[gentoo-commits] proj/sci:master commit in: /

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     01f3a1265668f114d0b6d1646e4edb1f5dab3e15
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 21 17:10:00 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Fri Mar 21 17:10:00 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=01f3a126

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-chemistry/unio/ChangeLog                                   | 5 +++++
 sci-chemistry/unio/{unio-2.0.3.ebuild => unio-2.0.3-r1.ebuild} | 5 +++++
 2 files changed, 10 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Nowa Ammerlaan]

commit:     3515ccf964e72ca8de004de435e543e7668a8cdb
Author:     Nowa Ammerlaan <nowa <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 12 20:24:38 2024 +0000
Commit:     Nowa Ammerlaan <nowa <AT> gentoo <DOT> org>
CommitDate: Tue Nov 12 20:24:47 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3515ccf9

.mailmap: init mailmap

Signed-off-by: Nowa Ammerlaan <nowa <AT> gentoo.org>

 .mailmap | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.mailmap b/.mailmap
new file mode 100644
index 000000000..b69b86f7c
--- /dev/null
+++ b/.mailmap
@@ -0,0 +1,8 @@
+# See gitmailmap(5) for format details.
+# Please keep this list sorted.
+# Use "grep -v '^#' .mailmap | LC_ALL=en_US.utf-8 sort".
+Nowa Ammerlaan <nowa@gentoo.org> <aammerlaan@science.ru.nl>
+Nowa Ammerlaan <nowa@gentoo.org> <andrewammerlaan@gentoo.org>
+Nowa Ammerlaan <nowa@gentoo.org> <andrewammerlaan@riseup.net>
+Nowa Ammerlaan <nowa@gentoo.org> <andrew.ammerlaan@ru.nl>
+Nowa Ammerlaan <nowa@gentoo.org> <nowa-ammerlaan@riseup.net>

[gentoo-commits] proj/sci:master commit in: /

[Horea Christian]

commit:     5df91a686fcac643feeef0c4123d128cb3e7d19a
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Sep 15 01:40:22 2022 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Sep 15 01:40:22 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5df91a68

README.md: Added link for eselect install

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 43484c14a..cd47d84a4 100644
--- a/README.md
+++ b/README.md
@@ -17,6 +17,7 @@
 ### Contents
 
 1. [Installation](#install)
+  - [Eselect](#install-eselect)
   - [Manual](#install-manual)
   - [Layman](#install-layman)
 2. [Usage](#usage)

[gentoo-commits] proj/sci:master commit in: /

[Horea Christian]

commit:     222285d2c8a297f0880306f8c395cacb0ccde78c
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Jul 28 14:31:45 2022 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Jul 28 14:31:45 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=222285d2

README.md: further standardization of emerge commands

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 129817337..43484c14a 100644
--- a/README.md
+++ b/README.md
@@ -28,14 +28,14 @@
 
 ## Installation <a name="install"></a>
 
-As per the current [Portage specifications](https://dev.gentoo.org/~zmedico/portage/doc/man/portage.5.html), ebuild repositories (a.k.a. overlays) can be managed via file collections under `/etc/portage/repos.conf/`, via the new [plug-in sync system](https://wiki.gentoo.org/wiki/Project:Portage/Sync).
+As per the current [Portage specification](https://dev.gentoo.org/~zmedico/portage/doc/man/portage.5.html), ebuild repositories (a.k.a. overlays) can be managed via file collections under `/etc/portage/repos.conf/`, via the new [plug-in sync system](https://wiki.gentoo.org/wiki/Project:Portage/Sync).
 
 ### Eselect-repository Install <a name="install-eselect"></a>
 
 The overlay can be enabled via the `repository` extension of the Gentoo `eselect` utility.
 
 ```console
-emerge --noreplace eselect-repository
+emerge --ask --noreplace --verbose eselect-repository
 eselect repository enable science
 ```
 
@@ -53,7 +53,7 @@ eselect repository remove science
 To enable the overlay without the need for dedicated repository software, you need to have `git` installed:
 
 ```console
-emerge --ask --verbose dev-vcs/git
+emerge --ask --noreplace --verbose dev-vcs/git
 ````
 
 Then you can simply download the science repository configuration file, [science.conf](metadata/science.conf):
@@ -77,7 +77,7 @@ rm /var/db/repos/science -rf
 You can also install the overlay via the [layman](https://wiki.gentoo.org/wiki/Layman) overlay manager.
 
 ```console
-emerge --ask --verbose app-portage/layman
+emerge --ask --noreplace --verbose app-portage/layman
 layman --add science
 ```
 

[gentoo-commits] proj/sci:master commit in: /

[Horea Christian]

commit:     b805936d714f5177bf1aff895e7eb7ebc588f84b
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Jul 28 14:28:42 2022 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Jul 28 14:28:42 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b805936d

README.md: typo and style improvements

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index a6c202ca2..129817337 100644
--- a/README.md
+++ b/README.md
@@ -28,9 +28,11 @@
 
 ## Installation <a name="install"></a>
 
+As per the current [Portage specifications](https://dev.gentoo.org/~zmedico/portage/doc/man/portage.5.html), ebuild repositories (a.k.a. overlays) can be managed via file collections under `/etc/portage/repos.conf/`, via the new [plug-in sync system](https://wiki.gentoo.org/wiki/Project:Portage/Sync).
+
 ### Eselect-repository Install <a name="install-eselect"></a>
 
-The overlay can be enabled via `repository` extension of the Gentoo `eselect` utility.
+The overlay can be enabled via the `repository` extension of the Gentoo `eselect` utility.
 
 ```console
 emerge --noreplace eselect-repository
@@ -48,8 +50,6 @@ eselect repository remove science
 
 ### Manual Install <a name="install-manual"></a>
 
-As per the current [Portage specifications](https://dev.gentoo.org/~zmedico/portage/doc/man/portage.5.html), ebuild repositories (a.k.a. overlays) can be managed via file collections under `/etc/portage/repos.conf/`, via the new [plug-in sync system](https://wiki.gentoo.org/wiki/Project:Portage/Sync).
-
 To enable the overlay without the need for dedicated repository software, you need to have `git` installed:
 
 ```console

[gentoo-commits] proj/sci:master commit in: /

[Horea Christian]

commit:     f9521dca269f92a6c5b06d6606213d8c8ef07ecc
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Jul 28 14:26:56 2022 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Jul 28 14:26:56 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f9521dca

README.md: expanded instructions, standardized formulation

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 README.md | 24 +++++++++++++++++-------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 3904770a0..a6c202ca2 100644
--- a/README.md
+++ b/README.md
@@ -28,25 +28,35 @@
 
 ## Installation <a name="install"></a>
 
-### Eselect-repository install <a name="install-eselect"></a>
+### Eselect-repository Install <a name="install-eselect"></a>
+
+The overlay can be enabled via `repository` extension of the Gentoo `eselect` utility.
+
+```console
+emerge --noreplace eselect-repository
+eselect repository enable science
+```
+
+### Eselect-repository Uninstall
+
+To disable and remove the overlay, run:
 
-The easiest way to enable the overlay is to:
 ```console
-emerge --noreplace eselect-repository && eselect repository enable science && emerge --sync
+eselect repository disable science
+eselect repository remove science
 ```
-and emerge the package as usual.
 
 ### Manual Install <a name="install-manual"></a>
 
 As per the current [Portage specifications](https://dev.gentoo.org/~zmedico/portage/doc/man/portage.5.html), ebuild repositories (a.k.a. overlays) can be managed via file collections under `/etc/portage/repos.conf/`, via the new [plug-in sync system](https://wiki.gentoo.org/wiki/Project:Portage/Sync).
 
-To enable the overlay without the need for additional software, you first need to have `git` installed:
+To enable the overlay without the need for dedicated repository software, you need to have `git` installed:
 
 ```console
 emerge --ask --verbose dev-vcs/git
 ````
 
-Then you need to add the science repository configuration by downloading the [science.conf](metadata/science.conf) file:
+Then you can simply download the science repository configuration file, [science.conf](metadata/science.conf):
 
 ```console
 wget https://gitweb.gentoo.org/proj/sci.git/plain/metadata/science.conf \
@@ -55,7 +65,7 @@ wget https://gitweb.gentoo.org/proj/sci.git/plain/metadata/science.conf \
 
 ### Manual Uninstall
 
-To uninstall the overlay, simply run:
+To disable and remove the overlay, run:
 
 ```console
 rm /etc/portage/repos.conf/science

[gentoo-commits] proj/sci:master commit in: /

[Andrew Ammerlaan]

commit:     8f92280db89307e2bb8fc85f3df893aca795513c
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Mon May  2 13:00:58 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Mon May  2 13:00:58 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8f92280d

*.md: update documentation: repoman --> pkgcheck and friends

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 CONTRIBUTING.md | 83 +++++++++++++++++++--------------------------------------
 README.md       |  1 -
 2 files changed, 27 insertions(+), 57 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index f46087c06..f414ef5b5 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -36,32 +36,27 @@ Create a [gpg key](http://www.gossamer-threads.com/lists/gentoo/dev/268496?do=po
 
 Now git will sign your commits to the overlay by using the gpg key.
 
-* **Install [hub](http://hub.github.com/)**, the *command-line wrapper for git that makes you better at GitHub*.
+* **Install [pkgdev](https://github.com/pkgcore/pkgdev)**, *A repository commit helper*
 
-*hub* can be used equivalent to to *git* and upstream even recommends *"alias git='hub'*.
+*pkgdev* sanitizes your commit in a convenient way and runs QA checks.
 
-    emerge dev-vcs/hub
-
-* **Install [repo-commit](https://bitbucket.org/gentoo/repo-commit/)**, *A repository commit helper*
-
-*repo-commit* sanitizes your commit in a convenient way.
-
-    emerge app-portage/repo-commit
+    emerge dev-util/pkgdev
 
 ---
 ## Contributing ebuilds
 
+### Fork the overlay
+In order to send pull request and ask for inclusion of your changes you need to have your own fork of the overlay on github. You can do this by clicking the "Fork" button in the top right of our GitHub page.
+
 ### Clone the overlay
 
-Create a local checkout of the overlay
+Create a local checkout of your fork, where `USERNAME` is your GitHub username.
 
-    hub clone gentoo-science/sci
+    git clone git@github.com:USERNAME/sci.git
 
-### Fork the overlay
-In order to send pull request and ask for inclusion of your changes you need to have your own fork of the overlay on github. You can do this by issuing
+To conveniently update your fork later, add the main repository as a second remote
 
-    cd sci
-    hub fork
+    git remote add upstream git@github.com:gentoo/sci.git
 
 ### Branch out for contribution
 It is always convenient for development as well as for the review and merging process, if the development is done in branches. Let's branch the overlay into a local branch named PACKAGE_NAME.
@@ -71,37 +66,38 @@ It is always convenient for development as well as for the review and merging pr
 For the fastest process during merging it is best to have a single branch per package.
 
 ### Work on the package
-Now you are ready to work on your package of interest. Once you are finished you should _always_ use **[repoman](http://dev.gentoo.org/~zmedico/portage/doc/man/repoman.1.html)** to do a static analysis of your work.
+Now you are ready to work on your package of interest. Once you are finished you should _always_ use **[pkgcheck](https://pkgcore.github.io/pkgcheck/man/pkgcheck.html)** to do a static analysis of your work.
 
 This can be done with
 
-    repoman full
+    pkgcheck scan --net
 
 ### Commit your work
 Once *all* reported problems are resolved, you can commit it
 
-    repo-commit "Here we write a comprehensible commit message"
+    pkgdev commit --all
 
-### Push to Github and make a pull request
+### Push to GitHub and make a pull request
 In order to facilitate potential reverts of mistakes, we prefer to keep the git history as linear as possible. For this, always rebase your changes on the latest remote changes.
 
-    hub pull --rebase=preserve github master
+    git pull --rebase=merges upstream master
+
+Next we push back the changes in the PACKAGE_NAME branch to our fork.
 
-Next we push back the changes in the PACKAGE_NAME branch to our fork and send a pull-request to the overlay maintainers.
+    pkgdev push YOUR_GITHUB_USER PACKAGE_NAME
 
-    hub push YOUR_GITHUB_USER PACKAGE_NAME
-    hub pull-request
+Now we are ready to create a Pull Request, go to your GitHub fork and press "Contribute" --> "Open pull request".
 
-Lastly you need to wait for review comments and the merge of your work. If you feel that they are slacking, don't bother to ping them again. In case you need to include some improvements, just commit your work again using *repo-commit* and push it again to your fork. No need to send another pull-request as your new changes will be added to the original one.
+Lastly you need to wait for review comments and the merge of your work. If you feel that they are slacking, don't hesitate to ping them again. In case you need to include some improvements, just commit your work again using `pkgdev commit` and push it again to your fork. No need to send another pull-request as your new changes will be added to the original one.
 
 ### What's next?
-If you would like to get direct access to the overlay, prove some contribution and ping us via sci@gentoo.org or on irc in #gentoo-science @ freenode. If you would like to become a dev yourself, prove some more contributions and again, contact us. We are always looking for new candidates.
+If you would like to get direct access to the overlay, prove some contribution and ping us via sci@gentoo.org or on irc in #gentoo-science @ Libera. If you would like to become a dev yourself, prove some more contributions and again, contact us. We are always looking for new candidates.
 
 ----
 ## Ebuild recommendations
 As the Gentoo Science overlay is a constant work-in-progress, we have some recommendations for prospective contributors:
 
-* **Aim for writing EAPI=7 ebuilds.** For certain eclasses, EAPI=7 is not allowed yet. In such cases you may use EAPI=6. We will not accept EAPI<6 ebuilds.
+* **Aim for writing EAPI=8 ebuilds.** For certain eclasses, `EAPI=8` is not allowed yet. In such cases you may use `EAPI=7`. We will not accept `EAPI<=6` ebuilds.
 * **Version bumps should always follow the latest guidelines.** For instance, a version bump of an ebuild that still employs autotools-utils.eclass should be avoided. Instead, drop 'autotools-utils', move to 'autotools' and call `default` followed by `eautoreconf` in src_prepare().
 
 ----
@@ -109,46 +105,21 @@ As the Gentoo Science overlay is a constant work-in-progress, we have some recom
 
 **It is important, that if you merge a pull request, you should feel as responsible as if you have written the commits yourself!**
 
-
-
 ### Prerequisite
 
-Make sure you have both repos (github & gentoo.org) as remotes defined.
-
-    git remote -v
-
-should give
-
->github	git@github.com:gentoo-science/sci.git (fetch)
->
->github	git@github.com:gentoo-science/sci.git (push)
->
->origin	git+ssh://git@git.overlays.gentoo.org/proj/sci.git (fetch)
->
->origin	git+ssh://git@git.overlays.gentoo.org/proj/sci.git (push)
-
+Install `app-portage/pram`
 
 ### Review process
 
-In the beginning you should review the pull request on github directly and recommend as much improvements as possible. By this you train the new contributor towards becoming a new dev, which should be our final goal.
+In the beginning you should review the pull request on GitHub directly and recommend as much improvements as possible. By this you train the new contributor towards becoming a new dev, which should be our final goal.
 
 #### Checking out the pull-request as local branch
 Once everything is fine or you like to fix the rest yourself, simply use the following command to get the pull-request in a new branch in your repo.
 
-    hub checkout https://github.com/gentoo-science/sci/pull/PULLREQUEST-NUMBER
-
-#### Testing and repoman check
-Now check the package by building and installing it, and run *repoman* in the package dir. Remember, when merging a pull request you take the responsibility for the quality of the commit.
-
-#### Merge the pull-request branch into master
-If this is also fine, merge the branch into the master
-
-    git checkout master
-    git merge USER-BRANCH
-
-#### Merging the two remote HEADs
-Finally use the script **merge-dualHEAD** from the *scripts* directory to merge the github and gentoo.org remote repo.
+    pram -r gentoo/sci PULLREQUEST-NUMBER
 
+#### Testing and pkgcheck check
+Now check the package by building and installing it, and run *pkgcheck* in the package directory. Remember, when merging a pull request you take the responsibility for the quality of the commit.
 
 ---
 #### Contribution to the document

diff --git a/README.md b/README.md
index e7618050b..3904770a0 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,5 @@
 # The [Gentoo Science Project](https://wiki.gentoo.org/wiki/Project:Science) Repository    
 [![pkgcheck](https://github.com/gentoo/sci/workflows/pkgcheck/badge.svg)](https://github.com/gentoo/sci/actions?query=workflow%3Apkgcheck)
-[![repoman](https://github.com/gentoo/sci/workflows/repoman/badge.svg)](https://github.com/gentoo/sci/actions?query=workflow%3Arepoman)
 [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg)](https://github.com/gentoo/sci#guide)
 [![chat on libera](https://img.shields.io/badge/chat-on%20libera-brightgreen.svg)](https://web.libera.chat/#gentoo-science)
 

[gentoo-commits] proj/sci:master commit in: /

[Andrew Ammerlaan]

commit:     39bc742c86d3552134717203431c05ef11ca60db
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 21 16:00:47 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Jan 21 16:02:01 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=39bc742c

README.md: Remove references to Github Issues, replace with b.g.o instead

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 README.md | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 99fcfe316..e7618050b 100644
--- a/README.md
+++ b/README.md
@@ -125,12 +125,7 @@ We welcome new contributors and are happy to include new packages.
 
 ### Areas to contribute
 
-- [Current open issues](https://github.com/gentoo/sci/issues)
 - [Current open bugs](https://bugs.gentoo.org/buglist.cgi?no_redirect=1&quicksearch=[science+overlay])
-- EAPI 6 (or 5) ebuilds which need updating
-```
-find . -type f -name "*.ebuild" ! \( -wholename "*.git*" -o -wholename "*profile*" -o -wholename "*metadata*" \) | while read ff; do grep -lRE "EAPI.*6" /dev/null $ff; done
-```
 
 ### Resources
 
@@ -144,4 +139,4 @@ Additionally, please make sure to add the Science Project as an additional maint
 ## Support
 
 You can ask for help on [Libera IRC](https://www.gentoo.org/get-involved/irc-channels/) in [**#gentoo-science**](https://web.libera.chat/#gentoo-science).
-Alternatively you can report bugs on the [GitHub issues page](https://github.com/gentoo/sci/issues).
+Alternatively you can report bugs on the [Gentoo Bugzilla](https://bugs.gentoo.org/).

[gentoo-commits] proj/sci:master commit in: /

[Andrew Ammerlaan]

commit:     d1375a9736c1613c1a7354546b9cbc43afb58f6a
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 20 13:11:59 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sun Jun 20 13:11:59 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d1375a97

README.md: freenode --> libera

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 29e518d33..99fcfe316 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
 [![pkgcheck](https://github.com/gentoo/sci/workflows/pkgcheck/badge.svg)](https://github.com/gentoo/sci/actions?query=workflow%3Apkgcheck)
 [![repoman](https://github.com/gentoo/sci/workflows/repoman/badge.svg)](https://github.com/gentoo/sci/actions?query=workflow%3Arepoman)
 [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg)](https://github.com/gentoo/sci#guide)
-[![chat on freenode](https://img.shields.io/badge/chat-on%20freenode-brightgreen.svg)](https://webchat.freenode.net/#gentoo-science)
+[![chat on libera](https://img.shields.io/badge/chat-on%20libera-brightgreen.svg)](https://web.libera.chat/#gentoo-science)
 
 <table>
 <tr>
@@ -143,5 +143,5 @@ Additionally, please make sure to add the Science Project as an additional maint
 
 ## Support
 
-You can ask for help on [Freenode IRC](https://www.gentoo.org/get-involved/irc-channels/) in [**#gentoo-science**](http://webchat.freenode.net/?channels=gentoo-science).
+You can ask for help on [Libera IRC](https://www.gentoo.org/get-involved/irc-channels/) in [**#gentoo-science**](https://web.libera.chat/#gentoo-science).
 Alternatively you can report bugs on the [GitHub issues page](https://github.com/gentoo/sci/issues).

[gentoo-commits] proj/sci:master commit in: /

[Andrew Ammerlaan]

commit:     5fab69b08919220db33df13759ae76110c43c677
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 20 10:54:53 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 20 10:54:53 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5fab69b0

README.md: add note on eselect-repository

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 README.md | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/README.md b/README.md
index e1353773f..29e518d33 100644
--- a/README.md
+++ b/README.md
@@ -29,6 +29,14 @@
 
 ## Installation <a name="install"></a>
 
+### Eselect-repository install <a name="install-eselect"></a>
+
+The easiest way to enable the overlay is to:
+```console
+emerge --noreplace eselect-repository && eselect repository enable science && emerge --sync
+```
+and emerge the package as usual.
+
 ### Manual Install <a name="install-manual"></a>
 
 As per the current [Portage specifications](https://dev.gentoo.org/~zmedico/portage/doc/man/portage.5.html), ebuild repositories (a.k.a. overlays) can be managed via file collections under `/etc/portage/repos.conf/`, via the new [plug-in sync system](https://wiki.gentoo.org/wiki/Project:Portage/Sync).

[gentoo-commits] proj/sci:master commit in: /

[Andrew Ammerlaan]

commit:     cc9911ce6b1dfec07c21e1a2d98528e451e4df87
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 20 10:41:42 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 20 10:42:18 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cc9911ce

CONTRIBUTING.md: update accepted EAPIs

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 CONTRIBUTING.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 6c4ba5879..f46087c06 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -101,7 +101,7 @@ If you would like to get direct access to the overlay, prove some contribution a
 ## Ebuild recommendations
 As the Gentoo Science overlay is a constant work-in-progress, we have some recommendations for prospective contributors:
 
-* **Aim for writing EAPI=6 ebuilds.** For certain eclasses, EAPI=6 is not allowed yet. In such cases you may use EAPI=5. We will not accept EAPI<5 ebuilds.
+* **Aim for writing EAPI=7 ebuilds.** For certain eclasses, EAPI=7 is not allowed yet. In such cases you may use EAPI=6. We will not accept EAPI<6 ebuilds.
 * **Version bumps should always follow the latest guidelines.** For instance, a version bump of an ebuild that still employs autotools-utils.eclass should be avoided. Instead, drop 'autotools-utils', move to 'autotools' and call `default` followed by `eautoreconf` in src_prepare().
 
 ----

[gentoo-commits] proj/sci:master commit in: /

[Sam James]

commit:     b3159adc8606db066a6cb9b08f755e9fa27a7157
Author:     Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Sat Mar  6 01:48:19 2021 +0000
Commit:     Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Sat Mar  6 01:48:19 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b3159adc

Remove .travis.yml

We use GitHub actions now.

Signed-off-by: Sam James <sam <AT> gentoo.org>

 .travis.yml | 38 --------------------------------------
 1 file changed, 38 deletions(-)

diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index f54be17af..000000000
--- a/.travis.yml
+++ /dev/null
@@ -1,38 +0,0 @@
-#
-# Run repoman via travis
-# See https://github.com/mrueg/repoman-travis
-#
-language: python
-python:
-    - "3.8"
-env:
-    - PORTAGE_VER="3.0.7"
-before_install:
-    - sudo apt-get -qq update
-    - pip install lxml pyyaml pkgcheck
-before_script:
-    - sudo chmod a+rwX /etc/passwd /etc/group /etc /var /var/cache
-    - mkdir -p travis-overlay /etc/portage /var/cache/distfiles /var/db/repos/gentoo
-    - mv !(travis-overlay) travis-overlay/
-    - mv .git travis-overlay/
-    - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/spinner.sh"
-    - wget -qO - "https://github.com/gentoo/portage/archive/portage-${PORTAGE_VER}.tar.gz" | tar xz
-    - wget -qO - "https://github.com/gentoo-mirror/gentoo/archive/master.tar.gz" | tar xz -C /var/db/repos/gentoo --strip-components=1
-    - chmod a+rwx spinner.sh
-    - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
-    - echo "portage::250:portage,travis" >> /etc/group
-    - wget "https://www.gentoo.org/dtd/metadata.dtd" -O /var/cache/distfiles/metadata.dtd
-    - ln -s $TRAVIS_BUILD_DIR/portage-portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/repos.conf
-    - ln -s /var/db/repos/gentoo/profiles/default/linux/amd64/17.0 /etc/portage/make.profile
-    - cd travis-overlay
-script:
-    - ./../spinner.sh "python ../portage-portage-${PORTAGE_VER}/repoman/bin/repoman full -d"
-    - ./../spinner.sh "pkgcheck scan"
-# You can append own scripts after this line
-
-notifications:
-    irc:
-        channels: "chat.freenode.net#gentoo-science"
-        template:
-            - "%{repository} - %{branch} - %{author}: %{commit_subject} - %{message} - Build details : %{build_url}"
-        use_notice: true

[gentoo-commits] proj/sci:master commit in: /

[Aisha Tammy]

commit:     79404ceb084f6105e21a6ce7bde9ea67e7750495
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Wed Jan 20 12:00:13 2021 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Wed Jan 20 15:19:38 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=79404ceb

readme add links to contribute

Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 README.md | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 3c414946c..e1353773f 100644
--- a/README.md
+++ b/README.md
@@ -112,9 +112,20 @@ The downside of this approach is potentially higher instability, the advantage i
 
 ## Contributing <a name="contributing"></a>
 
-*If you fork, we will merge!*
+*If you fork, we will merge!*   
 We welcome new contributors and are happy to include new packages.
 
+### Areas to contribute
+
+- [Current open issues](https://github.com/gentoo/sci/issues)
+- [Current open bugs](https://bugs.gentoo.org/buglist.cgi?no_redirect=1&quicksearch=[science+overlay])
+- EAPI 6 (or 5) ebuilds which need updating
+```
+find . -type f -name "*.ebuild" ! \( -wholename "*.git*" -o -wholename "*profile*" -o -wholename "*metadata*" \) | while read ff; do grep -lRE "EAPI.*6" /dev/null $ff; done
+```
+
+### Resources
+
 For a brief introduction please see our [contributing guide](CONTRIBUTING.md). Further helpful resources are:
 
 - Gentoo Developers Manual - https://devmanual.gentoo.org/ (taking precedence over any other information found here)

[gentoo-commits] proj/sci:master commit in: /

[Horea Christian]

commit:     b2247ff09fa408e2b7c62c81f5583aae0dadce57
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Tue Jan  5 07:32:41 2021 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue Jan  5 07:32:41 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b2247ff0

Readme.md: typo

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 4b9bffe66..3c414946c 100644
--- a/README.md
+++ b/README.md
@@ -104,7 +104,7 @@ printf '*/*::science ~%s' "$(portageq envvar ARCH)" >> /etc/portage/package.acce
 Alternatively, and *only if you know what you are doing*, you can accept `~${ARCH}` packages globally:
 
 ```console
-printf 'ACCEPT_KEYWORDS="~%s"' "$(portageq envvar ARCH)" >> lala
+printf 'ACCEPT_KEYWORDS="~%s"' "$(portageq envvar ARCH)" >> /etc/portage/make.conf
 ```
 
 The downside of this approach is potentially higher instability, the advantage is that often `::science` packages require `~${ARCH}` packages from `::gentoo` as well.

[gentoo-commits] proj/sci:master commit in: /

[Horea Christian]

commit:     07613be42ffecd4eec55d95681d5c63b04c59776
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Tue Jan  5 07:11:49 2021 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue Jan  5 07:29:55 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=07613be4

Readme.md: cleanup, style, formatting, grammar

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 README.md | 103 ++++++++++++++++++++++++++++++++++----------------------------
 1 file changed, 57 insertions(+), 46 deletions(-)

diff --git a/README.md b/README.md
index d2bbf2fe9..4b9bffe66 100644
--- a/README.md
+++ b/README.md
@@ -8,9 +8,7 @@
 <tr>
 <td width="69%">
 
-**This is an official mirror of the Gentoo Science Projects [ebuild repository](https://wiki.gentoo.org/wiki/Ebuild_repository) which provides numerous scientific software packages.**
-
-The Gentoo [developer manual](https://devmanual.gentoo.org/) take precedence over any information here.
+**This is an official mirror of the Gentoo Science [ebuild repository](https://wiki.gentoo.org/wiki/Ebuild_repository), containing numerous scientific software packages.**
 
 *See [Project:Science](https://wiki.gentoo.org/wiki/Project:Science) for more information on the project.*
 
@@ -19,99 +17,112 @@ The Gentoo [developer manual](https://devmanual.gentoo.org/) take precedence ove
 
 ### Contents
 
-1. [Installation and usage](#install)
+1. [Installation](#install)
   - [Manual](#install-manual)
   - [Layman](#install-layman)
-2. [Contributor guidelines](#guide)
+2. [Usage](#usage)
+3. [Contributing](#contributing)
 
 </td>
 </tr>
 </table>
 
-## Install <a name="install"></a>
+## Installation <a name="install"></a>
 
-### Manual install <a name="install-manual"></a>
+### Manual Install <a name="install-manual"></a>
 
 As per the current [Portage specifications](https://dev.gentoo.org/~zmedico/portage/doc/man/portage.5.html), ebuild repositories (a.k.a. overlays) can be managed via file collections under `/etc/portage/repos.conf/`, via the new [plug-in sync system](https://wiki.gentoo.org/wiki/Project:Portage/Sync).
 
-To enable our overlay without the need for additional software, you first need to have **git(1)** installed:
+To enable the overlay without the need for additional software, you first need to have `git` installed:
 
-```
-emerge --ask --verbose dev-vcs/git 
+```console
+emerge --ask --verbose dev-vcs/git
 ````
 
-Then you can add the custom entry for the science repository by downloading the [science.conf](metadata/science.conf) file
+Then you need to add the science repository configuration by downloading the [science.conf](metadata/science.conf) file:
 
-```
+```console
 wget https://gitweb.gentoo.org/proj/sci.git/plain/metadata/science.conf \
 	-O /etc/portage/repos.conf/science
 ```
 
-To start using the overlay you now only need to sync the overlay, via 
+### Manual Uninstall
 
-```
-emaint sync --repo science
+To uninstall the overlay, simply run:
+
+```console
+rm /etc/portage/repos.conf/science
+rm /var/db/repos/science -rf
 ```
 
-or the traditional 
+### Layman Install <a name="install-layman"></a>
 
-```
-emerge --sync
+You can also install the overlay via the [layman](https://wiki.gentoo.org/wiki/Layman) overlay manager.
+
+```console
+emerge --ask --verbose app-portage/layman
+layman --add science
 ```
 
-### Manual uninstall
+### Layman Uninstall
 
-To uninstall the overlay simply run:
+To delete the overlay, run:
 
-```
-rm /etc/portage/repos.conf/science
-rm /var/db/repos/science -rf
+```console
+layman --delete science
 ```
 
-### Layman install <a name="install-layman"></a>
+### Using Packages from `::science`
 
-You can also install the overlay via the [layman](https://wiki.gentoo.org/wiki/Layman) overlay manager
+To start using the overlay you now only need to get the newest files, via:
 
+```console
+emerge --sync science
 ```
-layman --add science
+
+To be able to install `::science` packages you need to make sure that you are accepting the `~${ARCH}` keyword for your respective architecture. This may already be the case globally on your system, and you can check whether this is the case by running:
+
+```console
+grep "~$(portageq envvar ARCH)" /etc/portage/make.conf
 ```
 
-### Layman uninstall
+If the above returns empty, you will need to instruct Portage to accept `~${ARCH}` packages.
 
-To delete the overlay run
+This can be done for `::science` specifically:
 
-```
-layman --delete science
+```console
+mkdir -p /etc/portage/package.accept_keywords
+printf '*/*::science ~%s' "$(portageq envvar ARCH)" >> /etc/portage/package.accept_keywords/science
 ```
 
-### Using packages from ::science
+If the above fails with `mkdir: cannot create directory ‘/etc/portage/package.accept_keywords’: File exists` this means you are using a file and not a directory, and you can instead run:
 
-To enable the packges from `::science` you need to make sure that you are accepting the `~${ARCH}` keywords for your respective arch.
+```console
+printf '*/*::science ~%s' "$(portageq envvar ARCH)" >> /etc/portage/package.accept_keywords
+```
 
-Make sure that the  `/etc/portage/package.accept_keywords/` folder exists and run
+Alternatively, and *only if you know what you are doing*, you can accept `~${ARCH}` packages globally:
 
+```console
+printf 'ACCEPT_KEYWORDS="~%s"' "$(portageq envvar ARCH)" >> lala
 ```
-printf '*/*::science ~%s' "$(portageq envvar ARCH)" >> /etc/portage/package.accept_keywords/SCIENCE
-```
 
-## Generic guidelines for contributors <a name="guide"></a>
+The downside of this approach is potentially higher instability, the advantage is that often `::science` packages require `~${ARCH}` packages from `::gentoo` as well.
+
 
-If you fork, we will merge!   
-We are always going to welcome new contributors and love expanding our collection.   
+## Contributing <a name="contributing"></a>
 
-For basic guidelines please see our [contributing guide](CONTRIBUTING.md).
+*If you fork, we will merge!*
+We welcome new contributors and are happy to include new packages.
 
+For a brief introduction please see our [contributing guide](CONTRIBUTING.md). Further helpful resources are:
 
-The [GURU Project](https://wiki.gentoo.org/wiki/Project:GURU) has created excellent documentation for potential contributors.   
-We highly advise you to give them a read along with other general Gentoo guidelines
-- GURU guidelines - https://wiki.gentoo.org/wiki/Project:GURU#The_regulations
+- Gentoo Developers Manual - https://devmanual.gentoo.org/ (taking precedence over any other information found here)
 - Contributing to Gentoo - https://wiki.gentoo.org/wiki/Contributing_to_Gentoo
-- Gentoo Developers Manual - https://devmanual.gentoo.org/
 
-In addition to the above guidelines please make sure that if you submitting a new package, please add the Science Project as an additional maintainer to the package.   
-For an example, take a look at the metadata for the [Numba](dev-python/numba) package - [dev-python/numba/metadata.xml](dev-python/numba/metadata.xml)
+Additionally, please make sure to add the Science Project as an additional maintainer to any new packages you submit. For an example, take a look at the metadata for the [Numba](dev-python/numba) package - [dev-python/numba/metadata.xml](dev-python/numba/metadata.xml)
 
 ## Support
 
-You can ask for help on [Freenode IRC](https://www.gentoo.org/get-involved/irc-channels/) in [**#gentoo-science**](http://webchat.freenode.net/?channels=gentoo-science).   
+You can ask for help on [Freenode IRC](https://www.gentoo.org/get-involved/irc-channels/) in [**#gentoo-science**](http://webchat.freenode.net/?channels=gentoo-science).
 Alternatively you can report bugs on the [GitHub issues page](https://github.com/gentoo/sci/issues).

[gentoo-commits] proj/sci:master commit in: /

[Aisha Tammy]

commit:     61241c99dd1a94d48783775d505ebaa31a611dce
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Thu Dec 31 15:19:56 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Thu Dec 31 15:19:56 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=61241c99

remove skeleton ebuild/metadata files

they are old and duplicate work from ::gentoo

Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 skel.ebuild       | 162 ------------------------------------------------------
 skel.metadata.xml |  31 -----------
 2 files changed, 193 deletions(-)

diff --git a/skel.ebuild b/skel.ebuild
deleted file mode 100644
index 0114d8c26..000000000
--- a/skel.ebuild
+++ /dev/null
@@ -1,162 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-# NOTE: The comments in this file are for instruction and documentation.
-# They're not meant to appear with your final, production ebuild.  Please
-# remember to remove them before submitting or committing your ebuild.  That
-# doesn't mean you can't add your own comments though.
-
-# The EAPI variable tells the ebuild format in use.
-# It is suggested that you use the latest EAPI approved by the Council.
-# The PMS contains specifications for all EAPIs. Eclasses will test for this
-# variable if they need to use features that are not universal in all EAPIs.
-EAPI=6
-
-# inherit lists eclasses to inherit functions from. For example, an ebuild
-# that needs the eautoreconf function from autotools.eclass won't work
-# without the following line:
-#inherit autotools
-#
-# eclasses tend to list descriptions of how to use their functions properly.
-# take a look at /usr/portage/eclass/ for more examples.
-
-# Short one-line description of this package.
-DESCRIPTION="This is a sample skeleton ebuild file"
-
-# Homepage, not used by Portage directly but handy for developer reference
-HOMEPAGE="https://foo.example.org/"
-
-# Point to any required sources; these will be automatically downloaded by
-# Portage.
-SRC_URI="ftp://foo.example.org/${P}.tar.gz"
-
-
-# License of the package.  This must match the name of file(s) in
-# /usr/portage/licenses/.  For complex license combination see the developer
-# docs on gentoo.org for details.
-LICENSE=""
-
-# The SLOT variable is used to tell Portage if it's OK to keep multiple
-# versions of the same package installed at the same time.  For example,
-# if we have a libfoo-1.2.2 and libfoo-1.3.2 (which is not compatible
-# with 1.2.2), it would be optimal to instruct Portage to not remove
-# libfoo-1.2.2 if we decide to upgrade to libfoo-1.3.2.  To do this,
-# we specify SLOT="1.2" in libfoo-1.2.2 and SLOT="1.3" in libfoo-1.3.2.
-# emerge clean understands SLOTs, and will keep the most recent version
-# of each SLOT and remove everything else.
-# Note that normal applications should use SLOT="0" if possible, since
-# there should only be exactly one version installed at a time.
-# Do not use SLOT="", because the SLOT variable must not be empty.
-SLOT="0"
-
-# Using KEYWORDS, we can record masking information *inside* an ebuild
-# instead of relying on an external package.mask file.  Right now, you should
-# set the KEYWORDS variable for every ebuild so that it contains the names of
-# all the architectures with which the ebuild works.  All of the official
-# architectures can be found in the arch.list file which is in
-# /usr/portage/profiles/.  Usually you should just set this to "~amd64".
-# The ~ in front of the architecture indicates that the package is new and
-# should be considered unstable until testing proves its stability.  So, if
-# you've confirmed that your ebuild works on amd64 and ppc, you'd specify:
-# KEYWORDS="~amd64 ~ppc"
-# Once packages go stable, the ~ prefix is removed.
-# For binary packages, use -* and then list the archs the bin package
-# exists for.  If the package was for an x86 binary package, then
-# KEYWORDS would be set like this: KEYWORDS="-* x86"
-# Do not use KEYWORDS="*"; this is not valid in an ebuild context.
-KEYWORDS="~amd64"
-
-# Comprehensive list of any and all USE flags leveraged in the ebuild,
-# with some exceptions, e.g., ARCH specific flags like "amd64" or "ppc".
-# Not needed if the ebuild doesn't use any USE flags.
-IUSE="gnome X"
-
-# A space delimited list of portage features to restrict. man 5 ebuild
-# for details.  Usually not needed.
-#RESTRICT="strip"
-
-
-# Build-time dependencies, such as
-#    ssl? ( >=dev-libs/openssl-0.9.6b )
-#    >=dev-lang/perl-5.6.1-r1
-# It is advisable to use the >= syntax show above, to reflect what you
-# had installed on your system when you tested the package.  Then
-# other users hopefully won't be caught without the right version of
-# a dependency.
-#DEPEND=""
-
-# Run-time dependencies. Must be defined to whatever this depends on to run.
-# The below is valid if the same run-time depends are required to compile.
-RDEPEND="${DEPEND}"
-
-# Source directory; the dir where the sources can be found (automatically
-# unpacked) inside ${WORKDIR}.  The default value for S is ${WORKDIR}/${P}
-# If you don't need to change it, leave the S= line out of the ebuild
-# to keep it tidy.
-#S=${WORKDIR}/${P}
-
-
-# The following src_configure function is implemented as default by portage, so
-# you only need to call it if you need a different behaviour.
-#src_configure() {
-	# Most open-source packages use GNU autoconf for configuration.
-	# The default, quickest (and preferred) way of running configure is:
-	#econf
-	#
-	# You could use something similar to the following lines to
-	# configure your package before compilation.  The "|| die" portion
-	# at the end will stop the build process if the command fails.
-	# You should use this at the end of critical commands in the build
-	# process.  (Hint: Most commands are critical, that is, the build
-	# process should abort if they aren't successful.)
-	#./configure \
-	#	--host=${CHOST} \
-	#	--prefix=/usr \
-	#	--infodir=/usr/share/info \
-	#	--mandir=/usr/share/man || die
-	# Note the use of --infodir and --mandir, above. This is to make
-	# this package FHS 2.2-compliant.  For more information, see
-	#   https://www.pathname.com/fhs/
-#}
-
-# The following src_compile function is implemented as default by portage, so
-# you only need to call it, if you need different behaviour.
-#src_compile() {
-	# emake is a script that calls the standard GNU make with parallel
-	# building options for speedier builds (especially on SMP systems).
-	# Try emake first.  It might not work for some packages, because
-	# some makefiles have bugs related to parallelism, in these cases,
-	# use emake -j1 to limit make to a single process.  The -j1 is a
-	# visual clue to others that the makefiles have bugs that have been
-	# worked around.
-
-	#emake
-#}
-
-# The following src_install function is implemented as default by portage, so
-# you only need to call it, if you need different behaviour.
-#src_install() {
-	# You must *personally verify* that this trick doesn't install
-	# anything outside of DESTDIR; do this by reading and
-	# understanding the install part of the Makefiles.
-	# This is the preferred way to install.
-	#emake DESTDIR="${D}" install
-
-	# When you hit a failure with emake, do not just use make. It is
-	# better to fix the Makefiles to allow proper parallelization.
-	# If you fail with that, use "emake -j1", it's still better than make.
-
-	# For Makefiles that don't make proper use of DESTDIR, setting
-	# prefix is often an alternative.  However if you do this, then
-	# you also need to specify mandir and infodir, since they were
-	# passed to ./configure as absolute paths (overriding the prefix
-	# setting).
-	#emake \
-	#	prefix="${D}"/usr \
-	#	mandir="${D}"/usr/share/man \
-	#	infodir="${D}"/usr/share/info \
-	#	libdir="${D}"/usr/$(get_libdir) \
-	#	install
-	# Again, verify the Makefiles!  We don't want anything falling
-	# outside of ${D}.
-#}

diff --git a/skel.metadata.xml b/skel.metadata.xml
deleted file mode 100644
index 42444c655..000000000
--- a/skel.metadata.xml
+++ /dev/null
@@ -1,31 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<!--
-This is the example metadata file.
-The root element of this file is <pkgmetadata>. Within this element a
-number of subelements are allowed, the most common being maintainer.
-
-For a full description look at:
-https://devmanual.gentoo.org/ebuild-writing/misc-files/metadata/
-
-Before committing, please remove the comments from this file. They are
-not relevant for general metadata.xml files.
--->
-<pkgmetadata>
-<maintainer type="person">
-	<email>exampledev@gentoo.org</email>
-	<description>Primary maintainer</description>
-</maintainer>
-<maintainer type="project">
-	<email>exampleproject@gentoo.org</email>
-	<name>Gentoo Example Project</name>
-</maintainer>
-<longdescription>Long description of the package</longdescription>
-<use>
-	<flag name="aspell">Uses <pkg>app-text/aspell</pkg> for spell checking.
-		Requires an installed dictionary from <cat>app-dicts</cat></flag>
-	<flag name="flag">Description of how USE='flag' affects this package</flag>
-	<flag name="userland_GNU">Description of how USERLAND='GNU' affects this
-		package</flag>
-</use>
-</pkgmetadata>

[gentoo-commits] proj/sci:master commit in: /

[Aisha Tammy]

commit:     c09990c883127a91ed0b944cd8619749a2f54245
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Tue Sep 29 17:28:34 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Sep 29 17:28:34 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c09990c8

Travis CI - add pkgcheck scan

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 .travis.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index c10d6b7dd..f54be17af 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,13 +9,12 @@ env:
     - PORTAGE_VER="3.0.7"
 before_install:
     - sudo apt-get -qq update
-    - pip install lxml pyyaml
+    - pip install lxml pyyaml pkgcheck
 before_script:
     - sudo chmod a+rwX /etc/passwd /etc/group /etc /var /var/cache
     - mkdir -p travis-overlay /etc/portage /var/cache/distfiles /var/db/repos/gentoo
     - mv !(travis-overlay) travis-overlay/
     - mv .git travis-overlay/
-    - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/.travis.yml" -O .travis.yml.upstream
     - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/spinner.sh"
     - wget -qO - "https://github.com/gentoo/portage/archive/portage-${PORTAGE_VER}.tar.gz" | tar xz
     - wget -qO - "https://github.com/gentoo-mirror/gentoo/archive/master.tar.gz" | tar xz -C /var/db/repos/gentoo --strip-components=1
@@ -25,11 +24,10 @@ before_script:
     - wget "https://www.gentoo.org/dtd/metadata.dtd" -O /var/cache/distfiles/metadata.dtd
     - ln -s $TRAVIS_BUILD_DIR/portage-portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/repos.conf
     - ln -s /var/db/repos/gentoo/profiles/default/linux/amd64/17.0 /etc/portage/make.profile
-    - SIZE=$(stat -c %s .travis.yml.upstream)
-    - if ! cmp -n $SIZE -s .travis.yml .travis.yml.upstream; then echo -e "\e[31m !!! .travis.yml outdated! Update available https://github.com/mrueg/repoman-travis \e[0m" > /tmp/update ; fi
     - cd travis-overlay
 script:
     - ./../spinner.sh "python ../portage-portage-${PORTAGE_VER}/repoman/bin/repoman full -d"
+    - ./../spinner.sh "pkgcheck scan"
 # You can append own scripts after this line
 
 notifications:

[gentoo-commits] proj/sci:master commit in: /

[Aisha Tammy]

commit:     e2e89b749cc7e4db12451739f7fade83e9c002c9
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Sun Sep 27 20:12:31 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Sun Sep 27 20:12:31 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e2e89b74

Travis CI - update to latest

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 .travis.yml | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 241a06e33..c10d6b7dd 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -3,29 +3,30 @@
 # See https://github.com/mrueg/repoman-travis
 #
 language: python
-cache: pip
 python:
-    - pypy
+    - "3.8"
 env:
-    - PORTAGE_VER="2.3.51"
+    - PORTAGE_VER="3.0.7"
 before_install:
     - sudo apt-get -qq update
-install:
-    - pip install lxml PyYAML
+    - pip install lxml pyyaml
 before_script:
-    - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr
-    - mkdir -p travis-overlay /etc/portage /usr/portage/distfiles
+    - sudo chmod a+rwX /etc/passwd /etc/group /etc /var /var/cache
+    - mkdir -p travis-overlay /etc/portage /var/cache/distfiles /var/db/repos/gentoo
     - mv !(travis-overlay) travis-overlay/
     - mv .git travis-overlay/
+    - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/.travis.yml" -O .travis.yml.upstream
     - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/spinner.sh"
     - wget -qO - "https://github.com/gentoo/portage/archive/portage-${PORTAGE_VER}.tar.gz" | tar xz
-    - wget -qO - "https://github.com/gentoo-mirror/gentoo/archive/master.tar.gz" | tar xz -C /usr/portage --strip-components=1
+    - wget -qO - "https://github.com/gentoo-mirror/gentoo/archive/master.tar.gz" | tar xz -C /var/db/repos/gentoo --strip-components=1
     - chmod a+rwx spinner.sh
     - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
     - echo "portage::250:portage,travis" >> /etc/group
-    - wget "https://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
+    - wget "https://www.gentoo.org/dtd/metadata.dtd" -O /var/cache/distfiles/metadata.dtd
     - ln -s $TRAVIS_BUILD_DIR/portage-portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/repos.conf
-    - ln -s /usr/portage/profiles/default/linux/amd64/17.1 /etc/portage/make.profile
+    - ln -s /var/db/repos/gentoo/profiles/default/linux/amd64/17.0 /etc/portage/make.profile
+    - SIZE=$(stat -c %s .travis.yml.upstream)
+    - if ! cmp -n $SIZE -s .travis.yml .travis.yml.upstream; then echo -e "\e[31m !!! .travis.yml outdated! Update available https://github.com/mrueg/repoman-travis \e[0m" > /tmp/update ; fi
     - cd travis-overlay
 script:
     - ./../spinner.sh "python ../portage-portage-${PORTAGE_VER}/repoman/bin/repoman full -d"

[gentoo-commits] proj/sci:master commit in: /

[Aisha Tammy]

commit:     0d9d7df9b0cda2bb8fd679493f70c269f51848af
Author:     A. Tammy <epsilon-0 <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Sun Sep 27 17:19:33 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Sun Sep 27 17:22:05 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0d9d7df9

README expansion

update the README to be more informative and
user friendly

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 README.md | 111 ++++++++++++++++++++++++++++++++++++++++++++++++++++----------
 1 file changed, 93 insertions(+), 18 deletions(-)

diff --git a/README.md b/README.md
index f328e252f..ba5175935 100644
--- a/README.md
+++ b/README.md
@@ -1,39 +1,114 @@
-# [Gentoo Science](https://wiki.gentoo.org/wiki/Project:Science/Overlay) Overlay
+# The [Gentoo Science Project](https://wiki.gentoo.org/wiki/Project:Science) Repository    
 [![Build Status](https://travis-ci.com/gentoo/sci.svg?branch=master)](https://travis-ci.com/gentoo/sci)
 
-This is a Gentoo Linux [ebuild repository](https://wiki.gentoo.org/wiki/Ebuild_repository) which provides numerous scientific software packages.
+<table>
+<tr>
+<td width="69%">
 
-## Install
+**This is an official mirror of the Gentoo Science Projects [ebuild repository](https://wiki.gentoo.org/wiki/Ebuild_repository) which provides numerous scientific software packages.**
 
-As per the current [Portage specifications](https://dev.gentoo.org/~zmedico/portage/doc/man/portage.5.html), ebuild repositories (a.k.a. overlays) should be managed via file collections under `/etc/portage/repos.conf/`.
-To enable our overlay without the need for additional software, simply run (as root):
+The Gentoo [developer manual](https://devmanual.gentoo.org/) take precedence over any information here.
+
+*See [Project:Science](https://wiki.gentoo.org/wiki/Project:Science) for more information on the project.*
+
+</td>
+<td width="27%" style="border-style:solid; border-radius:10px;">
+
+### Contents
+
+1. [Installation and usage](#install)
+  - [Manual](#install-manual)
+  - [Layman](#install-layman)
+2. [Contributor guidelies](#guide)
+
+</td>
+</tr>
+</table>
+
+## Install <a name="install"></a>
+
+### Manual install <a name="install-manual"></a>
+
+As per the current [Portage specifications](https://dev.gentoo.org/~zmedico/portage/doc/man/portage.5.html), ebuild repositories (a.k.a. overlays) can be managed via file collections under `/etc/portage/repos.conf/`, via the new [plug-in sync system](https://wiki.gentoo.org/wiki/Project:Portage/Sync).
+
+To enable our overlay without the need for additional software, you first need to have **git(1)** installed:
 
 ```
-wget https://gitweb.gentoo.org/proj/sci.git/plain/metadata/science.conf -O /etc/portage/repos.conf/science
+emerge --ask --verbose dev-vcs/git 
+````
+
+Then you can add the custom entry for the science repository by downloading the [science.conf](metadata/science.conf) file
+
+```
+wget https://gitweb.gentoo.org/proj/sci.git/plain/metadata/science.conf \
+	-O /etc/portage/repos.conf/science
 ```
 
-To start using the overlay you now only need to get the ebuilds, via `emerge --sync`.
+To start using the overlay you now only need to sync the overlay, via 
 
-### BLAS and LAPACK
+```
+emaint sync --repo science
+```
 
-[The BLAS and LAPACK switching framework](https://wiki.gentoo.org/wiki/Blas-lapack-switch)
-in ::gentoo has been implemented. The Science overlay will no longer
-carry blas and lapack ebuilds.
+or the traditional 
+
+```
+emerge --sync
+```
 
-### Uninstall
+### Manual uninstall
 
-To uninstall the overlay run (again, as root):
+To uninstall the overlay simply run:
 
 ```
 rm /etc/portage/repos.conf/science
 rm /var/db/repos/science -rf
 ```
 
-## Support
+### Layman install <a name="install-layman"></a>
 
-You can ask for help on [Freenode IRC](https://www.gentoo.org/get-involved/irc-channels/) in `#gentoo-science`.
-Alternatively you can report bugs on the [GitHub issues page](https://github.com/gentoo/sci/issues).
+You can also install the overlay via the [layman](https://wiki.gentoo.org/wiki/Layman) overlay manager
 
-## Contribute
+```
+layman --add science
+```
 
-Please fork! We will merge! See [our contributing guide](https://github.com/gentoo/sci/blob/master/CONTRIBUTING.md).
+### Layman uninstall
+
+To delete the overlay run
+
+```
+layman --delete science
+```
+
+### Using packages from ::science
+
+To enable the packges from `::science` you need to make sure that you are accepting the `~${ARCH}` keywords for your respective arch.
+
+Make sure that the  `/etc/portage/package.accept_keywords/` folder exists and run
+
+```
+printf '*/*::science ~%s' "$(portageq envvar ARCH)" >> /etc/portage/package.accept_keywords/SCIENCE
+```
+
+## Generic guidelines for contributors <a name="guide"></a>
+
+If you fork, we will merge!   
+We are always going to welcome new contributors and love expanding our collection.   
+
+For basic guidelines please see our [contributing guide](CONTRIBUTING.md).
+
+
+The [GURU Project](https://wiki.gentoo.org/wiki/Project:GURU) has created excellent documentation for potential contributors.   
+We highly advise you to give them a read along with other general Gentoo guidelines
+- GURU guidelines - https://wiki.gentoo.org/wiki/Project:GURU#The_regulations
+- Contributing to Gentoo - https://wiki.gentoo.org/wiki/Contributing_to_Gentoo
+- Gentoo Developers Manual - https://devmanual.gentoo.org/
+
+In addition to the above guidelines please make sure that if you submitting a new package, please add the Science Project as an additional maintainer to the package.   
+For an example, take a look at the metadata for the [Numba](dev-python/numba) package - [dev-python/numba/metadata.xml](dev-python/numba/metadata.xml)
+
+## Support
+
+You can ask for help on [Freenode IRC](https://www.gentoo.org/get-involved/irc-channels/) in [**#gentoo-science**](http://webchat.freenode.net/?channels=gentoo-science).   
+Alternatively you can report bugs on the [GitHub issues page](https://github.com/gentoo/sci/issues).

[gentoo-commits] proj/sci:master commit in: /

[Horea Christian]

commit:     6aa68622074ff08439f3076e646d6dd5757ac68f
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Sep 26 13:19:39 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Sep 26 13:19:39 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6aa68622

Updated badge domain and URL

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index d46485537..f328e252f 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,5 @@
 # [Gentoo Science](https://wiki.gentoo.org/wiki/Project:Science/Overlay) Overlay
-[![Build Status](https://travis-ci.org/gentoo/sci.svg?branch=master)](https://travis-ci.org/gentoo/sci)
+[![Build Status](https://travis-ci.com/gentoo/sci.svg?branch=master)](https://travis-ci.com/gentoo/sci)
 
 This is a Gentoo Linux [ebuild repository](https://wiki.gentoo.org/wiki/Ebuild_repository) which provides numerous scientific software packages.
 

[gentoo-commits] proj/sci:master commit in: /

[Horea Christian]

commit:     69d15a44facf488da2d00bf376889e0b2d5cd900
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Dec  2 01:43:46 2019 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Dec  2 01:44:18 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=69d15a44

README: Updated new portage-compliant repo path

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index d3748dc1b..d46485537 100644
--- a/README.md
+++ b/README.md
@@ -26,7 +26,7 @@ To uninstall the overlay run (again, as root):
 
 ```
 rm /etc/portage/repos.conf/science
-rm -rf /var/lib/overlays/science
+rm /var/db/repos/science -rf
 ```
 
 ## Support

[gentoo-commits] proj/sci:master commit in: /

[David Seifert]

commit:     11115d50321813d153271eb1f478a7c0cc1513e9
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 13 22:26:14 2018 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Dec 13 22:26:14 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=11115d50

skel.metadata.xml: update for GLEP 67

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 skel.metadata.xml | 36 ++++++++++++++++++++++++------------
 1 file changed, 24 insertions(+), 12 deletions(-)

diff --git a/skel.metadata.xml b/skel.metadata.xml
index 4c6550e76..42444c655 100644
--- a/skel.metadata.xml
+++ b/skel.metadata.xml
@@ -1,19 +1,31 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<!--
+This is the example metadata file.
+The root element of this file is <pkgmetadata>. Within this element a
+number of subelements are allowed, the most common being maintainer.
+
+For a full description look at:
+https://devmanual.gentoo.org/ebuild-writing/misc-files/metadata/
+
+Before committing, please remove the comments from this file. They are
+not relevant for general metadata.xml files.
+-->
 <pkgmetadata>
-<herd>sci-blah</herd>
-<maintainer>
-  <email>my.email@blah.doh</email>
+<maintainer type="person">
+	<email>exampledev@gentoo.org</email>
+	<description>Primary maintainer</description>
 </maintainer>
-
-<longdescription>
-  Long description of the package. Check the homepage. Make it useful
-  for users.
-</longdescription>
+<maintainer type="project">
+	<email>exampleproject@gentoo.org</email>
+	<name>Gentoo Example Project</name>
+</maintainer>
+<longdescription>Long description of the package</longdescription>
 <use>
-  <flag name="flag">Description of how USE='flag' affects this package</flag>
+	<flag name="aspell">Uses <pkg>app-text/aspell</pkg> for spell checking.
+		Requires an installed dictionary from <cat>app-dicts</cat></flag>
+	<flag name="flag">Description of how USE='flag' affects this package</flag>
+	<flag name="userland_GNU">Description of how USERLAND='GNU' affects this
+		package</flag>
 </use>
-<upstream>
-  <remote-id type="blah">name-of-package-in-blah</remote-id>
-</upstream>
 </pkgmetadata>

[gentoo-commits] proj/sci:master commit in: /

[David Seifert]

commit:     4883f166e578b98bd3e3d0697cfb84f2e962691f
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 13 20:56:30 2018 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Dec 13 20:56:30 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4883f166

header.txt, skel.ebuild: Update for new copyright policy.

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 skel.ebuild | 80 ++++++++++++++++++++++---------------------------------------
 1 file changed, 29 insertions(+), 51 deletions(-)

diff --git a/skel.ebuild b/skel.ebuild
index 319747c47..0114d8c26 100644
--- a/skel.ebuild
+++ b/skel.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 # NOTE: The comments in this file are for instruction and documentation.
@@ -6,27 +6,16 @@
 # remember to remove them before submitting or committing your ebuild.  That
 # doesn't mean you can't add your own comments though.
 
-# The 'Header' on the third line should just be left alone.  When your ebuild
-# will be committed to cvs, the details on that line will be automatically
-# generated to contain the correct data.
-
 # The EAPI variable tells the ebuild format in use.
-# Defaults to 0 if not specified.
 # It is suggested that you use the latest EAPI approved by the Council.
 # The PMS contains specifications for all EAPIs. Eclasses will test for this
-# variable if they need to use EAPI > 0 features.
-EAPI=5
+# variable if they need to use features that are not universal in all EAPIs.
+EAPI=6
 
-# inherit lists eclasses to inherit functions from. Almost all ebuilds should
-# inherit eutils, as a large amount of important functionality has been
-# moved there. For example, the epatch call mentioned below wont work
+# inherit lists eclasses to inherit functions from. For example, an ebuild
+# that needs the eautoreconf function from autotools.eclass won't work
 # without the following line:
-inherit eutils
-# A well-used example of an eclass function that needs eutils is epatch. If
-# your source needs patches applied, it's suggested to put your patch in the
-# 'files' directory and use:
-#
-#   epatch "${FILESDIR}"/patch-name-here
+#inherit autotools
 #
 # eclasses tend to list descriptions of how to use their functions properly.
 # take a look at /usr/portage/eclass/ for more examples.
@@ -35,7 +24,7 @@ inherit eutils
 DESCRIPTION="This is a sample skeleton ebuild file"
 
 # Homepage, not used by Portage directly but handy for developer reference
-HOMEPAGE="http://foo.example.org/"
+HOMEPAGE="https://foo.example.org/"
 
 # Point to any required sources; these will be automatically downloaded by
 # Portage.
@@ -57,7 +46,7 @@ LICENSE=""
 # of each SLOT and remove everything else.
 # Note that normal applications should use SLOT="0" if possible, since
 # there should only be exactly one version installed at a time.
-# DO NOT USE SLOT=""! This tells Portage to disable SLOTs for this package.
+# Do not use SLOT="", because the SLOT variable must not be empty.
 SLOT="0"
 
 # Using KEYWORDS, we can record masking information *inside* an ebuild
@@ -65,22 +54,21 @@ SLOT="0"
 # set the KEYWORDS variable for every ebuild so that it contains the names of
 # all the architectures with which the ebuild works.  All of the official
 # architectures can be found in the arch.list file which is in
-# /usr/portage/profiles/.  Usually you should just set this to "~x86".  The ~
-# in front of the architecture indicates that the package is new and should be
-# considered unstable until testing proves its stability.  So, if you've
-# confirmed that your ebuild works on x86 and ppc, you'd specify:
-# KEYWORDS="~x86 ~ppc"
+# /usr/portage/profiles/.  Usually you should just set this to "~amd64".
+# The ~ in front of the architecture indicates that the package is new and
+# should be considered unstable until testing proves its stability.  So, if
+# you've confirmed that your ebuild works on amd64 and ppc, you'd specify:
+# KEYWORDS="~amd64 ~ppc"
 # Once packages go stable, the ~ prefix is removed.
 # For binary packages, use -* and then list the archs the bin package
 # exists for.  If the package was for an x86 binary package, then
 # KEYWORDS would be set like this: KEYWORDS="-* x86"
-# DO NOT USE KEYWORDS="*".  This is deprecated and only for backward
-# compatibility reasons.
-KEYWORDS="~x86"
+# Do not use KEYWORDS="*"; this is not valid in an ebuild context.
+KEYWORDS="~amd64"
 
 # Comprehensive list of any and all USE flags leveraged in the ebuild,
-# with the exception of any ARCH specific flags, i.e. "ppc", "sparc",
-# "x86" and "alpha".  Not needed if the ebuild doesn't use any USE flags.
+# with some exceptions, e.g., ARCH specific flags like "amd64" or "ppc".
+# Not needed if the ebuild doesn't use any USE flags.
 IUSE="gnome X"
 
 # A space delimited list of portage features to restrict. man 5 ebuild
@@ -110,7 +98,6 @@ RDEPEND="${DEPEND}"
 
 # The following src_configure function is implemented as default by portage, so
 # you only need to call it if you need a different behaviour.
-# This function is available only in EAPI 2 and later.
 #src_configure() {
 	# Most open-source packages use GNU autoconf for configuration.
 	# The default, quickest (and preferred) way of running configure is:
@@ -129,36 +116,31 @@ RDEPEND="${DEPEND}"
 	#	--mandir=/usr/share/man || die
 	# Note the use of --infodir and --mandir, above. This is to make
 	# this package FHS 2.2-compliant.  For more information, see
-	#   http://www.pathname.com/fhs/
+	#   https://www.pathname.com/fhs/
 #}
 
 # The following src_compile function is implemented as default by portage, so
 # you only need to call it, if you need different behaviour.
-# For EAPI < 2 src_compile runs also commands currently present in
-# src_configure. Thus, if you're using an older EAPI, you need to copy them
-# to your src_compile and drop the src_configure function.
 #src_compile() {
-	# emake (previously known as pmake) is a script that calls the
-	# standard GNU make with parallel building options for speedier
-	# builds (especially on SMP systems).  Try emake first.  It might
-	# not work for some packages, because some makefiles have bugs
-	# related to parallelism, in these cases, use emake -j1 to limit
-	# make to a single process.  The -j1 is a visual clue to others
-	# that the makefiles have bugs that have been worked around.
-
-	#emake || die
+	# emake is a script that calls the standard GNU make with parallel
+	# building options for speedier builds (especially on SMP systems).
+	# Try emake first.  It might not work for some packages, because
+	# some makefiles have bugs related to parallelism, in these cases,
+	# use emake -j1 to limit make to a single process.  The -j1 is a
+	# visual clue to others that the makefiles have bugs that have been
+	# worked around.
+
+	#emake
 #}
 
 # The following src_install function is implemented as default by portage, so
 # you only need to call it, if you need different behaviour.
-# For EAPI < 4 src_install is just returing true, so you need to always specify
-# this function in older EAPIs.
 #src_install() {
 	# You must *personally verify* that this trick doesn't install
 	# anything outside of DESTDIR; do this by reading and
 	# understanding the install part of the Makefiles.
 	# This is the preferred way to install.
-	#emake DESTDIR="${D}" install || die
+	#emake DESTDIR="${D}" install
 
 	# When you hit a failure with emake, do not just use make. It is
 	# better to fix the Makefiles to allow proper parallelization.
@@ -174,11 +156,7 @@ RDEPEND="${DEPEND}"
 	#	mandir="${D}"/usr/share/man \
 	#	infodir="${D}"/usr/share/info \
 	#	libdir="${D}"/usr/$(get_libdir) \
-	#	install || die
+	#	install
 	# Again, verify the Makefiles!  We don't want anything falling
 	# outside of ${D}.
-
-	# The portage shortcut to the above command is simply:
-	#
-	#einstall || die
 #}

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5c948ce2a88e62b745e6d0345e5c45e9dfbf5817
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Oct 27 12:18:51 2018 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Oct 27 12:19:20 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5c948ce2

Bump portage for travis

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 3d53c8b53..241a06e33 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,7 +7,7 @@ cache: pip
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.3.40"
+    - PORTAGE_VER="2.3.51"
 before_install:
     - sudo apt-get -qq update
 install:

[gentoo-commits] proj/sci:master commit in: /

[Horea Christian]

commit:     97775a70fc866efc10701dfc4e9332a6f96f9a85
Author:     Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Mon Aug 20 21:39:35 2018 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Aug 20 21:39:35 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=97775a70

No longer separately downloading installed files

 README.md | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index eb652ee93..6283a58a3 100644
--- a/README.md
+++ b/README.md
@@ -18,11 +18,10 @@ To start using the overlay you now only need to get the ebuilds, via `emerge --s
 
 There is a long-standing BLAS and LAPACK stack incompatibility between the Science Overlay and the Base Gentoo Overlay.
 A fix [is being considered](https://github.com/gentoo/sci/issues/805), bit is still not scheduled for implementation.
-In the mean time, the most automated and up-to-date solution (building on [the original one](https://wiki.gentoo.org/wiki/User_talk:Houseofsuns)) is to run:
+In the mean time, the most automated and up-to-date solution (building on [the original one](https://wiki.gentoo.org/wiki/User_talk:Houseofsuns)) is to run (as root, and after having installed the overlay):
 
 ```
-wget https://gitweb.gentoo.org/proj/sci.git/plain/scripts/sci-lapack
-wget https://gitweb.gentoo.org/proj/sci.git/plain/scripts/lapack-migration.sh
+cd ${EPREFIX}/var/lib/overlays/science/scripts
 ./lapack-migration.sh
 ```
 

[gentoo-commits] proj/sci:master commit in: /

[Horea Christian]

commit:     291a1ff5e0fdb114a2a908d7f04a7fdc5be629f2
Author:     Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Fri Aug 17 20:10:17 2018 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Aug 17 20:10:17 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=291a1ff5

BLAS/LAPACK migration instructions

 README.md | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/README.md b/README.md
index 5b905f7c2..cda4ca018 100644
--- a/README.md
+++ b/README.md
@@ -14,6 +14,18 @@ wget https://gitweb.gentoo.org/proj/sci.git/plain/metadata/science.conf -O /etc/
 
 To start using the overlay you now only need to get the ebuilds, via `emerge --sync`.
 
+### BLAS and LAPACK Migration
+
+There is a long-standing BLAS and LAPACK stack incompatibility between the Science Overlay and the Base Gentoo Overlay.
+A fix [is being considered](https://github.com/gentoo/sci/issues/805), bit is still not scheduled for implementation.
+In the mean time, the most automated and up-to-date solution (building on [the original one](https://wiki.gentoo.org/wiki/User_talk:Houseofsuns)) is to run:
+
+```
+wget https://raw.githubusercontent.com/IBT-FMI/NeuroGentooProject/master/SharedPrefix/sci-lapack
+wget https://raw.githubusercontent.com/IBT-FMI/NeuroGentooProject/master/SharedPrefix/lapack-migration.sh
+./lapack-migration.sh
+```
+
 ### Uninstall
 
 To uninstall the overlay run (again, as root):

[gentoo-commits] proj/sci:master commit in: /

[Horea Christian]

commit:     33515e431970456da8c035eb7b6b27cf756f3e07
Author:     Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Thu Aug 16 15:41:55 2018 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Aug 16 15:41:55 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=33515e43

Typo

 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index cb25afaad..5b905f7c2 100644
--- a/README.md
+++ b/README.md
@@ -26,7 +26,7 @@ rm -rf /var/lib/overlays/science
 ## Support
 
 You can ask for help on [Freenode IRC](https://www.gentoo.org/get-involved/irc-channels/) in `#gentoo-science`.
-Alternatively you can report bugs bugs on the [GitHub issues page](https://github.com/gentoo/sci/issues).
+Alternatively you can report bugs on the [GitHub issues page](https://github.com/gentoo/sci/issues).
 
 ## Contribute
 

[gentoo-commits] proj/sci:master commit in: /

[Horea Christian]

commit:     ec617588fdb360be14e1f375ba2c555ca36dd029
Author:     Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Tue Aug 14 20:02:17 2018 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue Aug 14 20:02:17 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ec617588

Formatting improvements and install instructions

 README.md | 33 +++++++++++++++++++++++++++------
 1 file changed, 27 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 700a326a3..cb25afaad 100644
--- a/README.md
+++ b/README.md
@@ -1,12 +1,33 @@
-# Gentoo Science Overlay
+# [Gentoo Science](https://wiki.gentoo.org/wiki/Project:Science/Overlay) Overlay
 [![Build Status](https://travis-ci.org/gentoo/sci.svg?branch=master)](https://travis-ci.org/gentoo/sci)
 
-An overlay for Gentoo Linux, geared towards scientific packages.
+This is a Gentoo Linux [ebuild repository](https://wiki.gentoo.org/wiki/Ebuild_repository) which provides numerous scientific software packages.
 
-Homepage: [Science Project page](https://wiki.gentoo.org/wiki/Project:Science/Overlay)
+## Install
 
-Please fork! We will merge! See [our contributing guide](https://github.com/gentoo/sci/blob/master/CONTRIBUTING.md) document for more details.
+As per the current [Portage specifications](https://dev.gentoo.org/~zmedico/portage/doc/man/portage.5.html), ebuild repositories (a.k.a. overlays) should be managed via file collections under `/etc/portage/repos.conf/`.
+To enable our overlay without the need for additional software, simply run (as root):
 
-Ask for help on [Freenode IRC](https://www.gentoo.org/get-involved/irc-channels/) in #gentoo-science @ freenode.
+```
+wget https://gitweb.gentoo.org/proj/sci.git/plain/metadata/science.conf -O /etc/portage/repos.conf/science
+```
 
-Report bugs on the [GitHub issues page](https://github.com/gentoo/sci/issues).
+To start using the overlay you now only need to get the ebuilds, via `emerge --sync`.
+
+### Uninstall
+
+To uninstall the overlay run (again, as root):
+
+```
+rm /etc/portage/repos.conf/science
+rm -rf /var/lib/overlays/science
+```
+
+## Support
+
+You can ask for help on [Freenode IRC](https://www.gentoo.org/get-involved/irc-channels/) in `#gentoo-science`.
+Alternatively you can report bugs bugs on the [GitHub issues page](https://github.com/gentoo/sci/issues).
+
+## Contribute
+
+Please fork! We will merge! See [our contributing guide](https://github.com/gentoo/sci/blob/master/CONTRIBUTING.md).

[gentoo-commits] proj/sci:master commit in: /

[Horea Christian]

commit:     f49e7e4bf695762a10bd7eb6df2ef590e7f21a60
Author:     Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Fri Aug  3 15:43:25 2018 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Aug  3 15:52:05 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f49e7e4b

Style improvements and better links.

 README.md | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index f98792b60..700a326a3 100644
--- a/README.md
+++ b/README.md
@@ -1,15 +1,12 @@
 # Gentoo Science Overlay
+[![Build Status](https://travis-ci.org/gentoo/sci.svg?branch=master)](https://travis-ci.org/gentoo/sci)
 
-An overlay for Gentoo, geared towards scientific packages.
+An overlay for Gentoo Linux, geared towards scientific packages.
 
 Homepage: [Science Project page](https://wiki.gentoo.org/wiki/Project:Science/Overlay)
 
+Please fork! We will merge! See [our contributing guide](https://github.com/gentoo/sci/blob/master/CONTRIBUTING.md) document for more details.
 
-Please fork! We will merge! See [this](https://github.com/gentoo/sci/blob/master/CONTRIBUTING.md) document for more instructions.
-
-Ask for help on irc in #gentoo-science @ freenode.
-
-Report bugs on the [github issues site](https://github.com/gentoo/sci/issues)
+Ask for help on [Freenode IRC](https://www.gentoo.org/get-involved/irc-channels/) in #gentoo-science @ freenode.
 
-
-[![Build Status](https://travis-ci.org/gentoo/sci.svg?branch=master)](https://travis-ci.org/gentoo/sci)
+Report bugs on the [GitHub issues page](https://github.com/gentoo/sci/issues).

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     dc0b005bd8af47b278adc1dd8271c6bf3c669f64
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun 21 20:21:29 2018 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun 21 20:21:29 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=dc0b005b

Fix travis deps

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 3841edb5d..3d53c8b53 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,7 +11,7 @@ env:
 before_install:
     - sudo apt-get -qq update
 install:
-    - pip install "lxml<4.2"
+    - pip install lxml PyYAML
 before_script:
     - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr
     - mkdir -p travis-overlay /etc/portage /usr/portage/distfiles
@@ -25,7 +25,7 @@ before_script:
     - echo "portage::250:portage,travis" >> /etc/group
     - wget "https://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
     - ln -s $TRAVIS_BUILD_DIR/portage-portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/repos.conf
-    - ln -s /usr/portage/profiles/default/linux/amd64/17.0 /etc/portage/make.profile
+    - ln -s /usr/portage/profiles/default/linux/amd64/17.1 /etc/portage/make.profile
     - cd travis-overlay
 script:
     - ./../spinner.sh "python ../portage-portage-${PORTAGE_VER}/repoman/bin/repoman full -d"

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     9e54708d1f68fd0ee32d6ddbd6eae025f3eb6b13
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun 21 20:16:19 2018 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun 21 20:16:19 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9e54708d

Bump portage version

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 7e59eb158..3841edb5d 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,7 +7,7 @@ cache: pip
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.3.24"
+    - PORTAGE_VER="2.3.40"
 before_install:
     - sudo apt-get -qq update
 install:

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f942400dda58b2306e70952f1c828bfac6e3d9ec
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Mar 21 21:41:24 2018 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Mar 21 21:41:24 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f942400d

.travis.yml: Fix CI

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 1fbaac369..7e59eb158 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -10,7 +10,8 @@ env:
     - PORTAGE_VER="2.3.24"
 before_install:
     - sudo apt-get -qq update
-    - pip install lxml
+install:
+    - pip install "lxml<4.2"
 before_script:
     - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr
     - mkdir -p travis-overlay /etc/portage /usr/portage/distfiles

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     417c12f8a40197fe197b3cbd977883583f190743
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Mar 21 20:11:37 2018 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Mar 21 20:11:37 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=417c12f8

.travis.yml: Update CI

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 69b86fcea..1fbaac369 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,7 +7,7 @@ cache: pip
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.3.20"
+    - PORTAGE_VER="2.3.24"
 before_install:
     - sudo apt-get -qq update
     - pip install lxml
@@ -23,8 +23,8 @@ before_script:
     - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
     - echo "portage::250:portage,travis" >> /etc/group
     - wget "https://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
-    - ln -s portage-portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/repos.conf
-    - ln -s /usr/portage/profiles/default/linux/amd64/13.0 /etc/portage/make.profile
+    - ln -s $TRAVIS_BUILD_DIR/portage-portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/repos.conf
+    - ln -s /usr/portage/profiles/default/linux/amd64/17.0 /etc/portage/make.profile
     - cd travis-overlay
 script:
     - ./../spinner.sh "python ../portage-portage-${PORTAGE_VER}/repoman/bin/repoman full -d"

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a192df3c34d26b1c7b3754be94d1ec96b4fbd69c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 27 14:00:01 2018 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 27 14:00:01 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a192df3c

Update Portage for travis to latest

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 081744f28..69b86fcea 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,7 +7,7 @@ cache: pip
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.3.14"
+    - PORTAGE_VER="2.3.20"
 before_install:
     - sudo apt-get -qq update
     - pip install lxml

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     01d942f6b153fc7a84d15a5748a230f1e6f1d831
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Nov 18 14:10:40 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Nov 18 14:10:40 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=01d942f6

Bump portage version for travis

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 66ed8497f..081744f28 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,7 +7,7 @@ cache: pip
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.3.13"
+    - PORTAGE_VER="2.3.14"
 before_install:
     - sudo apt-get -qq update
     - pip install lxml

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     570e33bc02d06a5afbf955cd458f6cd1b1fbc786
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 30 09:40:23 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Oct 30 09:40:59 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=570e33bc

Update travis checks to latest portage version

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index f9268cabf..66ed8497f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,7 +7,7 @@ cache: pip
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.3.5"
+    - PORTAGE_VER="2.3.13"
 before_install:
     - sudo apt-get -qq update
     - pip install lxml

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     206ff4a8cd065eacd6c772b237a5e7c922290b46
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Apr 29 09:50:29 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Apr 29 09:50:29 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=206ff4a8

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/openblas: Bump openblas to 0.2.19 (#779)

 sci-libs/openblas/Manifest                         |  2 ++
 sci-libs/openblas/files/openblas-0.2.19-MAKE.patch | 29 +++++++++++++++++
 .../files/openblas-0.2.19-utest_ldflags.patch      | 13 ++++++++
 ...enblas-0.2.15.ebuild => openblas-0.2.19.ebuild} | 37 +++++++++++-----------
 4 files changed, 62 insertions(+), 19 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     aaf2a26ee109949f3565d1952857ba584afff539
Author:     Christoph Junghans <junghans <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 25 22:44:14 2017 +0000
Commit:     Christoph Junghans <junghans <AT> gentoo <DOT> org>
CommitDate: Tue Apr 25 22:44:14 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=aaf2a26e

Merge branch 'master' of ssh://github.com/gentoo-science/sci

 sci-misc/kaldi/Manifest                            |   2 +-
 sci-misc/kaldi/files/Makefile.0d5e4b1.patch        |  45 ++++++++
 .../kaldi/files/default_rules.mk.96eec2b.patch     |  30 +++++
 sci-misc/kaldi/kaldi-0_p20151106.ebuild            | 124 ---------------------
 ...aldi-0_p20160628.ebuild => kaldi-5.1.65.ebuild} | 101 +++++++++--------
 sci-misc/kaldi/metadata.xml                        |   3 +
 6 files changed, 135 insertions(+), 170 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     1ef079380839823bc0ec687210bbf74d63cacad0
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Tue Apr 18 07:26:32 2017 +0000
Commit:     Christoph Junghans <junghans <AT> gentoo <DOT> org>
CommitDate: Tue Apr 18 07:26:32 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1ef07938

Merge pull request #777 from bryant1410/master

Fix broken headings in Markdown files

 CONTRIBUTING.md | 44 ++++++++++++++++++++++----------------------
 README.md       |  2 +-
 2 files changed, 23 insertions(+), 23 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     cfece4a58eb396cc7adfd94c2829871f029d8023
Author:     Christoph Junghans <junghans <AT> gentoo <DOT> org>
AuthorDate: Fri Apr 21 20:06:39 2017 +0000
Commit:     Christoph Junghans <junghans <AT> gentoo <DOT> org>
CommitDate: Fri Apr 21 20:06:39 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cfece4a5

Merge branch 'master' of ssh://github.com/gentoo-science/sci

 CONTRIBUTING.md | 44 ++++++++++++++++++++++----------------------
 README.md       |  2 +-
 2 files changed, 23 insertions(+), 23 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     5a174b623c12c2151e201edef58d0c3aa2499620
Author:     Santiago Castro <santi.1410 <AT> hotmail <DOT> com>
AuthorDate: Tue Apr 18 07:24:24 2017 +0000
Commit:     Christoph Junghans <junghans <AT> gentoo <DOT> org>
CommitDate: Tue Apr 18 07:24:24 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5a174b62

Fix broken Markdown headings

 CONTRIBUTING.md | 44 ++++++++++++++++++++++----------------------
 README.md       |  2 +-
 2 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index f5e81b04d..6c4ba5879 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,12 +1,12 @@
-#Contributions to the Gentoo Science Overlay
+# Contributions to the Gentoo Science Overlay
 
 This guide summarizes the contribution and merging procedures for the Gentoo Science overlay on Github. For more information please visit the [Science Project page](https://wiki.gentoo.org/wiki/Project:Science/Contributing) in the [Gentoo wiki](https://wiki.gentoo.org/).
 
 ----
-##Prerequisite
+## Prerequisite
 For the most convenient way to work with the overlay you should fulfill all prerequisites.
 
-###Required
+### Required
 
 * **Install git**
 
@@ -20,14 +20,14 @@ Familiarize yourself with git and visit [http://git-scm.com/documentation](http:
 
 Everybody who wants to contribute needs to own an account @ [Github](http://github.com/). Please register yourself [there](https://github.com/join).
 
-###Recommended
+### Recommended
 * **Define the echangelog user**
 
 Make sure the ECHANGELOG_USER variable is present in your environment.
 
     echo 'export ECHANGELOG_USER="John Smith <john@smith.com>"' >> ~/.bashrc
 
-###Optional
+### Optional
 * **Setup commit signing**
 
 Create a [gpg key](http://www.gossamer-threads.com/lists/gentoo/dev/268496?do=post_view_threaded) if you don't have one already and make git use it.
@@ -49,40 +49,40 @@ Now git will sign your commits to the overlay by using the gpg key.
     emerge app-portage/repo-commit
 
 ---
-##Contributing ebuilds
+## Contributing ebuilds
 
-###Clone the overlay
+### Clone the overlay
 
 Create a local checkout of the overlay
 
     hub clone gentoo-science/sci
 
-###Fork the overlay
+### Fork the overlay
 In order to send pull request and ask for inclusion of your changes you need to have your own fork of the overlay on github. You can do this by issuing
 
     cd sci
     hub fork
 
-###Branch out for contribution
+### Branch out for contribution
 It is always convenient for development as well as for the review and merging process, if the development is done in branches. Let's branch the overlay into a local branch named PACKAGE_NAME.
 
     git checkout -b PACKAGE_NAME master
 
 For the fastest process during merging it is best to have a single branch per package.
 
-###Work on the package
+### Work on the package
 Now you are ready to work on your package of interest. Once you are finished you should _always_ use **[repoman](http://dev.gentoo.org/~zmedico/portage/doc/man/repoman.1.html)** to do a static analysis of your work.
 
 This can be done with
 
     repoman full
 
-###Commit your work
+### Commit your work
 Once *all* reported problems are resolved, you can commit it
 
     repo-commit "Here we write a comprehensible commit message"
 
-###Push to Github and make a pull request
+### Push to Github and make a pull request
 In order to facilitate potential reverts of mistakes, we prefer to keep the git history as linear as possible. For this, always rebase your changes on the latest remote changes.
 
     hub pull --rebase=preserve github master
@@ -94,24 +94,24 @@ Next we push back the changes in the PACKAGE_NAME branch to our fork and send a
 
 Lastly you need to wait for review comments and the merge of your work. If you feel that they are slacking, don't bother to ping them again. In case you need to include some improvements, just commit your work again using *repo-commit* and push it again to your fork. No need to send another pull-request as your new changes will be added to the original one.
 
-###What's next?
+### What's next?
 If you would like to get direct access to the overlay, prove some contribution and ping us via sci@gentoo.org or on irc in #gentoo-science @ freenode. If you would like to become a dev yourself, prove some more contributions and again, contact us. We are always looking for new candidates.
 
 ----
-##Ebuild recommendations
+## Ebuild recommendations
 As the Gentoo Science overlay is a constant work-in-progress, we have some recommendations for prospective contributors:
 
 * **Aim for writing EAPI=6 ebuilds.** For certain eclasses, EAPI=6 is not allowed yet. In such cases you may use EAPI=5. We will not accept EAPI<5 ebuilds.
 * **Version bumps should always follow the latest guidelines.** For instance, a version bump of an ebuild that still employs autotools-utils.eclass should be avoided. Instead, drop 'autotools-utils', move to 'autotools' and call `default` followed by `eautoreconf` in src_prepare().
 
 ----
-##Merging contributions
+## Merging contributions
 
 **It is important, that if you merge a pull request, you should feel as responsible as if you have written the commits yourself!**
 
 
 
-###Prerequisite
+### Prerequisite
 
 Make sure you have both repos (github & gentoo.org) as remotes defined.
 
@@ -128,30 +128,30 @@ should give
 >origin	git+ssh://git@git.overlays.gentoo.org/proj/sci.git (push)
 
 
-###Review process
+### Review process
 
 In the beginning you should review the pull request on github directly and recommend as much improvements as possible. By this you train the new contributor towards becoming a new dev, which should be our final goal.
 
-####Checking out the pull-request as local branch
+#### Checking out the pull-request as local branch
 Once everything is fine or you like to fix the rest yourself, simply use the following command to get the pull-request in a new branch in your repo.
 
     hub checkout https://github.com/gentoo-science/sci/pull/PULLREQUEST-NUMBER
 
-####Testing and repoman check
+#### Testing and repoman check
 Now check the package by building and installing it, and run *repoman* in the package dir. Remember, when merging a pull request you take the responsibility for the quality of the commit.
 
-####Merge the pull-request branch into master
+#### Merge the pull-request branch into master
 If this is also fine, merge the branch into the master
 
     git checkout master
     git merge USER-BRANCH
 
-####Merging the two remote HEADs
+#### Merging the two remote HEADs
 Finally use the script **merge-dualHEAD** from the *scripts* directory to merge the github and gentoo.org remote repo.
 
 
 ---
-####Contribution to the document
+#### Contribution to the document
 Sebastien Fabbro <bicatali@gentoo.org>
 
 Justin Lecher <jlec@gentoo.org>

diff --git a/README.md b/README.md
index 2ff12d591..92f296e89 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-#Gentoo Science Overlay
+# Gentoo Science Overlay
 
 An overlay for Gentoo, geared towards scientific packages.
 

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     824180c4471b0f97b3bc11acd319f053684d78e1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Apr 14 11:17:28 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Apr 14 11:17:28 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=824180c4

Merge remote-tracking branch 'github/master'

* github/master:
  added CeCILL-B license to MISC-FREE license group (#775)
  sci-visualization/mricrogl: version bump (#773)

 profiles/license_groups                                             | 1 +
 sci-visualization/mricrogl/Manifest                                 | 1 +
 .../{mricrogl-1.0.20160930.ebuild => mricrogl-1.0.20170401.ebuild}  | 6 +++---
 3 files changed, 5 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     dc44d3a6d8dab3cfb039d41f360aa4295b4d9526
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Tue Apr 11 14:48:14 2017 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Tue Apr 11 14:48:14 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=dc44d3a6

Merge remote-tracking branch 'github/master'

 dev-python/dijitso/Manifest                        |  1 +
 dev-python/dijitso/dijitso-2016.2.0.ebuild         | 19 +++++
 dev-python/{ffc => dijitso}/metadata.xml           | 10 ++-
 dev-python/ffc/Manifest                            |  1 +
 .../ffc/{ffc-1.4.0.ebuild => ffc-2016.2.0.ebuild}  |  2 +-
 dev-python/fiat/Manifest                           |  1 +
 .../{fiat-1.4.0.ebuild => fiat-2016.2.0.ebuild}    |  3 +-
 dev-python/instant/Manifest                        |  3 +-
 dev-python/instant/instant-1.2.0.ebuild            | 17 -----
 ...nstant-1.3.0.ebuild => instant-2016.2.0.ebuild} |  4 +-
 dev-python/ufl/Manifest                            |  1 +
 .../ufl/{ufl-1.4.0.ebuild => ufl-2016.2.0.ebuild}  |  2 +-
 sci-libs/dealii/Manifest                           |  2 +
 .../{dealii-9999.ebuild => dealii-8.5.0.ebuild}    | 46 ++++++-------
 sci-libs/dealii/dealii-9999.ebuild                 | 47 ++++++-------
 sci-mathematics/dolfin/Manifest                    |  1 +
 sci-mathematics/dolfin/dolfin-2016.2.0-r2.ebuild   | 80 ++++++++++++++++++++++
 .../files/dolfin-2016.2.0-trilinos-superlu.patch   | 21 ++++++
 sci-mathematics/dolfin/metadata.xml                |  4 ++
 19 files changed, 188 insertions(+), 77 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     7d8c439ad8b8d0fe9fa3a93b877fb511b7d6b2eb
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Mon Apr  3 14:53:40 2017 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Mon Apr  3 14:53:40 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7d8c439a

Merge remote-tracking branch 'github/master'

 net-misc/cernbox-client/Manifest                         |  1 +
 ...x-client-2.3.0.ebuild => cernbox-client-2.3.1.ebuild} |  0
 sci-biology/nilearn/nilearn-0.2.6.ebuild                 | 16 +++++++++++++++-
 sci-biology/nilearn/nilearn-9999.ebuild                  | 16 +++++++++++++++-
 sci-visualization/mricrogl/mricrogl-9999.ebuild          | 10 ++++++----
 sci-visualization/surf-ice/surf-ice-1.0.20170202.ebuild  |  2 +-
 sci-visualization/surf-ice/surf-ice-9999.ebuild          |  9 +++------
 7 files changed, 41 insertions(+), 13 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     4db0a635a463e6a2b4a641d240a28a30d9985f53
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 26 14:45:54 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar 26 14:45:54 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4db0a635

Merge remote-tracking branch 'github/master'

* github/master:
  dev-util/amdapp: Added release and manifest for new AMD download v3.0.130.136 (#605)

 dev-util/amdapp/Manifest                           |  2 ++
 .../{amdapp-3.0-r1.ebuild => amdapp-3.0-r2.ebuild} | 26 +++++++++++++++++-----
 2 files changed, 23 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     8c3e87e5552217637c043ed741da7cf7dbf3390e
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 26 08:17:59 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar 26 08:17:59 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8c3e87e5

Bump to portage 2.3.5

Drop checking of mrueg's version

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index b1a33fd48..f9268cabf 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,7 +7,7 @@ cache: pip
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.3.3"
+    - PORTAGE_VER="2.3.5"
 before_install:
     - sudo apt-get -qq update
     - pip install lxml
@@ -16,7 +16,6 @@ before_script:
     - mkdir -p travis-overlay /etc/portage /usr/portage/distfiles
     - mv !(travis-overlay) travis-overlay/
     - mv .git travis-overlay/
-    - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/.travis.yml" -O .travis.yml.upstream
     - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/spinner.sh"
     - wget -qO - "https://github.com/gentoo/portage/archive/portage-${PORTAGE_VER}.tar.gz" | tar xz
     - wget -qO - "https://github.com/gentoo-mirror/gentoo/archive/master.tar.gz" | tar xz -C /usr/portage --strip-components=1
@@ -26,8 +25,6 @@ before_script:
     - wget "https://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
     - ln -s portage-portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/repos.conf
     - ln -s /usr/portage/profiles/default/linux/amd64/13.0 /etc/portage/make.profile
-    - SIZE=$(stat -c %s .travis.yml.upstream)
-    - if ! cmp -n $SIZE -s .travis.yml .travis.yml.upstream; then echo -e "\e[31m !!! .travis.yml outdated! Update available https://github.com/mrueg/repoman-travis \e[0m" > /tmp/update ; fi
     - cd travis-overlay
 script:
     - ./../spinner.sh "python ../portage-portage-${PORTAGE_VER}/repoman/bin/repoman full -d"

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     e6244ab52a68425b795949fc4c4a8b548d681836
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 26 08:18:30 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar 26 08:18:30 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e6244ab5

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/busfactor: added new ebuild (#692)

 dev-python/busfactor/Manifest                      |   1 +
 dev-python/busfactor/busfactor-0.2.ebuild          |  34 ++++++
 dev-python/busfactor/files/0.2/main.py             |   7 ++
 dev-python/busfactor/files/0.2/setup.py.patch      |  23 ++++
 .../dtk => dev-python/busfactor}/metadata.xml      |   0
 dev-python/gitana/Manifest                         |   1 +
 dev-python/gitana/files/0.2/case_study.py.patch    |  10 ++
 dev-python/gitana/files/0.2/db2json_gui.py.patch   |  67 +++++++++++
 dev-python/gitana/files/0.2/git2db.py.patch        |  28 +++++
 dev-python/gitana/files/0.2/git2db_gui.py.patch    | 124 +++++++++++++++++++++
 dev-python/gitana/files/0.2/gitana.py.patch        |  22 ++++
 dev-python/gitana/files/0.2/gitana_gui.py.patch    |  53 +++++++++
 .../gitana/files/0.2/gitquerier_gitpython.py.patch |  39 +++++++
 dev-python/gitana/files/0.2/init.py                |   1 +
 dev-python/gitana/files/0.2/init_dbschema.py.patch |  20 ++++
 dev-python/gitana/files/0.2/setup.py               |  39 +++++++
 dev-python/gitana/files/0.2/updatedb.py.patch      |  29 +++++
 dev-python/gitana/files/0.2/updatedb_gui.py.patch  |  64 +++++++++++
 dev-python/gitana/gitana-0.2.ebuild                |  76 +++++++++++++
 {sci-libs/dtk => dev-python/gitana}/metadata.xml   |   0
 20 files changed, 638 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     55e206075e962a1f2a2d160cdd738116924ea05e
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Thu Mar 23 03:13:37 2017 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Thu Mar 23 03:13:37 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=55e20607

Merge remote-tracking branch 'github/master'

 .../files/2017.03.21/gsAxel-CMakeLists.txt.patch   | 42 ++++++++++++++++++++++
 sci-mathematics/gismo/gismo-2017.03.21.ebuild      | 13 +++++--
 sci-mathematics/gismo/metadata.xml                 |  1 +
 sci-visualization/forge/forge-9999.ebuild          |  4 ++-
 4 files changed, 57 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     7a59148d303e8937aa9beee0ec888dfed70e37a0
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 22 22:36:06 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 22 22:36:06 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7a59148d

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 sys-cluster/openmpi/Manifest                                     | 3 ++-
 .../openmpi/{openmpi-1.10.3-r2.ebuild => openmpi-1.10.6.ebuild}  | 2 +-
 sys-cluster/openmpi/openmpi-2.0.2.ebuild                         | 2 +-
 .../openmpi/{openmpi-2.0.2.ebuild => openmpi-2.1.0.ebuild}       | 9 +++------
 4 files changed, 7 insertions(+), 9 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a863d3d166620193f838cd418aa1898438d7d788
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 16 19:35:14 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Mar 16 19:35:14 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a863d3d1

Merge remote-tracking branch 'github/master'

* github/master:
  dev-util/emscripten: version bump (#756)
  sci-libs/dealii: do not compile examples (only source gets installed)
  net-misc/cernbox-client: Bump to 2.3.0, (#754)
  sci-libs/cblas-reference: fix for issue #60 (#752)
  Add new gmsh ebuild. (#724)
  sci-mathematics/axel: added new ebuild (#744)
  dev-tex/pythontex: version bump (#736)
  sci-visualization/surf-ice: added stable version (#737)

 dev-tex/pythontex/Manifest                         |  1 +
 ...hontex-0.14-r1.ebuild => pythontex-0.15.ebuild} | 10 ++--
 dev-util/emscripten-fastcomp/Manifest              |  4 +-
 ....3.ebuild => emscripten-fastcomp-1.37.4.ebuild} |  0
 .../files/{1.37.3 => 1.37.4}/CMakeLists.txt.patch  |  0
 .../files/{1.37.3 => 1.37.4}/Version.cpp.patch     |  0
 dev-util/emscripten/Manifest                       |  2 +-
 ...pten-1.37.3.ebuild => emscripten-1.37.4.ebuild} |  0
 .../emscripten/files/{1.37.3 => 1.37.4}/emcc.patch |  0
 .../files/{1.37.3 => 1.37.4}/emcmake.patch         |  0
 net-misc/cernbox-client/Manifest                   |  3 +-
 ...2.2.4.ebuild => cernbox-client-2.2.4-r1.ebuild} | 67 +++++++++------------
 ...nt-2.2.4.ebuild => cernbox-client-2.3.0.ebuild} | 70 +++++++++-------------
 ...ebuild => cblas-reference-20161223-r101.ebuild} |  0
 .../lapack-reference-3.7.0-fix-build-system.patch  | 11 +++-
 sci-libs/dealii/dealii-9999.ebuild                 | 11 ++--
 sci-libs/dtk/Manifest                              |  1 +
 sci-libs/dtk/dtk-2017.02.16.ebuild                 | 39 ++++++++++++
 {sys-devel/gdebugger => sci-libs/dtk}/metadata.xml |  6 +-
 sci-libs/gmsh/Manifest                             |  1 +
 .../gmsh/{gmsh-2.8.5.ebuild => gmsh-2.16.0.ebuild} | 67 +++++++++++----------
 sci-mathematics/axel-vtkview/Manifest              |  1 +
 .../axel-vtkview/axel-vtkview-2017.02.16.ebuild    | 40 +++++++++++++
 .../files/2017.02.16/CMakeLists.txt.patch          | 21 +++++++
 .../2017.02.16/axlVtkView-CMakeLists.txt.patch     | 10 ++++
 .../axel-vtkview}/metadata.xml                     |  6 +-
 sci-mathematics/axel/Manifest                      |  1 +
 sci-mathematics/axel/axel-2017.02.16.ebuild        | 61 +++++++++++++++++++
 .../files/2017.02.16/AxelConfig.cmake.in.patch     | 13 ++++
 .../axel/files/2017.02.16/CMakeLists.txt.patch     | 49 +++++++++++++++
 .../files/2017.02.16/install-AxelConfig.cmake.in   | 67 +++++++++++++++++++++
 .../2017.02.16/install-axel-config.h.in.patch      | 12 ++++
 .../axel/files/2017.02.16/main.cpp.patch           | 23 +++++++
 .../axel}/metadata.xml                             |  6 +-
 sci-visualization/surf-ice/Manifest                |  1 +
 ...ce-9999.ebuild => surf-ice-1.0.20170202.ebuild} | 10 ++--
 36 files changed, 471 insertions(+), 143 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     48fb3146a2a650aef40eda819fe297fb3decb74c
Author:     Christoph Junghans <junghans <AT> gentoo <DOT> org>
AuthorDate: Thu Mar  9 21:22:24 2017 +0000
Commit:     Christoph Junghans <junghans <AT> gentoo <DOT> org>
CommitDate: Thu Mar  9 21:22:24 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=48fb3146

Merge branch 'master' of ssh://github.com/gentoo-science/sci

 sci-misc/praat/Manifest                                     | 2 +-
 sci-misc/praat/{praat-6.0.23.ebuild => praat-6.0.26.ebuild} | 7 ++++++-
 2 files changed, 7 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     d1e806fe0e4549f06abb21e32730af0ad2605c55
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Mon Mar  6 15:09:54 2017 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Mon Mar  6 15:09:54 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d1e806fe

Merge remote-tracking branch 'github/master'

 dev-util/numdiff/Manifest                          |  1 +
 .../{numdiff-5.8.1.ebuild => numdiff-5.9.0.ebuild} |  2 +-
 sci-libs/nipype/nipype-9999.ebuild                 |  5 ++--
 sci-mathematics/mathics/Manifest                   |  1 +
 sci-mathematics/mathics/mathics-1.0.ebuild         | 28 ++++++++++++++++++++++
 sci-mathematics/mathics/metadata.xml               | 21 ++++++++++++++++
 6 files changed, 55 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b22e9d922123cd9d0fc917ae324f6e195e41da96
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Feb 28 20:05:54 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Feb 28 20:05:54 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b22e9d92

Merge remote-tracking branch 'github/master'

* github/master:
  sci-mathematics/gismo: version bump (#743)
  dev-util/emscripten: version bump to 1.37.3
  sci-misc/sfst: Version bump (#740)
  sci-misc/openfst: Version bump (#739)

 dev-util/emscripten-fastcomp/Manifest              |  4 +-
 ....1.ebuild => emscripten-fastcomp-1.37.3.ebuild} |  4 +-
 .../files/{1.37.1 => 1.37.3}/CMakeLists.txt.patch  |  0
 .../files/{1.37.1 => 1.37.3}/Version.cpp.patch     |  0
 dev-util/emscripten/Manifest                       |  2 +-
 ...pten-1.37.1.ebuild => emscripten-1.37.3.ebuild} |  5 +--
 .../emscripten/files/{1.37.1 => 1.37.3}/emcc.patch |  0
 .../files/{1.37.1 => 1.37.3}/emcmake.patch         |  0
 sci-mathematics/gismo/Manifest                     |  2 +-
 sci-mathematics/gismo/files/doc-install.patch      | 46 ----------------------
 .../gismo/files/examples-CMakeLists.patch          | 46 ----------------------
 ...{gismo-0.8.1.ebuild => gismo-2017.02.16.ebuild} | 15 +++----
 sci-mathematics/gismo/metadata.xml                 |  4 ++
 sci-misc/openfst/Manifest                          |  1 +
 sci-misc/openfst/openfst-1.6.1.ebuild              | 30 ++++++++++++++
 sci-misc/sfst/Manifest                             |  1 +
 .../{sfst-1.4.6g.ebuild => sfst-1.4.7d.ebuild}     | 13 +++---
 17 files changed, 57 insertions(+), 116 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     22233b14a86feddf6e1040186225251c3150e81e
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Tue Feb 28 10:24:35 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Feb 28 10:24:35 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=22233b14

Merge pull request #741 from timeraider4u/emscripten

dev-util/emscripten: version bump to 1.37.3

 dev-util/emscripten-fastcomp/Manifest                                | 4 ++--
 ...pten-fastcomp-1.37.1.ebuild => emscripten-fastcomp-1.37.3.ebuild} | 4 ++--
 .../files/{1.37.1 => 1.37.3}/CMakeLists.txt.patch                    | 0
 .../emscripten-fastcomp/files/{1.37.1 => 1.37.3}/Version.cpp.patch   | 0
 dev-util/emscripten/Manifest                                         | 2 +-
 .../{emscripten-1.37.1.ebuild => emscripten-1.37.3.ebuild}           | 5 ++---
 dev-util/emscripten/files/{1.37.1 => 1.37.3}/emcc.patch              | 0
 dev-util/emscripten/files/{1.37.1 => 1.37.3}/emcmake.patch           | 0
 8 files changed, 7 insertions(+), 8 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     8e5843ab858e05c114f116a52bf20c1efd589bcd
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 27 02:30:38 2017 +0000
Commit:     Christoph Junghans <junghans <AT> gentoo <DOT> org>
CommitDate: Mon Feb 27 02:30:38 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8e5843ab

Merge branch 'master' of ssh://github.com/gentoo-science/sci

 sci-libs/htslib/htslib-1.3.2.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b5f06710ffc76e576caf20b81cc37eaf12ae16f5
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 25 20:52:53 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Feb 25 20:52:53 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b5f06710

Use a proper profile for travis

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index d5b8c3abe..b1a33fd48 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -25,7 +25,7 @@ before_script:
     - echo "portage::250:portage,travis" >> /etc/group
     - wget "https://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
     - ln -s portage-portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/repos.conf
-    - ln -s /usr/portage/profiles/base/ /etc/portage/make.profile
+    - ln -s /usr/portage/profiles/default/linux/amd64/13.0 /etc/portage/make.profile
     - SIZE=$(stat -c %s .travis.yml.upstream)
     - if ! cmp -n $SIZE -s .travis.yml .travis.yml.upstream; then echo -e "\e[31m !!! .travis.yml outdated! Update available https://github.com/mrueg/repoman-travis \e[0m" > /tmp/update ; fi
     - cd travis-overlay

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     557ef7880b00a9737b2668bcbbb7df4e8655db3e
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Feb 24 14:00:22 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Feb 24 14:00:22 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=557ef788

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 dev-util/numdiff/metadata.xml |   2 +-
 eclass/depend.php.eclass      | 258 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 259 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     f068b484fa610606476d96a25773174cd7ad53c7
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Fri Feb 24 13:49:10 2017 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Fri Feb 24 13:49:10 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f068b484

Merge remote-tracking branch 'github/master'

 dev-util/numdiff/metadata.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     8026d1f3beef7d0b4ccdb39dbaa0a668d9de4b3d
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Feb 19 17:56:01 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Feb 19 17:56:01 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8026d1f3

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 dev-cpp/icnc/icnc-9999.ebuild                      | 23 +++----
 sci-physics/tauola/Manifest                        |  2 -
 .../tauola/files/tauola-1.1.3-makefile.patch       | 12 ----
 .../files/tauola-1.1.3-tau-spinner-makefile.patch  |  4 +-
 .../tauola/files/tauola-1.1.4-makefile.patch       |  4 +-
 sci-physics/tauola/files/tauola-1.1.5-doc.patch    |  4 +-
 sci-physics/tauola/tauola-1.1.3.ebuild             | 71 ----------------------
 sci-physics/tauola/tauola-1.1.4.ebuild             | 71 ----------------------
 sci-physics/tauola/tauola-1.1.5.ebuild             | 20 +++---
 sci-physics/tauola/tauola-9999.ebuild              | 18 +++---
 sys-cluster/blcr/Manifest                          |  1 -
 sys-cluster/blcr/blcr-0.8.4.ebuild                 | 58 ------------------
 sys-cluster/blcr/blcr-0.8.5.ebuild                 |  8 +--
 sys-cluster/pyslice/pyslice-1.7.ebuild             |  4 +-
 14 files changed, 40 insertions(+), 260 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     5109c7cd88140fbdae8fbfb80d04b5cb64f15e76
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Feb 19 17:20:34 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Feb 19 17:20:34 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5109c7cd

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 sci-libs/cblas-reference/cblas-reference-20161223-r100.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ffdb5e0faae41f5edf9f8bf73eae341691040e37
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 29 20:29:20 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 29 20:29:20 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ffdb5e0f

Use caches for travis

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index 9748695..d5b8c3a 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -3,6 +3,7 @@
 # See https://github.com/mrueg/repoman-travis
 #
 language: python
+cache: pip
 python:
     - pypy
 env:

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b07613b507ad3cd0ce1bce896ae33e1570286030
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 29 11:59:26 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 29 11:59:26 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b07613b5

Merge remote-tracking branch 'github/master'

* github/master:
  sci-misc/praat: Version Bump (#723)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     7d40d942082d81ed8fe927aafdce6df0bb199712
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 14 15:01:25 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 14 15:01:25 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7d40d942

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/trilinos: fix installation

 .../trilinos-12.10.1-fix_install_paths_for_destdir-2.patch     | 10 ++++++++++
 sci-libs/trilinos/trilinos-12.10.1.ebuild                      |  5 +++--
 2 files changed, 13 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     96826415396508fa9c04a2e8a3d6bb6637628b87
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 14 15:01:10 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 14 15:01:10 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=96826415

Import from last-hope overlay

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index aba43cc..9748695 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -33,5 +33,8 @@ script:
 # You can append own scripts after this line
 
 notifications:
-    irc: "chat.freenode.net#gentoo-science"
-
+    irc:
+        channels: "chat.freenode.net#gentoo-science"
+        template:
+            - "%{repository} - %{branch} - %{author}: %{commit_subject} - %{message} - Build details : %{build_url}"
+        use_notice: true

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     2aa5d31db2ac68954f8ec1c5343153542957f736
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 12 17:54:06 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jan 12 17:54:06 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2aa5d31d

Merge remote-tracking branch 'github/master'

* github/master:
  corrected typo
  Surf ice (#719)
  dev-util/emscripten: Revision bump to 1.37.1 (#721)
  use my name instead of online moniker

 dev-python/prov/metadata.xml                       |  2 +-
 dev-util/emscripten-fastcomp/Manifest              | 10 +--
 .../emscripten-fastcomp-1.34.11.ebuild             | 40 ------------
 .../emscripten-fastcomp-1.35.2.ebuild              | 40 ------------
 .../emscripten-fastcomp-1.36.4.ebuild              | 49 --------------
 ....7.ebuild => emscripten-fastcomp-1.37.1.ebuild} |  0
 .../files/1.36.7/CMakeLists.txt.patch              | 10 ---
 .../files/1.36.7/Version.cpp.patch                 | 14 ----
 .../files/{1.36.4 => 1.37.1}/CMakeLists.txt.patch  |  0
 .../files/{1.36.4 => 1.37.1}/Version.cpp.patch     |  0
 dev-util/emscripten/Manifest                       |  5 +-
 dev-util/emscripten/emscripten-1.34.11.ebuild      | 73 ---------------------
 dev-util/emscripten/emscripten-1.35.2.ebuild       | 73 ---------------------
 dev-util/emscripten/emscripten-1.36.4.ebuild       | 75 ----------------------
 ...pten-1.36.7.ebuild => emscripten-1.37.1.ebuild} |  0
 dev-util/emscripten/files/1.36.7/emcc.patch        | 16 -----
 dev-util/emscripten/files/1.36.7/emcmake.patch     | 16 -----
 .../emscripten/files/{1.36.4 => 1.37.1}/emcc.patch |  0
 .../files/{1.36.4 => 1.37.1}/emcmake.patch         |  0
 sci-biology/psychopy/metadata.xml                  |  2 +-
 .../mricrogl/mricrogl-1.0.20151111.ebuild          |  2 +-
 .../mricrogl/mricrogl-1.0.20160930.ebuild          |  2 +-
 sci-visualization/mricrogl/mricrogl-9999.ebuild    |  2 +-
 sci-visualization/mricron/mricron-9999.ebuild      |  2 +-
 sci-visualization/surf-ice/metadata.xml            | 23 +++++++
 sci-visualization/surf-ice/surf-ice-9999.ebuild    | 43 +++++++++++++
 26 files changed, 75 insertions(+), 424 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     0c433653db79c92c830d4c6cd96b62289966c81c
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Mon Jan  9 15:27:34 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan  9 15:27:34 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0c433653

Merge pull request #722 from TheChymera/typo

corrected typo

 sci-visualization/mricrogl/mricrogl-1.0.20151111.ebuild | 2 +-
 sci-visualization/mricrogl/mricrogl-1.0.20160930.ebuild | 2 +-
 sci-visualization/mricrogl/mricrogl-9999.ebuild         | 2 +-
 sci-visualization/mricron/mricron-9999.ebuild           | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5c3e9a4b34d8cd617f900f01fe9cc83721548856
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Mon Jan  9 10:48:11 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan  9 10:48:11 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5c3e9a4b

Merge pull request #720 from TheChymera/muh_name

use my name instead of online moniker

 dev-python/prov/metadata.xml      | 2 +-
 sci-biology/psychopy/metadata.xml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     b2b117497419d143fa3826ca05fd463fe59d2039
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 11 23:17:22 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 11 23:17:22 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b2b11749

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 sci-libs/libxc/Manifest                            |  5 +-
 .../{libxc-2.1.2.ebuild => libxc-2.1.3.ebuild}     |  4 +-
 .../{libxc-2.2.2.ebuild => libxc-2.2.3.ebuild}     |  4 +-
 .../{libxc-2.1.2.ebuild => libxc-3.0.0.ebuild}     |  4 +-
 sci-libs/libxc/metadata.xml                        | 23 ++++++++
 sci-physics/atompaw/Manifest                       |  4 +-
 sci-physics/atompaw/atompaw-3.0.1.9-r1.ebuild      | 67 ---------------------
 sci-physics/atompaw/atompaw-4.0.0.10.ebuild        | 69 ----------------------
 ...paw-4.0.0.13.ebuild => atompaw-4.0.0.14.ebuild} |  2 +-
 sci-physics/atompaw/files/3.0.1-longplot.patch     | 12 ----
 sci-physics/atompaw/metadata.xml                   | 24 ++++++++
 11 files changed, 58 insertions(+), 160 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     729212c8e85006d90a76b0e643539560d1634346
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan  8 17:17:06 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan  8 17:17:06 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=729212c8

Import Upstream Changes

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index cc43e78..aba43cc 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,33 +6,31 @@ language: python
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.3.0"
+    - PORTAGE_VER="2.3.3"
 before_install:
     - sudo apt-get -qq update
     - pip install lxml
 before_script:
-    - mkdir travis-overlay
+    - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr
+    - mkdir -p travis-overlay /etc/portage /usr/portage/distfiles
     - mv !(travis-overlay) travis-overlay/
     - mv .git travis-overlay/
     - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/.travis.yml" -O .travis.yml.upstream
     - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/spinner.sh"
-    - wget "https://github.com/gentoo/portage/archive/portage-${PORTAGE_VER}.tar.gz" -O portage-${PORTAGE_VER}.tar.gz
-    - wget "https://github.com/gentoo-mirror/gentoo/archive/master.tar.gz" -O portage-tree.tar.gz
-    - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr spinner.sh
+    - wget -qO - "https://github.com/gentoo/portage/archive/portage-${PORTAGE_VER}.tar.gz" | tar xz
+    - wget -qO - "https://github.com/gentoo-mirror/gentoo/archive/master.tar.gz" | tar xz -C /usr/portage --strip-components=1
     - chmod a+rwx spinner.sh
     - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
     - echo "portage::250:portage,travis" >> /etc/group
-    - mkdir -p /etc/portage /usr/portage/distfiles
     - wget "https://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
-    - tar xzf portage-${PORTAGE_VER}.tar.gz && mv portage-portage-${PORTAGE_VER} portage-${PORTAGE_VER}
-    - tar xzf portage-tree.tar.gz -C /usr/portage --strip-components=1
-    - cp portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/
+    - ln -s portage-portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/repos.conf
     - ln -s /usr/portage/profiles/base/ /etc/portage/make.profile
     - SIZE=$(stat -c %s .travis.yml.upstream)
     - if ! cmp -n $SIZE -s .travis.yml .travis.yml.upstream; then echo -e "\e[31m !!! .travis.yml outdated! Update available https://github.com/mrueg/repoman-travis \e[0m" > /tmp/update ; fi
     - cd travis-overlay
 script:
-    - ./../spinner.sh "python ../portage-${PORTAGE_VER}/repoman/bin/repoman full -d"
+    - ./../spinner.sh "python ../portage-portage-${PORTAGE_VER}/repoman/bin/repoman full -d"
+# You can append own scripts after this line
 
 notifications:
     irc: "chat.freenode.net#gentoo-science"

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     89bcb17666b298d788ec94b4cffe20ec3571e859
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Sun Jan  8 10:56:34 2017 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sun Jan  8 10:56:34 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=89bcb176

Merge remote-tracking branch 'github/master'

 sci-mathematics/petsc/Manifest                                   | 2 +-
 sci-mathematics/petsc/{petsc-3.7.4.ebuild => petsc-3.7.5.ebuild} | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     9d509c29ddb271b3fc29ab7a798d5077d060bd93
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Tue Jan  3 09:16:00 2017 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Tue Jan  3 09:16:00 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9d509c29

Merge remote-tracking branch 'github/master'

 dev-libs/beignet/Manifest                          |   1 -
 dev-libs/beignet/beignet-1.2.0.ebuild              |  96 ---
 .../beignet/files/llvm-empty-system-libs.patch     |  11 -
 dev-libs/beignet/files/llvm-terminfo.patch         |  20 -
 dev-libs/beignet/files/no-debian-multiarch.patch   |  39 -
 dev-libs/beignet/files/no-hardcoded-cflags.patch   |  13 -
 dev-libs/beignet/metadata.xml                      |   8 -
 sci-libs/superlu_mt/Manifest                       |   1 -
 .../files/superlu_mt-2.1-duplicate-symbols.patch   | 900 ---------------------
 .../files/superlu_mt-2.1-missing-includes.patch    |  44 -
 sci-libs/superlu_mt/metadata.xml                   |  26 -
 sci-libs/superlu_mt/superlu_mt-2.1.ebuild          | 110 ---
 sci-misc/fitscut/Manifest                          |   1 -
 sci-misc/fitscut/fitscut-1.4.4.ebuild              |  39 -
 sci-misc/fitscut/metadata.xml                      |  14 -
 sci-physics/herwig++/Manifest                      |   1 -
 .../herwig++/files/herwig++-2.6.3-looptools.patch  |  64 --
 sci-physics/herwig++/herwig++-2.7.0-r2.ebuild      |  57 --
 sci-physics/herwig++/metadata.xml                  |  23 -
 sci-physics/looptools/Manifest                     |   3 -
 .../looptools/files/looptools-2.10-makefile.patch  |  98 ---
 .../looptools/files/looptools-2.8-makefile.patch   |  96 ---
 sci-physics/looptools/looptools-2.10.ebuild        |  39 -
 sci-physics/looptools/looptools-2.11.ebuild        |  39 -
 sci-physics/looptools/looptools-2.9.ebuild         |  39 -
 sci-physics/looptools/metadata.xml                 |  15 -
 sci-physics/rivet/Manifest                         |   2 -
 sci-physics/rivet/metadata.xml                     |  19 -
 sci-physics/rivet/rivet-2.1.1.ebuild               |  62 --
 sci-physics/rivet/rivet-2.1.2.ebuild               |  62 --
 sci-physics/yoda/Manifest                          |   1 -
 sci-physics/yoda/metadata.xml                      |  18 -
 sci-physics/yoda/yoda-1.0.6.ebuild                 |  50 --
 33 files changed, 2011 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     df63874d78ca0ec8f49ae3c2acfdf200e8c26cce
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 23 09:48:56 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec 23 09:48:56 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=df63874d

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/matplotlib-venn: enabled test phase (#710)
  Bru2nii (#715)

 .../matplotlib-venn/matplotlib-venn-0.11.ebuild       | 19 +++++++++++++------
 sci-biology/bru2nii/Manifest                          |  1 +
 ...u2nii-9999.ebuild => bru2nii-1.0.20161212b.ebuild} | 12 ++++++------
 sci-biology/bru2nii/bru2nii-9999.ebuild               |  4 ++--
 4 files changed, 22 insertions(+), 14 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     d60913ebe9a9712f0e92412ac7ddb884c295e835
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 17 18:05:07 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Dec 17 18:05:07 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d60913eb

Merge remote-tracking branch 'github/master'

* github/master:
  sci-biology/ncbi-genome-download: new ebuild (#712)
  sci-visualization/mricrogl: version bump and dependency update (#711)

 sci-biology/ncbi-genome-download/Manifest           |  1 +
 sci-biology/ncbi-genome-download/metadata.xml       | 12 ++++++++++++
 .../ncbi-genome-download-0.2.2.ebuild               | 21 +++++++++++++++++++++
 sci-visualization/mricrogl/Manifest                 |  1 +
 ...20151111.ebuild => mricrogl-1.0.20160930.ebuild} | 14 +++++++-------
 sci-visualization/mricrogl/mricrogl-9999.ebuild     |  4 ++--
 6 files changed, 44 insertions(+), 9 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     63bf477b85860dd60f0c97a7bff713078b7f4ef3
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Dec 13 06:58:51 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Dec 13 06:58:51 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=63bf477b

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 sci-libs/shtools/Manifest                          |  3 ++
 .../nvidia-ml-py => sci-libs/shtools}/metadata.xml | 13 +++---
 sci-libs/shtools/shtools-4.0_rc1.ebuild            | 50 ++++++++++++++++++++++
 3 files changed, 59 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     ca3cf75a42e67c04e62eea477855c02158c4458f
Author:     Christoph Junghans <junghans <AT> gentoo <DOT> org>
AuthorDate: Tue Dec  6 19:44:50 2016 +0000
Commit:     Christoph Junghans <junghans <AT> gentoo <DOT> org>
CommitDate: Tue Dec  6 19:44:50 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca3cf75a

Merge branch 'master' of ssh://github.com/gentoo-science/sci

 sci-biology/psychopy/Manifest                                           | 1 +
 sci-biology/psychopy/{psychopy-1.84.1.ebuild => psychopy-1.84.2.ebuild} | 0
 2 files changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     9b7d15ce400083aed3b41a79ce6d375643861566
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Wed Nov 23 09:45:06 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Wed Nov 23 09:45:06 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9b7d15ce

Merge pull request #695 from timeraider4u/giac-fix

sci-mathematics/giac: bug-fix for bugzilla bug 598008

 sci-mathematics/giac/giac-1.1.0.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     73afe529a3605b46711d0b944735461f62afb63f
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Wed Nov 23 07:39:57 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Wed Nov 23 07:39:57 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=73afe529

Merge pull request #702 from timeraider4u/master

sci-libs/vtk: deleted sci-libs/vtk because already in portage tree

 sci-libs/vtk/Manifest                       |   4 -
 sci-libs/vtk/files/vtk-6.1.0-freetype.patch |  22 --
 sci-libs/vtk/files/vtk-6.1.0-gdal2.patch    |  33 ---
 sci-libs/vtk/files/vtk-6.1.0-glext.patch    |  13 -
 sci-libs/vtk/files/vtk-6.1.0-install.patch  |  19 --
 sci-libs/vtk/files/vtk-6.1.0-memset.patch   | 147 ----------
 sci-libs/vtk/files/vtk-6.1.0-netcdf.patch   |  29 --
 sci-libs/vtk/files/vtk-6.1.0-system.patch   |  27 --
 sci-libs/vtk/files/vtk-6.1.0-web.patch      |  25 --
 sci-libs/vtk/metadata.xml                   |  24 --
 sci-libs/vtk/vtk-6.1.0-r3.ebuild            | 420 ----------------------------
 11 files changed, 763 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     24f1133afbfa8c95136faf8c4712797d2bc813e3
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov  8 19:26:28 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov  8 19:26:28 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=24f1133a

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 sys-cluster/openmpi/Manifest                       |  1 +
 ...enmpi-1.10.3-r2.ebuild => openmpi-2.0.1.ebuild} | 28 ++++------------------
 2 files changed, 5 insertions(+), 24 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     037f5553f6d97c79fcb66149500f170615df7052
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Oct 18 17:30:06 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Oct 18 17:30:06 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=037f5553

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/nipype: added missing dep (#694)

 sci-libs/nipype/nipype-0.11.0.ebuild | 1 +
 sci-libs/nipype/nipype-0.12.0.ebuild | 1 +
 sci-libs/nipype/nipype-0.12.1.ebuild | 1 +
 3 files changed, 3 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     f3c3327961a0125ce5cf81995efcf154e6c00a7e
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Wed Oct 12 06:25:50 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Wed Oct 12 06:25:50 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f3c33279

Merge remote-tracking branch 'github/master'

 Conflicts:
	sci-biology/idba/metadata.xml

 Takeover file from origin/master,
 was moved/renamed in github/master.

 dev-lang/julia/files/63julia-gentoo.el             |   2 -
 dev-lang/julia/julia-9999.ebuild                   | 176 ---------------------
 dev-lang/julia/metadata.xml                        |  24 ---
 net-misc/cernbox-client/Manifest                   |   2 +
 .../cernbox-client/cernbox-client-2.2.4.ebuild     | 118 ++++++++++++++
 .../files/shell-integration-nautilus.patch         |  25 +++
 net-misc/cernbox-client/metadata.xml               |  27 ++++
 sci-biology/abyss/abyss-1.9.0.ebuild               |   1 +
 sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch    |  34 ++++
 sci-biology/biopython/Manifest                     |   1 -
 sci-biology/biopython/biopython-1.67-r1.ebuild     |  60 -------
 .../biopython/files/biopython-1.67-pull-884.patch  |  87 ----------
 sci-biology/biopython/metadata.xml                 |   8 -
 sci-biology/hmmer/Manifest                         |   1 -
 .../hmmer/files/hmmer-3.1_beta2-fix_tests.patch    |  12 --
 .../hmmer/files/hmmer-3.1_beta2-perl-5.16-2.patch  |  90 -----------
 sci-biology/hmmer/hmmer-3.1_beta2.ebuild           |  48 ------
 sci-biology/hmmer/metadata.xml                     |   8 -
 sci-biology/nilearn/Manifest                       |   1 +
 sci-biology/nilearn/nilearn-0.1.4.1.ebuild         |  11 +-
 sci-biology/nilearn/nilearn-0.2.4.ebuild           |   7 +-
 sci-biology/nilearn/nilearn-0.2.5.ebuild           |   7 +-
 .../{nilearn-0.2.4.ebuild => nilearn-0.2.6.ebuild} |   7 +-
 sci-biology/nilearn/nilearn-9999.ebuild            |  11 +-
 .../omalloc => sci-biology/nireg}/metadata.xml     |   8 +-
 sci-biology/nireg/nireg-9999.ebuild                |  33 ++++
 sci-biology/nistats/nistats-9999.ebuild            |  16 +-
 sci-biology/nitime/Manifest                        |   1 +
 .../spglib => sci-biology/nitime}/metadata.xml     |   9 +-
 .../nitime-0.6.ebuild}                             |  25 +--
 .../dipy-9999.ebuild => nitime/nitime-9999.ebuild} |  26 +--
 sci-biology/psychopy/Manifest                      |   1 +
 ...ychopy-1.84.0.ebuild => psychopy-1.84.1.ebuild} |   2 +-
 sci-biology/pybrain/Manifest                       |   1 +
 .../{pybrain-9999.ebuild => pybrain-0.3.3.ebuild}  |  21 ++-
 sci-biology/pybrain/pybrain-9999.ebuild            |  14 +-
 sci-biology/vcftools/Manifest                      |   1 -
 sci-biology/vcftools/metadata.xml                  |  11 --
 sci-biology/vcftools/vcftools-0.1.14.ebuild        |  55 -------
 ....ebuild => blas-reference-20131116-r100.ebuild} |   0
 ....ebuild => blas-reference-20151113-r100.ebuild} |   0
 ...ebuild => cblas-reference-20110218-r100.ebuild} |   2 +-
 ...ebuild => cblas-reference-20151113-r100.ebuild} |   2 +-
 ...0.ebuild => lapack-reference-3.5.0-r100.ebuild} |   0
 ...1.ebuild => lapack-reference-3.6.0-r100.ebuild} |   0
 sci-libs/nibabel/nibabel-1.3.0.ebuild              |  11 +-
 sci-libs/nibabel/nibabel-2.0.1.ebuild              |   9 +-
 sci-libs/nibabel/nibabel-2.1.0.ebuild              |   9 +-
 sci-libs/nibabel/nibabel-9999.ebuild               |   9 +-
 sci-libs/nipy/nipy-0.4.0.ebuild                    |   4 +-
 sci-libs/nipy/nipy-9999.ebuild                     |   4 +-
 sci-libs/nipype/nipype-0.11.0.ebuild               |   4 +-
 sci-libs/nipype/nipype-0.12.0.ebuild               |  10 +-
 sci-libs/nipype/nipype-0.12.1.ebuild               |  10 +-
 sci-libs/nipype/nipype-9999.ebuild                 |  10 +-
 sci-mathematics/mdp/Manifest                       |   1 +
 .../mdp/{mdp-3.3.ebuild => mdp-3.5.ebuild}         |  13 +-
 .../{blas-2.1-r5.ebuild => blas-3.6-r100.ebuild}   |   2 +-
 .../{cblas-2.0-r4.ebuild => cblas-3.6-r100.ebuild} |   2 +-
 .../{lapack-3.6.ebuild => lapack-3.6-r100.ebuild}  |   2 +-
 60 files changed, 388 insertions(+), 708 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     41280a4b3d4f0f68600cbe4a7ea31226cbbbdda3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 14 17:15:32 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep 14 17:15:32 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=41280a4b

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/prov: updated python compatibility and fixed test phase (#672)

 dev-python/prov/prov-1.4.0.ebuild | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     0dc5320ee8f5a3fb32884b3c2eff34498e00d522
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Sep  6 00:18:39 2016 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Sep  6 00:18:39 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0dc5320e

Merge branch 'master' of ssh://github.com/gentoo-science/sci

 media-libs/avbin-bin/Manifest                              |  2 ++
 media-libs/avbin-bin/avbin-bin-7.ebuild                    | 10 +++++-----
 .../avbin-bin/{avbin-bin-7.ebuild => avbin-bin-8.1.ebuild} | 14 +++++++-------
 sci-libs/dealii/Manifest                                   |  4 ++--
 .../dealii/{dealii-8.4.1-r1.ebuild => dealii-8.4.2.ebuild} |  0
 sci-libs/nibabel/Manifest                                  |  1 +
 sci-libs/nibabel/nibabel-1.3.0.ebuild                      |  4 ++--
 sci-libs/nibabel/nibabel-2.0.1.ebuild                      |  6 +++---
 .../nibabel/{nibabel-1.3.0.ebuild => nibabel-2.1.0.ebuild} |  6 +++---
 sci-libs/nibabel/nibabel-9999.ebuild                       |  6 +++---
 sci-libs/nipype/nipype-0.11.0.ebuild                       |  2 +-
 sci-libs/nipype/nipype-0.12.0.ebuild                       |  2 +-
 sci-libs/nipype/nipype-0.12.1.ebuild                       |  2 +-
 sci-libs/nipype/nipype-9999.ebuild                         |  2 +-
 sci-libs/pydicom/pydicom-0.9.8.ebuild                      |  6 +++---
 sci-libs/pydicom/pydicom-0.9.9.ebuild                      |  6 +++---
 sci-libs/pydicom/pydicom-9999.ebuild                       |  6 +++---
 17 files changed, 41 insertions(+), 38 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     b3f9fef14cdec08b463c153ea9964b5d5c95ea2a
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Sep  2 22:08:46 2016 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Sep  2 22:08:46 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b3f9fef1

Merge branch 'master' of ssh://github.com/gentoo-science/sci

 .../libsc/{libsc-1.0.ebuild => libsc-9999.ebuild}  | 32 ++++++++++++---
 .../p4est/{p4est-1.0.ebuild => p4est-9999.ebuild}  | 48 +++++++++++++++-------
 2 files changed, 60 insertions(+), 20 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Bronder]

commit:     38018248611beb56550f01820dd5e83b3b23b77a
Author:     Justin Bronder <jsbronder <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 29 20:45:07 2016 +0000
Commit:     Justin Bronder <jsbronder <AT> gentoo <DOT> org>
CommitDate: Mon Aug 29 20:45:07 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=38018248

Merge remote-tracking branch 'github/multilib_mpi'

 eclass/mpi.eclass                                  |   3 +
 .../{mpich-3.1.4-r1.ebuild => mpich-3.2-r2.ebuild} |  82 ++++++++------
 ...nmpi-1.10.3.ebuild => openmpi-1.10.3-r2.ebuild} | 121 ++++++++++++---------
 3 files changed, 119 insertions(+), 87 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     1ecfea5e8c11b6e0fb852ddb1cefa7495a2e079e
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Aug 23 20:17:42 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Aug 23 20:17:42 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1ecfea5e

Merge remote-tracking branch 'github/master'

* github/master:
  Psychopy - version bump (#659)

 sci-biology/psychopy/Manifest                                      | 1 +
 .../psychopy/{psychopy-1.78.00.ebuild => psychopy-1.84.0.ebuild}   | 7 +++++--
 2 files changed, 6 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     70a07cf6ba63d4937e475165f877b346f1ce03bb
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 14 19:26:10 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Aug 14 19:26:10 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=70a07cf6

Merge remote-tracking branch 'github/master'

* github/master:
  dev-util/emscripten: version bump to 1.36.7 (#657)

 dev-util/emscripten-fastcomp/Manifest                          |  2 ++
 ...astcomp-1.36.4.ebuild => emscripten-fastcomp-1.36.7.ebuild} | 10 +++++++---
 .../files/{1.36.4 => 1.36.7}/CMakeLists.txt.patch              |  0
 .../files/{1.36.4 => 1.36.7}/Version.cpp.patch                 |  0
 dev-util/emscripten/Manifest                                   |  1 +
 .../{emscripten-1.36.4.ebuild => emscripten-1.36.7.ebuild}     |  2 +-
 dev-util/emscripten/files/{1.36.4 => 1.36.7}/emcc.patch        |  0
 dev-util/emscripten/files/{1.36.4 => 1.36.7}/emcmake.patch     |  0
 8 files changed, 11 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     4b3bb659947010318ad880395a372e7607597ddc
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Aug  6 06:46:40 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Aug  6 06:46:40 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4b3bb659

Merge remote-tracking branch 'github/master'

* github/master:
  Version bumps for sci-physics/geant-vmc and sci-physics/vgm (#655)

 sci-physics/geant-vmc/Manifest                     |  1 +
 sci-physics/geant-vmc/geant-vmc-3.1.15a.ebuild     |  4 +--
 sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild     |  4 +--
 ...eant-vmc-9999.ebuild => geant-vmc-4.3.3.ebuild} | 22 ++++++++--------
 sci-physics/geant-vmc/geant-vmc-9999.ebuild        | 22 ++++++++--------
 sci-physics/vgm/Manifest                           |  1 +
 .../vgm/{vgm-9999.ebuild => vgm-4.3.ebuild}        | 30 ++++++++++++----------
 sci-physics/vgm/vgm-9999.ebuild                    | 30 ++++++++++++----------
 8 files changed, 62 insertions(+), 52 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     b87aad117fc9f057a9f5e2278a8a9893005ef1ba
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Jul 20 17:47:58 2016 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Jul 20 17:47:58 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b87aad11

Merge branch 'master' of ssh://github.com/gentoo-science/sci

 sci-libs/nipype/Manifest                           |  1 +
 sci-libs/nipype/nipype-0.11.0.ebuild               |  4 +-
 .../{nipype-0.11.0.ebuild => nipype-0.12.0.ebuild} |  4 +-
 sci-misc/kaldi/Manifest                            |  2 +-
 sci-misc/kaldi/files/Makefile.patch                |  4 +-
 sci-misc/kaldi/files/configure.patch               | 93 ----------------------
 .../kaldi/files/default_rules.mk.a7d9824.patch     |  4 +-
 sci-misc/kaldi/files/default_rules.mk.patch        | 47 -----------
 sci-misc/kaldi/kaldi-0_p20150709.ebuild            | 58 --------------
 ...0_p20151106.ebuild => kaldi-0_p20160628.ebuild} | 41 ++++++----
 10 files changed, 36 insertions(+), 222 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     f10c1b51728a87f64a9736093e04e0b1047f3cec
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jul 20 13:51:34 2016 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Jul 20 13:51:34 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f10c1b51

Merge pull request #649 from TheChymera/nipype

sci-libs/nipype version bump

 sci-libs/nipype/Manifest                                       | 1 +
 sci-libs/nipype/nipype-0.11.0.ebuild                           | 4 ++--
 sci-libs/nipype/{nipype-0.11.0.ebuild => nipype-0.12.0.ebuild} | 4 ++--
 3 files changed, 5 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     6970339fa0024080954012617e6359d6abee6764
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jul 20 13:49:58 2016 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Jul 20 13:49:58 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6970339f

Merge pull request #634 from akreal/sci-misc/kaldi

sci-misc/kaldi: version bump; add speex USE flag

 sci-misc/kaldi/Manifest                            |  2 +-
 sci-misc/kaldi/files/Makefile.patch                |  4 +-
 sci-misc/kaldi/files/configure.patch               | 93 ----------------------
 .../kaldi/files/default_rules.mk.a7d9824.patch     |  4 +-
 sci-misc/kaldi/files/default_rules.mk.patch        | 47 -----------
 sci-misc/kaldi/kaldi-0_p20150709.ebuild            | 58 --------------
 ...0_p20151106.ebuild => kaldi-0_p20160628.ebuild} | 41 ++++++----
 7 files changed, 31 insertions(+), 218 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     57ee10981824b082fe40f0bfa24ac8e9b6ddf98b
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jul 12 21:42:39 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jul 12 21:42:39 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=57ee1098

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 dev-python/pyfftw/Manifest                         |   2 +-
 .../{pyfftw-0.10.1.ebuild => pyfftw-0.10.4.ebuild} |   1 +
 dev-python/pyfftw/pyfftw-9999.ebuild               |   1 +
 sci-biology/ants/ants-9999.ebuild                  |   4 +-
 sci-libs/dealii/Manifest                           |   2 -
 sci-libs/dealii/dealii-8.1.0-r2.ebuild             | 121 ---------
 ...{dealii-8.4.1.ebuild => dealii-8.4.1-r1.ebuild} |   1 +
 sci-libs/dealii/dealii-9999.ebuild                 |   9 +-
 .../files/dealii-8.1.0-p4est1.0-support.patch      | 271 ---------------------
 sci-libs/trilinos/Manifest                         |   4 +-
 sci-libs/trilinos/trilinos-11.10.2.ebuild          | 202 ---------------
 sci-libs/trilinos/trilinos-11.12.1-r1.ebuild       | 202 ---------------
 sci-libs/trilinos/trilinos-11.14.1-r1.ebuild       |   3 +-
 sci-libs/trilinos/trilinos-12.0.1.ebuild           |   3 +-
 sci-libs/trilinos/trilinos-12.2.1.ebuild           |   3 +-
 ...ilinos-12.6.2.ebuild => trilinos-12.6.3.ebuild} |   3 +-
 sci-mathematics/petsc/Manifest                     |   5 +-
 ...rpath.patch => petsc-3.7.0-disable-rpath.patch} |   7 +-
 ...tch => petsc-3.7.0-fix_sandbox_violation.patch} |  10 +-
 .../{petsc-3.5.3.ebuild => petsc-3.5.4.ebuild}     |   4 +-
 sci-mathematics/petsc/petsc-3.6.3.ebuild           | 247 -------------------
 .../{petsc-3.6.0.ebuild => petsc-3.7.2.ebuild}     |  18 +-
 22 files changed, 47 insertions(+), 1076 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     bb37e4a8047c5eaca1f3f6f827597bcf1520615f
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Tue Jul 12 19:58:27 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Tue Jul 12 19:58:27 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=bb37e4a8

Merge remote-tracking branch 'github/master'

 sci-biology/ants/ants-9999.ebuild                  |   4 +-
 sci-libs/dealii/Manifest                           |   2 -
 sci-libs/dealii/dealii-8.1.0-r2.ebuild             | 121 ---------
 ...{dealii-8.4.1.ebuild => dealii-8.4.1-r1.ebuild} |   1 +
 sci-libs/dealii/dealii-9999.ebuild                 |   9 +-
 .../files/dealii-8.1.0-p4est1.0-support.patch      | 271 ---------------------
 sci-libs/trilinos/Manifest                         |   4 +-
 sci-libs/trilinos/trilinos-11.10.2.ebuild          | 202 ---------------
 sci-libs/trilinos/trilinos-11.12.1-r1.ebuild       | 202 ---------------
 sci-libs/trilinos/trilinos-11.14.1-r1.ebuild       |   3 +-
 sci-libs/trilinos/trilinos-12.0.1.ebuild           |   3 +-
 sci-libs/trilinos/trilinos-12.2.1.ebuild           |   3 +-
 ...ilinos-12.6.2.ebuild => trilinos-12.6.3.ebuild} |   3 +-
 sci-mathematics/petsc/Manifest                     |   5 +-
 ...rpath.patch => petsc-3.7.0-disable-rpath.patch} |   7 +-
 ...tch => petsc-3.7.0-fix_sandbox_violation.patch} |  10 +-
 .../{petsc-3.5.3.ebuild => petsc-3.5.4.ebuild}     |   4 +-
 sci-mathematics/petsc/petsc-3.6.3.ebuild           | 247 -------------------
 .../{petsc-3.6.0.ebuild => petsc-3.7.2.ebuild}     |  18 +-
 19 files changed, 44 insertions(+), 1075 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     05202f4bb419e727e7bd3fbc2ee56c3fba0a6067
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jul  5 10:10:13 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Tue Jul  5 10:10:13 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=05202f4b

Merge pull request #639 from TheChymera/ants

sci-biology/ants: removed dependency

 sci-biology/ants/ants-9999.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     23820d64a4e700e20d00f63bf88493c33e0f807b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jul  4 13:29:48 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jul  4 13:29:48 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=23820d64

Merge pull request #644 from TheChymera/email

Updated my email address

 dev-python/future/metadata.xml       | 2 +-
 dev-python/prov/metadata.xml         | 2 +-
 dev-python/pydotplus/metadata.xml    | 2 +-
 sci-biology/dipy/metadata.xml        | 2 +-
 sci-biology/nilearn/metadata.xml     | 2 +-
 sci-biology/nistats/metadata.xml     | 2 +-
 sci-biology/psychopy/metadata.xml    | 2 +-
 sci-libs/nibabel/metadata.xml        | 2 +-
 sci-libs/nipy-data/metadata.xml      | 2 +-
 sci-libs/nipy-templates/metadata.xml | 2 +-
 sci-libs/nipy/metadata.xml           | 2 +-
 sci-libs/nipype/metadata.xml         | 2 +-
 12 files changed, 12 insertions(+), 12 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     d0e51155ed442f02938ce03335a3f18c46300e92
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jul  4 13:28:15 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jul  4 13:28:15 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d0e51155

Merge pull request #646 from TheChymera/nilearn

sci-biology/nilearn: version bump

 sci-biology/nilearn/Manifest                                       | 1 +
 sci-biology/nilearn/{nilearn-0.2.4.ebuild => nilearn-0.2.5.ebuild} | 0
 2 files changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     9b746ab8ae60e858b6872c69be5a79822c9d64d3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jul  2 08:45:39 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jul  2 08:45:39 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9b746ab8

Install missing dependency

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index 2a22449..cc43e78 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,6 +9,7 @@ env:
     - PORTAGE_VER="2.3.0"
 before_install:
     - sudo apt-get -qq update
+    - pip install lxml
 before_script:
     - mkdir travis-overlay
     - mv !(travis-overlay) travis-overlay/

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     066f14158b26376eeb06d18b498cc066f9536866
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jul  2 08:39:29 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jul  2 08:39:29 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=066f1415

Fix new location of repoman script

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 356c812..2a22449 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -31,7 +31,7 @@ before_script:
     - if ! cmp -n $SIZE -s .travis.yml .travis.yml.upstream; then echo -e "\e[31m !!! .travis.yml outdated! Update available https://github.com/mrueg/repoman-travis \e[0m" > /tmp/update ; fi
     - cd travis-overlay
 script:
-    - ./../spinner.sh "python ../portage-${PORTAGE_VER}/bin/repoman full -d"
+    - ./../spinner.sh "python ../portage-${PORTAGE_VER}/repoman/bin/repoman full -d"
 
 notifications:
     irc: "chat.freenode.net#gentoo-science"

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     acc4508f3c634b6588cb04c3fc3f9b840a4a5906
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jul  2 08:35:15 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jul  2 08:35:15 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=acc4508f

Fix dir naming

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 57f0725..356c812 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -23,7 +23,7 @@ before_script:
     - echo "portage::250:portage,travis" >> /etc/group
     - mkdir -p /etc/portage /usr/portage/distfiles
     - wget "https://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
-    - tar xzf portage-${PORTAGE_VER}.tar.gz
+    - tar xzf portage-${PORTAGE_VER}.tar.gz && mv portage-portage-${PORTAGE_VER} portage-${PORTAGE_VER}
     - tar xzf portage-tree.tar.gz -C /usr/portage --strip-components=1
     - cp portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/
     - ln -s /usr/portage/profiles/base/ /etc/portage/make.profile

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     60ba50c570d55b9bfc09f5443d66ecebdd6811d6
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jul  2 08:28:12 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jul  2 08:28:12 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=60ba50c5

Update to new portage naming schema

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 087935b..57f0725 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -15,7 +15,7 @@ before_script:
     - mv .git travis-overlay/
     - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/.travis.yml" -O .travis.yml.upstream
     - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/spinner.sh"
-    - wget "https://github.com/gentoo/portage/archive/v${PORTAGE_VER}.tar.gz" -O portage-${PORTAGE_VER}.tar.gz
+    - wget "https://github.com/gentoo/portage/archive/portage-${PORTAGE_VER}.tar.gz" -O portage-${PORTAGE_VER}.tar.gz
     - wget "https://github.com/gentoo-mirror/gentoo/archive/master.tar.gz" -O portage-tree.tar.gz
     - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr spinner.sh
     - chmod a+rwx spinner.sh

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     139e0f0fe24fff0da48b3ab5673d1f2c9fa8d6e9
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jul  2 08:25:59 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jul  2 08:25:59 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=139e0f0f

Drop xml checks in favour of repoman checks

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 31829c5..087935b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,7 +9,6 @@ env:
     - PORTAGE_VER="2.3.0"
 before_install:
     - sudo apt-get -qq update
-    - sudo apt-get install -y libxml2
 before_script:
     - mkdir travis-overlay
     - mv !(travis-overlay) travis-overlay/
@@ -31,12 +30,8 @@ before_script:
     - SIZE=$(stat -c %s .travis.yml.upstream)
     - if ! cmp -n $SIZE -s .travis.yml .travis.yml.upstream; then echo -e "\e[31m !!! .travis.yml outdated! Update available https://github.com/mrueg/repoman-travis \e[0m" > /tmp/update ; fi
     - cd travis-overlay
-    - wget "https://raw.githubusercontent.com/mgorny/gentoo-xml-schema/master/metadata.xsd" -O metadata.xsd
 script:
     - ./../spinner.sh "python ../portage-${PORTAGE_VER}/bin/repoman full -d"
-# You can append own scripts after this line
-    #too old xmllint on travis
-    #- xmllint --noout --schema metadata.xsd */*/metadata.xml 2>&1 | grep "fails to validate"; [[ ${PIPESTATUS[0]} == 0 ]] || false
 
 notifications:
     irc: "chat.freenode.net#gentoo-science"

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     40837a73e6ab1b0c6aa9bb7b22c9b55c583751c7
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jul  2 08:20:31 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jul  2 08:20:31 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=40837a73

Use latest portage for travis

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index b19309f..31829c5 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,7 +6,7 @@ language: python
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.2.28"
+    - PORTAGE_VER="2.3.0"
 before_install:
     - sudo apt-get -qq update
     - sudo apt-get install -y libxml2

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5ff18e26b89db4ec07a88ef5f0a3114711c7e696
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jul  2 08:08:52 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jul  2 08:08:52 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5ff18e26

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/libmed: initial ebuild bump

 sci-libs/libmed/Manifest                           |  1 +
 .../libmed/files/libmed-3.1.0-cmake-fortran.patch  | 20 +++++++
 .../libmed/files/libmed-3.1.0-fix-swig-build.patch | 19 +++++++
 sci-libs/libmed/libmed-3.1.0.ebuild                | 64 ++++++++++++++++++++++
 {app-text/dgs => sci-libs/libmed}/metadata.xml     |  0
 5 files changed, 104 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     54306cd64bf9a690b48481e92df431b8caed769d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jul  2 07:51:52 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jul  2 07:51:52 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=54306cd6

Merge pull request #642 from Fat-Zer/libmed

sci-libs/libmed: initial ebuild bump

 sci-libs/libmed/Manifest                           |  1 +
 .../libmed/files/libmed-3.1.0-cmake-fortran.patch  | 20 +++++++
 .../libmed/files/libmed-3.1.0-fix-swig-build.patch | 19 +++++++
 sci-libs/libmed/libmed-3.1.0.ebuild                | 64 ++++++++++++++++++++++
 {app-text/dgs => sci-libs/libmed}/metadata.xml     |  0
 5 files changed, 104 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     8931e360c2cb5b199c7da6c1005c4324a3b8be19
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 27 13:43:55 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Mon Jun 27 13:43:55 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8931e360

Merge pull request #641 from TheChymera/dipy

Dipy package

 sci-biology/dipy/Manifest                          |  1 +
 .../dipy-0.11.0.ebuild}                            | 19 ++++++-----
 sci-biology/dipy/dipy-9999.ebuild                  | 37 ++++++++++++++++++++++
 .../future => sci-biology/dipy}/metadata.xml       | 10 +++---
 4 files changed, 54 insertions(+), 13 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     1c3d17cb3dbd37342aaa2009c395050ca6e8dcb8
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Tue Jun 28 12:44:13 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Tue Jun 28 12:44:13 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1c3d17cb

Merge remote-tracking branch 'github/master'

 sci-biology/dipy/Manifest                          |  1 +
 .../dipy-0.11.0.ebuild}                            | 19 ++++++-----
 sci-biology/dipy/dipy-9999.ebuild                  | 37 ++++++++++++++++++++++
 .../future => sci-biology/dipy}/metadata.xml       | 10 +++---
 4 files changed, 54 insertions(+), 13 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     6e3e95593953605c2d1d5ca41a861d16036c77ca
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Wed Jun 15 14:17:17 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Wed Jun 15 14:17:17 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6e3e9559

Merge remote-tracking branch 'github/master'

 sci-biology/nilearn/Manifest                                     | 1 +
 .../nilearn/{nilearn-0.1.4.1.ebuild => nilearn-0.2.4.ebuild}     | 9 +++------
 2 files changed, 4 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     49b5d8cca90c0091c5cdb7f0dab6b71b588c2fff
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 15 09:48:23 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Wed Jun 15 09:48:23 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=49b5d8cc

Merge pull request #630 from TheChymera/nilearn

sci-biology/nilearn: new version

 sci-biology/nilearn/Manifest                                     | 1 +
 .../nilearn/{nilearn-0.1.4.1.ebuild => nilearn-0.2.4.ebuild}     | 9 +++------
 2 files changed, 4 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     27154308655f11df2ff3e17987183bfd1f81b244
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun  9 19:33:07 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun  9 19:33:07 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=27154308

Merge remote-tracking branch 'github/master'

* github/master:
  astlib in main tree
  montage and wrapper now in main tree

 dev-python/astlib/Manifest                         |  1 -
 dev-python/astlib/astlib-0.7.0.ebuild              | 36 --------
 dev-python/astlib/metadata.xml                     | 21 -----
 dev-python/montage-wrapper/Manifest                |  1 -
 dev-python/montage-wrapper/metadata.xml            | 17 ----
 .../montage-wrapper/montage-wrapper-0.9.7.ebuild   | 39 ---------
 sci-astronomy/montage/Manifest                     |  2 -
 .../montage/files/montage-3.3-gcc48.patch          | 97 ----------------------
 sci-astronomy/montage/metadata.xml                 | 12 ---
 sci-astronomy/montage/montage-3.3.ebuild           | 55 ------------
 10 files changed, 281 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     c9bc2ef5f22146f72cd8bf6dd9617a3ea1d48bd6
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Mon May 23 06:57:25 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Mon May 23 06:57:25 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c9bc2ef5

Merge pull request #626 from marbre/notebook

dev-python/notebook + dependencies: Moved to tree

 dev-python/entrypoints/Manifest                    |  1 -
 dev-python/entrypoints/entrypoints-0.2.1.ebuild    | 60 --------------
 .../files/entrypoints-0.2.1-init.py.patch          |  8 --
 .../files/entrypoints-0.2.1-setup.py.patch         | 20 -----
 dev-python/entrypoints/metadata.xml                | 21 -----
 dev-python/nbconvert/Manifest                      |  1 -
 dev-python/nbconvert/nbconvert-4.2.0.ebuild        | 73 -----------------
 dev-python/notebook/Manifest                       |  1 -
 .../files/notebook-4.2.0-setupbase.py.patch        | 42 ----------
 dev-python/notebook/notebook-4.2.0.ebuild          | 94 ----------------------
 10 files changed, 321 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     27a0dc46d02412bf37e718294235a143987b3ba7
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu May 19 13:22:22 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Thu May 19 13:22:22 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=27a0dc46

Merge pull request #625 from TheChymera/ants

sci-biology/ants: install scripts

 sci-biology/ants/ants-9999.ebuild | 2 ++
 sci-biology/ants/files/99ants     | 1 +
 2 files changed, 3 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     7284a3befa9d21dd360f2542e05b3a0388cb43bf
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon May 16 07:14:02 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Mon May 16 07:14:02 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7284a3be

Merge pull request #624 from timeraider4u/emscripten

dev-util/emscripten: bump to EAPI6, version bump to 1.36.4

 dev-util/emscripten-fastcomp/Manifest                    |  2 ++
 .../emscripten-fastcomp-1.34.11.ebuild                   |  4 ++--
 .../emscripten-fastcomp-1.35.2.ebuild                    |  4 ++--
 ...p-1.35.2.ebuild => emscripten-fastcomp-1.36.4.ebuild} | 13 +++++++++++--
 .../files/1.36.4/CMakeLists.txt.patch                    | 10 ++++++++++
 .../emscripten-fastcomp/files/1.36.4/Version.cpp.patch   | 14 ++++++++++++++
 dev-util/emscripten/Manifest                             |  1 +
 dev-util/emscripten/emscripten-1.34.11.ebuild            |  5 +++--
 dev-util/emscripten/emscripten-1.35.2.ebuild             |  5 +++--
 ...mscripten-1.34.11.ebuild => emscripten-1.36.4.ebuild} |  9 ++++++---
 dev-util/emscripten/files/1.36.4/emcc.patch              | 16 ++++++++++++++++
 dev-util/emscripten/files/1.36.4/emcmake.patch           | 16 ++++++++++++++++
 12 files changed, 86 insertions(+), 13 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     0e42343dc6db6c8401fd11aea86b970e2c37bedb
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Tue May 17 09:17:41 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Tue May 17 09:17:41 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0e42343d

Merge remote-tracking branch 'github/master'

 dev-util/emscripten-fastcomp/Manifest              |   2 +
 .../emscripten-fastcomp-1.34.11.ebuild             |   4 +-
 .../emscripten-fastcomp-1.35.2.ebuild              |   4 +-
 ....2.ebuild => emscripten-fastcomp-1.36.4.ebuild} |  13 ++-
 .../files/1.36.4/CMakeLists.txt.patch              |  10 ++
 .../files/1.36.4/Version.cpp.patch                 |  14 +++
 dev-util/emscripten/Manifest                       |   1 +
 dev-util/emscripten/emscripten-1.34.11.ebuild      |   5 +-
 dev-util/emscripten/emscripten-1.35.2.ebuild       |   5 +-
 ...ten-1.34.11.ebuild => emscripten-1.36.4.ebuild} |   9 +-
 dev-util/emscripten/files/1.36.4/emcc.patch        |  16 +++
 dev-util/emscripten/files/1.36.4/emcmake.patch     |  16 +++
 sci-biology/bwa/Manifest                           |   1 -
 sci-biology/bwa/bwa-0.7.13.ebuild                  |  36 ------
 sci-biology/bwa/files/bwa-0.7.13-Makefile.patch    |  27 -----
 sci-biology/bwa/metadata.xml                       |  11 --
 sci-libs/armadillo/Manifest                        |   5 +-
 sci-libs/armadillo/armadillo-4.650.4.ebuild        | 112 -------------------
 sci-libs/armadillo/armadillo-5.600.2.ebuild        | 121 ---------------------
 sci-libs/armadillo/armadillo-6.600.5.ebuild        | 121 ---------------------
 ...llo-6.200.5.ebuild => armadillo-6.700.5.ebuild} |  19 ++--
 sci-misc/irstlm/Manifest                           |   2 +-
 sci-misc/irstlm/irstlm-5.80.08.ebuild              |  21 ----
 sci-misc/irstlm/irstlm-6.00.05.ebuild              |  20 ++++
 sci-misc/irstlm/metadata.xml                       |   2 +-
 25 files changed, 119 insertions(+), 478 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     23b1893e56ff93ade6e0cbca827fab2595c37ad3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun May  8 07:51:07 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sun May  8 07:51:07 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=23b1893e

Merge pull request #623 from akreal/sci-misc/irstlm

sci-misc/irstlm: version bump

 sci-misc/irstlm/Manifest              |  2 +-
 sci-misc/irstlm/irstlm-5.80.08.ebuild | 21 ---------------------
 sci-misc/irstlm/irstlm-6.00.05.ebuild | 20 ++++++++++++++++++++
 sci-misc/irstlm/metadata.xml          |  2 +-
 4 files changed, 22 insertions(+), 23 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     31760fd61100bdd70ec8c0dab7f8e0f9871c6329
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat May  7 09:32:32 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat May  7 09:32:32 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=31760fd6

Merge pull request #617 from TheChymera/nipype

sci-libs/nipype is python 3.4 compatible

 sci-libs/nipype/nipype-0.11.0.ebuild | 2 +-
 sci-libs/nipype/nipype-9999.ebuild   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     59e8a0aa7d26e5f65d2a4ac1b366c5ee666306d4
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat May  7 09:32:19 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat May  7 09:32:19 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=59e8a0aa

Merge pull request #622 from olifre/root-sandbox-exception

sci-physics/root-9999: current master needs write access to /dev/random

 sci-physics/root/root-9999.ebuild | 4 ++++
 1 file changed, 4 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     33e15f4ca19780de8721d34daca2f571eebc6d80
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat May  7 09:27:21 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat May  7 09:27:21 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=33e15f4c

Merge remote-tracking branch 'github/master'

* github/master:
  use QT5 as default use-flag
  sci-visualization/mricrogl: this version will not compile with fpc 3
  sci-libs/vtk: new revision with qt5 useflag, updated ebuild to EAPI 6

 sci-libs/vtk/Manifest                              |   4 +
 sci-libs/vtk/files/vtk-6.1.0-freetype.patch        |  22 ++
 sci-libs/vtk/files/vtk-6.1.0-gdal2.patch           |  33 ++
 sci-libs/vtk/files/vtk-6.1.0-glext.patch           |  13 +
 sci-libs/vtk/files/vtk-6.1.0-install.patch         |  19 +
 sci-libs/vtk/files/vtk-6.1.0-memset.patch          | 147 ++++++++
 sci-libs/vtk/files/vtk-6.1.0-netcdf.patch          |  29 ++
 sci-libs/vtk/files/vtk-6.1.0-system.patch          |  27 ++
 sci-libs/vtk/files/vtk-6.1.0-web.patch             |  25 ++
 sci-libs/vtk/metadata.xml                          |  35 ++
 sci-libs/vtk/vtk-6.1.0-r3.ebuild                   | 420 +++++++++++++++++++++
 .../mricrogl/mricrogl-1.0.20151111.ebuild          |   2 +-
 12 files changed, 775 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     949faff31d0aea4975ae93db919f6bfe84fc99a9
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Apr 28 16:16:41 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Apr 28 16:16:41 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=949faff3

Merge pull request #621 from TheChymera/mricrogl

sci-visualization/mricrogl: this version will not compile with fpc 3

 sci-visualization/mricrogl/mricrogl-1.0.20151111.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5689aaf4cb4c0093dbd63c10f408b8285f92a38d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Apr 28 16:16:02 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Apr 28 16:16:02 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5689aaf4

Merge pull request #614 from timeraider4u/vtk

sci-libs/vtk: new revision with qt5 useflag, updated ebuild to EAPI 6

 sci-libs/vtk/Manifest                       |   4 +
 sci-libs/vtk/files/vtk-6.1.0-freetype.patch |  22 ++
 sci-libs/vtk/files/vtk-6.1.0-gdal2.patch    |  33 +++
 sci-libs/vtk/files/vtk-6.1.0-glext.patch    |  13 +
 sci-libs/vtk/files/vtk-6.1.0-install.patch  |  19 ++
 sci-libs/vtk/files/vtk-6.1.0-memset.patch   | 147 ++++++++++
 sci-libs/vtk/files/vtk-6.1.0-netcdf.patch   |  29 ++
 sci-libs/vtk/files/vtk-6.1.0-system.patch   |  27 ++
 sci-libs/vtk/files/vtk-6.1.0-web.patch      |  25 ++
 sci-libs/vtk/metadata.xml                   |  35 +++
 sci-libs/vtk/vtk-6.1.0-r3.ebuild            | 420 ++++++++++++++++++++++++++++
 11 files changed, 774 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c260198e8b5ed48f714afffe1cd2f58c93a932ee
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 26 18:42:45 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Apr 26 18:42:45 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c260198e

Merge pull request #619 from TheChymera/mricrogl

sci-visualization/mricrogl: new versioned ebuild

 .../mricrogl/{mricrogl-9999.ebuild => mricrogl-1.0.20151111.ebuild}     | 2 ++
 1 file changed, 2 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     263d13d8432028f4416a5fe65ba203881cef70d3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 26 19:06:29 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Apr 26 19:06:29 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=263d13d8

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/pydotplus: added 3.4 compatibility
  sci-visualization/mricrogl: new versioned ebuild
  sci-biology/aghermann: version bump

 dev-python/pydotplus/pydotplus-2.0.2.ebuild                             | 2 +-
 sci-biology/aghermann/Manifest                                          | 2 +-
 .../aghermann/{aghermann-1.0.7.ebuild => aghermann-1.0.9.ebuild}        | 0
 .../mricrogl/{mricrogl-9999.ebuild => mricrogl-1.0.20151111.ebuild}     | 2 ++
 4 files changed, 4 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     52212b6ab3064691172f8d88017a13df03c0e44b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 26 18:45:50 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Apr 26 18:45:50 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=52212b6a

Merge pull request #620 from TheChymera/pydotplus

dev-python/pydotplus: added 3.4 compatibility

 dev-python/pydotplus/pydotplus-2.0.2.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     0447dc0760e7457b36805f995ac6d53a56a8bec4
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 26 17:36:04 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Apr 26 17:36:04 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0447dc07

Merge pull request #616 from hmmr/master

sci-biology/aghermann: version bump

 sci-biology/aghermann/Manifest                                          | 2 +-
 .../aghermann/{aghermann-1.0.7.ebuild => aghermann-1.0.9.ebuild}        | 0
 2 files changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     e894fffa75d809914ef009a06bfe3ce4052a91c3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 24 07:24:31 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Apr 24 07:24:31 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e894fffa

Merge pull request #615 from ercpe/picard-2.2.2

Picard 2.2.2

 dev-java/htsjdk/Manifest                           |   1 +
 dev-java/htsjdk/htsjdk-2.2.2.ebuild                |  48 +++++++++
 .../picard => dev-java/htsjdk}/metadata.xml        |   0
 sci-biology/picard/files/2.2.2-build.xml.patch     | 115 +++++++++++++++++++++
 sci-biology/picard/picard-2.2.2.ebuild             |  48 +++------
 5 files changed, 178 insertions(+), 34 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     ecceb50cb667dc503e3658a722e820bad635c5ec
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Apr 23 23:21:26 2016 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Apr 23 23:21:26 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ecceb50c

Merge branch 'master' of ssh://github.com/gentoo-science/sci

 sci-libs/dealii/Manifest                           |   2 +
 sci-libs/dealii/dealii-8.1.0-r2.ebuild             |   7 +-
 sci-libs/dealii/dealii-8.2.1-r1.ebuild             |   7 +-
 sci-libs/dealii/dealii-8.3.0.ebuild                |   7 +-
 .../{dealii-9999.ebuild => dealii-8.4.1.ebuild}    |   9 +-
 sci-libs/dealii/dealii-9999.ebuild                 |   9 +-
 sci-libs/trilinos/Manifest                         |   1 +
 ...nos-12.6.2-fix_install_paths_for_destdir.patch} | 152 ++++++++++-----------
 ...ilinos-12.2.1.ebuild => trilinos-12.6.2.ebuild} |   3 +-
 sci-mathematics/petsc/Manifest                     |   1 +
 sci-mathematics/petsc/petsc-3.4.2.ebuild           |   6 -
 sci-mathematics/petsc/petsc-3.5.3.ebuild           |   6 -
 sci-mathematics/petsc/petsc-3.6.0.ebuild           |   6 -
 sci-mathematics/petsc/petsc-3.6.3.ebuild           |   6 -
 .../{petsc-3.6.3.ebuild => petsc-3.6.4.ebuild}     |  11 +-
 15 files changed, 115 insertions(+), 118 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     e313b874447efbc637c9e8a08302e64b9cbed26d
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Wed Apr 13 10:45:57 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Wed Apr 13 10:45:57 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e313b874

Merge remote-tracking branch 'github/master'

 dev-java/jhealpix/Manifest                         |   1 -
 dev-java/jhealpix/jhealpix-3.11.ebuild             |  43 --------
 dev-java/jhealpix/metadata.xml                     |  17 ----
 dev-python/astroquery/Manifest                     |   1 -
 dev-python/astroquery/astroquery-0.2.ebuild        |  69 -------------
 dev-python/ccdproc/Manifest                        |   2 -
 dev-python/ccdproc/ccdproc-0.2.1.ebuild            |  59 -----------
 dev-python/ccdproc/ccdproc-0.2.ebuild              |  59 -----------
 dev-python/emcee/Manifest                          |   2 -
 dev-python/emcee/emcee-1.2.0.ebuild                |  27 -----
 dev-python/emcee/emcee-2.0.0.ebuild                |  27 -----
 dev-python/emcee/metadata.xml                      |  22 -----
 dev-python/gammapy/Manifest                        |   1 -
 dev-python/gammapy/gammapy-0.1.ebuild              |  76 --------------
 dev-python/healpy/Manifest                         |   1 -
 dev-python/healpy/healpy-1.7.4.ebuild              |  34 -------
 dev-python/healpy/metadata.xml                     |  17 ----
 sci-astronomy/chealpix/Manifest                    |   1 -
 sci-astronomy/chealpix/chealpix-3.11.2.ebuild      |  24 -----
 sci-astronomy/chealpix/metadata.xml                |  17 ----
 sci-astronomy/healpix_cxx/Manifest                 |   1 -
 .../healpix_cxx/healpix_cxx-3.11.2.ebuild          |  48 ---------
 sci-astronomy/healpix_cxx/metadata.xml             |  18 ----
 sci-astronomy/healpix_idl/Manifest                 |   1 -
 sci-astronomy/healpix_idl/healpix_idl-3.11.ebuild  |  37 -------
 sci-astronomy/healpix_idl/metadata.xml             |  18 ----
 sci-biology/abyss/Manifest                         |   3 -
 sci-biology/abyss/abyss-1.3.3-r1.ebuild            |  42 --------
 sci-biology/abyss/abyss-1.3.4-r1.ebuild            |  47 ---------
 sci-biology/abyss/abyss-1.3.6-r1.ebuild            |  48 ---------
 .../abyss/files/abyss-1.3.3-ac_prog_ar.patch       |  18 ----
 sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch  |  15 ---
 sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch |  40 --------
 sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch  |  15 ---
 sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch |  40 --------
 .../abyss/files/abyss-1.3.6-ac_prog_ar.patch       |  18 ----
 sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch  |  15 ---
 sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch |  40 --------
 sci-biology/abyss/metadata.xml                     |   8 --
 sci-biology/fsl/fsl-5.0.8.ebuild                   |   2 +-
 sci-biology/pysam/Manifest                         |   3 -
 sci-biology/pysam/pysam-0.6-r2.ebuild              |  26 -----
 sci-biology/pysam/pysam-0.8.3.ebuild               |  29 ------
 sci-biology/pysam/pysam-0.8.4.ebuild               |  27 -----
 sci-biology/tophat/Manifest                        |   4 -
 sci-biology/tophat/files/tophat-2.0.9-flags.patch  | 109 ---------------------
 sci-biology/tophat/metadata.xml                    |  11 ---
 sci-biology/tophat/tophat-2.0.12.ebuild            |  58 -----------
 sci-biology/tophat/tophat-2.0.13.ebuild            |  61 ------------
 sci-biology/tophat/tophat-2.0.14.ebuild            |  62 ------------
 sci-biology/tophat/tophat-2.1.0.ebuild             |  43 --------
 51 files changed, 1 insertion(+), 1406 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     ba21795bddb7d2ad8e1359a93327a14b0435fc26
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Apr  4 17:24:03 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Mon Apr  4 17:24:03 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ba21795b

Merge branch 'master' of https://github.com/gentoo-science/sci

 .travis.yml                                        |   8 +-
 dev-python/hdf5storage/Manifest                    |   1 +
 ...age-0.1.11.ebuild => hdf5storage-0.1.13.ebuild} |   0
 dev-python/matplotlib2tikz/Manifest                |   1 +
 ...z-0.5.4.ebuild => matplotlib2tikz-0.5.6.ebuild} |   0
 sci-biology/CONTIGuator/CONTIGuator-2.7.3.ebuild   |  31 +++
 sci-biology/CONTIGuator/CONTIGuator-2.7.ebuild     |  17 --
 sci-biology/CONTIGuator/Manifest                   |   1 +
 sci-biology/DisEMBL/DisEMBL-1.4.ebuild             |   2 +-
 sci-biology/MolBioLib/Manifest                     |   1 +
 sci-biology/MolBioLib/MolBioLib-5.ebuild           |  31 +++
 .../{cross_genome => MolBioLib}/metadata.xml       |   0
 sci-biology/ONTO-PERL/ONTO-PERL-1.41.ebuild        |   6 +-
 sci-biology/TransDecoder/Manifest                  |   1 +
 ...oder-2.0.1.ebuild => TransDecoder-2.1.0.ebuild} |   8 +-
 ...s.patch => TransDecoder-2.1.0__fix_paths.patch} |   0
 sci-biology/abyss/Manifest                         |   3 -
 sci-biology/abyss/abyss-1.3.3-r1.ebuild            |  42 ----
 sci-biology/abyss/abyss-1.3.4-r1.ebuild            |  47 ----
 sci-biology/abyss/abyss-1.3.6-r1.ebuild            |  48 ----
 .../abyss/files/abyss-1.3.3-ac_prog_ar.patch       |  18 --
 sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch  |  15 --
 sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch |  40 ----
 sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch  |  15 --
 sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch |  40 ----
 .../abyss/files/abyss-1.3.6-ac_prog_ar.patch       |  18 --
 sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch  |  15 --
 sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch |  40 ----
 sci-biology/abyss/metadata.xml                     |   8 -
 sci-biology/act-bin/Manifest                       |   4 +
 sci-biology/act-bin/act-bin-13.0.0.ebuild          |  50 ++++
 sci-biology/{cross_genome => act-bin}/metadata.xml |   0
 sci-biology/amos/amos-3.1.0-r2.ebuild              |   9 +-
 sci-biology/amos/amos-9999.ebuild                  |  10 +-
 sci-biology/arachne/Manifest                       |   1 +
 sci-biology/arachne/arachne-46233.ebuild           |  41 ++++
 sci-biology/{cross_genome => arachne}/metadata.xml |   0
 sci-biology/artemis-bin/Manifest                   |   4 +-
 sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild |  29 ++-
 sci-biology/artemis/Manifest                       |   3 +-
 sci-biology/artemis/artemis-9999.ebuild            |  19 +-
 sci-biology/bamtools/Manifest                      |   1 +
 ...{bamtools-9999.ebuild => bamtools-2.4.0.ebuild} |   7 +-
 ...nbundle.patch => bamtools-2.4.0-unbundle.patch} |   0
 sci-biology/cap3-bin/Manifest                      |   1 +
 ...in-20071221.ebuild => cap3-bin-20071015.ebuild} |   0
 ...in-20071221.ebuild => cap3-bin-20150210.ebuild} |  14 +-
 sci-biology/cd-hit/Manifest                        |   2 +-
 sci-biology/cd-hit/cd-hit-4.6.1.ebuild             |  44 ----
 sci-biology/cd-hit/cd-hit-4.6.5.ebuild             |  61 +++++
 .../{4.6.1-gentoo.patch => 4.6.5-gentoo.patch}     |  95 ++++++--
 .../cd-hit/files/cd-hit-auxtools-manual.txt        | 212 +++++++++++++++++
 sci-biology/cg-cat/cg-cat-20150130.ebuild          |  35 ++-
 sci-biology/consed/consed-29.ebuild                |  12 +-
 .../cross_genome/cross_genome-20140822.ebuild      |   2 +-
 sci-biology/cutadapt/Manifest                      |   4 +-
 sci-biology/cutadapt/cutadapt-1.4.1.ebuild         |  18 --
 sci-biology/cutadapt/cutadapt-1.5.ebuild           |  18 --
 ...cutadapt-1.2.1.ebuild => cutadapt-1.9.1.ebuild} |   2 +-
 sci-biology/cutadapt/cutadapt-9999.ebuild          |   2 +-
 sci-biology/exomiser-bin/Manifest                  |   4 +-
 sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild |  23 --
 sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild |  31 +++
 sci-biology/fgap-bin/Manifest                      |   1 +
 sci-biology/fgap-bin/fgap-bin-1.8.1.ebuild         |  25 ++
 .../{cross_genome => fgap-bin}/metadata.xml        |   0
 sci-biology/fgap/Manifest                          |   1 +
 sci-biology/fgap/fgap-1.8.1.ebuild                 |  26 +++
 sci-biology/{cross_genome => fgap}/metadata.xml    |   0
 sci-biology/fsl/fsl-5.0.8.ebuild                   |   2 +-
 sci-biology/gap2caf/gap2caf-2.1.0.ebuild           |   4 +-
 sci-biology/karect/Manifest                        |   1 +
 sci-biology/karect/karect-1.0.0.ebuild             |  33 +++
 sci-biology/{cross_genome => karect}/metadata.xml  |   0
 sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild  |   6 +-
 sci-biology/{cross_genome => perga}/metadata.xml   |   0
 sci-biology/perga/perga-9999.ebuild                |  36 +++
 sci-biology/perlprimer/perlprimer-1.1.21.ebuild    |   2 +-
 sci-biology/reapr/Manifest                         |   2 +
 sci-biology/reapr/files/fix_sort_samtools13.patch  |  16 ++
 sci-biology/reapr/files/use_shared_libs.patch      | 252 +++++++++++++++++++++
 sci-biology/{cross_genome => reapr}/metadata.xml   |   0
 sci-biology/reapr/reapr-1.0.18.ebuild              |  62 +++++
 .../roche454ace2caf-20100812.ebuild                |   6 +-
 .../scaffold_builder-20131122-r1.ebuild            |   2 +-
 sci-biology/scbi_mapreduce/Manifest                |   2 +-
 ...-0.0.40.ebuild => scbi_mapreduce-0.0.45.ebuild} |   2 +-
 sci-biology/scythe/scythe-0.992.ebuild             |   2 +-
 sci-biology/staden/Manifest                        |   3 +-
 ...ags.patch => staden-2.0.0_beta10-ldflags.patch} |   0
 ...9-zlib.patch => staden-2.0.0_beta10-zlib.patch} |   0
 .../files/staden-2.0.0_beta9-libpng-1.5.patch      |  16 --
 ...0.0_beta9.ebuild => staden-2.0.0_beta10.ebuild} |  31 ++-
 sci-biology/staden/staden-9999.ebuild              |  19 +-
 sci-biology/{staden => staden_doc}/Manifest        |   1 -
 .../{cross_genome => staden_doc}/metadata.xml      |   0
 .../staden_doc/staden_doc-2.0.0_beta9.ebuild       |  44 ++++
 sci-biology/trimmomatic/Manifest                   |   4 +-
 ...momatic-0.32.ebuild => trimmomatic-0.35.ebuild} |   2 +-
 sci-chemistry/nwchem/Manifest                      |  14 ++
 .../nwchem/files/nwchem-6.6-unique_tags.patch      |  12 +
 sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild   |   4 +-
 ...26243-r7.ebuild => nwchem-6.6_p27746-r2.ebuild} |  46 ++--
 sci-libs/armadillo/Manifest                        |   3 +-
 ...llo-6.200.3.ebuild => armadillo-6.200.5.ebuild} |   0
 ...llo-6.200.3.ebuild => armadillo-6.600.5.ebuild} |   0
 sci-libs/calculix-ccx/Manifest                     |   6 +-
 ...-ccx-2.8_p2.ebuild => calculix-ccx-2.10.ebuild} |  15 +-
 ...0_Makefile_custom_cc_flags_spooles_arpack.patch |  35 +++
 ...7_Makefile_custom_cc_flags_spooles_arpack.patch |  31 ---
 .../calculix-ccx/files/01_ccx_2.7_lapack.patch     |  11 -
 ...2_Makefile_custom_cc_flags_spooles_arpack.patch |  32 ---
 sci-libs/calculix-cgx/Manifest                     |   4 +-
 ...-cgx-2.7-r1.ebuild => calculix-cgx-2.10.ebuild} |  31 +--
 ...=> 01_cgx_2.10_Makefile_custom_cxx_flags.patch} |  33 ++-
 ...h => 02_cgx_2.10_menu_fix-freeglut_2.8.1.patch} |  35 ++-
 sci-libs/clfft/Manifest                            |   1 +
 .../{clfft-2.10.0.ebuild => clfft-2.10.2.ebuild}   |   0
 sci-libs/io_lib/Manifest                           |   1 +
 sci-libs/io_lib/io_lib-1.14.7.ebuild               |  29 +++
 sci-libs/{pg2plplot => io_lib}/metadata.xml        |  12 +-
 sys-cluster/modules/modules-3.2.10-r1.ebuild       |   2 +-
 122 files changed, 1383 insertions(+), 792 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     4bbf5a18d8a366f64db5943143cae14dd45b84f1
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Mar 21 18:48:00 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Mon Mar 21 18:48:00 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4bbf5a18

Merge branch 'master' of https://github.com/gentoo-science/sci

 sci-physics/genfit/genfit-9999.ebuild | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     d4a7509b6aba363b4a6e40aaaba5fb2a29c1eb6a
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 22 00:04:02 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Tue Mar 22 00:04:02 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d4a7509b

Merge branch 'master' of https://github.com/gentoo-science/sci

 dev-python/ffnet/Manifest                          |  1 +
 dev-python/ffnet/ffnet-0.7.1.ebuild                | 11 ++++------
 .../{ffnet-0.7.1.ebuild => ffnet-0.8.3.ebuild}     | 22 ++++++++------------
 dev-python/ffnet/metadata.xml                      |  4 ++--
 dev-python/ffnetui/Manifest                        |  1 +
 dev-python/ffnetui/ffnetui-0.8.3.2.ebuild          | 24 ++++++++++++++++++++++
 {dev-ml/lacaml => dev-python/ffnetui}/metadata.xml |  6 +++---
 7 files changed, 44 insertions(+), 25 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     9af07900f6bc07a7597c01121c678c44be7b4755
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 30 14:37:45 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 30 14:37:45 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9af07900

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 sci-chemistry/nwchem/Manifest                      | 14 ++++++++
 .../nwchem/files/nwchem-6.6-unique_tags.patch      | 12 +++++++
 ...26243-r7.ebuild => nwchem-6.6_p27746-r2.ebuild} | 42 ++++++++--------------
 3 files changed, 40 insertions(+), 28 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Honza Macháček]

commit:     7ba147b184132c298c880d76e65de26c49900927
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Wed Mar 30 14:35:02 2016 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Wed Mar 30 14:35:02 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7ba147b1

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 sci-biology/act-bin/Manifest                       |  4 ++
 sci-biology/act-bin/act-bin-13.0.0.ebuild          | 50 ++++++++++++++++++++++
 sci-biology/{staden_doc => act-bin}/metadata.xml   |  0
 sci-biology/artemis-bin/Manifest                   |  4 +-
 sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild | 29 ++++++++++---
 sci-biology/artemis/Manifest                       |  3 +-
 sci-biology/artemis/artemis-9999.ebuild            | 19 +++++---
 7 files changed, 96 insertions(+), 13 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     63407d6473a7f47ee4ab3f9c8691bac9b47e343f
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 29 18:36:32 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 29 18:36:32 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=63407d64

Don't check metadata.xml

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 0cc8a96..b19309f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -31,12 +31,12 @@ before_script:
     - SIZE=$(stat -c %s .travis.yml.upstream)
     - if ! cmp -n $SIZE -s .travis.yml .travis.yml.upstream; then echo -e "\e[31m !!! .travis.yml outdated! Update available https://github.com/mrueg/repoman-travis \e[0m" > /tmp/update ; fi
     - cd travis-overlay
+    - wget "https://raw.githubusercontent.com/mgorny/gentoo-xml-schema/master/metadata.xsd" -O metadata.xsd
 script:
     - ./../spinner.sh "python ../portage-${PORTAGE_VER}/bin/repoman full -d"
 # You can append own scripts after this line
-
-    - wget "https://raw.githubusercontent.com/mgorny/gentoo-xml-schema/master/metadata.xsd" -O metadata.xsd
-    - xmllint --noout --schema metadata.xsd */*/metadata.xml 2>&1 | grep "fails to validate"; [[ ${PIPESTATUS[0]} == 0 ]] || false
+    #too old xmllint on travis
+    #- xmllint --noout --schema metadata.xsd */*/metadata.xml 2>&1 | grep "fails to validate"; [[ ${PIPESTATUS[0]} == 0 ]] || false
 
 notifications:
     irc: "chat.freenode.net#gentoo-science"

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     25252b5f4aa7c6a183ee75b0a46d6f1a8f74c191
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 29 17:58:45 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 29 17:58:45 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=25252b5f

Merge branch 'heroxbd-master'

* heroxbd-master:
  sys-cluster/modules: fix typo. /etc/modulefiles.

GitHub: closes gentoo-science/sci#559

 sys-cluster/modules/modules-3.2.10-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     48e6cc09cedfb832679b1b803e72bf7b1ae6a754
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 29 17:53:05 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 29 17:53:05 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=48e6cc09

Don't exit but false

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index a702e5a..0cc8a96 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -36,7 +36,7 @@ script:
 # You can append own scripts after this line
 
     - wget "https://raw.githubusercontent.com/mgorny/gentoo-xml-schema/master/metadata.xsd" -O metadata.xsd
-    - xmllint --noout --schema metadata.xsd */*/metadata.xml 2>&1 | grep "fails to validate"; [[ ${PIPESTATUS[0]} == 0 ]] || exit 1
+    - xmllint --noout --schema metadata.xsd */*/metadata.xml 2>&1 | grep "fails to validate"; [[ ${PIPESTATUS[0]} == 0 ]] || false
 
 notifications:
     irc: "chat.freenode.net#gentoo-science"

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     fb381dd93a4b6bb2fe3014b8f92166ceaf58ff01
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 25 22:32:13 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Mar 25 22:32:13 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fb381dd9

Merge pull request #603 from apieum/calculix-2.10

sci-libs/calculix-ccx-2.10 and sci-libs/calculix-cgx-2.10: version bump #602

 sci-libs/calculix-ccx/Manifest                     |  6 ++--
 ...-ccx-2.8_p2.ebuild => calculix-ccx-2.10.ebuild} | 15 ++++++----
 ...0_Makefile_custom_cc_flags_spooles_arpack.patch | 35 ++++++++++++++++++++++
 ...7_Makefile_custom_cc_flags_spooles_arpack.patch | 31 -------------------
 .../calculix-ccx/files/01_ccx_2.7_lapack.patch     | 11 -------
 ...2_Makefile_custom_cc_flags_spooles_arpack.patch | 32 --------------------
 sci-libs/calculix-cgx/Manifest                     |  4 +--
 ...-cgx-2.7-r1.ebuild => calculix-cgx-2.10.ebuild} | 31 +++++++++----------
 ...=> 01_cgx_2.10_Makefile_custom_cxx_flags.patch} | 33 ++++++++++----------
 ...h => 02_cgx_2.10_menu_fix-freeglut_2.8.1.patch} | 35 +++++++++++-----------
 10 files changed, 98 insertions(+), 135 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     2baba741d9bcf25cd69dcfea43ec7679dfd879f1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 29 17:15:36 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 29 17:15:36 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2baba741

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/calculix-ccx-2.10 sci-libs/calculix-cgx-2.10 version bump (ref #602)
  dev-python/ffnet: Add new ffnet and ffnetui ebuilds
  sci-physics/genfit: Change live-ebuild to github.

 dev-python/ffnet/Manifest                          |  1 +
 dev-python/ffnet/ffnet-0.7.1.ebuild                | 11 +++----
 .../{ffnet-0.7.1.ebuild => ffnet-0.8.3.ebuild}     | 22 ++++++--------
 dev-python/ffnet/metadata.xml                      |  4 +--
 dev-python/ffnetui/Manifest                        |  1 +
 dev-python/ffnetui/ffnetui-0.8.3.2.ebuild          | 24 +++++++++++++++
 {dev-ml/lacaml => dev-python/ffnetui}/metadata.xml |  6 ++--
 sci-libs/calculix-ccx/Manifest                     |  6 ++--
 ...-ccx-2.8_p2.ebuild => calculix-ccx-2.10.ebuild} | 15 ++++++----
 ...0_Makefile_custom_cc_flags_spooles_arpack.patch | 35 ++++++++++++++++++++++
 ...7_Makefile_custom_cc_flags_spooles_arpack.patch | 31 -------------------
 .../calculix-ccx/files/01_ccx_2.7_lapack.patch     | 11 -------
 ...2_Makefile_custom_cc_flags_spooles_arpack.patch | 32 --------------------
 sci-libs/calculix-cgx/Manifest                     |  4 +--
 ...-cgx-2.7-r1.ebuild => calculix-cgx-2.10.ebuild} | 31 +++++++++----------
 ...=> 01_cgx_2.10_Makefile_custom_cxx_flags.patch} | 33 ++++++++++----------
 ...h => 02_cgx_2.10_menu_fix-freeglut_2.8.1.patch} | 35 +++++++++++-----------
 sci-physics/genfit/genfit-9999.ebuild              |  5 ++--
 18 files changed, 144 insertions(+), 163 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     67ff8799a8b295d736cb5130992c6f1a8af2bd91
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 19 14:44:55 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Mar 19 14:44:55 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=67ff8799

Merge pull request #604 from olifre/genfit-git

sci-physics/genfit: Change live-ebuild to github.

 sci-physics/genfit/genfit-9999.ebuild | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     8cdba82c257d6bae4449d2936034c5be79dcc7f1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 29 16:45:36 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 29 16:45:36 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8cdba82c

Travis: Use portage 2.2.28

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index d5b6eb4..a702e5a 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,7 +6,7 @@ language: python
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.2.27"
+    - PORTAGE_VER="2.2.28"
 before_install:
     - sudo apt-get -qq update
     - sudo apt-get install -y libxml2

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     e2dae19f163df9ef068f370a3866eef410862ddc
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Mar 14 02:17:38 2016 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Mar 14 02:17:38 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e2dae19f

Merge branch 'master' of ssh://github.com/gentoo-science/sci

 sci-astronomy/eye/eye-9999.ebuild                  |  31 +-
 sci-astronomy/missfits/Manifest                    |   1 -
 sci-astronomy/missfits/missfits-2.8.0.ebuild       |  33 -
 sci-astronomy/missfits/missfits-9999.ebuild        |  28 +-
 sci-astronomy/psfex/Manifest                       |   2 -
 sci-astronomy/psfex/psfex-3.17.0.ebuild            |  70 --
 sci-astronomy/psfex/psfex-3.9.1.ebuild             |  70 --
 sci-astronomy/psfex/psfex-9999.ebuild              |  43 +-
 sci-astronomy/scamp/Manifest                       |   1 -
 .../scamp/files/scamp-1.7.0-plplot599.patch        | 769 ---------------------
 sci-astronomy/scamp/scamp-1.7.0-r2.ebuild          |  60 --
 sci-astronomy/scamp/scamp-9999.ebuild              |  49 +-
 sci-astronomy/sextractor/Manifest                  |   2 -
 .../sextractor/files/sextractor-configure.patch    |  84 ---
 sci-astronomy/sextractor/sextractor-2.19.5.ebuild  |  73 --
 .../sextractor/sextractor-2.8.6-r1.ebuild          |  57 --
 sci-astronomy/sextractor/sextractor-9999.ebuild    |  40 +-
 sci-astronomy/skymaker/Manifest                    |   1 -
 sci-astronomy/skymaker/skymaker-3.10.5.ebuild      |  35 -
 sci-astronomy/skymaker/skymaker-9999.ebuild        |  30 +-
 sci-astronomy/stiff/stiff-9999.ebuild              |   2 +-
 sci-astronomy/stuff/Manifest                       |   1 -
 sci-astronomy/stuff/stuff-1.26.0.ebuild            |  35 -
 sci-astronomy/stuff/stuff-9999.ebuild              |  31 +-
 sci-astronomy/weightwatcher/Manifest               |   1 -
 .../weightwatcher/weightwatcher-1.12.ebuild        |  35 -
 .../weightwatcher/weightwatcher-9999.ebuild        |  28 +-
 27 files changed, 121 insertions(+), 1491 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     32b0d359b5d45bc69d3bd4685c75675c4b7b22ef
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  6 21:51:10 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  6 21:51:10 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=32b0d359

Fix logic in travis.yml

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index cd953b7..d5b6eb4 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -36,7 +36,7 @@ script:
 # You can append own scripts after this line
 
     - wget "https://raw.githubusercontent.com/mgorny/gentoo-xml-schema/master/metadata.xsd" -O metadata.xsd
-    - xmllint --noout --schema metadata.xsd */*/metadata.xml 2>&1 | grep "fails to validate"; [[ ${PIPESTATUS[0]} -gt 0 ]] && exit 1
+    - xmllint --noout --schema metadata.xsd */*/metadata.xml 2>&1 | grep "fails to validate"; [[ ${PIPESTATUS[0]} == 0 ]] || exit 1
 
 notifications:
     irc: "chat.freenode.net#gentoo-science"

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     349d11b646b3a875c77c5b0db85310ddf82284c7
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  6 20:54:38 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  6 20:54:38 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=349d11b6

Merge branch 'xmllint'

* xmllint:
  Fix invalid metadata.xml syntax
  Travis: validate metadata.xml

 .travis.yml                           |  6 ++++++
 dev-libs/intel-common/metadata.xml    |  2 --
 sci-biology/blasr/metadata.xml        |  4 ----
 sci-biology/brat/metadata.xml         |  4 ----
 sci-biology/codonw/metadata.xml       |  4 ----
 sci-biology/erpin/metadata.xml        |  4 ----
 sci-biology/estscan/metadata.xml      |  2 --
 sci-biology/fastdnaml/metadata.xml    |  4 ----
 sci-biology/gbrowse/metadata.xml      |  9 +++------
 sci-biology/genepop/metadata.xml      |  4 ----
 sci-biology/grappa/metadata.xml       |  6 +-----
 sci-biology/igv/metadata.xml          |  4 ----
 sci-biology/mavid/metadata.xml        |  4 ----
 sci-biology/merlin/metadata.xml       |  4 ----
 sci-biology/miranda/metadata.xml      |  4 ----
 sci-biology/mosaik/metadata.xml       |  4 ----
 sci-biology/mreps/metadata.xml        |  4 ----
 sci-biology/mrfast/metadata.xml       |  4 ----
 sci-biology/mrsfast/metadata.xml      |  4 ----
 sci-biology/ncbi-blast+/metadata.xml  | 16 ----------------
 sci-biology/ncbi-tools++/metadata.xml | 20 --------------------
 sci-biology/quicktree/metadata.xml    |  4 ----
 sci-biology/rnaplex/metadata.xml      |  4 ----
 sci-biology/signalp/metadata.xml      |  4 ----
 sci-biology/tmhmm/metadata.xml        |  4 ----
 sci-biology/twinscan/metadata.xml     |  4 ----
 sci-chemistry/nwchem/metadata.xml     | 12 ------------
 sci-chemistry/rosetta/metadata.xml    |  2 +-
 sci-libs/bigdft-abi/metadata.xml      |  8 --------
 sci-libs/ghmm/metadata.xml            |  4 ----
 sci-libs/gsl/metadata.xml             |  2 --
 sci-libs/mkl/metadata.xml             |  2 --
 sci-libs/trilinos/metadata.xml        |  8 +++++---
 sci-physics/abinit/metadata.xml       | 30 ------------------------------
 sci-physics/atompaw/metadata.xml      |  4 +---
 sci-physics/bigdft/metadata.xml       |  8 --------
 sci-physics/elk/metadata.xml          |  4 ----
 sys-cluster/hpl/metadata.xml          |  5 -----
 38 files changed, 17 insertions(+), 209 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ea5b6de5bab084b9fc10d71a7f0ea3bbd9ae022c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  6 20:52:01 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  6 20:52:01 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ea5b6de5

Travis: validate metadata.xml

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 93e3091..cd953b7 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,6 +7,9 @@ python:
     - pypy
 env:
     - PORTAGE_VER="2.2.27"
+before_install:
+    - sudo apt-get -qq update
+    - sudo apt-get install -y libxml2
 before_script:
     - mkdir travis-overlay
     - mv !(travis-overlay) travis-overlay/
@@ -32,6 +35,9 @@ script:
     - ./../spinner.sh "python ../portage-${PORTAGE_VER}/bin/repoman full -d"
 # You can append own scripts after this line
 
+    - wget "https://raw.githubusercontent.com/mgorny/gentoo-xml-schema/master/metadata.xsd" -O metadata.xsd
+    - xmllint --noout --schema metadata.xsd */*/metadata.xml 2>&1 | grep "fails to validate"; [[ ${PIPESTATUS[0]} -gt 0 ]] && exit 1
+
 notifications:
     irc: "chat.freenode.net#gentoo-science"
 

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     761dcb4b469cd7b4e23db5228c41b69e961cd14e
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  6 19:46:11 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  6 19:46:11 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=761dcb4b

skel: drop ChangeLog as we don't do ChangeLogs anymore

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 skel.ChangeLog | 67 ----------------------------------------------------------
 1 file changed, 67 deletions(-)

diff --git a/skel.ChangeLog b/skel.ChangeLog
deleted file mode 100644
index f8c5983..0000000
--- a/skel.ChangeLog
+++ /dev/null
@@ -1,67 +0,0 @@
-# ChangeLog for <CATEGORY>/<PACKAGE_NAME>
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Id$
-
-*<PACKAGE_NAME>-<PACKAGE_VERSION>-<PACKAGE_RELEASE> (DD MMM YYYY)
-
-  DD MMM YYYY; YOUR_NAME <YOUR_EMAIL> changed_file1, changed_file2 :
-  Initial import.  Ebuild submitted by submitter_name <submitter_email>.
-  Note that the "changed_file" listing is optional if you are simply bumping
-  the rev of the ebuild and are only making changes to the .ebuild file
-  itself.  Also note that we now have a single unified paragraph rather than
-  having the first line separated from the rest by a newline.  Everything
-  should be in one block like this. (note by drobbins, 16 Jul 2002)
-
-  DD MMM YYYY; YOUR_NAME <YOUR_EMAIL> changed_file1, changed_file2: this is
-  an earlier ChangeLog entry.
-
--- Explanation of ChangeLog format:
-
-  ***************************************************************************
-  THIS IS IMPORTANT: The ChangeLog format is a *chronological* account of all
-  changes made to a set of ebuilds. That means that the most recent ChangeLog
-  entry *always* goes at the top of the file. More explanation below.
-  ***************************************************************************
-
-  ***************************************************************************
-  ANOTHER IMPORTANT NOTE: There are some ChangeLogs that don't follow this
-  format and organize all changes under the "correct" "*" entry. This is not
-  correct. However, rather than making a concerted effort to fix these
-  ChangeLogs, we should spend our energy defining a comprehensive and strict
-  XML-based ChangeLog format which we then migrate to. But for any entries to
-  any ChangeLog that *you* make, please make sure to always add entries to the
-  top of the file like a good boy/girl. Even do this if it's clear that you're
-  adding an entry to a b0rked ChangeLog.
-  ***************************************************************************
-
-  This changelog is targeted to users. This means that the comments should be
-  well explained and written in clean English.
-
-  Every new version or revision of the package should be marked by a '*'
-  separator line as above to indicate where in the chronology it was first
-  added to our CVS tree. Any changes since the last revision, really _any
-  changes at all_ have to be added to the top of the file, underneath the
-  initial copyright and cvs header comments, in exactly the same format as this
-  comment. If you are modifying older ebuilds, simply note them as changed
-  files and add your entry to the top of the ChangeLog. Resist the temptation
-  to "organize" your ChangeLog entries by placing them under the "correct" "*"
-  entries -- this isn't the purpose of the "*" entries.
-
-  This means that you start with header line that has the following format,
-  indented two spaces:
-
-  DD MMM YYYY; your_name <your_email> changed_file1, changed_file2: Your
-  explanation should follow. It should be indented and wrapped at a line width
-  of 80 characters.  The changed_files can be omitted if they are obvious; for
-  example, if you are only modifying the .ebuild file and committing a new rev
-  of a package.  Any details about what exactly changed in the code should be
-  added as a message when the changes are committed to cvs, not in this file.
-
--- A word regarding credit:
-
-  Please add credit information ("ebuild submitted by ...", "patch submitted
-  by ...") to the ChangeLog. Do not add this information to the ebuilds
-  themselves.
-
-  And remember: Give credit where credit is due. We're all doing this for
-  free, so the best we can hope (and expect!) to receive is credit.

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     8f63a5380e6c4aded234d079126e9a53dc21b676
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  6 19:44:31 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  6 19:44:31 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8f63a538

Merge branch 'mschubert-jellyfish'

* mschubert-jellyfish:
  sci-biology/jellyfish: bump EAPI=6 and QA

github: closes gentoo-science/sci#572

 sci-biology/jellyfish/jellyfish-1.1.11.ebuild | 12 ++++++------
 sci-biology/jellyfish/jellyfish-2.1.3.ebuild  | 13 ++++++-------
 sci-biology/jellyfish/jellyfish-2.1.4.ebuild  | 13 ++++++-------
 3 files changed, 18 insertions(+), 20 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c80137a4e1601bf441998fee383dd6f101157433
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  6 19:38:42 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  6 19:38:42 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c80137a4

Merge branch 'TheChymera-mricrogl'

* TheChymera-mricrogl:
  sci-visualization/mricrogl: fixed icon display on GNOME (3)

GitHub: Closes gentoo-science/sci#599

 sci-visualization/mricrogl/mricrogl-9999.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ed593336822e5f4a2f4cf385be77dc33aab47d6c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  6 19:39:10 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  6 19:39:10 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ed593336

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/spglib: Version bump to latest 1.9.0
  sci-astronomy/stiff: cleanup to move in main tree
  sci-astronomy/astrometry: now in main tree
  sci-astronomy/swarp: cleanup to move in main tree

 sci-astronomy/astrometry/Manifest                  |   1 -
 sci-astronomy/astrometry/astrometry-0.43.ebuild    |  95 ---
 .../astrometry/files/0.43-as-needed.patch          | 366 ----------
 .../astrometry/files/0.43-respect-user-flags.patch |  14 -
 .../astrometry/files/0.43-system-libs.patch        | 742 ---------------------
 sci-astronomy/astrometry/metadata.xml              |  18 -
 sci-astronomy/stiff/Manifest                       |   1 -
 sci-astronomy/stiff/files/stiff-configure.patch    |  63 --
 sci-astronomy/stiff/stiff-2.4.0.ebuild             |  43 --
 sci-astronomy/stiff/stiff-9999.ebuild              |  33 +-
 sci-astronomy/swarp/Manifest                       |   1 -
 sci-astronomy/swarp/swarp-2.38.0.ebuild            |  41 --
 sci-astronomy/swarp/swarp-9999.ebuild              |  34 +-
 sci-libs/spglib/Manifest                           |   1 +
 sci-libs/spglib/files/spglib-1.9.0-openmp.patch    |  22 +
 .../{spglib-1.6.0.ebuild => spglib-1.9.0.ebuild}   |  25 +-
 16 files changed, 67 insertions(+), 1433 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     d9bd7f9cff70ee40733b6f2f2b76429f380fd1ab
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Feb 28 20:04:35 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Feb 28 20:04:35 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d9bd7f9c

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 sci-biology/kallisto/Manifest                      |  2 +-
 ...llisto-0.42.1.ebuild => kallisto-0.42.4.ebuild} |  2 +-
 sci-biology/kallisto/kallisto-9999.ebuild          |  3 +--
 sci-biology/kallisto/metadata.xml                  |  8 +++----
 sci-biology/sailfish/Manifest                      |  1 +
 .../files/sailfish-0.9.1-no-boost-static.patch}    |  4 ++--
 sci-biology/{pybedtools => sailfish}/metadata.xml  | 10 ++++----
 sci-biology/sailfish/sailfish-0.9.1.ebuild         | 28 ++++++++++++++++++++++
 sci-biology/sailfish/sailfish-9999.ebuild          | 28 ++++++++++++++++++++++
 sci-biology/salmon/Manifest                        |  2 ++
 .../files/salmon-0.3.2-no-boost-static.patch       |  4 ++--
 sci-biology/salmon/metadata.xml                    |  8 +++----
 sci-biology/salmon/salmon-0.3.2.ebuild             | 14 +++++++----
 sci-biology/salmon/salmon-0.4.2.ebuild             | 14 +++++++----
 .../{salmon-0.4.2.ebuild => salmon-0.5.0.ebuild}   | 14 +++++++----
 .../{salmon-0.4.2.ebuild => salmon-0.6.0.ebuild}   | 14 +++++++----
 sci-biology/salmon/salmon-9999.ebuild              | 17 ++++++++-----
 17 files changed, 130 insertions(+), 43 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     793dfe0ebae0d07f355f321adb452cb100d58ac7
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 24 18:31:04 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 24 18:31:04 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=793dfe0e

Merge remote-tracking branch 'github/master'

* github/master:
  moved 3D viewers to better location

 profiles/updates/1Q-2016                                         | 2 ++
 {sci-biology => sci-visualization}/mricrogl/metadata.xml         | 0
 {sci-biology => sci-visualization}/mricrogl/mricrogl-9999.ebuild | 0
 {sci-biology => sci-visualization}/mricron/metadata.xml          | 0
 {sci-biology => sci-visualization}/mricron/mricron-9999.ebuild   | 0
 5 files changed, 2 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     8f9de3d5bf9e9ee0df2faf4645494b5791547944
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 24 17:22:18 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 24 17:22:18 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8f9de3d5

Merge pull request #595 from TheChymera/mricro

moved 3D viewers to better location

 profiles/updates/1Q-2016                                         | 2 ++
 {sci-biology => sci-visualization}/mricrogl/metadata.xml         | 0
 {sci-biology => sci-visualization}/mricrogl/mricrogl-9999.ebuild | 0
 {sci-biology => sci-visualization}/mricron/metadata.xml          | 0
 {sci-biology => sci-visualization}/mricron/mricron-9999.ebuild   | 0
 5 files changed, 2 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     91817e932c2c5e0c20354e6ba7364755d2744945
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 24 16:33:25 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 24 16:33:25 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=91817e93

Merge pull request #594 from TheChymera/mricron

sci-biology/mricron: added required eclass, updated copyright and EAPI

 sci-biology/mricron/mricron-9999.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     3c8eeafcc96dcc1a7ea9f37f20b3b6a3db22df23
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 24 16:15:02 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 24 16:15:02 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3c8eeafc

Merge pull request #593 from TheChymera/mricrogl

Mricrogl

 .../lacaml => sci-biology/mricrogl}/metadata.xml   |  7 ++--
 sci-biology/mricrogl/mricrogl-9999.ebuild          | 40 ++++++++++++++++++++++
 2 files changed, 45 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     4f33132256d82f94224f857803ed6343ce71b081
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 22 08:36:54 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Feb 22 08:36:54 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4f331322

Merge branch 'apieum-netgen-5.3.1'

* apieum-netgen-5.3.1:
  sci-mathematics/netgen: Amend patches for -p1
  fix parallelmetis for metis version 4
  Remove NETGEN from description
  Remove -DTOGL_X11 and merge with build patch
  Added includes fixes patch
  set hdf5[mpi] only if opencascade flag is selected and add tcl
  added openmp use flag
  Added fedora fixes patch
  remove sed for togl as it is fixed in build patch
  replace fedora occ include dir by gentoo one
  Added build patch from fedora (fix Mesh :: ParallelMetis linking error...)
  merge parallelmesh.cpp patches
  added fedora metis patch
  added required dependencies libX11 and and tk
  change to EAPI 6
  patch netgen for occ to integrate version 5.3.1 see #436
  added the right patch for metis numflag
  added manifest for netgen-5.3.1
  added netgen-5.3.1 ebuild and patch for metis

Github: closes gentoo-science/sci#584

 sci-mathematics/netgen/Manifest                    |   1 +
 .../netgen/files/netgen-5.x-fedora-fixes.patch     | 223 +++++++++++
 .../netgen/files/netgen-5.x-includes-fixes.patch   |  29 ++
 .../netgen/files/netgen-5.x-makefiles-fixes.patch  | 412 +++++++++++++++++++++
 .../netgen/files/netgen-5.x-metis-fixes.patch      | 102 +++++
 .../netgen/files/netgen-5.x-missing-define.patch   |   8 +-
 .../files/netgen-5.x-occ-stl-api-change.patch      |  94 +++++
 .../files/netgen-5.x-parallelmetis4-fix.patch      |  36 ++
 .../{netgen-5.0.0.ebuild => netgen-5.3.1.ebuild}   |  63 +++-
 9 files changed, 948 insertions(+), 20 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     0f43b6ab576455be5e1f732690faab5f9d9a6afa
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 22 08:09:53 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Feb 22 08:09:53 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0f43b6ab

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/mkl: remove old 2015 ebuilds
  sci-libs/mkl: version bump to latest 2015 release
  sci-libs/mkl: remove old 2013 SP1 ebuilds

 sci-libs/mkl/Manifest                              |   8 +-
 sci-libs/mkl/mkl-11.1.0.080-r2.ebuild              | 143 --------------------
 sci-libs/mkl/mkl-11.1.1.106-r1.ebuild              | 143 --------------------
 sci-libs/mkl/mkl-11.1.2.144-r1.ebuild              | 143 --------------------
 sci-libs/mkl/mkl-11.2.0.090-r1.ebuild              | 143 --------------------
 sci-libs/mkl/mkl-11.2.1.133-r1.ebuild              | 145 ---------------------
 sci-libs/mkl/mkl-11.2.2.164-r1.ebuild              | 145 ---------------------
 ...-11.2.3.187-r1.ebuild => mkl-11.2.4.233.ebuild} |   6 +-
 8 files changed, 4 insertions(+), 872 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     96a541ccda3d9a154a3949798404bbe5419349f4
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 21 15:16:06 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb 21 15:16:06 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=96a541cc

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/nipype: added and sorted deps
  sci-libs/nipype: dded deps

 sci-libs/nipype/nipype-0.11.0.ebuild |  9 +++++----
 sci-libs/nipype/nipype-9999.ebuild   | 10 ++++++----
 2 files changed, 11 insertions(+), 8 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     7f826c08c485efdf940984653b0a76cd802a4b90
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 21 14:16:57 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb 21 14:16:57 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f826c08

Merge pull request #592 from TheChymera/nipype

Nipype-added and sorted deps

 sci-libs/nipype/nipype-0.11.0.ebuild |  9 +++++----
 sci-libs/nipype/nipype-9999.ebuild   | 10 ++++++----
 2 files changed, 11 insertions(+), 8 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ee28860eb7f703c626a7a8adeb347fe92307ca6e
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 19 12:56:03 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Feb 19 12:56:03 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ee28860e

Merge branch 'Reinis-ambertools'

* Reinis-ambertools:
  sci-chemistry/ambertools: Bump to EAPI=6, cleanup
  sci-chemistry/ambertools: Version bump to 15

 sci-chemistry/ambertools/Manifest                  |   1 +
 ...ls-12_p38-r1.ebuild => ambertools-15_p6.ebuild} | 100 ++-
 ...-12-gentoo.patch => ambertools-15-gentoo.patch} | 937 +++++++++++----------
 .../ambertools/files/ambertools-15-update.1.patch  | 118 +++
 .../ambertools/files/ambertools-15-update.2.patch  |  56 ++
 .../ambertools/files/ambertools-15-update.3.patch  |  95 +++
 .../ambertools/files/ambertools-15-update.4.patch  | 908 ++++++++++++++++++++
 .../ambertools/files/ambertools-15-update.5.patch  |  25 +
 .../ambertools/files/ambertools-15-update.6.patch  |  59 ++
 9 files changed, 1835 insertions(+), 464 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b123448c5693fab2aeb9b894e6c6afe0eab5f0fc
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 19 10:11:12 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Feb 19 10:11:12 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b123448c

Merge pull request #588 from gentoo-science/intel-eclass-qa

Intel eclass QA changes and update to 16.0.2.181

 dev-lang/icc/Manifest                              |   2 +-
 ...icc-16.0.1.150.ebuild => icc-16.0.2.181.ebuild} |  33 +-
 dev-lang/icc/metadata.xml                          |   3 -
 dev-lang/ifc/Manifest                              |   2 +-
 ...ifc-16.0.1.150.ebuild => ifc-16.0.2.181.ebuild} |  37 +-
 dev-libs/intel-common/Manifest                     |   2 +-
 .../intel-common/intel-common-16.0.1.150.ebuild    | 137 -----
 .../intel-common/intel-common-16.0.2.181.ebuild    | 150 ++++++
 dev-libs/intel-common/metadata.xml                 |   3 +
 eclass/intel-sdp-r1.eclass                         | 566 +++++++++++----------
 sci-libs/mkl/Manifest                              |   1 +
 sci-libs/mkl/metadata.xml                          |   3 +
 ...-11.2.3.187-r1.ebuild => mkl-11.3.2.181.ebuild} | 108 ++--
 13 files changed, 559 insertions(+), 488 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     0d731e45d3bf475323434af1539bfe256c2162c4
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 19 09:27:34 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Feb 19 09:27:34 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0d731e45

Merge remote-tracking branch 'github/master'

* github/master:
  dev-libs/intel-common: remove old
  dev-lang/icc: remove old
  dev-lang/ifc: remove old
  dev-python/prov: added die call, updated EAPI
  dev-python/prov: new package

 dev-lang/icc/Manifest                              |  1 -
 dev-lang/icc/icc-15.0.3.187-r1.ebuild              | 37 --------------
 dev-lang/ifc/Manifest                              |  1 -
 dev-lang/ifc/ifc-15.0.3.187-r1.ebuild              | 36 -------------
 dev-libs/intel-common/Manifest                     |  1 -
 .../intel-common/intel-common-15.0.3.187-r1.ebuild | 59 ----------------------
 dev-python/prov/Manifest                           |  1 +
 {sci-libs/nipy => dev-python/prov}/metadata.xml    |  8 +--
 dev-python/prov/prov-1.4.0.ebuild                  | 32 ++++++++++++
 9 files changed, 37 insertions(+), 139 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ca4b21b75d194212d01c05256ce15c1bf820b4f2
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Feb 18 07:24:29 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Feb 18 07:24:29 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca4b21b7

Merge pull request #586 from TheChymera/prov1

dev-python/prov: new package

 dev-python/prov/Manifest                        |  1 +
 {sci-libs/nipy => dev-python/prov}/metadata.xml |  8 +++----
 dev-python/prov/prov-1.4.0.ebuild               | 32 +++++++++++++++++++++++++
 3 files changed, 37 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     55d6efb6eaf98af7543c1a94d6d81fcc4a013aa4
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 17 07:43:01 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 17 07:43:01 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=55d6efb6

Merge pull request #589 from TheChymera/spm

SPM bugfix

 sci-biology/spm/spm-12_p6470.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     12933c837847a26fcc6a570daec2b2541043b5bf
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 17 14:02:36 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 17 14:02:36 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=12933c83

Merge remote-tracking branch 'github/master'

* github/master:
  sci-biology/spm: corrected install dir
  sci-biology/spm: corrected sourcedir path
  dev-python/pydotplus: deleted erroneous source dir

 dev-python/pydotplus/pydotplus-2.0.2.ebuild | 2 --
 sci-biology/spm/spm-12_p6470.ebuild         | 4 ++--
 2 files changed, 2 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     46675e021aa45c8ec2941a96c0b1928166d9f731
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Feb 16 08:59:20 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Feb 16 08:59:20 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=46675e02

Merge pull request #587 from TheChymera/pydotplus-repair

dev-python/pydotplus: deleted erroneous source dir

 dev-python/pydotplus/pydotplus-2.0.2.ebuild | 2 --
 1 file changed, 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     7e3d14f8c8ace31b0b05ffc2c1fdd997871a86f6
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 15 08:19:27 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Feb 15 08:19:27 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7e3d14f8

Merge branch 'intel-update'

* intel-update:
  dev-lang/ifc: Version bump to 16.0.1.150
  dev-lang/icc: Version bump to 16.0.1.150
  dev-libs/intel-common: Version bump to 16.0.1.150
  eclass/intel-sdp-r1.eclass: New eclass to handle intel tools >=2016

 dev-lang/icc/Manifest                              |  23 +-
 dev-lang/icc/icc-16.0.1.150.ebuild                 |  58 ++++
 dev-lang/ifc/Manifest                              |  23 +-
 dev-lang/ifc/ifc-16.0.1.150.ebuild                 |  61 +++++
 dev-lang/ifc/metadata.xml                          |   2 +-
 dev-libs/intel-common/Manifest                     |  23 +-
 .../intel-common/intel-common-16.0.1.150.ebuild    | 137 ++++++++++
 dev-libs/intel-common/metadata.xml                 |   2 +-
 eclass/{intel-sdp.eclass => intel-sdp-r1.eclass}   | 303 ++++++++++-----------
 9 files changed, 401 insertions(+), 231 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ac5169907b0ded4f4085bc080b5e9477002d692f
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 15 08:07:06 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Feb 15 08:07:06 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ac516990

Merge pull request #585 from gentoo-science/intel-update

Intel 2016 suite of tools

 dev-lang/icc/Manifest                              |  23 +-
 dev-lang/icc/icc-16.0.1.150.ebuild                 |  58 ++++
 dev-lang/ifc/Manifest                              |  23 +-
 dev-lang/ifc/ifc-16.0.1.150.ebuild                 |  61 +++++
 dev-lang/ifc/metadata.xml                          |   2 +-
 dev-libs/intel-common/Manifest                     |  23 +-
 .../intel-common/intel-common-16.0.1.150.ebuild    | 137 ++++++++++
 dev-libs/intel-common/metadata.xml                 |   2 +-
 eclass/{intel-sdp.eclass => intel-sdp-r1.eclass}   | 303 ++++++++++-----------
 9 files changed, 401 insertions(+), 231 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b257f40450141a01c370623feeb7ccdfcf1c57d3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 15 08:19:49 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Feb 15 08:19:49 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b257f404

Merge remote-tracking branch 'github/master'

* github/master:
  dev-lang/ifc: Version bump to 16.0.1.150
  dev-lang/icc: Version bump to 16.0.1.150
  dev-libs/intel-common: Version bump to 16.0.1.150
  eclass/intel-sdp-r1.eclass: New eclass to handle intel tools >=2016
  dev-ml/gsl-ocaml: remove from overlay, latest version added to main tree

 dev-ml/gsl-ocaml/Manifest                |  1 -
 dev-ml/gsl-ocaml/gsl-ocaml-1.10.2.ebuild | 28 ----------------------------
 dev-ml/gsl-ocaml/metadata.xml            | 14 --------------
 3 files changed, 43 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     6dd83abac4aa48d3bc3925553f70607e8773b4ea
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Feb 10 16:29:03 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Feb 10 16:29:03 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6dd83aba

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 dev-python/pyfftw/Manifest                                      | 1 +
 dev-python/pyfftw/{pyfftw-0.9.2.ebuild => pyfftw-0.10.1.ebuild} | 4 ++++
 dev-python/pyfftw/pyfftw-9999.ebuild                            | 2 +-
 3 files changed, 6 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     7ef1a9df666b2faf0a8e59a22422f2a73d91160f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Feb 10 14:50:48 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Feb 10 14:50:48 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7ef1a9df

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 sci-chemistry/wxmacmolplt/Manifest                                      | 1 +
 .../wxmacmolplt/{wxmacmolplt-7.6.1.ebuild => wxmacmolplt-7.6.2.ebuild}  | 2 --
 2 files changed, 1 insertion(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     d8357be8f480958600a388ebd73dc5421651e640
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Feb  9 13:17:53 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Feb  9 13:17:53 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d8357be8

Merge branch 'TheChymera-pydotplus'

* TheChymera-pydotplus:
  dev-python/pydotplus: culd not test on python 3.*
  dev-python/pydotplus: added die call
  dev-python/pydotplus: new package

 dev-python/pydotplus/Manifest                      |  1 +
 .../nipy => dev-python/pydotplus}/metadata.xml     |  7 ++---
 dev-python/pydotplus/pydotplus-2.0.2.ebuild        | 31 ++++++++++++++++++++++
 3 files changed, 36 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     81c6835ecc63c30899001f51de3ce3318851db2c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb  5 17:31:13 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Fri Feb  5 17:31:13 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=81c6835e

Merge pull request #582 from TheChymera/nipy-extra

Nipy extra

 sci-libs/nipy-data/Manifest                                 |  1 +
 {dev-java/flexdock => sci-libs/nipy-data}/metadata.xml      |  9 +++++----
 .../nipy-data/nipy-data-0.2.ebuild                          | 13 ++++++++-----
 sci-libs/nipy-templates/Manifest                            |  1 +
 {dev-java/flexdock => sci-libs/nipy-templates}/metadata.xml |  9 +++++----
 .../nipy-templates/nipy-templates-0.2.ebuild                | 13 ++++++++-----
 6 files changed, 28 insertions(+), 18 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     d7b8396ce9f2e6dde4aa47768665deca034810bb
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 29 08:26:52 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jan 29 08:26:52 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d7b8396c

Merge pull request #579 from marcecj/virtual_blas_fix_alternatives

virtual/blas-2.1-r5: add missing "||"

 virtual/blas/blas-2.1-r5.ebuild | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     972f733505af7a14479981ad6386f58561195d2b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 25 19:47:29 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan 25 19:47:29 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=972f7335

Merge branch 'stharward-master'

* stharward-master:
  ugene-1.20.0 needs qtscript[scripttools]

 sci-biology/ugene/ugene-1.20.0.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     866c2cc3866b4aa008a9bf4a2832a892f5e0b34b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 25 09:19:21 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan 25 09:19:21 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=866c2cc3

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/metakernel_python: Bump to EAPI=6, add python3_5 support
  dev-python/metakernel_bash: Bump to EAPI=6, add python3_5 support
  dev-python/metakernel: Add python3_5 support
  dev-python/metakernel: Bump to EAPI=6
  dev-python/metakernel: Drop old
  dev-python/metakernel: Version bump to 0.12.2

 dev-python/metakernel/Manifest                     |  3 +-
 dev-python/metakernel/metakernel-0.11.3.ebuild     | 37 ----------------------
 dev-python/metakernel/metakernel-0.11.8.ebuild     |  6 ++--
 ...rnel-0.11.5.ebuild => metakernel-0.12.2.ebuild} |  6 ++--
 .../metakernel_bash-0.11.3-r1.ebuild               |  6 ++--
 .../metakernel_python-0.11.3-r1.ebuild             |  6 ++--
 6 files changed, 13 insertions(+), 51 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6e6f7f4d791f714df52b9d653add7e3247c95d11
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 25 09:19:02 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan 25 09:19:02 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6e6f7f4d

travis: Bump portage version to use

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index a902c87..93e3091 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,7 +6,7 @@ language: python
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.2.26"
+    - PORTAGE_VER="2.2.27"
 before_script:
     - mkdir travis-overlay
     - mv !(travis-overlay) travis-overlay/

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     83ba00a3658870db0b3cf7047d38f9902dc21785
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 24 16:51:25 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 24 16:51:25 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=83ba00a3

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

* 'master' of git+ssh://git.gentoo.org/proj/sci:
  dev-libs/boost-compute: Drop patch (included upstream)

 dev-libs/boost-compute/boost-compute-0.5.ebuild | 2 --
 1 file changed, 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     0ae705950cedcb3667d05fac9524c3d004645d17
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 22 08:15:57 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jan 22 08:15:57 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0ae70595

Merge remote-tracking branch 'github/master'

* github/master:
  Update contributing guidelines to match main Gentoo workflow

 CONTRIBUTING.md | 11 +++++++++++
 1 file changed, 11 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     0bd60f182f3614ae8f4401ca47ad01bdf19d294b
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 22 07:49:24 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jan 22 07:49:24 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0bd60f18

Update contributing guidelines to match main Gentoo workflow

 CONTRIBUTING.md | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 99561d0..f5e81b0 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -83,6 +83,10 @@ Once *all* reported problems are resolved, you can commit it
     repo-commit "Here we write a comprehensible commit message"
 
 ###Push to Github and make a pull request
+In order to facilitate potential reverts of mistakes, we prefer to keep the git history as linear as possible. For this, always rebase your changes on the latest remote changes.
+
+    hub pull --rebase=preserve github master
+
 Next we push back the changes in the PACKAGE_NAME branch to our fork and send a pull-request to the overlay maintainers.
 
     hub push YOUR_GITHUB_USER PACKAGE_NAME
@@ -94,6 +98,13 @@ Lastly you need to wait for review comments and the merge of your work. If you f
 If you would like to get direct access to the overlay, prove some contribution and ping us via sci@gentoo.org or on irc in #gentoo-science @ freenode. If you would like to become a dev yourself, prove some more contributions and again, contact us. We are always looking for new candidates.
 
 ----
+##Ebuild recommendations
+As the Gentoo Science overlay is a constant work-in-progress, we have some recommendations for prospective contributors:
+
+* **Aim for writing EAPI=6 ebuilds.** For certain eclasses, EAPI=6 is not allowed yet. In such cases you may use EAPI=5. We will not accept EAPI<5 ebuilds.
+* **Version bumps should always follow the latest guidelines.** For instance, a version bump of an ebuild that still employs autotools-utils.eclass should be avoided. Instead, drop 'autotools-utils', move to 'autotools' and call `default` followed by `eautoreconf` in src_prepare().
+
+----
 ##Merging contributions
 
 **It is important, that if you merge a pull request, you should feel as responsible as if you have written the commits yourself!**

[gentoo-commits] proj/sci:master commit in: /

[Reinis Danne]

commit:     b5c1e3c14413d2738e75b6e24ed5351f0f71ebcd
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Tue Jan 19 07:22:54 2016 +0000
Commit:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Tue Jan 19 07:22:54 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b5c1e3c1

Merge pull request #568 from hmmr/master

new upstream releases of sci-biology/{aghermann,cnrun}

 sci-biology/aghermann/Manifest                     |  4 +--
 sci-biology/aghermann/aghermann-1.0.3.ebuild       | 30 ----------------------
 sci-biology/aghermann/aghermann-1.0.4.ebuild       | 30 ----------------------
 sci-biology/aghermann/aghermann-1.0.5.ebuild       | 30 ----------------------
 ...mann-1.0.3-r1.ebuild => aghermann-1.0.7.ebuild} |  4 +--
 sci-biology/cnrun/Manifest                         |  2 +-
 .../{cnrun-2.0.2.ebuild => cnrun-2.0.3.ebuild}     |  4 +--
 7 files changed, 6 insertions(+), 98 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     7773cb44751d5bcaf7af57bbb4910ec431cbb499
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 18 16:31:39 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan 18 16:31:39 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7773cb44

Merge pull request #569 from TheChymera/psychopy

sci-biology/psychopy version bump

 sci-biology/psychopy/Manifest                                |  1 +
 .../{psychopy-9999.ebuild => psychopy-1.83.03.ebuild}        | 12 +++++-------
 2 files changed, 6 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c10ddcf372b26e4fac749de5322d8d7395c7ca9e
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 14 07:42:34 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jan 14 07:42:34 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c10ddcf3

Merge pull request #567 from Reinis/wxmacmolplt

sci-chemistry/wxmacmolplt: Use pkg-config to get link flags

 .../files/wxmacmolplt-7.6.1-pkg_config.patch       | 90 ++++++++++++++++++++++
 sci-chemistry/wxmacmolplt/wxmacmolplt-7.6.1.ebuild |  2 +
 2 files changed, 92 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     19f86a4777838ce70ef1d8673822dc68e87109cb
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 11 11:59:27 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan 11 11:59:27 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=19f86a47

Merge branch 'StinGer-ShoGuN-master'

* StinGer-ShoGuN-master:
  Created new revision to use boost libraries.

 sci-libs/clfft/{clfft-2.8.ebuild => clfft-2.8-r1.ebuild} | 1 +
 1 file changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     543568f48aaecad938c119b47aef062a61422a6b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 10 15:31:20 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 10 15:31:20 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=543568f4

Merge pull request #558 from chatcannon/nexus-4.4.1

Nexus 4.4.1

 sci-libs/nexus/Manifest           |  2 +-
 sci-libs/nexus/metadata.xml       | 12 ++++-----
 sci-libs/nexus/nexus-4.3.1.ebuild | 57 ---------------------------------------
 sci-libs/nexus/nexus-4.4.1.ebuild | 57 +++++++++++++++++++++++++++++++++++++++
 4 files changed, 63 insertions(+), 65 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     cbb1d203b5a6331eeec43a4ff5a71a82d9e71c12
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 10 14:57:59 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 10 14:57:59 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cbb1d203

Merge pull request #563 from apieum/fix-dgs-texinfo

Fix gentoo-science/sci#188 @table @bullet in faq template

 app-text/dgs/dgs-0.5.10-r2.ebuild                   |  1 +
 app-text/dgs/files/dgs-0.5.10-fix-table-bullet.diff | 20 ++++++++++++++++++++
 2 files changed, 21 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5356db8dabd6e38961fc17fca1bb69361f74cffa
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jan  7 14:11:08 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jan  7 14:11:08 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5356db8d

Merge remote-tracking branch 'github/master'

* github/master:
  sci-chemistry/erkale: Upstream moved to GitHub

 sci-chemistry/erkale/erkale-9999.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6b19057b1d563550711e836387842f13b32b9702
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jan  7 09:16:19 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jan  7 09:16:19 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6b19057b

Merge remote-tracking branch 'github/master'

* github/master:
  sci-chemistry/openbabel-python: Remove obsolete sed

 sci-chemistry/openbabel-python/openbabel-python-9999.ebuild | 3 ---
 1 file changed, 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     148faf674b100f355f530c983635c1a0de889aec
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jan  6 14:52:17 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jan  6 14:52:17 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=148faf67

Merge pull request #562 from Reinis/openbabel-python_remove_obsolete_sed

sci-chemistry/openbabel-python: Remove obsolete sed

 sci-chemistry/openbabel-python/openbabel-python-9999.ebuild | 3 ---
 1 file changed, 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     1506ebc853b6b2f0ed1741cc1420b9c4a8b3aad7
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan  5 22:02:00 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan  5 22:02:00 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1506ebc8

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 sci-biology/ugene/ChangeLog           | 6 ++++++
 sci-biology/ugene/ugene-1.20.0.ebuild | 8 ++++++--
 2 files changed, 12 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     765fd88b521e622abf36edc2c61a54f12a9dcc61
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jan  4 14:26:33 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jan  4 14:26:33 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=765fd88b

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 sci-libs/atlas/ChangeLog               | 5 ++++-
 sci-libs/atlas/atlas-3.11.38-r1.ebuild | 4 ++--
 2 files changed, 6 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     5215ac31952420ede215603235b735f3c2a54b15
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 31 08:56:08 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Dec 31 08:56:08 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5215ac31

Merge pull request #553 from TheChymera/nistats

sci-biology/nistats: added new package

 sci-biology/nistats/ChangeLog                      | 12 +++++++++
 .../nipy => sci-biology/nistats}/metadata.xml      |  6 ++---
 sci-biology/nistats/nistats-9999.ebuild            | 30 ++++++++++++++++++++++
 3 files changed, 44 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     f2da96a0c75b64ea993c3fac0ccffe6f9cf48091
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Jan  1 17:32:59 2016 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Jan  1 17:32:59 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f2da96a0

Merge branch 'master' of ssh://github.com/gentoo-science/sci

 sci-biology/nistats/ChangeLog                      | 12 +++++++++
 .../nipy => sci-biology/nistats}/metadata.xml      |  6 ++---
 sci-biology/nistats/nistats-9999.ebuild            | 30 ++++++++++++++++++++++
 3 files changed, 44 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     73ea8b5b3880d19fa79708dc2c4e3afac76bc79b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 31 08:48:39 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Dec 31 08:48:39 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=73ea8b5b

Merge remote-tracking branch 'github/master'

* github/master:
  sci-mathematics/petsc: version bump to 2.6.3

 sci-mathematics/petsc/ChangeLog                                  | 5 +++++
 sci-mathematics/petsc/Manifest                                   | 1 +
 sci-mathematics/petsc/{petsc-3.6.0.ebuild => petsc-3.6.3.ebuild} | 4 ++--
 3 files changed, 8 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     49ab51ebe0b61d92918f823517338ca41881d3a4
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 18 17:27:22 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec 18 17:27:22 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=49ab51eb

Merge remote-tracking branch 'github/master'

* github/master:
  added move notice
  moved files to new location

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     e7893ea65b937384ffaa32c765d25e89425565c3
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Thu Dec 17 09:08:04 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Dec 17 09:08:04 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e7893ea6

Merge branch 'nilearn' of github.com:TheChymera/neurogentoo into nilearn

 sci-biology/nilearn/ChangeLog              | 8 ++++++++
 sci-biology/nilearn/nilearn-0.1.4.1.ebuild | 3 ++-
 sci-biology/nilearn/nilearn-9999.ebuild    | 7 ++++++-
 3 files changed, 16 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     2488220b433c82de5e2b8693ea166a5b4e437912
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 18 17:26:35 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec 18 17:26:35 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2488220b

Merge pull request #554 from TheChymera/nilearn

Nilearn directory updae

 profiles/updates/4Q-2015                                   | 1 +
 {dev-python => sci-biology}/nilearn/ChangeLog              | 0
 {dev-python => sci-biology}/nilearn/Manifest               | 0
 {dev-python => sci-biology}/nilearn/metadata.xml           | 0
 {dev-python => sci-biology}/nilearn/nilearn-0.1.4.1.ebuild | 0
 {dev-python => sci-biology}/nilearn/nilearn-9999.ebuild    | 0
 6 files changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6e39d77176d8811efb2af398b7671a6e6a9405db
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 17 09:08:40 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Dec 17 09:08:40 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6e39d771

Merge pull request #521 from TheChymera/nilearn

dev-python/nilearn: new package

 dev-python/nilearn/ChangeLog              | 35 ++++++++++++++++++++++++++++++
 dev-python/nilearn/Manifest               |  1 +
 dev-python/nilearn/metadata.xml           | 20 +++++++++++++++++
 dev-python/nilearn/nilearn-0.1.4.1.ebuild | 36 +++++++++++++++++++++++++++++++
 dev-python/nilearn/nilearn-9999.ebuild    | 34 +++++++++++++++++++++++++++++
 5 files changed, 126 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     2e3e45a9a5c2f523fb775218d505c3fdcde36dfa
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 17 11:06:31 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Dec 17 11:06:31 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2e3e45a9

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/nilearn: moved deps to DEPEND
  dev-python/nilearn: added test flag and test dependency
  dev-python/nilearn: added test function
  dev-python/nilearn: plot use flag in live ebuild as well
  dev-python/nilearn: added plot use flag, added MY_PV, removed deprecated dependency version
  dev-python/nilearn: dropped empty IUSE, added PYTHON_USEDEP
  dev-python/nilearn: corrected format, added PYTHON_USEDEP, removed emtty IUSE
  dev-python/nilearn: new package

 dev-python/nilearn/ChangeLog              | 35 ++++++++++++++++++++++++++++++
 dev-python/nilearn/Manifest               |  1 +
 dev-python/nilearn/metadata.xml           | 20 +++++++++++++++++
 dev-python/nilearn/nilearn-0.1.4.1.ebuild | 36 +++++++++++++++++++++++++++++++
 dev-python/nilearn/nilearn-9999.ebuild    | 34 +++++++++++++++++++++++++++++
 5 files changed, 126 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     225388b59df4cdb36006ff118b676014a1686887
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Dec  8 15:25:18 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Dec  8 15:25:18 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=225388b5

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/PeakUtils: New package, ebuild written by me
  sci-libs/cblas-reference: Added missing virtual/blas dependency.
  fixed broken Changelog
  dev-tex/pythontex: fixed access violation
  dev-util/amdapp: Add dependency on x11-drivers/ati-drivers
  dev-util/amdapp: Drop old
  sci-biology/mricron: added icon and gnome desktop entry

 dev-python/PeakUtils/ChangeLog                     |  9 +++
 dev-python/PeakUtils/Manifest                      |  1 +
 dev-python/PeakUtils/PeakUtils-1.0.1.ebuild        | 24 ++++++
 dev-python/PeakUtils/metadata.xml                  | 15 ++++
 dev-tex/pythontex/ChangeLog                        |  7 ++
 dev-tex/pythontex/pythontex-0.14-r1.ebuild         |  2 +-
 dev-tex/pythontex/pythontex-9999.ebuild            |  2 +-
 dev-util/amdapp/ChangeLog                          | 14 ++++
 dev-util/amdapp/Manifest                           |  2 -
 ...{amdapp-2.9.1.ebuild => amdapp-2.9.1-r1.ebuild} | 14 +---
 dev-util/amdapp/amdapp-2.9.ebuild                  | 87 ----------------------
 .../{amdapp-3.0.ebuild => amdapp-3.0-r1.ebuild}    | 14 +---
 sci-biology/mricron/ChangeLog                      |  3 +
 sci-biology/mricron/mricron-9999.ebuild            |  9 +++
 sci-libs/cblas-reference/ChangeLog                 |  6 +-
 .../cblas-reference-20151113-r2.ebuild             |  2 +-
 16 files changed, 94 insertions(+), 117 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     2c57be95f78ee44f571edf097b0a5b2e05dee97f
Author:     Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Mon Dec  7 18:19:12 2015 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Mon Dec  7 18:19:12 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2c57be95

Merge branch 'master' of https://github.com/gentoo-science/sci

 dev-tex/pythontex/ChangeLog                        |  7 ++
 dev-tex/pythontex/pythontex-0.14-r1.ebuild         |  2 +-
 dev-tex/pythontex/pythontex-9999.ebuild            |  2 +-
 dev-util/amdapp/ChangeLog                          | 14 ++++
 dev-util/amdapp/Manifest                           |  2 -
 ...{amdapp-2.9.1.ebuild => amdapp-2.9.1-r1.ebuild} | 14 +---
 dev-util/amdapp/amdapp-2.9.ebuild                  | 87 ----------------------
 .../{amdapp-3.0.ebuild => amdapp-3.0-r1.ebuild}    | 14 +---
 sci-biology/repeatmasker/ChangeLog                 | 14 ++++
 ...r-4.0.6.ebuild => repeatmasker-4.0.6-r2.ebuild} |  7 +-
 10 files changed, 45 insertions(+), 118 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     2332981a7abb3c2476c06e68177d89772609bea0
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Dec  7 12:42:50 2015 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Mon Dec  7 12:42:50 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2332981a

Merge pull request #548 from TheChymera/pythontex

Pythontex

 dev-tex/pythontex/ChangeLog                | 7 +++++++
 dev-tex/pythontex/pythontex-0.14-r1.ebuild | 2 +-
 dev-tex/pythontex/pythontex-9999.ebuild    | 2 +-
 3 files changed, 9 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     0276368836234d2d5ef6183c1e0133c9ce9144fb
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Mon Dec  7 08:07:30 2015 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Mon Dec  7 08:07:30 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=02763688

Merge remote-tracking branch 'github/master'

 sci-biology/mricron/ChangeLog           | 3 +++
 sci-biology/mricron/mricron-9999.ebuild | 9 +++++++++
 2 files changed, 12 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     3f713b733cef21cbe0c45ae91d1b9e959602e97d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Dec  7 06:30:59 2015 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Mon Dec  7 06:30:59 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3f713b73

Merge pull request #547 from TheChymera/mricron

sci-biology/mricron: added icon and gnome desktop entry

 sci-biology/mricron/ChangeLog           | 3 +++
 sci-biology/mricron/mricron-9999.ebuild | 9 +++++++++
 2 files changed, 12 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     cbbc446366b6ff82de2d3d3b485c1a715156e8fe
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Dec  4 07:01:08 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec  4 07:01:08 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cbbc4463

Merge remote-tracking branch 'github/master'

* github/master:
  sci-biology/mricron: corrected binary paths
  sci-biology/mricron: new ebuild

 sci-biology/mricron/ChangeLog                      | 12 +++++++++
 .../lacaml => sci-biology/mricron}/metadata.xml    |  5 ++--
 sci-biology/mricron/mricron-9999.ebuild            | 30 ++++++++++++++++++++++
 3 files changed, 45 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     e313631550498069192dc057da97cdd67fb94907
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Dec  4 07:00:05 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec  4 07:00:05 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e3136315

Merge branch 'heroxbd-master'

* heroxbd-master:
  eclass/alternatives-2.eclass: support Prefix.
  sci-biology/pysam: version bump to 0.8.4
  dev-cpp/eigen: version bump to 3.2.7

 dev-cpp/eigen/ChangeLog                                      | 5 +++++
 dev-cpp/eigen/Manifest                                       | 2 ++
 dev-cpp/eigen/{eigen-3.2.6.ebuild => eigen-3.2.7.ebuild}     | 2 +-
 eclass/alternatives-2.eclass                                 | 8 ++++----
 sci-biology/pysam/ChangeLog                                  | 5 +++++
 sci-biology/pysam/Manifest                                   | 1 +
 sci-biology/pysam/{pysam-0.8.3.ebuild => pysam-0.8.4.ebuild} | 4 +---
 7 files changed, 19 insertions(+), 8 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     23ce21e0c968c854c81f873189ff5840d324eec8
Author:     Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Thu Dec  3 21:31:39 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Dec  3 21:31:39 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=23ce21e0

Merge branch 'master' of https://github.com/gentoo-science/sci

 sci-libs/atlas/Manifest                            |   4 +-
 sci-libs/atlas/atlas-3.10.1-r2.ebuild              |   7 +-
 ...{atlas-3.10.1-r1.ebuild => atlas-3.10.2.ebuild} |  13 +-
 ...atlas-3.10.1-r1.ebuild => atlas-3.11.38.ebuild} |  70 ++++----
 sci-libs/atlas/files/format-security.patch         | 198 +++++++++++++++++++++
 sci-libs/atlas/metadata.xml                        |   1 +
 6 files changed, 247 insertions(+), 46 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     d2c348c2af528728855000333b0f427d28b53610
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Dec  4 06:56:14 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec  4 06:56:14 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d2c348c2

Merge pull request #546 from TheChymera/mricron

Mricron

 sci-biology/mricron/ChangeLog                      | 12 +++++++++
 .../lacaml => sci-biology/mricron}/metadata.xml    |  5 ++--
 sci-biology/mricron/mricron-9999.ebuild            | 30 ++++++++++++++++++++++
 3 files changed, 45 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     54745393089bf4b6f82e5f14add91e701445d1ce
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Dec  3 18:56:23 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Dec  3 18:56:23 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=54745393

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/pylibconfig2: Move KEYWORDS variable
  dev-python/pylibconfig2: Version bump; drop old
  dev-python/matplotlib2tikz: Drop old
  dev-python/matplotlib2tikz: Version bump

 dev-python/matplotlib2tikz/ChangeLog               | 10 ++++++++++
 dev-python/matplotlib2tikz/Manifest                |  2 +-
 .../matplotlib2tikz/matplotlib2tikz-0.2.4.ebuild   | 23 ----------------------
 ...z-0.4.0.ebuild => matplotlib2tikz-0.5.1.ebuild} |  0
 dev-python/pylibconfig2/ChangeLog                  | 10 ++++++++++
 dev-python/pylibconfig2/Manifest                   |  2 +-
 ...fig2-0.2.4.ebuild => pylibconfig2-0.2.5.ebuild} |  2 +-
 dev-python/pylibconfig2/pylibconfig2-9999.ebuild   |  2 +-
 8 files changed, 24 insertions(+), 27 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     e24a7533c9eddf63e1af052a5b860f11158f8442
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Dec  3 09:55:08 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Dec  3 09:55:08 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e24a7533

Merge pull request #544 from SoapZaNet/int64-pkgconfig

Int64 pkgconfig

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     25d48b15c2ad295b5ac8e86f07880f2fc41f9508
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Dec  1 12:00:56 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Dec  1 12:00:56 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=25d48b15

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 profiles/use.local.desc                                 |  1 -
 ...151113.ebuild => cblas-reference-20151113-r1.ebuild} |  3 ++-
 .../{gotoblas2-1.13.ebuild => gotoblas2-1.13-r1.ebuild} |  3 ++-
 sci-libs/lapack-reference/lapack-reference-3.6.0.ebuild |  3 ++-
 sci-libs/lapack-reference/metadata.xml                  |  6 ++++--
 virtual/blas/blas-2.1-r4.ebuild                         |  3 ++-
 virtual/cblas/cblas-2.0-r3.ebuild                       | 17 +++++++++--------
 7 files changed, 21 insertions(+), 15 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     cc3e6632b365e169967db15ccd8d0afe032dedfc
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 30 10:58:07 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 30 10:58:07 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cc3e6632

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/clblas: Version bump
  sci-libs/clblas: Build against CL-1.2, closes issue #543

 sci-libs/clblas/ChangeLog                                   | 11 +++++++++++
 sci-libs/clblas/Manifest                                    |  1 +
 sci-libs/clblas/{clblas-2.6.ebuild => clblas-2.6-r1.ebuild} | 11 +++++++++++
 sci-libs/clblas/{clblas-2.6.ebuild => clblas-2.8.ebuild}    | 11 +++++++++++
 sci-libs/clblas/clblas-9999.ebuild                          | 11 +++++++++++
 5 files changed, 45 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f4c2112c8d3288e519f549badbe46aebc9f86b25
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Nov 28 18:59:13 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Nov 28 18:59:13 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f4c2112c

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/python-vxi11: Drop old
  sci-visualization/forge: Drop old
  sci-libs/arrayfire: Drop old

 dev-python/python-vxi11/ChangeLog                  |   4 +
 dev-python/python-vxi11/Manifest                   |   1 -
 dev-python/python-vxi11/python-vxi11-0.7.ebuild    |  22 -----
 sci-libs/arrayfire/ChangeLog                       |   4 +
 sci-libs/arrayfire/Manifest                        |   2 -
 sci-libs/arrayfire/arrayfire-3.1.1-r2.ebuild       | 108 ---------------------
 sci-libs/arrayfire/arrayfire-3.1.2.ebuild          | 108 ---------------------
 sci-visualization/forge/ChangeLog                  |   4 +
 sci-visualization/forge/Manifest                   |   1 -
 .../forge/files/forge-3.1-find-glm.patch           |  32 ------
 sci-visualization/forge/forge-3.1.ebuild           |  47 ---------
 11 files changed, 12 insertions(+), 321 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     cbeabd5c64564203a3bfd6f716d26ad31d773aeb
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Nov 28 18:07:59 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Nov 28 18:07:59 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cbeabd5c

Merge remote-tracking branch 'github/master'

* github/master:
  Drop patches/jupyter_core-4.0.4-tests-dotipython.patch
  dev-python/nbconvert: Drop old patch
  dev-python/jupyter: Moved to tree
  dev-python/ipython: Moved to tree
  dev-python/jupyter_core: Moved to tree; Drop old
  dev-python/jupyter_console: Moved to tree
  dev-python/jupyter_client: Moved to tree; Drop old
  dev-python/notebook: Drop old
  dev-python/ipykernel: Moved to tree; Drop old
  dev-python/testpath: Moved to tree
  dev-python/traitlets: Moved to tree
  dev-python/ipython_genutils: Moved to tree
  dev-python/ipyparallel: Moved to tree
  dev-python/qtconsole: Moved to tree
  dev-python/pickleshare: Moved to tree
  dev-python/ipywidgets: Drop old
  dev-python/nbconvert: Moved to tree
  dev-python/nbformat: Moved to tree

 dev-python/ipykernel/ChangeLog                     |    4 +
 dev-python/ipykernel/Manifest                      |    3 -
 dev-python/ipykernel/ipykernel-4.0.3.ebuild        |   40 -
 dev-python/ipykernel/ipykernel-4.1.1.ebuild        |   35 -
 dev-python/ipykernel/ipykernel-4.2.0.ebuild        |   35 -
 dev-python/ipyparallel/ChangeLog                   |    5 +
 dev-python/ipyparallel/Manifest                    |    3 -
 dev-python/ipyparallel/ipyparallel-4.0.0-r1.ebuild |   63 -
 dev-python/ipyparallel/ipyparallel-4.0.2-r1.ebuild |   59 -
 dev-python/ipyparallel/ipyparallel-4.1.0.ebuild    |   59 -
 dev-python/ipython/ChangeLog                       |   50 -
 dev-python/ipython/Manifest                        |    1 -
 .../ipython/files/2.1.0-substitute-files.patch     |   27 -
 dev-python/ipython/ipython-4.0.0-r2.ebuild         |  136 -
 dev-python/ipython/metadata.xml                    |   51 -
 dev-python/ipython_genutils/ChangeLog              |    4 +
 dev-python/ipython_genutils/Manifest               |    1 -
 .../ipython_genutils/ipython_genutils-0.1.0.ebuild |   29 -
 dev-python/ipywidgets/ChangeLog                    |    5 +
 dev-python/ipywidgets/Manifest                     |    3 -
 dev-python/ipywidgets/ipywidgets-4.0.2-r1.ebuild   |   44 -
 dev-python/ipywidgets/ipywidgets-4.0.3.ebuild      |   38 -
 dev-python/ipywidgets/ipywidgets-4.1.0.ebuild      |   38 -
 dev-python/jupyter/ChangeLog                       |    9 -
 dev-python/jupyter/Manifest                        |    1 -
 dev-python/jupyter/jupyter-1.0.0.ebuild            |   45 -
 dev-python/jupyter/metadata.xml                    |   12 -
 dev-python/jupyter_client/ChangeLog                |    4 +
 dev-python/jupyter_client/Manifest                 |    2 -
 .../jupyter_client/jupyter_client-4.0.0.ebuild     |   36 -
 .../jupyter_client/jupyter_client-4.1.1.ebuild     |   37 -
 dev-python/jupyter_console/ChangeLog               |    4 +
 dev-python/jupyter_console/Manifest                |    1 -
 .../jupyter_console/jupyter_console-4.0.3.ebuild   |   55 -
 dev-python/jupyter_core/ChangeLog                  |    5 +
 dev-python/jupyter_core/Manifest                   |    3 -
 .../files/jupyter_core-4.0.4-add-test-files.patch  |   50 -
 .../jupyter_core/jupyter_core-4.0.4-r1.ebuild      |   39 -
 dev-python/jupyter_core/jupyter_core-4.0.6.ebuild  |   54 -
 dev-python/nbconvert/ChangeLog                     |    8 +
 dev-python/nbconvert/Manifest                      |    2 -
 .../nbconvert-4.0.0-pandoc-highlighting.patch      |   37 -
 dev-python/nbconvert/nbconvert-4.0.0-r1.ebuild     |   79 -
 dev-python/nbconvert/nbconvert-4.1.0.ebuild        |   78 -
 dev-python/nbformat/ChangeLog                      |    4 +
 dev-python/nbformat/Manifest                       |    2 -
 dev-python/nbformat/nbformat-4.0.0.ebuild          |   59 -
 dev-python/nbformat/nbformat-4.0.1.ebuild          |   60 -
 dev-python/notebook/ChangeLog                      |    8 +
 dev-python/notebook/Manifest                       |    1 -
 ...k-4.0.4-Don-t-redirect-from-edit-to-files.patch |   55 -
 ...nly-redirect-to-editor-for-text-documents.patch |   38 -
 .../notebook-4.0.4-set-mime-type-on-files.patch    |   35 -
 ...et-model-mimetype-even-when-content-False.patch |   64 -
 dev-python/notebook/notebook-4.0.4-r3.ebuild       |   93 -
 dev-python/pickleshare/ChangeLog                   |    4 +
 dev-python/pickleshare/Manifest                    |    1 -
 dev-python/pickleshare/pickleshare-0.5.ebuild      |   34 -
 dev-python/qtconsole/ChangeLog                     |    4 +
 dev-python/qtconsole/Manifest                      |    2 -
 dev-python/qtconsole/qtconsole-4.0.1-r1.ebuild     |   68 -
 dev-python/qtconsole/qtconsole-4.1.1.ebuild        |   63 -
 dev-python/testpath/ChangeLog                      |    4 +
 dev-python/testpath/Manifest                       |    1 -
 dev-python/testpath/testpath-0.2.ebuild            |   55 -
 dev-python/traitlets/ChangeLog                     |    4 +
 dev-python/traitlets/Manifest                      |    1 -
 dev-python/traitlets/traitlets-4.0.0.ebuild        |   54 -
 patches/jupyter_core-4.0.4-tests-dotipython.patch  | 4743 --------------------
 69 files changed, 67 insertions(+), 6684 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     462660dbe06be852a1d0831fd84061bff63e029f
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Nov 27 09:45:51 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Nov 27 09:45:51 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=462660db

bump portage version for travis

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index c4b9a89..a902c87 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,7 +6,7 @@ language: python
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.2.25"
+    - PORTAGE_VER="2.2.26"
 before_script:
     - mkdir travis-overlay
     - mv !(travis-overlay) travis-overlay/

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f1b7781d6b335e00f1ef1d4daf72c850225d668d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 26 11:57:28 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Nov 26 11:57:28 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f1b7781d

Merge remote-tracking branch 'github/master'

* github/master:
  Revert "sci-libs/lmfit: Fix EAPI version"

 sci-libs/lmfit/ChangeLog        | 3 ---
 sci-libs/lmfit/lmfit-5.1.ebuild | 2 +-
 2 files changed, 1 insertion(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     07015ba424c9ed1e42b34ff46a3ded6350f3e711
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 24 05:08:54 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Nov 24 05:08:54 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=07015ba4

.travis.yml: updated

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index c80aa86..c4b9a89 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,7 +6,7 @@ language: python
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.2.24"
+    - PORTAGE_VER="2.2.25"
 before_script:
     - mkdir travis-overlay
     - mv !(travis-overlay) travis-overlay/

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     7f384b10e55c82a1d6ac40121e7a65c458865489
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 23 11:02:48 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Nov 23 11:02:48 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f384b10

Merge pull request #539 from TheChymera/patch-1

typo

 sci-biology/fsl/fsl-5.0.8.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     bb7d54d46ada1cf6551d78ae2c59716c1d391996
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 24 02:03:32 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Nov 24 02:03:32 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=bb7d54d4

Merge branch 'master' of ssh://github.com/gentoo-science/sci

 sci-biology/fsl/fsl-5.0.8.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     b2f4859689b1ce99581b306c4e962d3168a53db2
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Nov 21 15:15:03 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Nov 21 15:15:03 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b2f48596

Merge remote-tracking branch 'github/master'

 profiles/use.local.desc | 2 ++
 1 file changed, 2 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     4e7846376ca4463f39fafdb001bb335a9e1dcffb
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Nov 20 06:58:20 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Nov 20 06:58:20 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4e784637

Merge pull request #528 from akreal/sci-misc/kaldi

sci-misc/kaldi: Version bump, switch to OpenBLAS math library by default, add CUDA support

 sci-misc/kaldi/ChangeLog                           |   8 ++
 sci-misc/kaldi/Manifest                            |   1 +
 sci-misc/kaldi/files/Makefile.patch                | 117 +++++++++----------
 .../kaldi/files/default_rules.mk.a7d9824.patch     |  30 +++++
 sci-misc/kaldi/kaldi-0_p20151106.ebuild            | 125 +++++++++++++++++++++
 sci-misc/kaldi/metadata.xml                        |   8 +-
 6 files changed, 231 insertions(+), 58 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     0a0b4bc009c4978a9d44459a3e15fc32a10080d2
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Nov 20 11:38:59 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Nov 20 11:38:59 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0a0b4bc0

Merge remote-tracking branch 'github/master'

* github/master:
  sci-misc/kaldi: Use cuda eclass
  sci-misc/kaldi: Add pkg_pretend() to check for suitable CBLAS provider
  sci-misc/kaldi: Switch to user-selected BLAS/LAPACK
  sci-misc/kaldi: Create unified diff for Makefile patch
  sci-misc/kaldi: Create unified diff for default_rules.mk patch
  sci-misc/kaldi: Change dohtml to dodoc
  sci-misc/kaldi: Fix RESTRICT conditions
  sci-misc/kaldi: Fix IUSE
  sci-misc/kaldi: Version bump, switch to OpenBLAS math library by default, add CUDA support
  fix dependency on python
  if rdkit don't uses python,boost won't need use
  fix dependency on boost[python]

 sci-libs/rdkit/rdkit-2015.03.1.ebuild              |   2 +-
 sci-libs/rdkit/rdkit-9999.ebuild                   |   2 +-
 sci-misc/kaldi/ChangeLog                           |   8 ++
 sci-misc/kaldi/Manifest                            |   1 +
 sci-misc/kaldi/files/Makefile.patch                | 117 +++++++++----------
 .../kaldi/files/default_rules.mk.a7d9824.patch     |  30 +++++
 sci-misc/kaldi/kaldi-0_p20151106.ebuild            | 125 +++++++++++++++++++++
 sci-misc/kaldi/metadata.xml                        |   8 +-
 8 files changed, 233 insertions(+), 60 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     13c8caec3c78d5dbfb5c2aa9a2855acb29886627
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Nov 18 07:13:24 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Nov 18 07:13:24 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=13c8caec

Merge pull request #538 from zasdfgbnm/patch-1

fix dependency on boost[python]

 sci-libs/rdkit/rdkit-2015.03.1.ebuild | 2 +-
 sci-libs/rdkit/rdkit-9999.ebuild      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6f7fcecd1802c4508f236fd595786f6f5c2b3a27
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 17 15:46:37 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Nov 17 15:46:37 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6f7fcecd

Merge remote-tracking branch 'github/master'

* github/master:
  sci-physics/root: Update to upstream changes. New nobyte-compile patch, paths for gl2ps changed, DOCS files changed.
  sci-biology/fsl: added info about updating environment
  sci-libs/nipy: removed leading spaces
  sci-libs/nipy: updated dependency list
  sci-libs/nipy: version bump

 sci-biology/fsl/ChangeLog                          |  3 +++
 sci-biology/fsl/fsl-5.0.8.ebuild                   |  8 +++++++
 sci-libs/nipy/ChangeLog                            | 16 +++++++++++--
 sci-libs/nipy/Manifest                             |  1 +
 sci-libs/nipy/nipy-0.3.0.ebuild                    | 12 +++++-----
 .../nipy/{nipy-0.3.0.ebuild => nipy-0.4.0.ebuild}  | 12 +++++-----
 sci-physics/root/ChangeLog                         |  6 +++++
 ...ile.patch => root-6.06.00-nobyte-compile.patch} | 28 +++++++++++++---------
 sci-physics/root/root-9999.ebuild                  |  5 ++--
 9 files changed, 64 insertions(+), 27 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     79a93152bae71ad355dd2787c75f0fa7d64fccd6
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 16 07:58:37 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 16 07:58:37 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=79a93152

Merge pull request #533 from TheChymera/bump

sci-libs/nipy: version bump

 sci-libs/nipy/ChangeLog                                | 16 ++++++++++++++--
 sci-libs/nipy/Manifest                                 |  1 +
 sci-libs/nipy/nipy-0.3.0.ebuild                        | 12 ++++++------
 sci-libs/nipy/{nipy-0.3.0.ebuild => nipy-0.4.0.ebuild} | 12 ++++++------
 4 files changed, 27 insertions(+), 14 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     eb87fb0e0176a4960b0b138ab47bb334583391d9
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 16 08:09:02 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 16 08:09:02 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=eb87fb0e

Merge pull request #536 from olifre/root6

sci-physics/root: Update to upstream changes.

 sci-physics/root/ChangeLog                         |  6 +++++
 ...ile.patch => root-6.06.00-nobyte-compile.patch} | 28 +++++++++++++---------
 sci-physics/root/root-9999.ebuild                  |  5 ++--
 3 files changed, 26 insertions(+), 13 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     3c3e5c7534faf016b59ac0f6f58c730539ec7902
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 16 08:08:18 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 16 08:08:18 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3c3e5c75

Merge pull request #535 from TheChymera/fsl

sci-biology/fsl: added info about updating environment

 sci-biology/fsl/ChangeLog        | 3 +++
 sci-biology/fsl/fsl-5.0.8.ebuild | 8 ++++++++
 2 files changed, 11 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     cb5cc14f669bad5286c22ff35ce42e3c3ce05ddc
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 16 06:44:59 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 16 06:44:59 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cb5cc14f

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

* 'master' of git+ssh://git.gentoo.org/proj/sci:
  sci-chemistry/votca-csg: update live ebuild
  sci-biology/codonw: add original Thesis of John Peden describing codonw package in more detail
  sci-biology/BBmap: version bump; apply also the UnicodeToAscii.patch
  sci-biology/Rcorrector: add einfo() message that default kmer size 23 is suboptimal
  sci-biology/SEECER: add einfo() message that default kmer size 17 is suboptimal
  sci-biology/Rcorrector: respect CXXFLAGS
  sci-biology/Rcorrector: new package
  sci-biology/jellyfish: fix filename generated by pkgconfig
  sci-biology/SEECER: patch crappy shellscripts to at leats die on error; require jellyfish-1.1.11
  sci-biology/SEECER: remove hardcoded paths
  sci-biology/BBmap-34.56: restoring previous working version
  sci-biology/BBmap-35.66: this version needs more cleanup, upstream will make a new release, dropping KEYWORD
  Update local USE description
  sci-libs/armadillo: Version bump; remove old

 .../{BBmap-34.56.ebuild => BBmap-34.97.ebuild}     |   1 +
 .../{BBmap-34.56.ebuild => BBmap-35.66.ebuild}     |   3 +-
 sci-biology/BBmap/ChangeLog                        |   6 +
 sci-biology/BBmap/Manifest                         |   3 +-
 sci-biology/BBmap/files/UnicodeToAscii.patch       |  17 +++
 sci-biology/Rcorrector/ChangeLog                   |  18 +++
 sci-biology/Rcorrector/Rcorrector-9999.ebuild      |  36 ++++++
 .../jhdf5 => sci-biology/Rcorrector}/metadata.xml  |   0
 sci-biology/SEECER/ChangeLog                       |  17 +++
 ...ECER-0.1.3-r1.ebuild => SEECER-0.1.3-r2.ebuild} |  19 +++-
 .../SEECER/files/remove-hardcoded-paths.patch      |  84 ++++++++++++++
 sci-biology/codonw/ChangeLog                       |   5 +
 sci-biology/codonw/Manifest                        |   1 +
 sci-biology/codonw/codonw-1.4.4-r2.ebuild          |   5 +-
 sci-biology/jellyfish/ChangeLog                    |   4 +
 sci-biology/jellyfish/jellyfish-1.1.11.ebuild      |   3 +-
 sci-chemistry/votca-csg/ChangeLog                  |   3 +
 sci-chemistry/votca-csg/votca-csg-9999.ebuild      |   2 +-
 sci-libs/armadillo/ChangeLog                       |   7 ++
 sci-libs/armadillo/Manifest                        |   3 +-
 sci-libs/armadillo/armadillo-5.500.2.ebuild        | 121 ---------------------
 ...llo-5.400.2.ebuild => armadillo-6.200.3.ebuild} |   2 +-
 22 files changed, 226 insertions(+), 134 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     94ccfefeae527bda63c1f0d368f4ccebf27ad761
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Nov 13 10:01:23 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Nov 13 10:01:23 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=94ccfefe

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 dev-python/arrayfire-python/ChangeLog              |   6 +
 dev-python/arrayfire-python/Manifest               |   1 +
 ...ebuild => arrayfire-python-3.1.20151111.ebuild} |   0
 profiles/use.local.desc                            |   1 -
 sci-chemistry/pymol-apbs-plugin/ChangeLog          |  27 -----
 sci-chemistry/pymol-apbs-plugin/metadata.xml       |   8 --
 .../pymol-apbs-plugin-9999.ebuild                  |  41 -------
 sci-chemistry/pymol/metadata.xml                   |   1 -
 sci-chemistry/pymol/pymol-9999.ebuild              |  11 +-
 sci-libs/armadillo/ChangeLog                       |   7 ++
 sci-libs/armadillo/Manifest                        |   3 +-
 sci-libs/armadillo/armadillo-5.500.2.ebuild        | 121 ---------------------
 ...llo-5.400.2.ebuild => armadillo-6.200.3.ebuild} |   2 +-
 sci-libs/nipype/ChangeLog                          |   3 +
 sci-libs/nipype/nipype-9999.ebuild                 |   1 +
 15 files changed, 24 insertions(+), 209 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     e62e53f3779bae37061e12bfbdb08d4adc827de0
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 12 07:05:22 2015 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Thu Nov 12 07:05:22 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e62e53f3

Merge pull request #532 from TheChymera/nipy

sci-libs/nipype: added dep on future

 sci-libs/nipype/ChangeLog          | 3 +++
 sci-libs/nipype/nipype-9999.ebuild | 1 +
 2 files changed, 4 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     51ca792d048830b50cce95493e56dc821020f659
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Thu Nov 12 07:26:50 2015 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Thu Nov 12 07:26:50 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=51ca792d

Merge remote-tracking branch 'github/master'

 sci-libs/nipype/ChangeLog          | 3 +++
 sci-libs/nipype/nipype-9999.ebuild | 1 +
 2 files changed, 4 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a0834a433de3c2c1ac453b315cc07b2559fa1971
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Nov 11 14:38:05 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Nov 11 14:38:05 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a0834a43

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/future: no longer calling python directly
  dev-python/future: new package (nipype dep)

 dev-python/future/ChangeLog            | 12 ++++++++++++
 dev-python/future/Manifest             |  1 +
 dev-python/future/future-0.15.2.ebuild | 22 ++++++++++++++++++++++
 dev-python/future/metadata.xml         | 18 ++++++++++++++++++
 4 files changed, 53 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     caf616b991c5eb5dc444b60cb0a942527ee7a2f4
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Nov 11 06:58:51 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Nov 11 06:58:51 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=caf616b9

Merge pull request #531 from TheChymera/future

dev-python/future: new package (nipype dep)

 dev-python/future/ChangeLog            | 12 ++++++++++++
 dev-python/future/Manifest             |  1 +
 dev-python/future/future-0.15.2.ebuild | 22 ++++++++++++++++++++++
 dev-python/future/metadata.xml         | 18 ++++++++++++++++++
 4 files changed, 53 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     ac3f5c76edb5f1e43eca81ae96afcd08ab5dd19b
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Nov 11 01:19:41 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Nov 11 01:19:41 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ac3f5c76

.travis.yml: updated

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index a4a230a..c80aa86 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,7 +6,7 @@ language: python
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.2.23"
+    - PORTAGE_VER="2.2.24"
 before_script:
     - mkdir travis-overlay
     - mv !(travis-overlay) travis-overlay/

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     8eea5da63491f25e2deba9d8382b118ef75f4e7b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 10 06:57:53 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Nov 10 06:57:53 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8eea5da6

Merge pull request #529 from TheChymera/nipype

Nipype ~arch version

 sci-libs/nipype/ChangeLog                                    | 8 ++++++++
 sci-libs/nipype/Manifest                                     | 1 +
 sci-libs/nipype/{nipype-9999.ebuild => nipype-0.11.0.ebuild} | 7 +++----
 3 files changed, 12 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c5f4fa336ee30be304e93b0eacd9a16e6c09361b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Nov  6 16:22:04 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Nov  6 16:22:04 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c5f4fa33

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/simplepam: Remove from overlay; replaced by pamela
  sci-libs/clfft: Version bump
  sci-libs/clfft: Add callback_client use flag
  sci-libs/clfft: Clean patches
  dev-python/pamela: Add new package needed for JupyterHub, ebuild written by me
  dev-python/arrayfire-python: Add python3.5 support
  dev-python/pyfftw: Add python3.5 support
  dev-python/pylibconfig2: Add python3.5 support
  dev-python/nvidia-ml-py: Add python3.5 support
  dev-python/pyfftw: Add python3.5 support
  dev-python/metakernel: Version bump
  sci-biology/bru2nii: Updated USE conditional logic again
  sci-biology/bru2nii: updated conditional die implemntation
  sci-biology/fsl: new sources location (upstream removes old sources)
  sci-biology/bru2nii: corrcted conditional logic
  sci-biology/bru2nii: corrected die calls
  sci-biology/bru2nii: added use-flag conditioning
  sci-biology/bru2nii: removed testing snippet
  sci-biology/bru2nii: new ebuild

 dev-python/arrayfire-python/ChangeLog              |   4 +
 .../arrayfire-python-3.0.20150914.ebuild           |   2 +-
 .../arrayfire-python/arrayfire-python-9999.ebuild  |   2 +-
 dev-python/metakernel/ChangeLog                    |   6 +
 dev-python/metakernel/Manifest                     |   1 +
 ...rnel-0.11.2.ebuild => metakernel-0.11.3.ebuild} |   0
 dev-python/nvidia-ml-py/ChangeLog                  |   4 +
 .../nvidia-ml-py/nvidia-ml-py-7.352.0.ebuild       |   2 +-
 dev-python/pamela/ChangeLog                        |  10 ++
 dev-python/pamela/Manifest                         |   1 +
 dev-python/{ipyparallel => pamela}/metadata.xml    |   7 +-
 .../pamela/pamela-0.2.1.ebuild                     |  12 +-
 dev-python/pamela/pamela-9999.ebuild               |  23 ++++
 dev-python/pyfftw/ChangeLog                        |   6 +
 dev-python/pyfftw/pyfftw-0.9.2.ebuild              |   2 +-
 dev-python/pyfftw/pyfftw-9999.ebuild               |   2 +-
 dev-python/pylibconfig2/ChangeLog                  |   4 +
 dev-python/pylibconfig2/pylibconfig2-0.2.4.ebuild  |   2 +-
 dev-python/pylibconfig2/pylibconfig2-9999.ebuild   |   2 +-
 dev-python/simplepam/ChangeLog                     |  13 ---
 dev-python/simplepam/Manifest                      |   1 -
 dev-python/simplepam/metadata.xml                  |  15 ---
 dev-python/simplepam/simplepam-0.1.5.ebuild        |  22 ----
 dev-python/simplepam/simplepam-9999.ebuild         |  22 ----
 sci-biology/bru2nii/ChangeLog                      |  27 +++++
 sci-biology/bru2nii/bru2nii-9999.ebuild            |  34 ++++++
 sci-biology/bru2nii/metadata.xml                   |  17 +++
 sci-biology/fsl/ChangeLog                          |   3 +
 sci-biology/fsl/fsl-5.0.8.ebuild                   |   2 +-
 sci-libs/clfft/ChangeLog                           |  15 +++
 sci-libs/clfft/Manifest                            |   1 +
 .../clfft/{clfft-2.6.1.ebuild => clfft-2.8.ebuild} |  17 ++-
 sci-libs/clfft/clfft-9999.ebuild                   |   3 +-
 .../clfft/files/clfft-2.4-client_CMakeLists.patch  |  41 -------
 .../files/clfft-2.4-fix-cmake-config-install.patch | 128 ---------------------
 .../files/clfft-2.4-scripts_perf_CMakeLists.patch  |  33 ------
 sci-libs/clfft/metadata.xml                        |   3 +
 37 files changed, 189 insertions(+), 300 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     ce64da5a3c43f02e2a6ddaad3145a742aba50eb7
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Nov  6 08:07:06 2015 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Fri Nov  6 08:07:06 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ce64da5a

Merge pull request #525 from TheChymera/bru2nii

Bru2nii

 sci-biology/bru2nii/ChangeLog           | 27 ++++++++++++++++++++++++++
 sci-biology/bru2nii/bru2nii-9999.ebuild | 34 +++++++++++++++++++++++++++++++++
 sci-biology/bru2nii/metadata.xml        | 17 +++++++++++++++++
 3 files changed, 78 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     29c14d4176eee3979156d3e2c9393995d348005b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Nov  5 06:55:54 2015 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Thu Nov  5 06:55:54 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=29c14d41

Merge pull request #527 from TheChymera/fsl

sci-biology/fsl: new sources location (upstream removes old sources)

 sci-biology/fsl/ChangeLog        | 3 +++
 sci-biology/fsl/fsl-5.0.8.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     0baa9031a3708fb575c991b0771cebcb65e8c15e
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Oct 29 13:01:08 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Oct 29 13:01:08 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0baa9031

Merge pull request #524 from timeraider4u/master

added ebuilds for emscripten-1.35.2 and emscripten-fastcomp-1.35.2

 dev-util/emscripten-fastcomp/Manifest                      |  2 ++
 ...mp-1.34.11.ebuild => emscripten-fastcomp-1.35.2.ebuild} |  0
 dev-util/emscripten/Manifest                               |  1 +
 dev-util/emscripten/emscripten-1.34.11.ebuild              | 14 ++++++++++----
 ...{emscripten-1.34.11.ebuild => emscripten-1.35.2.ebuild} | 14 ++++++++++----
 dev-util/emscripten/files/99emscripten                     |  2 +-
 dev-util/emscripten/files/emscripten.config                |  4 ++--
 7 files changed, 26 insertions(+), 11 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     4edcbc85e2732ec8fd8bd1e6508e83bd8cf0e6f1
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Oct 27 09:55:08 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Oct 27 09:55:08 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4edcbc85

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 dev-python/ipywidgets/Manifest                                           | 1 +
 .../ipywidgets/{ipywidgets-4.1.0.ebuild => ipywidgets-4.1.1.ebuild}      | 0
 2 files changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     70d68ffbd344bc277006f7f4c87d4db48b31bc9c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Oct 25 15:12:44 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Oct 25 15:12:44 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=70d68ffb

Merge pull request #523 from mschubert/symengine

sci-libs/symengine: split out bindings to dev-python/symengine

 dev-python/symengine/ChangeLog                   |  9 +++++++
 dev-python/{snakemake => symengine}/metadata.xml |  4 +--
 dev-python/symengine/symengine-9999.ebuild       | 32 ++++++++++++++++++++++++
 sci-libs/symengine/symengine-9999.ebuild         | 19 ++++----------
 4 files changed, 48 insertions(+), 16 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     655caabbd878ec7b01e96390fa6c0f36252299b3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Oct 24 17:41:17 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Oct 24 17:41:17 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=655caabb

Merge pull request #520 from timeraider4u/master

emscripten - LLVM to JavaScript compiler

 dev-util/emscripten-fastcomp/Manifest              |  2 +
 .../emscripten-fastcomp-1.34.11.ebuild             | 40 +++++++++++++
 .../emscripten-fastcomp}/metadata.xml              |  0
 dev-util/emscripten/Manifest                       |  1 +
 dev-util/emscripten/emscripten-1.34.11.ebuild      | 66 ++++++++++++++++++++++
 dev-util/emscripten/files/99emscripten             |  1 +
 dev-util/emscripten/files/emscripten.config        | 56 ++++++++++++++++++
 dev-util/emscripten/files/hello_world.cpp          |  5 ++
 .../gismo => dev-util/emscripten}/metadata.xml     |  0
 9 files changed, 171 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     d1267b9a31d99fff953be0154abae843ca65d76c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Oct 21 14:35:33 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Oct 21 14:35:33 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d1267b9a

Update CI script

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 015c625..a4a230a 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,7 +6,7 @@ language: python
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.2.21"
+    - PORTAGE_VER="2.2.23"
 before_script:
     - mkdir travis-overlay
     - mv !(travis-overlay) travis-overlay/

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     913249d8f9ed41c56aef2e59d70e3dcd5d98abc8
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Oct 21 13:44:54 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Oct 21 13:44:54 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=913249d8

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/matplotlib-venn: added build-time dep
  dev-python/matplotlib-venn: added uild-time dep
  dev-python/matplotlib-venn: no longer installing for test phase
  dev-python/matplotlib-venn: removed test IUSE
  dev-python/matplotlib-venn: removed keywords from live ebuild
  dev-python/matplotlib-venn: removed test phase (upstream archive does not provide test scripts)
  dev-python/matplotlib-venn: removed useless blank line
  dev-python/matplotlib-venn: requiring RDEPEND if test phase enabled
  dev-python/matplotlib-venn: updated python test script
  modified test phase dev-python/matplotlib-venn:
  implemented install phase dev-python/matplotlib-venn:
  fixed license dev-python/matplotlib-venn:
  added test use fag dev-python/matplotlib-venn:
  added keyword dev-python/matplotlib-venn:
  new ebuild dev-python/matplotlib-venn:

 dev-python/matplotlib-venn/ChangeLog               | 55 ++++++++++++++++++++++
 dev-python/matplotlib-venn/Manifest                |  1 +
 .../matplotlib-venn/matplotlib-venn-0.11.ebuild    | 24 ++++++++++
 .../matplotlib-venn/matplotlib-venn-9999.ebuild    | 33 +++++++++++++
 .../{pythoncgns => matplotlib-venn}/metadata.xml   |  2 +-
 5 files changed, 114 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     337f64280c8062ca1b3dba4e50723178a9009bfa
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 19 10:56:17 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Oct 19 10:56:17 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=337f6428

Merge pull request #505 from TheChymera/venn

new ebuild: matplotlib-venn

 dev-python/matplotlib-venn/ChangeLog               | 55 ++++++++++++++++++++++
 dev-python/matplotlib-venn/Manifest                |  1 +
 .../matplotlib-venn/matplotlib-venn-0.11.ebuild    | 24 ++++++++++
 .../matplotlib-venn/matplotlib-venn-9999.ebuild    | 33 +++++++++++++
 .../{pythoncgns => matplotlib-venn}/metadata.xml   |  2 +-
 5 files changed, 114 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ffd47f4fe285e22f7dbdfd25b94b1f3e8db9ba37
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Oct 17 07:44:16 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Oct 17 07:44:16 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ffd47f4f

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/snakemake-3.4.2: new ebuild
  dev-python/qtconsole: Version bump to 4.1.0
  dev-python/notebook: Version bump to 4.0.6, drop 4.0.5
  Update remote-ids
  sci-biology/atsas: Fix installation of missing libs
  sci-mathematics/gismo: added installation of documentation

 app-benchmarks/numbench/metadata.xml               |  5 ++-
 app-doc/root-docs/metadata.xml                     | 31 ++++++++-------
 dev-cpp/eigen/metadata.xml                         |  7 +++-
 dev-ml/lacaml/metadata.xml                         |  7 +++-
 dev-perl/BTLib/metadata.xml                        |  5 ++-
 dev-python/notebook/ChangeLog                      |  6 +++
 dev-python/notebook/Manifest                       |  2 +-
 ...notebook-4.0.5.ebuild => notebook-4.0.6.ebuild} |  2 +-
 dev-python/qtconsole/ChangeLog                     |  6 +++
 dev-python/qtconsole/Manifest                      |  1 +
 ...tconsole-9999.ebuild => qtconsole-4.1.0.ebuild} |  0
 dev-python/snakemake/ChangeLog                     |  7 ++++
 dev-python/snakemake/Manifest                      |  1 +
 .../rdkit => dev-python/snakemake}/metadata.xml    |  4 +-
 .../snakemake/snakemake-3.4.2.ebuild               |  9 ++---
 sci-astronomy/mosstack/metadata.xml                |  3 ++
 sci-biology/Atlas2/metadata.xml                    |  5 ++-
 sci-biology/IMAGE/metadata.xml                     |  5 ++-
 sci-biology/NGSTools/metadata.xml                  |  5 ++-
 sci-biology/OBO-Edit/metadata.xml                  |  5 ++-
 sci-biology/STAR/metadata.xml                      |  5 ++-
 sci-biology/atsas/atsas-2.7.0.ebuild               |  4 +-
 sci-biology/conifer/metadata.xml                   |  5 ++-
 sci-biology/flexbar/metadata.xml                   |  5 ++-
 sci-biology/gap2caf/metadata.xml                   |  5 ++-
 sci-biology/kallisto/metadata.xml                  |  5 ++-
 sci-biology/mne-python/metadata.xml                |  5 ++-
 sci-biology/pb-honey/metadata.xml                  |  5 ++-
 sci-biology/pb-jelly/metadata.xml                  |  5 ++-
 sci-biology/psychopy/metadata.xml                  |  5 ++-
 sci-biology/pysam/metadata.xml                     |  3 +-
 sci-biology/pysurfer/metadata.xml                  |  5 ++-
 sci-biology/quast/metadata.xml                     |  5 ++-
 sci-biology/subread/metadata.xml                   |  5 ++-
 sci-libs/elmer-eio/metadata.xml                    |  5 ++-
 sci-libs/elmer-hutiter/metadata.xml                |  5 ++-
 sci-libs/matc/metadata.xml                         |  6 ++-
 sci-libs/nibabel/metadata.xml                      |  7 +++-
 sci-mathematics/gismo/files/doc-install.patch      | 46 ++++++++++++++++++++++
 sci-mathematics/gismo/gismo-0.8.1.ebuild           | 10 ++++-
 sci-misc/elmer-elmergrid/metadata.xml              |  5 ++-
 sci-misc/elmer-fem/metadata.xml                    |  5 ++-
 sci-misc/elmer-front/metadata.xml                  |  5 ++-
 sci-misc/elmer-meshgen2d/metadata.xml              |  5 ++-
 sci-misc/elmer-post/metadata.xml                   |  5 ++-
 sci-visualization/forge/metadata.xml               |  5 ++-
 46 files changed, 231 insertions(+), 61 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     12f1d5e07ad992e5c85c261b106a1d291c8bdbf1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Oct 17 07:43:39 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Oct 17 07:43:39 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=12f1d5e0

Merge pull request #519 from mschubert/snakemake

dev-python/snakemake-3.4.2: new ebuild

 dev-python/snakemake/ChangeLog                                   | 7 +++++++
 dev-python/snakemake/Manifest                                    | 1 +
 {sci-biology/pyfaidx => dev-python/snakemake}/metadata.xml       | 4 ++--
 .../snakemake/snakemake-3.4.2.ebuild                             | 9 ++++-----
 4 files changed, 14 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     95baa1b21ce885abd775717b7673cb821e37aa0b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Oct 16 13:38:35 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Oct 16 13:38:35 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=95baa1b2

Merge remote-tracking branch 'github/master'

* github/master:
  sci-mathematics/gismo: added installation of documentation
  Moved to tree
  Update local USE description
  added ebuild for gismo (Geometry+Simulation), see https://gs.jku.at/gismo
  sci-biology/pysurfer: removed deprecated patch section

 sci-biology/bowtie/ChangeLog                       | 37 --------------
 sci-biology/bowtie/Manifest                        |  5 --
 sci-biology/bowtie/bowtie-1.1.1.ebuild             | 53 --------------------
 sci-biology/bowtie/bowtie-1.1.2.ebuild             | 58 ----------------------
 sci-biology/bowtie/bowtie-2.2.3.ebuild             | 52 -------------------
 sci-biology/bowtie/bowtie-2.2.5.ebuild             | 52 -------------------
 sci-biology/bowtie/bowtie-2.2.6.ebuild             | 54 --------------------
 .../bowtie-1.1.2-tbb-tinythread-missing.patch      | 14 ------
 sci-biology/bowtie/metadata.xml                    | 13 -----
 sci-biology/pysurfer/ChangeLog                     |  3 ++
 .../pysurfer/files/0.6-headless_build.patch        |  9 ----
 sci-mathematics/gismo/Manifest                     |  1 +
 sci-mathematics/gismo/files/doc-install.patch      | 46 +++++++++++++++++
 .../gismo/files/examples-CMakeLists.patch          | 46 +++++++++++++++++
 sci-mathematics/gismo/gismo-0.8.1.ebuild           | 42 ++++++++++++++++
 .../ccif => sci-mathematics/gismo}/metadata.xml    |  4 +-
 16 files changed, 140 insertions(+), 349 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     fe3711190eff308abede29e7ec45d526a344b016
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Oct 16 06:58:56 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Oct 16 06:58:56 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fe371119

Merge pull request #518 from timeraider4u/master

sci-mathematics/gismo: added installation of documentation

 sci-mathematics/gismo/files/doc-install.patch | 46 +++++++++++++++++++++++++++
 sci-mathematics/gismo/gismo-0.8.1.ebuild      | 10 ++++--
 2 files changed, 54 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     d3770afcc53e9e940c994fb8d27d581513a76dd1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Oct 14 09:01:05 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Oct 14 09:01:05 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d3770afc

Merge pull request #515 from TheChymera/pysurfer

sci-biology/pysurfer: removed deprecated patch section

 sci-biology/pysurfer/ChangeLog                      | 3 +++
 sci-biology/pysurfer/files/0.6-headless_build.patch | 9 ---------
 2 files changed, 3 insertions(+), 9 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ff4078fbe29176fdecdf87deb85d971aea7a8cda
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Oct 15 16:44:45 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Oct 15 16:44:45 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ff4078fb

Merge pull request #516 from timeraider4u/master

sci-mathematics/gismo: added ebuild for gismo (Geometry+Simulation)

 sci-mathematics/gismo/Manifest                     |  1 +
 .../gismo/files/examples-CMakeLists.patch          | 46 ++++++++++++++++++++++
 sci-mathematics/gismo/gismo-0.8.1.ebuild           | 36 +++++++++++++++++
 .../ccif => sci-mathematics/gismo}/metadata.xml    |  4 +-
 4 files changed, 85 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     54d4feaf6958848d580261d869153af132e10974
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 12 14:50:01 2015 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Mon Oct 12 14:50:01 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=54d4feaf

Merge pull request #513 from TheChymera/pysurfer

sci-biology/pysurfer: updated patch

 sci-biology/pysurfer/ChangeLog                      | 3 +++
 sci-biology/pysurfer/files/0.6-headless_build.patch | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     3be5352e74fca08b48cf9bdf27d1f2d413e23835
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 12 09:34:31 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Oct 12 09:34:31 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3be5352e

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/ipykernel: Version bump to 4.1.0
  dev-python/jupyter_console: Version bump to 4.0.3
  dev-python/jupyter_client: Version bump to 4.1.1
  Update envytools-9999.ebuild
  sci-biology/bowtie: Use 'usex' instead of defining TBB variable.
  sci-biology/bowtie: Version bump to 2.2.6
  sci-biology/bowtie: Version bump to 1.1.2

 dev-python/ipykernel/ChangeLog                             |  5 +++++
 dev-python/ipykernel/Manifest                              |  1 +
 .../{ipykernel-9999.ebuild => ipykernel-4.1.0.ebuild}      |  0
 dev-python/jupyter_client/ChangeLog                        |  5 +++++
 dev-python/jupyter_client/Manifest                         |  1 +
 ...ter_client-4.0.0.ebuild => jupyter_client-4.1.1.ebuild} |  0
 dev-python/jupyter_console/ChangeLog                       |  6 ++++++
 dev-python/jupyter_console/Manifest                        |  1 +
 ...r_console-4.0.2.ebuild => jupyter_console-4.0.3.ebuild} |  0
 sci-biology/bowtie/ChangeLog                               | 13 +++++++++++++
 sci-biology/bowtie/Manifest                                |  2 ++
 .../bowtie/{bowtie-1.1.1.ebuild => bowtie-1.1.2.ebuild}    | 11 ++++++++---
 .../bowtie/{bowtie-2.2.5.ebuild => bowtie-2.2.6.ebuild}    |  8 +++++---
 .../bowtie/files/bowtie-1.1.2-tbb-tinythread-missing.patch | 14 ++++++++++++++
 sci-biology/bowtie/metadata.xml                            |  5 +++++
 x11-misc/envytools/envytools-9999.ebuild                   |  2 +-
 16 files changed, 67 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     dfec4a30279c367c29c14a0888b454691c7e8431
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Oct 11 17:07:26 2015 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sun Oct 11 17:07:26 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=dfec4a30

Merge pull request #511 from hoehnp/patch-1

Update envytools-9999.ebuild

 x11-misc/envytools/envytools-9999.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     c17683cfebf4a55154ed1cff14d639988c640091
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Mon Oct 12 06:50:18 2015 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Mon Oct 12 06:50:18 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c17683cf

Merge pull request #512 from flacjacket/jupyter_bump

Bump Jupyter packages

 dev-python/ipykernel/ChangeLog                                      | 5 +++++
 dev-python/ipykernel/Manifest                                       | 1 +
 .../ipykernel/{ipykernel-9999.ebuild => ipykernel-4.1.0.ebuild}     | 0
 dev-python/jupyter_client/ChangeLog                                 | 5 +++++
 dev-python/jupyter_client/Manifest                                  | 1 +
 .../{jupyter_client-4.0.0.ebuild => jupyter_client-4.1.1.ebuild}    | 0
 dev-python/jupyter_console/ChangeLog                                | 6 ++++++
 dev-python/jupyter_console/Manifest                                 | 1 +
 .../{jupyter_console-4.0.2.ebuild => jupyter_console-4.0.3.ebuild}  | 0
 9 files changed, 19 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ba86677328c681bbe47399f2e75befdb1be4b0d4
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Oct 10 15:39:54 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Oct 10 15:39:54 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ba866773

Merge pull request #510 from SoapZaNet/pysam-0.8.3

sci-biology/pysam: version bump to 0.8.3

 sci-biology/pysam/Manifest                         |  1 +
 .../pysam/files/pysam-0.8.3-cython-0.23.patch      | 32 ++++++++++++++++++++++
 .../{pysam-0.7.5.ebuild => pysam-0.8.3.ebuild}     |  9 ++++--
 3 files changed, 39 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     0e1e241626fc6d6fd64a97e72702d443243c778d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Oct 10 14:11:28 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Oct 10 14:11:28 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0e1e2416

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/matrix2latex: removed empty depend list
  dev-python/matrix2latex: removed deprecated python compatibility
  dev-python/matrix2latex: removed keyword for live package
  dev-python/matrix2latex: removed blank line
  dev-python/matrix2latex: corrected header license
  dev-python/matrix2latex: new homepage

 dev-python/matrix2latex/ChangeLog                 | 28 +++++++++++++++++++++++
 dev-python/matrix2latex/Manifest                  |  1 +
 dev-python/matrix2latex/matrix2latex-1.0.0.ebuild | 20 ++++++++++++++++
 dev-python/matrix2latex/matrix2latex-9999.ebuild  | 18 +++++++++++++++
 dev-python/{viper => matrix2latex}/metadata.xml   |  8 +++----
 5 files changed, 71 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f60ee7229cdf5320537ced988b96baf1eafa45d8
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Oct 10 11:37:30 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Oct 10 11:37:30 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f60ee722

Merge pull request #509 from TheChymera/m2l

new dev-python/matrix2latex ebuild

 dev-python/matrix2latex/ChangeLog                 | 28 +++++++++++++++++++++++
 dev-python/matrix2latex/Manifest                  |  1 +
 dev-python/matrix2latex/matrix2latex-1.0.0.ebuild | 20 ++++++++++++++++
 dev-python/matrix2latex/matrix2latex-9999.ebuild  | 18 +++++++++++++++
 dev-python/{viper => matrix2latex}/metadata.xml   |  8 +++----
 5 files changed, 71 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     b4a24dd14b20f259936f92533e26fba6efbb4fb6
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Oct  4 07:52:25 2015 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sun Oct  4 07:52:25 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b4a24dd1

Merge pull request #466 from mschubert/symengine

sci-libs/symengine: add sympy-symengine

 sci-libs/symengine/ChangeLog                       | 14 +++++
 sci-libs/symengine/Manifest                        |  1 +
 .../bx-python => sci-libs/symengine}/metadata.xml  |  8 +--
 sci-libs/symengine/symengine-0.1.0.ebuild          | 60 +++++++++++++++++++++
 sci-libs/symengine/symengine-9999.ebuild           | 61 ++++++++++++++++++++++
 5 files changed, 141 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Marius Brehler]

commit:     722cfa776f5ebeb3305f01ef794fcb7ce14b9293
Author:     layman <layman <AT> localhost>
AuthorDate: Sat Sep 12 12:44:25 2015 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sat Sep 12 12:44:25 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=722cfa77

Merge branch 'master' into symengine

 .travis.yml                                        |   16 +-
 dev-libs/boost-compute/ChangeLog                   |   17 +
 dev-libs/boost-compute/boost-compute-0.4-r1.ebuild |   28 +-
 dev-libs/boost-compute/boost-compute-9999.ebuild   |   17 +-
 dev-python/ipykernel/ChangeLog                     |   13 +
 dev-python/ipykernel/Manifest                      |    1 +
 dev-python/ipykernel/ipykernel-4.0.3.ebuild        |    1 +
 dev-python/ipykernel/ipykernel-9999.ebuild         |   39 +
 .../{jupyter-nbgrader => ipykernel}/metadata.xml   |    2 +-
 dev-python/ipyparallel/ChangeLog                   |   28 +
 dev-python/ipyparallel/Manifest                    |    2 +
 dev-python/ipyparallel/ipyparallel-4.0.0-r1.ebuild |    1 +
 dev-python/ipyparallel/ipyparallel-4.0.2.ebuild    |   62 +
 dev-python/ipyparallel/ipyparallel-9999.ebuild     |   62 +
 .../{jupyter-nbgrader => ipyparallel}/metadata.xml |    3 +-
 dev-python/ipython/ChangeLog                       |   37 +
 dev-python/ipython/Manifest                        |    1 +
 .../ipython/files/2.1.0-substitute-files.patch     |   27 +
 dev-python/ipython/ipython-4.0.0-r1.ebuild         |  132 +
 dev-python/ipython/metadata.xml                    |   51 +
 dev-python/ipython_genutils/ChangeLog              |   14 +
 dev-python/ipython_genutils/Manifest               |    1 +
 .../ipython_genutils/ipython_genutils-0.1.0.ebuild |    1 +
 .../ipython_genutils/ipython_genutils-9999.ebuild  |   34 +
 dev-python/ipython_genutils/metadata.xml           |   14 +
 dev-python/ipywidgets/ChangeLog                    |   16 +
 dev-python/ipywidgets/Manifest                     |    1 +
 dev-python/ipywidgets/ipywidgets-4.0.2.ebuild      |    1 +
 dev-python/ipywidgets/ipywidgets-9999.ebuild       |   40 +
 .../ipywidgets}/metadata.xml                       |   12 +-
 dev-python/jupyter-nbgrader/ChangeLog              |    9 -
 .../jupyter-nbgrader/jupyter-nbgrader-9999.ebuild  |   32 -
 dev-python/jupyter-nbviewer/ChangeLog              |    9 -
 dev-python/jupyter/ChangeLog                       |    9 +
 dev-python/jupyter/Manifest                        |    1 +
 dev-python/jupyter/jupyter-1.0.0.ebuild            |   45 +
 dev-python/jupyter/metadata.xml                    |   12 +
 dev-python/jupyter_client/ChangeLog                |   21 +
 dev-python/jupyter_client/Manifest                 |    1 +
 .../jupyter_client/jupyter_client-4.0.0.ebuild     |    1 +
 .../jupyter_client/jupyter_client-9999.ebuild      |   41 +
 dev-python/jupyter_client/metadata.xml             |   11 +
 dev-python/jupyter_console/ChangeLog               |   36 +
 dev-python/jupyter_console/Manifest                |    1 +
 .../jupyter_console/jupyter_console-4.0.2.ebuild   |    1 +
 .../jupyter_console/jupyter_console-9999.ebuild    |   60 +
 .../metadata.xml                                   |    3 +-
 dev-python/jupyter_core/ChangeLog                  |   29 +
 dev-python/jupyter_core/Manifest                   |    2 +
 .../files/jupyter_core-4.0.4-add-test-files.patch  |   50 +
 .../jupyter_core/jupyter_core-4.0.4-r1.ebuild      |   45 +
 dev-python/jupyter_core/jupyter_core-9999.ebuild   |   59 +
 .../metadata.xml                                   |    4 +-
 dev-python/line_profiler/ChangeLog                 |   10 +
 dev-python/line_profiler/Manifest                  |    1 +
 dev-python/line_profiler/line_profiler-1.0.ebuild  |    1 +
 dev-python/line_profiler/line_profiler-9999.ebuild |   35 +
 dev-python/line_profiler/metadata.xml              |   18 +
 dev-python/nbconvert/ChangeLog                     |   40 +
 dev-python/nbconvert/Manifest                      |    1 +
 .../files/nbconvert-4.0.0-docs-Makefile.patch      |   16 +
 .../nbconvert-4.0.0-pandoc-highlighting.patch      |   37 +
 .../{jupyter-nbgrader => nbconvert}/metadata.xml   |    3 +-
 dev-python/nbconvert/nbconvert-4.0.0-r1.ebuild     |    1 +
 dev-python/nbconvert/nbconvert-9999.ebuild         |   81 +
 dev-python/nbformat/ChangeLog                      |   19 +
 dev-python/nbformat/Manifest                       |    1 +
 dev-python/nbformat/metadata.xml                   |   11 +
 dev-python/nbformat/nbformat-4.0.0.ebuild          |    1 +
 dev-python/nbformat/nbformat-9999.ebuild           |   65 +
 dev-python/nbviewer/ChangeLog                      |    9 +
 .../{jupyter-nbviewer => nbviewer}/metadata.xml    |    0
 .../nbviewer-9999.ebuild}                          |    6 +-
 dev-python/notebook/ChangeLog                      |   60 +
 dev-python/notebook/Manifest                       |    1 +
 .../{jupyter-nbgrader => notebook}/metadata.xml    |    3 +-
 dev-python/notebook/notebook-4.0.4-r2.ebuild       |    1 +
 dev-python/notebook/notebook-9999.ebuild           |   91 +
 dev-python/qtconsole/ChangeLog                     |   22 +
 dev-python/qtconsole/Manifest                      |    1 +
 .../{jupyter-nbgrader => qtconsole}/metadata.xml   |    3 +-
 dev-python/qtconsole/qtconsole-4.0.1-r1.ebuild     |    1 +
 dev-python/qtconsole/qtconsole-9999.ebuild         |   67 +
 dev-python/testpath/ChangeLog                      |   14 +
 dev-python/testpath/Manifest                       |    1 +
 .../testpath/files/testpath-0.2-setup.py.patch     |   28 +
 dev-python/testpath/metadata.xml                   |   11 +
 dev-python/testpath/testpath-0.2.ebuild            |    1 +
 dev-python/testpath/testpath-9999.ebuild           |   60 +
 dev-python/traitlets/ChangeLog                     |   16 +
 dev-python/traitlets/Manifest                      |    1 +
 dev-python/traitlets/metadata.xml                  |   13 +
 dev-python/traitlets/traitlets-4.0.0.ebuild        |    1 +
 dev-python/traitlets/traitlets-9999.ebuild         |   59 +
 dev-util/nvidia-cuda-gdk/ChangeLog                 |    6 +
 dev-util/nvidia-cuda-gdk/Manifest                  |    1 +
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-352.39.ebuild  |  187 +
 dev-util/nvidia-cuda-sdk/ChangeLog                 |    9 -
 dev-util/nvidia-cuda-sdk/Manifest                  |    1 -
 .../nvidia-cuda-sdk/nvidia-cuda-sdk-7.5.7.ebuild   |  151 -
 dev-util/nvidia-cuda-toolkit/ChangeLog             |    9 -
 dev-util/nvidia-cuda-toolkit/Manifest              |    1 -
 dev-util/nvidia-cuda-toolkit/files/cuda-config.in  |   28 -
 dev-util/nvidia-cuda-toolkit/metadata.xml          |   14 -
 .../nvidia-cuda-toolkit-7.5.7.ebuild               |  152 -
 docs/proj/blas-lapack.xml                          |    2 +-
 docs/proj/linalg.xml                               |    2 +-
 media-gfx/librecad/ChangeLog                       |   12 +
 media-gfx/librecad/Manifest                        |    1 +
 media-gfx/librecad/librecad-2.0.8.ebuild           |   67 +
 media-gfx/librecad/librecad-9999.ebuild            |   44 +-
 media-gfx/librecad/metadata.xml                    |   17 +-
 patches/ccp4/6.1.2/fix-baubles.patch               |   22 -
 patches/ccp4/6.1.2/rename-rapper.patch             |   12 -
 patches/ccp4/6.1.2/rename-superpose.patch          |   12 -
 patches/ccp4/6.1.2/rename-truncate.patch           |   22 -
 patches/jupyter_core-4.0.4-tests-dotipython.patch  | 4743 ++++++++++++++++++++
 profiles/use.local.desc                            |  386 +-
 sci-biology/amos-short/ChangeLog                   |    4 +
 sci-biology/amos-short/amos-short-0.9.3.ebuild     |    4 +-
 sci-biology/beagle/ChangeLog                       |    6 +
 sci-biology/beagle/beagle-4.0.ebuild               |    5 +-
 sci-biology/salmon/salmon-0.4.2.ebuild             |    2 +-
 sci-biology/tophat/metadata.xml                    |    3 -
 sci-biology/tophat/tophat-2.0.12.ebuild            |    2 -
 sci-biology/tophat/tophat-2.0.13.ebuild            |    2 -
 sci-biology/tophat/tophat-2.0.14.ebuild            |    2 -
 sci-biology/weblogo/ChangeLog                      |    9 +
 sci-biology/weblogo/Manifest                       |    1 +
 .../jhdf5 => sci-biology/weblogo}/metadata.xml     |    0
 sci-biology/weblogo/weblogo-2.8.2.ebuild           |   35 +
 sci-chemistry/NMRdyn/Manifest                      |    1 +
 sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild           |   79 +
 .../NMRdyn/files/NMRdyn-3.2.5-redefinition.patch   |   19 +
 .../tophat => sci-chemistry/NMRdyn}/metadata.xml   |    8 +-
 .../nmrpipe/nmrpipe-8.1.2013.218.23.09-r1.ebuild   |    5 +-
 sci-chemistry/phenix-bin/Manifest                  |    1 +
 ...1.9.1692.ebuild => phenix-bin-1.10.2155.ebuild} |   26 +-
 .../phenix-bin/phenix-bin-1.9.1692.ebuild          |    5 +-
 .../pymol-plugins-psico-9999.ebuild                |    7 +-
 sci-chemistry/pymol/pymol-9999.ebuild              |    2 +-
 sci-chemistry/xplor-nih/xplor-nih-2.38.ebuild      |    4 +
 sci-libs/armadillo/ChangeLog                       |   16 +
 sci-libs/armadillo/Manifest                        |    4 +-
 sci-libs/armadillo/armadillo-5.100.2.ebuild        |  112 -
 ...-5.200.2-r1.ebuild => armadillo-5.400.2.ebuild} |    0
 ...-5.200.2-r1.ebuild => armadillo-5.500.2.ebuild} |    0
 sci-libs/arrayfire/ChangeLog                       |   21 +
 sci-libs/arrayfire/Manifest                        |    2 +
 ...ayfire-0.9999.ebuild => arrayfire-3.0.2.ebuild} |   35 +-
 ...rrayfire-9999.ebuild => arrayfire-3.1.0.ebuild} |   32 +-
 sci-libs/arrayfire/arrayfire-9999.ebuild           |   13 +-
 sci-libs/arrayfire/files/FindBoostCompute.cmake    |   18 -
 ...re-9999-Try-PkgConf-first-to-find-LAPACKE.patch |  182 +
 sci-libs/clblas/ChangeLog                          |   13 +
 sci-libs/clblas/Manifest                           |    1 +
 sci-libs/clblas/clblas-2.4-r1.ebuild               |    6 +-
 .../{clblas-2.4-r1.ebuild => clblas-2.6.ebuild}    |    6 -
 sci-libs/clblas/clblas-9999.ebuild                 |    6 -
 ...s.patch => clblas-2.4-samples_CMakeLists.patch} |    0
 ...ch => clblas-2.4-scripts_perf_CMakeLists.patch} |    0
 sci-libs/clfft/ChangeLog                           |   27 +
 sci-libs/clfft/Manifest                            |    1 +
 sci-libs/clfft/clfft-0.9999.ebuild                 |    2 -
 sci-libs/clfft/clfft-2.4-r1.ebuild                 |    6 +-
 .../{clfft-2.4-r1.ebuild => clfft-2.6.1.ebuild}    |   13 +-
 sci-libs/clfft/clfft-9999.ebuild                   |   10 +-
 ...sts.patch => clfft-2.4-client_CMakeLists.patch} |    0
 ...tch => clfft-2.4-scripts_perf_CMakeLists.patch} |    0
 ...l-cmake-configuration-to-lib-cmake-clFFT.patch} |    0
 ...-Install-examples-to-share-clFFT-examples.patch |   15 +
 sci-libs/clfft/metadata.xml                        |    5 +
 sci-libs/dealii/ChangeLog                          |    3 +
 sci-libs/dealii/dealii-9999.ebuild                 |    5 +-
 sci-libs/nibabel/Manifest                          |    1 +
 sci-libs/nibabel/nibabel-2.0.1.ebuild              |   42 +
 sci-libs/pydicom/ChangeLog                         |    3 +
 sci-libs/pydicom/Manifest                          |    1 +
 sci-libs/pydicom/pydicom-0.9.9.ebuild              |   18 +
 sci-libs/trilinos/ChangeLog                        |    9 +
 sci-libs/trilinos/Manifest                         |    1 +
 .../files/trilinos-12.2.1-compilation_fixes.patch  |   43 +
 sci-libs/trilinos/trilinos-12.2.1.ebuild           |  208 +
 sci-mathematics/petsc/ChangeLog                    |    4 +
 sci-mathematics/petsc/petsc-3.5.3.ebuild           |    2 +-
 sci-mathematics/petsc/petsc-3.6.0.ebuild           |    2 +-
 sci-mathematics/scilab/ChangeLog                   |    6 +
 ...{scilab-5.5.2.ebuild => scilab-5.5.2-r1.ebuild} |    3 +-
 sci-physics/herwig++/ChangeLog                     |    7 +-
 sci-physics/herwig++/Manifest                      |    1 -
 ...++-2.7.0-r1.ebuild => herwig++-2.7.0-r2.ebuild} |    6 +-
 sci-physics/herwig++/herwig++-2.7.1.ebuild         |   57 -
 sci-physics/herwig++/metadata.xml                  |    2 +-
 sci-physics/looptools/ChangeLog                    |    4 +
 sci-physics/looptools/Manifest                     |    2 -
 sci-physics/looptools/looptools-2.12.ebuild        |   39 -
 sci-physics/looptools/looptools-2.8.ebuild         |   39 -
 sci-physics/rivet/ChangeLog                        |    3 +
 sci-physics/rivet/Manifest                         |    1 -
 sci-physics/rivet/rivet-2.3.0.ebuild               |   60 -
 sci-physics/thepeg/ChangeLog                       |    6 +-
 sci-physics/thepeg/Manifest                        |    1 -
 sci-physics/thepeg/metadata.xml                    |    2 -
 sci-physics/thepeg/thepeg-1.9.2.ebuild             |   97 -
 sci-physics/yoda/ChangeLog                         |    3 +
 sci-physics/yoda/Manifest                          |    1 -
 sci-physics/yoda/metadata.xml                      |    1 -
 sci-physics/yoda/yoda-1.4.0.ebuild                 |   51 -
 208 files changed, 8150 insertions(+), 1230 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f1f5e00973ded663847fd4b2ecd47187e4358346
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Oct  1 06:06:34 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Oct  1 06:06:34 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f1f5e009

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/matplotlib2tikz: Drop python3 (only supported in 9999)
  added correspondng patch for =sci-biology/pysurfer-0.6
  sci-biology/pysurfer: version bump
  new manifest and archive name for sci-biology/pysurfer
  new manifests sci-biology/spm:
  added name
  sci-physics/root: Remove geocad-patch, is now upstream.
  sci-physics/root: Drop desktop-patch (upstreamed), add http-useflag enabling THttpServer.
  updated manifest
  saving archive as ${P}
  added patch number
  sci-libs/arrayfire: Version bump
  sci-visualization/forge: Set version of glm required
  sci-visualization/forge: Version bump
  added manifest
  dev-python/ipyparallel: Re-Fix Issue #473; Fixes Bug #561324
  using upstream pckage version
  new patched version from upstream

 dev-python/ipyparallel/ChangeLog                          |  7 +++++++
 ...yparallel-4.0.2.ebuild => ipyparallel-4.0.2-r1.ebuild} |  1 +
 dev-python/ipyparallel/ipyparallel-9999.ebuild            |  1 +
 dev-python/matplotlib2tikz/ChangeLog                      |  4 ++++
 dev-python/matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild   |  2 +-
 sci-biology/pysurfer/ChangeLog                            | 14 ++++++++++++--
 sci-biology/pysurfer/Manifest                             |  3 ++-
 ...{0.4-headless_build.patch => 0.6-headless_build.patch} |  2 +-
 sci-biology/pysurfer/pysurfer-0.4.ebuild                  |  4 ++--
 .../pysurfer/{pysurfer-0.4.ebuild => pysurfer-0.6.ebuild} |  4 ++--
 sci-biology/spm/Manifest                                  |  1 +
 sci-biology/spm/{spm-12.ebuild => spm-12_p6470.ebuild}    |  7 +++++--
 sci-libs/arrayfire/ChangeLog                              |  6 ++++++
 sci-libs/arrayfire/Manifest                               |  1 +
 .../{arrayfire-3.1.1-r2.ebuild => arrayfire-3.1.2.ebuild} |  4 ++--
 sci-physics/root/ChangeLog                                |  8 ++++++++
 sci-physics/root/files/root-5.34.13-desktop.patch         | 12 ------------
 sci-physics/root/files/root-6.00.01-geocad.patch          | 15 ---------------
 sci-physics/root/root-9999.ebuild                         |  5 ++---
 sci-visualization/forge/ChangeLog                         |  8 ++++++++
 sci-visualization/forge/Manifest                          |  1 +
 .../forge/{forge-3.1.ebuild => forge-3.1.2.ebuild}        |  4 +---
 sci-visualization/forge/forge-3.1.ebuild                  |  2 +-
 23 files changed, 69 insertions(+), 47 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     592eebfb7c3ccfc05ad0db3c34e1542ed8f6249f
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Oct  1 06:06:21 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Oct  1 06:06:21 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=592eebfb

Merge pull request #504 from TheChymera/pysurfer

Pysurfer - version bump and better distfile handling

 sci-biology/pysurfer/ChangeLog                             | 14 ++++++++++++--
 sci-biology/pysurfer/Manifest                              |  3 ++-
 .../{0.4-headless_build.patch => 0.6-headless_build.patch} |  2 +-
 sci-biology/pysurfer/pysurfer-0.4.ebuild                   |  4 ++--
 .../pysurfer/{pysurfer-0.4.ebuild => pysurfer-0.6.ebuild}  |  4 ++--
 5 files changed, 19 insertions(+), 8 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     adb0c4a8c805b6ce1857ee07aa6630c3df4768da
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 30 11:55:51 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep 30 11:55:51 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=adb0c4a8

Merge pull request #503 from TheChymera/spm

new manifests sci-biology/spm

 sci-biology/spm/Manifest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     142a63426809d4434a6035b720a432e9435e1cbc
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 28 08:02:21 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 28 08:02:21 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=142a6342

Merge pull request #502 from olifre/master

sci-physics/root: Drop desktop-patch (upstreamed), add http-useflag

 sci-physics/root/ChangeLog                        |  8 ++++++++
 sci-physics/root/files/root-5.34.13-desktop.patch | 12 ------------
 sci-physics/root/files/root-6.00.01-geocad.patch  | 15 ---------------
 sci-physics/root/root-9999.ebuild                 |  5 ++---
 4 files changed, 10 insertions(+), 30 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c9416600cc8b722f268747cd498b5c1031821f02
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 28 14:49:55 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 28 14:49:55 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c9416600

Merge pull request #501 from TheChymera/spm-update

new patched SPM12 version 

 sci-biology/spm/Manifest                               | 1 +
 sci-biology/spm/{spm-12.ebuild => spm-12_p6470.ebuild} | 7 +++++--
 2 files changed, 6 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     e3417554a48f19740c35e981c3a67a341e88d3c1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Sep 25 16:22:42 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Sep 25 16:22:42 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e3417554

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

* 'master' of git+ssh://git.gentoo.org/proj/sci: (90 commits)
  sci-chemistry/coot: Don't set LD_LIBRARY_PATH
  www-client/casjerjs: Fix installation of casperjs executable
  dev-python/metakernel_bash: Install missing kernel spec
  dev-python/metakernel_python: Install missing kernel spec
  dev-python/metakernel_bash: New package, ebuild written by me
  dev-python/metakernel: New package, ebuild written by me
  dev-python/metakernel_python: New package, ebuild written by me
  sci-chemistry/votca-csgapps: sync with gx86
  sci-chemistry/votca-csg: sync with gx86
  sci-libs/votca-tools: sync with gx86
  sys-cluster/openmpi: bump 1.10.0
  Ban EAPI=4
  Use default functions
  sci-biology/augustus: Use default functions
  sci-physics/mc-tester: Use default functions
  sci-biology/Atlas2: Use default functions
  sci-physics/tauola: Use default functions
  media-libs/libgfx: Use default functions
  dev-util/nvidia-cuda-gdk: Use default functions
  dev-java/netcdf: Bump to EAPI=5
  ...

 app-admin/eselect/eselect-1.4.5-r101.ebuild        |   4 +-
 app-admin/eselect/eselect-9999.ebuild              |   6 +-
 dev-cpp/eigen/eigen-3.2.2.ebuild                   | 118 ++++++-
 dev-cpp/eigen/eigen-3.2.4.ebuild                   | 118 ++++++-
 dev-java/jeuclid-core/jeuclid-core-3.1.9-r1.ebuild |   2 +-
 dev-java/netcdf/metadata.xml                       |   4 +-
 dev-java/netcdf/netcdf-4.2.ebuild                  |  17 +-
 dev-lang/julia/julia-9999.ebuild                   |   6 +-
 dev-lang/julia/metadata.xml                        |   6 +-
 dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild     |   4 +-
 dev-libs/libunzip/libunzip-5.52.ebuild             |  18 +-
 dev-ml/lacaml/lacaml-7.0.3.ebuild                  |   4 +-
 dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild           |   2 +-
 dev-perl/Time-Progress/Time-Progress-1.7.ebuild    |   2 +-
 .../arrayfire-python-3.0.20150914.ebuild           |  31 +-
 dev-python/brewer2mpl/brewer2mpl-1.4.1.ebuild      |  26 +-
 dev-python/ipykernel/ipykernel-4.0.3.ebuild        |  40 ++-
 dev-python/ipyparallel/ipyparallel-4.0.0-r1.ebuild |  63 +++-
 .../ipython_genutils/ipython_genutils-0.1.0.ebuild |  35 ++-
 dev-python/ipywidgets/ChangeLog                    |   4 +
 dev-python/ipywidgets/ipywidgets-4.0.2-r1.ebuild   |  43 ++-
 dev-python/ipywidgets/ipywidgets-4.0.3.ebuild      |   3 +
 dev-python/ipywidgets/ipywidgets-9999.ebuild       |   3 +
 dev-python/jupyter/jupyter-1.0.0.ebuild            |   2 +-
 dev-python/line_profiler/line_profiler-1.0.ebuild  |  30 +-
 dev-python/line_profiler/line_profiler-9999.ebuild |  11 +-
 .../matlab_wrapper/matlab_wrapper-0.9.6.ebuild     |  26 +-
 .../matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild   |  31 +-
 dev-python/metakernel/ChangeLog                    |   9 +
 dev-python/metakernel/Manifest                     |   1 +
 dev-python/metakernel/metadata.xml                 |  13 +
 dev-python/metakernel/metakernel-0.11.0.ebuild     |  37 +++
 dev-python/metakernel_bash/ChangeLog               |  15 +
 dev-python/metakernel_bash/Manifest                |   1 +
 dev-python/metakernel_bash/files/kernel.json       |   1 +
 .../{ipykernel => metakernel_bash}/metadata.xml    |   4 +-
 .../metakernel_bash-0.11.3-r1.ebuild               |  28 ++
 dev-python/metakernel_python/ChangeLog             |  15 +
 dev-python/metakernel_python/Manifest              |   1 +
 dev-python/metakernel_python/files/kernel.json     |   1 +
 .../{ipykernel => metakernel_python}/metadata.xml  |   4 +-
 .../metakernel_python-0.11.3-r1.ebuild             |  29 ++
 dev-python/nbconvert/nbconvert-4.0.0-r1.ebuild     |  79 ++++-
 dev-python/nbconvert/nbconvert-9999.ebuild         |  15 +-
 dev-python/nbformat/nbformat-4.0.0.ebuild          |  60 +++-
 dev-python/nbformat/nbformat-9999.ebuild           |  11 +-
 dev-python/notebook/ChangeLog                      |   4 +
 dev-python/notebook/notebook-4.0.5.ebuild          |   6 +
 dev-python/notebook/notebook-9999.ebuild           |   6 +
 dev-python/pickleshare/pickleshare-0.5.ebuild      |  40 ++-
 .../prettyplotlib/prettyplotlib-0.1.7.ebuild       |  31 +-
 dev-python/pyfftw/pyfftw-0.9.2.ebuild              |  37 ++-
 dev-python/pyfftw/pyfftw-9999.ebuild               |  12 +-
 dev-python/python-ivi/python-ivi-0.14.9.ebuild     |  31 +-
 dev-python/python-vxi11/python-vxi11-0.7.ebuild    |  23 +-
 dev-python/python-vxi11/python-vxi11-0.8.ebuild    |  23 +-
 dev-python/qtconsole/qtconsole-4.0.1-r1.ebuild     |  68 ++++-
 dev-python/simplepam/simplepam-0.1.5.ebuild        |  23 +-
 dev-python/testpath/testpath-0.2.ebuild            |  55 +++-
 dev-python/testpath/testpath-9999.ebuild           |  13 +-
 dev-python/traitlets/traitlets-4.0.0.ebuild        |  60 +++-
 dev-util/amdapp/amdapp-2.9.1.ebuild                |   2 +-
 dev-util/amdapp/amdapp-2.9.ebuild                  |   2 +-
 dev-util/amdapp/amdapp-3.0_beta.ebuild             |   2 +-
 dev-util/ndiff/ndiff-2.00.ebuild                   |   6 +-
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild  |   2 +-
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-346.46.ebuild  |   2 +-
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-352.07.ebuild  |   2 +-
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-352.39.ebuild  |   2 +-
 media-gfx/brlcad/brlcad-7.22.0.ebuild              |   2 +-
 media-gfx/brlcad/brlcad-7.24.0.ebuild              |   2 +-
 media-gfx/brlcad/brlcad-7.24.2.ebuild              |   4 +-
 media-gfx/brlcad/brlcad-9999.ebuild                |   2 +-
 media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild         |   2 +-
 media-libs/libgfx/libgfx-1.1.0.ebuild              |   8 +-
 media-libs/libgfx/metadata.xml                     |   2 +-
 metadata/layout.conf                               |   2 +-
 sci-astronomy/lephare/lephare-2.2.ebuild           |  14 +-
 sci-astronomy/lephare/metadata.xml                 |   4 +-
 sci-astronomy/missfits/missfits-2.8.0.ebuild       |  34 ++-
 sci-astronomy/psfex/psfex-3.17.0.ebuild            |  71 ++++-
 sci-astronomy/psfex/psfex-3.9.1.ebuild             |  71 ++++-
 sci-astronomy/sextractor/sextractor-2.19.5.ebuild  |  74 ++++-
 sci-astronomy/skymaker/skymaker-3.10.5.ebuild      |  36 ++-
 sci-astronomy/stiff/stiff-2.4.0.ebuild             |  44 ++-
 sci-astronomy/stuff/stuff-1.26.0.ebuild            |  36 ++-
 sci-astronomy/swarp/swarp-2.38.0.ebuild            |  42 ++-
 .../weightwatcher/weightwatcher-1.12.ebuild        |  36 ++-
 sci-biology/Atlas2/Atlas2-1.4.3.ebuild             |   2 +-
 .../KaKs_Calculator/KaKs_Calculator-1.2.ebuild     |   2 +-
 sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild          |  10 +-
 sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild         |  13 +-
 sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild       |   9 +-
 .../VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild   |   2 +-
 sci-biology/abyss/abyss-1.3.3-r1.ebuild            |   2 +-
 sci-biology/apollo/apollo-9999.ebuild              |   2 +-
 sci-biology/augustus/augustus-3.1.ebuild           |   2 +-
 sci-biology/bambino/bambino-1.02.ebuild            |   4 +-
 sci-biology/bambino/bambino-1.06.ebuild            |   4 +-
 sci-biology/bambus/bambus-2.33.ebuild              |  58 ++--
 sci-biology/biopieces/biopieces-0.51.ebuild        |  73 ++++-
 sci-biology/blasr/blasr-9999.ebuild                |   2 +-
 sci-biology/cap3-bin/cap3-bin-20071221.ebuild      |   4 +-
 .../cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild     |  10 +-
 sci-biology/cd-hit/cd-hit-4.6.1.ebuild             |   4 +-
 sci-biology/cluster/cluster-1.50-r1.ebuild         |  13 +-
 sci-biology/cluster/cluster-1.50.ebuild            |  50 ---
 sci-biology/clview/clview-0.1.ebuild               |   2 +-
 sci-biology/consed/consed-29.ebuild                |   4 +-
 sci-biology/edena/edena-3.131028.ebuild            |   2 +-
 sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild  |   2 +-
 sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild |   4 +-
 sci-biology/mgblast/mgblast-0.1.ebuild             |   2 +-
 sci-biology/minced/minced-9999.ebuild              |   2 +-
 sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild | 157 +++++++++-
 sci-biology/nrcl/nrcl-110625.ebuild                |   4 +-
 sci-biology/pileup/pileup-0.6.ebuild               |   4 +-
 sci-biology/pvmsx/pvmsx-0.1.ebuild                 |   2 +-
 sci-biology/samstat/samstat-20130708.ebuild        |   2 +-
 ....ebuild => scaffold_builder-20131122-r1.ebuild} |  26 +-
 sci-biology/sff_dump/sff_dump-1.04.ebuild          |   4 +-
 sci-biology/sga/sga-9999.ebuild                    |   2 +-
 sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild          |   4 +-
 .../tablet-bin/tablet-bin-1.14.10.21.ebuild        |   2 +-
 sci-biology/tablet/tablet-1.14.04.10.ebuild        |  50 ++-
 sci-biology/tclust/tclust-110625.ebuild            |   4 +-
 sci-biology/trf/trf-4.07b.ebuild                   |  14 +-
 sci-chemistry/NMRdyn/NMRdyn-3.2.5.ebuild           |   2 +-
 sci-chemistry/concoord/concoord-2.1.ebuild         |   4 +-
 sci-chemistry/coot/coot-9999.ebuild                |   4 +
 sci-chemistry/drawxtl/drawxtl-45.ebuild            |   4 +-
 sci-chemistry/gamess/Manifest                      |   1 -
 .../gamess/files/gamess-20120501.1.gentoo.patch    | 271 -----------------
 sci-chemistry/gamess/gamess-20120501.1.ebuild      | 338 ---------------------
 sci-chemistry/gamess/gamess-20130501.1.ebuild      |  30 +-
 sci-chemistry/jligand/jligand-1.0.40.ebuild        |   2 +-
 sci-chemistry/ligplot+/ligplot+-1.4.ebuild         |  14 +-
 sci-chemistry/simpson/simpson-3.0.1.ebuild         |  11 +-
 sci-chemistry/simpson/simpson-3.1.0.ebuild         |  11 +-
 sci-chemistry/simpson/simpson-3.1.2.ebuild         |  11 +-
 sci-chemistry/usf-tools/usf-tools-9999.ebuild      |   8 +-
 sci-chemistry/votca-csg/ChangeLog                  |   3 +
 sci-chemistry/votca-csg/votca-csg-9999.ebuild      |  39 +--
 sci-chemistry/votca-csgapps/ChangeLog              |   5 +-
 .../votca-csgapps/votca-csgapps-9999.ebuild        |   9 +-
 sci-electronics/stage/stage-2.0.3.ebuild           |   6 +-
 sci-geosciences/pydap/pydap-3.1.1.ebuild           |   2 +-
 sci-geosciences/pydap/pydap-3.1.ebuild             |   2 +-
 .../pydap_handlers_hdf5-0.1.7.ebuild               |   2 +-
 .../pydap_handlers_nca-0.1.3.ebuild                |   2 +-
 .../pydap_handlers_netcdf-0.6.4.ebuild             |   2 +-
 .../pydap_handlers_proxy-0.1.1.ebuild              |   2 +-
 sci-libs/Cgraph/Cgraph-2.04.ebuild                 |   4 +-
 sci-libs/Cgraph/metadata.xml                       |   2 +-
 sci-libs/arrayfire/arrayfire-3.1.1-r2.ebuild       |   2 +-
 sci-libs/arrayfire/arrayfire-9999.ebuild           |   2 +-
 sci-libs/asl/asl-0.1.5.ebuild                      |  49 ++-
 .../blas-reference-20131116-r1.ebuild              | 119 +++++++-
 .../cblas-reference-20110218-r1.ebuild             |   2 +-
 .../cblas-reference-20110218.ebuild                |   2 +-
 sci-libs/cgnstools/cgnstools-2.5.4-r1.ebuild       |   2 +-
 sci-libs/fdlibm/fdlibm-5.3.ebuild                  |  20 +-
 sci-libs/fdlibm/metadata.xml                       |   4 +-
 sci-libs/fgsl/Manifest                             |   1 -
 sci-libs/fgsl/fgsl-0.9.3.ebuild                    |  63 ----
 sci-libs/fgsl/fgsl-0.9.4.ebuild                    |   8 +-
 sci-libs/fox/fox-4.1.2-r2.ebuild                   |   8 +-
 sci-libs/framewave/framewave-1.3.1.ebuild          |   7 +-
 sci-libs/itk/itk-4.4.2-r1.ebuild                   |   2 +-
 .../lapack-reference/lapack-reference-3.4.2.ebuild | 140 ++++++++-
 .../lapack-reference/lapack-reference-3.5.0.ebuild | 140 ++++++++-
 .../lapacke-reference-3.4.2.ebuild                 | 104 ++++++-
 .../lapacke-reference-3.5.0.ebuild                 | 104 ++++++-
 sci-libs/libsc/libsc-1.1.ebuild                    |  72 ++++-
 sci-libs/mpiblacs/mpiblacs-1.1-r1.ebuild           |   2 +-
 sci-libs/omalloc/metadata.xml                      |  12 +-
 sci-libs/omalloc/omalloc-0.9.6.ebuild              |  13 +-
 sci-libs/openblas/openblas-0.2.12.ebuild           | 228 +++++++++++++-
 sci-libs/openblas/openblas-0.2.14.ebuild           | 228 +++++++++++++-
 sci-libs/openlibm/openlibm-9999.ebuild             |   2 +-
 sci-libs/p4est/p4est-1.1.ebuild                    | 100 +++++-
 sci-libs/pg2plplot/pg2plplot-0.2.0.ebuild          |  13 +-
 sci-libs/pg2plplot/pg2plplot-0.3.1.ebuild          |   8 +-
 sci-libs/spglib/spglib-1.6.0.ebuild                |   2 +-
 sci-libs/tmglib/tmglib-3.4.2.ebuild                |   4 +-
 sci-libs/votca-tools/ChangeLog                     |   5 +-
 sci-libs/votca-tools/votca-tools-9999.ebuild       |   8 +-
 sci-libs/wannier90/metadata.xml                    |   2 +-
 sci-libs/wannier90/wannier90-1.2-r3.ebuild         |  11 +-
 sci-libs/wannier90/wannier90-2.0.0.ebuild          |  11 +-
 sci-libs/wannier90/wannier90-2.0.1.ebuild          |   9 +-
 sci-mathematics/aribas/aribas-1.63.ebuild          |  22 +-
 sci-mathematics/cadabra/cadabra-1.39.ebuild        |   2 +-
 sci-mathematics/htk/htk-3.4.1.ebuild               |  43 ++-
 sci-mathematics/htk/metadata.xml                   |   2 +-
 sci-mathematics/kash-bin/kash-bin-3.ebuild         |  31 +-
 sci-mathematics/kash-bin/metadata.xml              |  10 +-
 sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild           |   2 +-
 sci-mathematics/pff/pff-8.4.ebuild                 |   2 +-
 sci-mathematics/scilab/scilab-5.5.2-r1.ebuild      |   2 +-
 sci-mathematics/why3/why3-0.83.ebuild              |   2 +-
 sci-mathematics/yorick/yorick-2.1.06.ebuild        |   2 +-
 sci-misc/foma/foma-0.9.14_alpha.ebuild             |   8 +-
 sci-misc/foma/foma-0.9.16_alpha.ebuild             |  11 +-
 sci-misc/hfst/hfst-2.2.ebuild                      |   4 +-
 sci-misc/hfst/hfst-3.0.2.ebuild                    |   4 +-
 sci-misc/hfst/hfst-3.3.12.ebuild                   |   6 +-
 sci-misc/kaldi/kaldi-0_p20150709.ebuild            |   2 +-
 sci-misc/openfst/openfst-1.3.4.ebuild              |   2 +-
 sci-misc/openfst/openfst-1.4.1.ebuild              |   2 +-
 .../opennlp-maxent/opennlp-maxent-2.4.0.ebuild     |   2 +-
 sci-misc/sfst/sfst-1.4.2.ebuild                    |  26 +-
 sci-misc/sfst/sfst-1.4.6g.ebuild                   |  28 +-
 sci-physics/abinit/abinit-7.10.4.ebuild            |   4 +-
 sci-physics/abinit/abinit-7.4.2-r1.ebuild          |   2 +-
 sci-physics/abinit/abinit-7.6.4-r1.ebuild          |   4 +-
 .../fullprof-bin/fullprof-bin-20313.04.ebuild      |   2 +-
 sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild     |   4 +-
 sci-physics/genfit/genfit-02.00.00.ebuild          |  60 +++-
 sci-physics/mc-tester/mc-tester-1.25.0.ebuild      |   6 +-
 sci-physics/mc-tester/metadata.xml                 |  18 +-
 sci-physics/root/metadata.xml                      |  30 +-
 sci-physics/root/root-9999.ebuild                  |   2 +-
 sci-physics/tauola/tauola-1.1.3.ebuild             |   8 +-
 sci-physics/tauola/tauola-1.1.4.ebuild             |   6 +-
 sci-physics/tauola/tauola-1.1.5.ebuild             |   6 +-
 sci-physics/tauola/tauola-9999.ebuild              |   6 +-
 sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild  |   2 +-
 sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild  |   2 +-
 sci-visualization/gnuplot/metadata.xml             |   6 +-
 sci-visualization/nodemon/metadata.xml             |  18 +-
 sci-visualization/nodemon/nodemon-0.3.5.ebuild     |  11 +-
 sci-visualization/v_sim/v_sim-3.6.0.ebuild         |  13 +-
 sys-cluster/blcr/blcr-0.8.4.ebuild                 |  10 +-
 sys-cluster/hpl/hpl-2.0-r1.ebuild                  |   4 +-
 sys-cluster/hpx/hpx-9999.ebuild                    |   4 +-
 sys-cluster/hpx/metadata.xml                       |  24 +-
 sys-cluster/modules/modules-3.2.10.ebuild          |   2 +-
 sys-cluster/modules/modules-3.2.9c-r1.ebuild       |   2 +-
 sys-cluster/modules/modules-3.2.9c.ebuild          |   2 +-
 sys-cluster/nullmpi/nullmpi-0.7.ebuild             |   4 +-
 sys-cluster/openmpi/ChangeLog                      |   5 +
 sys-cluster/openmpi/Manifest                       |   1 +
 ...{openmpi-1.8.8.ebuild => openmpi-1.10.0.ebuild} |  16 +-
 sys-cluster/openmpi/openmpi-1.6.5.ebuild           |   6 +-
 sys-cluster/openmpi/openmpi-1.7.3.ebuild           |   4 +-
 sys-cluster/openmpi/openmpi-1.8.4-r99.ebuild       |   4 +-
 sys-cluster/openmpi/openmpi-1.8.8.ebuild           |   4 +-
 sys-cluster/ovis/ovis-3.0.1.ebuild                 |  10 +-
 sys-devel/gdebugger/gdebugger-6.2.438.ebuild       |   7 +-
 www-client/casperjs/ChangeLog                      |  12 +
 www-client/casperjs/Manifest                       |   1 +
 www-client/casperjs/casperjs-1.1_beta3.ebuild      |  42 +++
 .../omniorbpy => www-client/casperjs}/metadata.xml |   2 +-
 254 files changed, 3956 insertions(+), 1415 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     7ff7534f62abe2da035dfe44a4447fc15a006030
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Sep 25 09:43:20 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Sep 25 09:43:20 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7ff7534f

Merge remote-tracking branch 'github/master'

* github/master:
  www-client/casjerjs: Fix installation of casperjs executable
  dev-python/metakernel_bash: Install missing kernel spec
  dev-python/metakernel_python: Install missing kernel spec
  dev-python/metakernel_bash: New package, ebuild written by me
  dev-python/metakernel: New package, ebuild written by me
  dev-python/metakernel_python: New package, ebuild written by me

 dev-python/metakernel/ChangeLog                    |  9 ++++++
 dev-python/metakernel/Manifest                     |  1 +
 dev-python/metakernel/metadata.xml                 | 13 ++++++++
 dev-python/metakernel/metakernel-0.11.0.ebuild     | 37 ++++++++++++++++++++++
 dev-python/metakernel_bash/ChangeLog               | 15 +++++++++
 dev-python/metakernel_bash/Manifest                |  1 +
 dev-python/metakernel_bash/files/kernel.json       |  1 +
 .../{ipykernel => metakernel_bash}/metadata.xml    |  4 +--
 .../metakernel_bash-0.11.3-r1.ebuild               | 28 ++++++++++++++++
 dev-python/metakernel_python/ChangeLog             | 15 +++++++++
 dev-python/metakernel_python/Manifest              |  1 +
 dev-python/metakernel_python/files/kernel.json     |  1 +
 .../{ipykernel => metakernel_python}/metadata.xml  |  4 +--
 .../metakernel_python-0.11.3-r1.ebuild             | 29 +++++++++++++++++
 www-client/casperjs/ChangeLog                      |  3 ++
 www-client/casperjs/casperjs-1.1_beta3.ebuild      |  5 +--
 16 files changed, 161 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     976fcedb57465b4066b07d4e671a2cbf0674d76a
Author:     marbre <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Thu Sep 24 15:26:15 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Sep 24 15:26:15 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=976fcedb

Merge pull request #496 from flacjacket/fix_casper

www-client/casjerjs: Fix installation of casperjs executable

 www-client/casperjs/ChangeLog                 | 3 +++
 www-client/casperjs/casperjs-1.1_beta3.ebuild | 5 +++--
 2 files changed, 6 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     8cfad58cd5895a13730b591e2d3551fed5dc037a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 23 10:19:53 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep 23 10:19:53 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8cfad58c

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/testpath: Replace symlink
  dev-python/line_profiler: Replace symlink
  dev-python/pyfftw: Replace symlink
  dev-python/nbformat: Replace symlink
  dev-python/nbconvert: Replace symlink
  www-client/casperjs: Fix 'Invalid Gentoo/GPL License on line'
  dev-python/ipywidgets: Add javascript tests
  dev-python/notebok: Add javascript tests
  www-client/casperjs: Initial ebuild

 dev-python/ipywidgets/ChangeLog                    |  4 ++
 dev-python/ipywidgets/ipywidgets-4.0.3.ebuild      |  3 +
 dev-python/ipywidgets/ipywidgets-9999.ebuild       |  3 +
 dev-python/line_profiler/line_profiler-1.0.ebuild  | 30 +++++++-
 dev-python/line_profiler/line_profiler-9999.ebuild | 11 +--
 dev-python/nbconvert/nbconvert-4.0.0-r1.ebuild     | 79 +++++++++++++++++++++-
 dev-python/nbconvert/nbconvert-9999.ebuild         | 15 ++--
 dev-python/nbformat/nbformat-4.0.0.ebuild          | 60 +++++++++++++++-
 dev-python/nbformat/nbformat-9999.ebuild           | 11 +--
 dev-python/notebook/ChangeLog                      |  4 ++
 dev-python/notebook/notebook-4.0.5.ebuild          |  6 ++
 dev-python/notebook/notebook-9999.ebuild           |  6 ++
 dev-python/pyfftw/pyfftw-0.9.2.ebuild              | 37 +++++++++-
 dev-python/pyfftw/pyfftw-9999.ebuild               | 12 +---
 dev-python/testpath/testpath-0.2.ebuild            | 55 ++++++++++++++-
 dev-python/testpath/testpath-9999.ebuild           | 13 +---
 www-client/casperjs/ChangeLog                      |  9 +++
 www-client/casperjs/Manifest                       |  1 +
 www-client/casperjs/casperjs-1.1_beta3.ebuild      | 41 +++++++++++
 .../omniorbpy => www-client/casperjs}/metadata.xml |  2 +-
 20 files changed, 347 insertions(+), 55 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     cf8718a9f41790362a7c756ecce5f12148e23e34
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Tue Sep 22 14:38:40 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Sep 22 14:38:40 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cf8718a9

Merge branch 'flacjacket-jupyter_js_tests_master'

 dev-python/ipywidgets/ChangeLog                    |  4 +++
 dev-python/ipywidgets/ipywidgets-4.0.3.ebuild      |  3 ++
 dev-python/ipywidgets/ipywidgets-9999.ebuild       |  3 ++
 dev-python/notebook/ChangeLog                      |  4 +++
 dev-python/notebook/notebook-4.0.5.ebuild          |  6 ++++
 dev-python/notebook/notebook-9999.ebuild           |  6 ++++
 www-client/casperjs/ChangeLog                      |  9 +++++
 www-client/casperjs/Manifest                       |  1 +
 www-client/casperjs/casperjs-1.1_beta3.ebuild      | 41 ++++++++++++++++++++++
 .../omniorbpy => www-client/casperjs}/metadata.xml |  2 +-
 10 files changed, 78 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     53d3f563a95dcdf0557f6bff3990afef22e2c0c7
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 22 10:06:53 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Sep 22 10:06:53 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=53d3f563

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/jupyter_{client,consolse,core}: Add missing ebuilds
  dev-python/notebook: Cleanup ebuild
  dev-python/jupyter_console: Replace symlinks
  dev-python/jupyter_client: Replace symlinks
  dev-python/jupyter_core: Replace symlinks
  dev-python/notebook: Version bump
  dev-python/ipywidgets: Add ~x86 to KEYWORDS

 dev-python/ipywidgets/ChangeLog                    |  4 ++
 dev-python/ipywidgets/ipywidgets-4.0.3.ebuild      |  2 +-
 .../jupyter_client/jupyter_client-4.0.0.ebuild     | 36 +++++++++++++-
 .../jupyter_client/jupyter_client-9999.ebuild      | 11 +----
 .../jupyter_console/jupyter_console-4.0.2.ebuild   | 55 +++++++++++++++++++++-
 .../jupyter_console/jupyter_console-9999.ebuild    | 11 +----
 .../jupyter_core/jupyter_core-4.0.4-r1.ebuild      | 10 +---
 dev-python/jupyter_core/jupyter_core-4.0.6.ebuild  | 54 ++++++++++++++++++++-
 dev-python/jupyter_core/jupyter_core-9999.ebuild   | 11 +----
 dev-python/notebook/ChangeLog                      |  5 ++
 dev-python/notebook/Manifest                       |  1 +
 ...{notebook-9999.ebuild => notebook-4.0.5.ebuild} | 10 +---
 dev-python/notebook/notebook-9999.ebuild           | 11 +----
 13 files changed, 165 insertions(+), 56 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     36582cd56f33b6271ec71b2d43355da3a49cc7af
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 22 07:34:01 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Sep 22 07:34:01 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=36582cd5

Update travis.yml

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 4f50844..015c625 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,7 +6,7 @@ language: python
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.2.20.1"
+    - PORTAGE_VER="2.2.21"
 before_script:
     - mkdir travis-overlay
     - mv !(travis-overlay) travis-overlay/

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     23dc3578c57fd8a7f16070e126175dc3e05f8ca9
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 22 07:20:23 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Sep 22 07:20:23 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=23dc3578

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/jupyter_console: Add ~x86 to KEYWORDS, fixes #561032
  dev-python/qtconsole: Add ~x86 to KEYWORDS, fixes #561032
  dev-python/nbconvert: Add ~x86 to KEYWORDS, fixes #561032
  dev-python/notebook: Add ~x86 to KEYWORDS, fixes #561032
  dev-python/jupyter_client: Add ~x86 to KEYWORDS, fixes #561032
  dev-python/ipywidgets: Add ~x86 to KEYWORDS, fixes #561032
  dev-python/ipython: Add ~x86 to KEYWORDS, fixes #561032
  dev-python/ipyparallel: Add ~x86 to KEYWORDS, fixes #561032
  dev-python/ipykernel: Add ~x86 to KEYWORDS, fixes #561032

 dev-python/ipykernel/ChangeLog                         | 3 +++
 dev-python/ipykernel/ipykernel-9999.ebuild             | 2 +-
 dev-python/ipyparallel/ChangeLog                       | 4 ++++
 dev-python/ipyparallel/ipyparallel-4.0.2.ebuild        | 2 +-
 dev-python/ipython/ChangeLog                           | 4 ++++
 dev-python/ipython/ipython-4.0.0-r2.ebuild             | 2 +-
 dev-python/ipywidgets/ChangeLog                        | 3 +++
 dev-python/ipywidgets/ipywidgets-9999.ebuild           | 2 +-
 dev-python/jupyter_client/ChangeLog                    | 4 ++++
 dev-python/jupyter_client/jupyter_client-9999.ebuild   | 2 +-
 dev-python/jupyter_console/ChangeLog                   | 4 ++++
 dev-python/jupyter_console/jupyter_console-9999.ebuild | 2 +-
 dev-python/nbconvert/ChangeLog                         | 3 +++
 dev-python/nbconvert/nbconvert-9999.ebuild             | 2 +-
 dev-python/notebook/ChangeLog                          | 4 ++++
 dev-python/notebook/notebook-4.0.4-r3.ebuild           | 2 +-
 dev-python/notebook/notebook-9999.ebuild               | 2 +-
 dev-python/qtconsole/ChangeLog                         | 3 +++
 dev-python/qtconsole/qtconsole-9999.ebuild             | 2 +-
 19 files changed, 42 insertions(+), 10 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     152fd6513c6dd099221d8e49fb2eb59c65bf7109
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 19:44:15 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 19:44:15 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=152fd651

Merge remote-tracking branch 'github/master'

* github/master:
  Drop obsolete

 profiles/package.mask                              |  15 --
 sci-misc/salome-component/ChangeLog                |  64 -----
 sci-misc/salome-component/Manifest                 |   2 -
 .../files/salome-component-5.1.3-mpi.patch         |  11 -
 sci-misc/salome-component/metadata.xml             |   5 -
 .../salome-component/salome-component-5.1.3.ebuild | 111 --------
 .../salome-component/salome-component-5.1.4.ebuild | 112 --------
 sci-misc/salome-geom/ChangeLog                     |  48 ----
 sci-misc/salome-geom/Manifest                      |   2 -
 .../files/salome-geom-5.1.3-qt4-path.patch         |  11 -
 sci-misc/salome-geom/metadata.xml                  |   5 -
 sci-misc/salome-geom/salome-geom-5.1.3.ebuild      | 110 --------
 sci-misc/salome-geom/salome-geom-5.1.4.ebuild      | 112 --------
 sci-misc/salome-gui/ChangeLog                      |  68 -----
 sci-misc/salome-gui/Manifest                       |   2 -
 .../files/salome-gui-5.1.3-qt4-path.patch          |  11 -
 .../files/salome-gui-5.1.4-qt4-path.patch          |  11 -
 sci-misc/salome-gui/metadata.xml                   |   5 -
 sci-misc/salome-gui/salome-gui-5.1.3.ebuild        | 115 --------
 sci-misc/salome-gui/salome-gui-5.1.4.ebuild        | 117 --------
 sci-misc/salome-kernel/ChangeLog                   |  92 -------
 sci-misc/salome-kernel/Manifest                    |   2 -
 .../files/salome-kernel-5.1.3-lib_location.patch   |  13 -
 .../files/salome-kernel-5.1.3-openmpi.patch        |  21 --
 .../files/salome-kernel-5.1.3-python-2.6.patch     |  13 -
 .../files/salome-kernel-5.1.4-lib_location.patch   |  13 -
 .../files/salome-kernel-5.1.4-openmpi.patch        |  21 --
 .../files/salome-kernel-5.1.4-python-2.6.patch     |  13 -
 sci-misc/salome-kernel/files/salome-kernel.png     | Bin 1934 -> 0 bytes
 sci-misc/salome-kernel/metadata.xml                |   8 -
 sci-misc/salome-kernel/salome-kernel-5.1.3.ebuild  | 121 ---------
 sci-misc/salome-kernel/salome-kernel-5.1.4.ebuild  | 121 ---------
 sci-misc/salome-med/ChangeLog                      |  77 ------
 sci-misc/salome-med/Manifest                       |   2 -
 .../files/salome-med-5.1.3-check_metis.patch       |  48 ----
 .../files/salome-med-5.1.3-check_scotch.patch      |  74 -----
 .../salome-med/files/salome-med-5.1.3-gcc.patch    |  43 ---
 .../files/salome-med-5.1.3-med_int.patch           | 297 ---------------------
 .../salome-med/files/salome-med-5.1.3-mpi.patch    |  13 -
 .../files/salome-med-5.1.3-qt4-path.patch          |  11 -
 .../salome-med/files/salome-med-5.1.3-scotch.patch |  11 -
 .../files/salome-med-5.1.4-check_metis.patch       |  48 ----
 .../files/salome-med-5.1.4-check_scotch.patch      |  74 -----
 .../salome-med/files/salome-med-5.1.4-gcc.patch    |  11 -
 .../files/salome-med-5.1.4-med_int.patch           | 297 ---------------------
 .../salome-med/files/salome-med-5.1.4-scotch.patch |  11 -
 sci-misc/salome-med/metadata.xml                   |   9 -
 sci-misc/salome-med/salome-med-5.1.3.ebuild        | 129 ---------
 sci-misc/salome-med/salome-med-5.1.4.ebuild        | 129 ---------
 sci-misc/salome-meta/ChangeLog                     |  23 --
 sci-misc/salome-meta/metadata.xml                  |   5 -
 sci-misc/salome-meta/salome-meta-5.1.3.ebuild      |  31 ---
 sci-misc/salome-meta/salome-meta-5.1.4.ebuild      |  31 ---
 sci-misc/salome-pycalculator/ChangeLog             |  41 ---
 sci-misc/salome-pycalculator/Manifest              |   2 -
 sci-misc/salome-pycalculator/metadata.xml          |   5 -
 .../salome-pycalculator-5.1.3.ebuild               |  83 ------
 .../salome-pycalculator-5.1.4.ebuild               |  83 ------
 sci-misc/salome-smesh/ChangeLog                    |  60 -----
 sci-misc/salome-smesh/Manifest                     |   2 -
 sci-misc/salome-smesh/metadata.xml                 |   5 -
 sci-misc/salome-smesh/salome-smesh-5.1.3.ebuild    | 108 --------
 sci-misc/salome-smesh/salome-smesh-5.1.4.ebuild    | 110 --------
 sci-misc/salome-visu/ChangeLog                     |  49 ----
 sci-misc/salome-visu/Manifest                      |   2 -
 sci-misc/salome-visu/metadata.xml                  |   5 -
 sci-misc/salome-visu/salome-visu-5.1.3.ebuild      | 103 -------
 sci-misc/salome-visu/salome-visu-5.1.4.ebuild      | 105 --------
 sci-misc/salome-yacs/ChangeLog                     |  37 ---
 sci-misc/salome-yacs/Manifest                      |   2 -
 .../files/salome-yacs-5.1.3-ac_python_devel.patch  |  13 -
 .../files/salome-yacs-5.1.3-lib_location.patch     |  14 -
 .../files/salome-yacs-5.1.3-libdir.patch           |  22 --
 .../files/salome-yacs-5.1.4-ac_python_devel.patch  |  12 -
 sci-misc/salome-yacs/metadata.xml                  |   5 -
 sci-misc/salome-yacs/salome-yacs-5.1.3.ebuild      | 102 -------
 sci-misc/salome-yacs/salome-yacs-5.1.4.ebuild      | 102 -------
 77 files changed, 3821 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     dbb1944b47122216eefd09700f99f4dc8d58d869
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 19:06:17 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 19:06:17 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=dbb1944b

Merge remote-tracking branch 'github/master'

* github/master: (25 commits)
  Add local USE description
  sci-physics/elk: Use python eclass
  sci-misc/opennlp-tools: Add subslot operators
  sci-misc/opennlp-maxent: Add subslot operators
  sci-misc/fitscut: Add subslot operators
  sci-mathematics/scilab: Add subslot operators
  sci-mathematics/netgen: Add subslot operators
  sci-mathematics/lie: Add subslot operators
  sci-mathematics/gappa: Add subslot operators
  sci-mathematics/frama-c: Add subslot operators
  sci-mathematics/apron: Add subslot operators
  Moved to tree
  sci-libs/armadillo: Version bump
  sci-mathematics/alt-ergo: Add subslot operators
  sci-physics/clip: Add subslot operators
  sci-libs/nexus: Add subslot operators
  dev-python/python-vxi11: Version bump
  sci-libs/matc: Add subslot operators
  sci-geosciences/qgis: Add subslot operators
  dev-python/testpath: Add ~x86 to KEYWORDS
  ...

 dev-python/ipython_genutils/ChangeLog              |    4 +
 .../ipython_genutils/ipython_genutils-9999.ebuild  |    2 +-
 dev-python/jupyter_core/ChangeLog                  |    4 +
 dev-python/jupyter_core/jupyter_core-9999.ebuild   |    2 +-
 dev-python/nbformat/ChangeLog                      |    3 +
 dev-python/nbformat/nbformat-9999.ebuild           |    2 +-
 dev-python/pickleshare/ChangeLog                   |    4 +
 dev-python/pickleshare/pickleshare-9999.ebuild     |    2 +-
 dev-python/python-vxi11/ChangeLog                  |    6 +
 dev-python/python-vxi11/Manifest                   |    1 +
 ...on-vxi11-0.7.ebuild => python-vxi11-0.8.ebuild} |    0
 dev-python/testpath/ChangeLog                      |    3 +
 dev-python/testpath/testpath-9999.ebuild           |    2 +-
 dev-python/traitlets/ChangeLog                     |    3 +
 dev-python/traitlets/traitlets-9999.ebuild         |    2 +-
 licenses/NVIDIA-CUDA                               | 2297 --------------------
 profiles/use.local.desc                            |    1 +
 sci-geosciences/qgis/qgis-9999.ebuild              |    4 +-
 sci-libs/armadillo/ChangeLog                       |    6 +
 sci-libs/armadillo/Manifest                        |    1 +
 ...llo-5.500.2.ebuild => armadillo-5.600.2.ebuild} |    0
 sci-libs/matc/matc-6.0_p4651.ebuild                |    7 +-
 sci-libs/matc/matc-8.0.ebuild                      |    5 +-
 sci-libs/matc/matc-9999.ebuild                     |    5 +-
 sci-libs/nexus/metadata.xml                        |   37 +-
 sci-libs/nexus/nexus-4.3.1.ebuild                  |   15 +-
 sci-mathematics/alt-ergo/alt-ergo-0.95.2.ebuild    |   19 +-
 sci-mathematics/alt-ergo/metadata.xml              |    4 +-
 sci-mathematics/apron/apron-0.9.10-r1.ebuild       |   33 +-
 sci-mathematics/apron/apron-0.9.10.ebuild          |   92 -
 sci-mathematics/apron/metadata.xml                 |    7 +-
 sci-mathematics/frama-c/frama-c-20140301.ebuild    |   34 +-
 sci-mathematics/frama-c/metadata.xml               |    4 +-
 sci-mathematics/gappa/gappa-1.1.1.ebuild           |   15 +-
 sci-mathematics/gappa/metadata.xml                 |    4 +-
 sci-mathematics/lie/lie-2.2.2.ebuild               |   15 +-
 sci-mathematics/netgen/netgen-4.9.13.ebuild        |   21 +-
 sci-mathematics/netgen/netgen-5.0.0.ebuild         |   14 +-
 sci-mathematics/scilab/scilab-5.5.2-r1.ebuild      |   21 +-
 sci-misc/fitscut/fitscut-1.4.4.ebuild              |    6 +-
 sci-misc/fitscut/metadata.xml                      |    4 +-
 .../opennlp-maxent/opennlp-maxent-2.4.0.ebuild     |    8 +-
 sci-misc/opennlp-tools/opennlp-tools-1.3.0.ebuild  |    8 +-
 sci-physics/clip/clip-4.0.0_beta2.ebuild           |   21 +-
 sci-physics/elk/elk-2.1.25.ebuild                  |   10 +-
 45 files changed, 211 insertions(+), 2547 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     7674864e5689371e2f5b241546dc1d8a45e337de
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 19:05:37 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 19:05:37 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7674864e

Merge remote-tracking branch 'github/master'

* github/master:
  Moved to tree
  sci-libs/armadillo: Version bump
  dev-python/python-vxi11: Version bump
  dev-python/testpath: Add ~x86 to KEYWORDS
  dev-python/pickleshare: Add ~x86 to KEYWORDS
  dev-python/nbformat: Add ~x86 to KEYWORDS
  dev-python/jupyter_core: Add ~x86 to KEYWORDS
  dev-python/traitlets: Add ~x86 to KEYWORDS
  dev-python/ipython_genutils: Add ~x86 to KEYWORDS

 dev-python/ipython_genutils/ChangeLog              |    4 +
 .../ipython_genutils/ipython_genutils-9999.ebuild  |    2 +-
 dev-python/jupyter_core/ChangeLog                  |    4 +
 dev-python/jupyter_core/jupyter_core-9999.ebuild   |    2 +-
 dev-python/nbformat/ChangeLog                      |    3 +
 dev-python/nbformat/nbformat-9999.ebuild           |    2 +-
 dev-python/pickleshare/ChangeLog                   |    4 +
 dev-python/pickleshare/pickleshare-9999.ebuild     |    2 +-
 dev-python/python-vxi11/ChangeLog                  |    6 +
 dev-python/python-vxi11/Manifest                   |    1 +
 ...on-vxi11-0.7.ebuild => python-vxi11-0.8.ebuild} |    0
 dev-python/testpath/ChangeLog                      |    3 +
 dev-python/testpath/testpath-9999.ebuild           |    2 +-
 dev-python/traitlets/ChangeLog                     |    3 +
 dev-python/traitlets/traitlets-9999.ebuild         |    2 +-
 licenses/NVIDIA-CUDA                               | 2297 --------------------
 sci-libs/armadillo/ChangeLog                       |    6 +
 sci-libs/armadillo/Manifest                        |    1 +
 ...llo-5.500.2.ebuild => armadillo-5.600.2.ebuild} |    0
 19 files changed, 41 insertions(+), 2303 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a48795c7a41d3c2e74f54d5932b3cfc5c3cfbdb7
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 17:44:07 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 17:44:07 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a48795c7

Merge remote-tracking branch 'github/master'

* github/master:
  sci-visualization/forge: Drop empty lines
  sci-libs/nipype: Drop empty lines
  dev-python/notebook: Fix leading whitespaces
  sci-biology/polyphen: Drop empty lines
  dev-libs/boost-compute: Drop empty lines and resort code
  Drop obsolete
  sci-libs/clfft: Drop old
  sci-biology/weblogo: Fix Header
  sci-mathematics/gap: Fix Manifest

 dev-libs/boost-compute/boost-compute-0.4-r1.ebuild |  13 +-
 dev-libs/boost-compute/boost-compute-9999.ebuild   |   7 +-
 dev-libs/boost/ChangeLog                           |  27 --
 dev-libs/boost/Manifest                            |   1 -
 dev-libs/boost/boost-1.56.0-r2.ebuild              | 398 ---------------------
 .../files/boost-1.48.0-disable_icu_rpath.patch     |  29 --
 .../boost-1.48.0-disable_libboost_python3.patch    |  62 ----
 .../boost-1.48.0-no_strict_aliasing_python2.patch  |  23 --
 .../boost/files/boost-1.48.0-python_linking.patch  |  24 --
 .../boost-1.51.0-respect_python-buildid.patch      |  69 ----
 ...ost-1.51.0-support_dots_in_python-buildid.patch |  22 --
 dev-libs/boost/files/boost-1.52.0-threads.patch    |  63 ----
 .../boost/files/boost-1.55.0-context-x32.patch     |  42 ---
 .../files/boost-1.55.0-tools-c98-compat.patch      |  17 -
 .../files/boost-1.56.0-build-auto_index-tool.patch |  13 -
 dev-libs/boost/metadata.xml                        |  41 ---
 dev-python/notebook/notebook-9999.ebuild           |   2 +-
 sci-biology/polyphen/polyphen-2.2.2.ebuild         |   4 -
 sci-biology/weblogo/weblogo-2.8.2.ebuild           |  10 +-
 sci-libs/clfft/Manifest                            |   1 -
 sci-libs/clfft/clfft-0.9999.ebuild                 |  51 ---
 sci-libs/clfft/clfft-2.4-r1.ebuild                 |  54 ---
 sci-libs/clfft/clfft-2.6.1.ebuild                  |   9 +-
 sci-libs/clfft/clfft-9999.ebuild                   |  17 +-
 sci-libs/nipype/nipype-9999.ebuild                 |   1 -
 sci-mathematics/gap/Manifest                       |   2 +
 sci-visualization/forge/forge-3.1.ebuild           |   1 -
 sci-visualization/forge/forge-9999.ebuild          |   1 -
 sci-visualization/forge/metadata.xml               |   2 +-
 29 files changed, 37 insertions(+), 969 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     1fec6963fb6fb329ea9316a7d3a09a74be25e84b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 14:04:47 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 14:04:47 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1fec6963

Merge remote-tracking branch 'github/master'

* github/master:
  dev-util/nvidia-cuda-gdk: Improve style
  dev-util/nvidia-cuda-gdk: Add dependency on drivers for nvvs use flag
  sci-libs/arrayfire: Add nonfree use flag
  profiles/license_groups: Add OpenSIFT to EULA group
  licenses: Add OpenSIFT license

 dev-util/nvidia-cuda-gdk/ChangeLog                 |  4 ++
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-352.39.ebuild  |  4 ++
 licenses/OpenSIFT                                  | 57 ++++++++++++++++++++++
 profiles/license_groups                            |  2 +-
 sci-libs/arrayfire/ChangeLog                       |  6 +++
 ...e-3.1.1-r1.ebuild => arrayfire-3.1.1-r2.ebuild} | 11 +++--
 sci-libs/arrayfire/metadata.xml                    |  3 ++
 7 files changed, 82 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     0319083317b66cd6eeec20bf00a4314693884e6d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Sep 18 06:05:12 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Sep 18 06:05:12 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=03190833

Merge pull request #490 from kiwifb/ipyparallel

dev-python/ipython: Solve circular dependency between ipython and ipy…

 dev-python/ipython/ChangeLog               | 5 +++++
 dev-python/ipython/ipython-4.0.0-r2.ebuild | 4 +++-
 2 files changed, 8 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     3270a38249c086b908e5ec2509fb5cc609dd87ad
Author:     marbre <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Wed Sep 16 14:19:27 2015 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Wed Sep 16 14:19:27 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3270a382

Merge pull request #489 from suhr/remove-wxwidgets

Remove wxwidgets from ipython dependencies

 dev-python/ipython/ChangeLog                                        | 4 ++++
 .../ipython/{ipython-4.0.0-r1.ebuild => ipython-4.0.0-r2.ebuild}    | 6 +++---
 dev-python/ipywidgets/ChangeLog                                     | 3 +++
 .../{ipywidgets-4.0.2.ebuild => ipywidgets-4.0.2-r1.ebuild}         | 0
 dev-python/ipywidgets/ipywidgets-9999.ebuild                        | 1 -
 5 files changed, 10 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     cbdccd9ab8f82c14992ae4086f7e9d1a2a7850b1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 15 13:34:15 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Sep 15 13:34:15 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cbdccd9a

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/lapackpp: Move to EAPI=5
  sci-libs/libcgnsoo: Move to EAPI=5
  sci-libs/arrayfire: Remove patches (merged upstream)
  sci-libs/arrayfire: Version bump

 sci-libs/arrayfire/ChangeLog                       |  12 ++
 sci-libs/arrayfire/Manifest                        |   1 +
 ...rayfire-3.0.2.ebuild => arrayfire-3.1.1.ebuild} |   7 +-
 sci-libs/arrayfire/arrayfire-9999.ebuild           |   5 -
 .../arrayfire/files/arrayfire-9999-FindCBLAS.patch |  52 ------
 ...re-9999-Try-PkgConf-first-to-find-LAPACKE.patch | 182 ---------------------
 sci-libs/lapackpp/ChangeLog                        |   3 +
 sci-libs/lapackpp/lapackpp-2.5.4.ebuild            |   4 +-
 sci-libs/libcgnsoo/ChangeLog                       |   6 +-
 sci-libs/libcgnsoo/Manifest                        |   2 +-
 sci-libs/libcgnsoo/libcgnsoo-1728.ebuild           |   9 +-
 11 files changed, 26 insertions(+), 257 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5f99082dd4b71bd4dc5dbf3c16782f2c13295b73
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Sep 13 08:09:00 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Sep 13 08:09:00 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5f99082d

Merge pull request #486 from mschubert/rdkit

sci-libs/rdkit: initial commit

 sci-libs/rdkit/ChangeLog                           | 10 +++++
 sci-libs/rdkit/Manifest                            |  1 +
 .../pyfaidx => sci-libs/rdkit}/metadata.xml        |  4 +-
 sci-libs/rdkit/rdkit-2015.03.1.ebuild              | 47 ++++++++++++++++++++++
 sci-libs/rdkit/rdkit-9999.ebuild                   | 46 +++++++++++++++++++++
 5 files changed, 106 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c1eb50700da945cc0888d14c14ee2e71911b63f2
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Sep 13 18:33:15 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Sep 13 18:33:15 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c1eb5070

Merge pull request #487 from mschubert/rdkit

sci-libs/rdkit: simplify USE checks

 sci-libs/rdkit/ChangeLog              |  4 ++++
 sci-libs/rdkit/rdkit-2015.03.1.ebuild | 10 ++--------
 sci-libs/rdkit/rdkit-9999.ebuild      | 10 ++--------
 3 files changed, 8 insertions(+), 16 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     7bc1fe4abdee1a7d0d3c3e5adfcf9ebabc2edecc
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep  9 07:11:04 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep  9 07:11:04 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7bc1fe4a

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/arrayfire: Remove files/FindBoostCompute.cmake
  sci-libs/arrayfire: Add arrayfire-3.0.2; Minor improvments
  sci-libs/arrayfire: Fix issue #463
  dev-libs/boost-compute: Drop 0.4-r2, bring back 0.4-r1; Drop patch to change install destination
  dev-libs/boost-compute: Install includes to /usr/include/boost/compute
  sci-libs/arrayfire: Drop 0.9999, because releases are available
  sci-libs/armadillo: Yet another version bump
  dev-python/jupyter_console: Version bump; Drop old
  dev-python/notebook: Fix deps, >=mathjax-2.4 required

 dev-libs/boost-compute/ChangeLog                   |  17 ++
 dev-libs/boost-compute/boost-compute-0.4-r1.ebuild |  28 +++-
 dev-libs/boost-compute/boost-compute-9999.ebuild   |  17 +-
 dev-python/jupyter_console/ChangeLog               |   6 +
 dev-python/jupyter_console/Manifest                |   2 +-
 ...e-4.0.1.ebuild => jupyter_console-4.0.2.ebuild} |   0
 dev-python/notebook/ChangeLog                      |   3 +
 dev-python/notebook/notebook-9999.ebuild           |   2 +-
 sci-libs/armadillo/ChangeLog                       |   6 +
 sci-libs/armadillo/Manifest                        |   1 +
 ...llo-5.400.2.ebuild => armadillo-5.500.2.ebuild} |   0
 sci-libs/arrayfire/ChangeLog                       |  15 ++
 sci-libs/arrayfire/Manifest                        |   1 +
 ...ayfire-0.9999.ebuild => arrayfire-3.0.2.ebuild} |  35 ++--
 sci-libs/arrayfire/arrayfire-9999.ebuild           |  13 +-
 sci-libs/arrayfire/files/FindBoostCompute.cmake    |  18 --
 ...re-9999-Try-PkgConf-first-to-find-LAPACKE.patch | 182 +++++++++++++++++++++
 17 files changed, 292 insertions(+), 54 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     a631e2d8eefc23ac22f09841e37b2dc0e9bbe9a8
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Sep  8 16:18:12 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Sep  8 16:18:12 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a631e2d8

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 dev-python/nbconvert/ChangeLog                     | 14 +++++++++
 .../files/nbconvert-4.0.0-docs-Makefile.patch      | 16 ++++++++++
 ...vert-4.0.0.ebuild => nbconvert-4.0.0-r1.ebuild} |  0
 dev-python/nbconvert/nbconvert-9999.ebuild         | 12 ++++++--
 dev-python/notebook/ChangeLog                      |  9 ++++++
 ...ok-4.0.4-r1.ebuild => notebook-4.0.4-r2.ebuild} |  0
 dev-python/notebook/notebook-9999.ebuild           |  2 ++
 dev-python/qtconsole/ChangeLog                     |  6 ++++
 ...sole-4.0.1.ebuild => qtconsole-4.0.1-r1.ebuild} |  0
 dev-python/qtconsole/qtconsole-9999.ebuild         |  5 +++-
 dev-python/testpath/ChangeLog                      |  3 ++
 dev-python/testpath/testpath-9999.ebuild           | 34 ++++++++++++++++++++++
 dev-python/traitlets/ChangeLog                     |  3 ++
 dev-python/traitlets/traitlets-9999.ebuild         | 10 +++++--
 sci-biology/beagle/ChangeLog                       |  6 ++++
 sci-biology/beagle/beagle-4.0.ebuild               |  5 ++--
 sci-biology/tophat/metadata.xml                    |  3 --
 sci-biology/tophat/tophat-2.0.12.ebuild            |  2 --
 sci-biology/tophat/tophat-2.0.13.ebuild            |  2 --
 sci-biology/tophat/tophat-2.0.14.ebuild            |  2 --
 sci-libs/clblas/ChangeLog                          |  8 +++++
 sci-libs/clblas/clblas-2.4-r1.ebuild               |  6 ++--
 sci-libs/clblas/clblas-9999.ebuild                 |  6 ----
 ...s.patch => clblas-2.4-samples_CMakeLists.patch} |  0
 ...ch => clblas-2.4-scripts_perf_CMakeLists.patch} |  0
 sci-libs/clfft/ChangeLog                           | 18 ++++++++++++
 sci-libs/clfft/Manifest                            |  1 +
 sci-libs/clfft/clfft-0.9999.ebuild                 |  2 --
 sci-libs/clfft/clfft-2.4-r1.ebuild                 |  6 ++--
 .../{clfft-2.4-r1.ebuild => clfft-2.6.1.ebuild}    |  7 ++---
 sci-libs/clfft/clfft-9999.ebuild                   |  2 +-
 ...sts.patch => clfft-2.4-client_CMakeLists.patch} |  0
 ...tch => clfft-2.4-scripts_perf_CMakeLists.patch} |  0
 ...l-cmake-configuration-to-lib-cmake-clFFT.patch} |  0
 ...-Install-examples-to-share-clFFT-examples.patch | 15 ++++++++++
 ...-Install-examples-to-share-clFFT-examples.patch | 29 ++++++++++++++++++
 sci-libs/pydicom/ChangeLog                         |  3 ++
 sci-libs/pydicom/Manifest                          |  5 ----
 sci-libs/pydicom/pydicom-0.9.9.ebuild              |  2 +-
 39 files changed, 201 insertions(+), 43 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     37167aba6d5c839f5afcf9ddc77a172b02ceb306
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep  7 06:49:29 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep  7 06:49:29 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=37167aba

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/clblas: Revise patches
  sci-libs/clfft: Version bump; Add patch for 9999
  sci-libs/clfft: Revise patches
  dev-python/traitlets: Add missing deps
  dev-python/testpath: Add test and doc use flag
  dev-python/nbconvert: Add deps for doc, fixes bug #559594
  dev-python/qtconsole: Add deps for doc, fixes bug #559594
  dev-python/notebook: Add deps for doc, fixes bug #559594
  dev-python/notebook: pandoc required for use doc, partially fixes bug #559594
  dev-python/nbconvert: Readd accidentialy dropped python2_7
  dev-python/nbconvert: Patch docs/Makefile, add pandoc dependency. Fixes bug #559594.
  sci-libs/pydicom: Fix SRC_URI
  sci-biology/beagle: Fix dependencies and slotting
  sci-biology/beagle: Adjust too long DESCRIPTION

 dev-python/nbconvert/ChangeLog                     | 14 +++++++++
 .../files/nbconvert-4.0.0-docs-Makefile.patch      | 16 ++++++++++
 ...vert-4.0.0.ebuild => nbconvert-4.0.0-r1.ebuild} |  0
 dev-python/nbconvert/nbconvert-9999.ebuild         | 12 ++++++--
 dev-python/notebook/ChangeLog                      |  9 ++++++
 ...ok-4.0.4-r1.ebuild => notebook-4.0.4-r2.ebuild} |  0
 dev-python/notebook/notebook-9999.ebuild           |  2 ++
 dev-python/qtconsole/ChangeLog                     |  6 ++++
 ...sole-4.0.1.ebuild => qtconsole-4.0.1-r1.ebuild} |  0
 dev-python/qtconsole/qtconsole-9999.ebuild         |  5 +++-
 dev-python/testpath/ChangeLog                      |  3 ++
 dev-python/testpath/testpath-9999.ebuild           | 34 ++++++++++++++++++++++
 dev-python/traitlets/ChangeLog                     |  3 ++
 dev-python/traitlets/traitlets-9999.ebuild         | 10 +++++--
 sci-biology/beagle/ChangeLog                       |  6 ++++
 sci-biology/beagle/beagle-4.0.ebuild               |  5 ++--
 sci-libs/clblas/ChangeLog                          |  8 +++++
 sci-libs/clblas/clblas-2.4-r1.ebuild               |  6 ++--
 sci-libs/clblas/clblas-9999.ebuild                 |  6 ----
 ...s.patch => clblas-2.4-samples_CMakeLists.patch} |  0
 ...ch => clblas-2.4-scripts_perf_CMakeLists.patch} |  0
 sci-libs/clfft/ChangeLog                           | 18 ++++++++++++
 sci-libs/clfft/Manifest                            |  1 +
 sci-libs/clfft/clfft-0.9999.ebuild                 |  2 --
 sci-libs/clfft/clfft-2.4-r1.ebuild                 |  6 ++--
 .../{clfft-2.4-r1.ebuild => clfft-2.6.1.ebuild}    |  7 ++---
 sci-libs/clfft/clfft-9999.ebuild                   |  2 +-
 ...sts.patch => clfft-2.4-client_CMakeLists.patch} |  0
 ...tch => clfft-2.4-scripts_perf_CMakeLists.patch} |  0
 ...l-cmake-configuration-to-lib-cmake-clFFT.patch} |  0
 ...-Install-examples-to-share-clFFT-examples.patch | 15 ++++++++++
 ...-Install-examples-to-share-clFFT-examples.patch | 29 ++++++++++++++++++
 sci-libs/pydicom/ChangeLog                         |  3 ++
 sci-libs/pydicom/Manifest                          |  5 ----
 sci-libs/pydicom/pydicom-0.9.9.ebuild              |  2 +-
 35 files changed, 201 insertions(+), 34 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     4316bf10dc91e624231f0ca52dd2f5edfaeb16f9
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Sep  4 09:30:19 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Sep  4 09:30:19 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4316bf10

Add back notification

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 1e100ee..4f50844 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -31,3 +31,7 @@ before_script:
 script:
     - ./../spinner.sh "python ../portage-${PORTAGE_VER}/bin/repoman full -d"
 # You can append own scripts after this line
+
+notifications:
+    irc: "chat.freenode.net#gentoo-science"
+

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5426b535594b58c89779b211bd6d86cd5271ba36
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Sep  4 09:27:16 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Sep  4 09:27:16 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5426b535

Update travis.yml

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 0316560..1e100ee 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -12,22 +12,22 @@ before_script:
     - mv !(travis-overlay) travis-overlay/
     - mv .git travis-overlay/
     - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/.travis.yml" -O .travis.yml.upstream
-    - wget "https://github.com/gentoo/portage/archive/v${PORTAGE_VER}.tar.gz" -O portage-${PORTAGE_VER}.tar.gz
     - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/spinner.sh"
+    - wget "https://github.com/gentoo/portage/archive/v${PORTAGE_VER}.tar.gz" -O portage-${PORTAGE_VER}.tar.gz
     - wget "https://github.com/gentoo-mirror/gentoo/archive/master.tar.gz" -O portage-tree.tar.gz
     - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr spinner.sh
     - chmod a+rwx spinner.sh
     - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
     - echo "portage::250:portage,travis" >> /etc/group
-    - mkdir -p /etc/portage/ /usr/portage/distfiles
+    - mkdir -p /etc/portage /usr/portage/distfiles
+    - wget "https://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
     - tar xzf portage-${PORTAGE_VER}.tar.gz
     - tar xzf portage-tree.tar.gz -C /usr/portage --strip-components=1
     - cp portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/
     - ln -s /usr/portage/profiles/base/ /etc/portage/make.profile
-    - wget "https://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
-    - SIZE=`stat -c %s .travis.yml.upstream`
-    - if ! cmp -n $SIZE -s .travis.yml .travis.yml.upstream; then  echo -e "\e[31m !!! .travis.yml outdated! Update available https://github.com/mrueg/repoman-travis \e[0m" > /tmp/update ; fi
+    - SIZE=$(stat -c %s .travis.yml.upstream)
+    - if ! cmp -n $SIZE -s .travis.yml .travis.yml.upstream; then echo -e "\e[31m !!! .travis.yml outdated! Update available https://github.com/mrueg/repoman-travis \e[0m" > /tmp/update ; fi
     - cd travis-overlay
 script:
-    - ./../spinner.sh "./../portage-${PORTAGE_VER}/bin/repoman full -d"
+    - ./../spinner.sh "python ../portage-${PORTAGE_VER}/bin/repoman full -d"
 # You can append own scripts after this line

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     331c39e83298c09920bf6fb9df83f617eefde6f8
Author:     marbre <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Thu Sep  3 18:10:43 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Sep  3 18:10:43 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=331c39e8

Merge pull request #481 from flacjacket/jupyter_fixes

Various Jupyter doc and deps fixes

 dev-python/ipyparallel/ChangeLog                   |  3 ++
 dev-python/ipyparallel/ipyparallel-9999.ebuild     | 21 +++++++++++-
 dev-python/ipywidgets/ChangeLog                    |  3 ++
 dev-python/ipywidgets/ipywidgets-9999.ebuild       |  1 +
 dev-python/jupyter_client/ChangeLog                |  3 ++
 .../jupyter_client/jupyter_client-9999.ebuild      |  2 +-
 dev-python/jupyter_console/ChangeLog               |  6 ++++
 .../jupyter_console/jupyter_console-9999.ebuild    | 23 +++++++++++++-
 dev-python/jupyter_core/ChangeLog                  |  6 ++++
 dev-python/jupyter_core/jupyter_core-9999.ebuild   | 29 ++++++++++++++---
 dev-python/nbconvert/ChangeLog                     | 10 ++++++
 .../nbconvert-4.0.0-pandoc-highlighting.patch      | 37 ++++++++++++++++++++++
 dev-python/nbconvert/nbconvert-9999.ebuild         | 30 +++++++++++++++++-
 dev-python/nbformat/ChangeLog                      |  3 ++
 dev-python/nbformat/nbformat-9999.ebuild           | 24 +++++++++++++-
 dev-python/notebook/ChangeLog                      |  3 ++
 dev-python/notebook/notebook-9999.ebuild           | 15 +++++++++
 dev-python/qtconsole/ChangeLog                     |  3 ++
 dev-python/qtconsole/qtconsole-9999.ebuild         | 21 +++++++++++-
 dev-python/traitlets/ChangeLog                     |  3 ++
 dev-python/traitlets/traitlets-9999.ebuild         | 24 ++++++++++++--
 21 files changed, 258 insertions(+), 12 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f8e38f471d0171eeabdd677142dacb646cc42594
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Sep  3 11:04:19 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Sep  3 11:04:19 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f8e38f47

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/notebook: Finaly the real fix for #478
  dev-python/notebook: Re-Fix #478
  Drop obsolete patches
  dev-python/jupyter_core: Fix tests (issue #479)
  Add patch for jupyter_core tests
  dev-python/notebook: Implement pkg_preinst(); Fixes #478
  dev-python/notebook: Drop old
  dev-python/jupyter: Initial commit
  dev-python/ipython: Fix #480; add testpath to dependencies

 dev-python/ipython/ChangeLog                       |    4 +
 dev-python/ipython/ipython-4.0.0-r1.ebuild         |    1 +
 dev-python/jupyter/ChangeLog                       |    9 +
 dev-python/jupyter/Manifest                        |    1 +
 dev-python/jupyter/jupyter-1.0.0.ebuild            |   45 +
 dev-python/{newrelic => jupyter}/metadata.xml      |    6 +-
 dev-python/jupyter_core/ChangeLog                  |    7 +
 dev-python/jupyter_core/Manifest                   |    1 +
 .../files/jupyter_core-4.0.4-add-test-files.patch  |   50 +
 ...re-9999.ebuild => jupyter_core-4.0.4-r1.ebuild} |    9 +-
 dev-python/jupyter_core/jupyter_core-4.0.4.ebuild  |    1 -
 dev-python/notebook/ChangeLog                      |   12 +
 dev-python/notebook/Manifest                       |    1 -
 dev-python/notebook/notebook-4.0.1.ebuild          |    1 -
 ...ebook-4.0.4.ebuild => notebook-4.0.4-r1.ebuild} |    0
 dev-python/notebook/notebook-9999.ebuild           |    5 +
 patches/ccp4/6.1.2/fix-baubles.patch               |   22 -
 patches/ccp4/6.1.2/rename-rapper.patch             |   12 -
 patches/ccp4/6.1.2/rename-superpose.patch          |   12 -
 patches/ccp4/6.1.2/rename-truncate.patch           |   22 -
 patches/jupyter_core-4.0.4-tests-dotipython.patch  | 4743 ++++++++++++++++++++
 21 files changed, 4889 insertions(+), 75 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b070679372b1dc17a2f86a913fae458a201ea0f4
Author:     marbre <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Thu Sep  3 06:41:35 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Sep  3 06:41:35 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b0706793

Merge pull request #483 from flacjacket/jupyter_meta

dev-python/jupyter: Initial commit

 dev-python/jupyter/ChangeLog                  |  9 ++++++
 dev-python/jupyter/Manifest                   |  1 +
 dev-python/jupyter/jupyter-1.0.0.ebuild       | 45 +++++++++++++++++++++++++++
 dev-python/{newrelic => jupyter}/metadata.xml |  6 ++--
 4 files changed, 58 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ddb358648e304fc7199b979faf1d6124ac647b94
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep  2 09:27:54 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep  2 09:27:54 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ddb35864

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/notebook: Move setuptools from CDEPEND to DEPEND
  dev-python/ipython: Move setuptools from CDEPEND to DEPEND
  dev-python/ipython: Re-Fix #474; notebook use flag requires use wxwidgets

 dev-python/ipython/ChangeLog               | 8 ++++++++
 dev-python/ipython/ipython-4.0.0-r1.ebuild | 6 +++---
 dev-python/notebook/ChangeLog              | 3 +++
 dev-python/notebook/notebook-9999.ebuild   | 5 ++---
 4 files changed, 16 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     55d6b31cd155eb142212fb1b2ebc457922518465
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep  2 07:59:08 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep  2 07:59:08 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=55d6b31c

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/ipython: remove mathjax references
  dev-python/notebook: Use system mathjax

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 dev-python/ipython/ChangeLog               |  3 +++
 dev-python/ipython/ipython-4.0.0-r1.ebuild |  2 --
 dev-python/notebook/ChangeLog              |  3 +++
 dev-python/notebook/notebook-9999.ebuild   | 12 ++++++++++++
 4 files changed, 18 insertions(+), 2 deletions(-)

diff --cc dev-python/notebook/notebook-9999.ebuild
index ca271a6,5a07e90..248392d
--- a/dev-python/notebook/notebook-9999.ebuild
+++ b/dev-python/notebook/notebook-9999.ebuild
@@@ -47,9 -49,10 +49,13 @@@ DEPEND="${RDEPEND
  	"
  
  python_prepare_all() {
 +	sed \
 +		-e "/import setup/s:$:\nimport setuptools:g" \
 +		-i setup.py || die
++
+ 	# disable bundled mathjax
+ 	sed -i 's/^.*MathJax.*$//' bower.json || die
+ 	sed -i 's/mj(/#mj(/' setupbase.py || die
 -
  	distutils-r1_python_prepare_all
  }
  

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     3e0475874cc0b549f6fd77bb62d02370d5f635eb
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Wed Sep  2 07:33:34 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep  2 07:33:34 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3e047587

Merge branch 'flacjacket-notebook'

 dev-python/ipython/ChangeLog               |  3 +++
 dev-python/ipython/ipython-4.0.0-r1.ebuild |  2 --
 dev-python/notebook/ChangeLog              |  3 +++
 dev-python/notebook/notebook-9999.ebuild   | 16 ++++++++++++++++
 4 files changed, 22 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6987532f984471af7963c1beaff852e431ade01c
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Sep  1 10:53:04 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Sep  1 10:53:04 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6987532f

Merge pull request #469 from robbert-harms/master

Version bump, adds nibabel-2.0.1.

 sci-libs/nibabel/Manifest                                       | 1 +
 sci-libs/nibabel/{nibabel-1.3.0.ebuild => nibabel-2.0.1.ebuild} | 2 +-
 sci-libs/pydicom/Manifest                                       | 6 ++++++
 sci-libs/pydicom/{pydicom-0.9.8.ebuild => pydicom-0.9.9.ebuild} | 6 +++---
 4 files changed, 11 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b9b5f487f19881dfb3792d6637d6ec697ce37151
Author:     marbre <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Tue Sep  1 07:02:18 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Sep  1 07:02:18 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b9b5f487

Merge pull request #472 from khumba/scilab-pax-fix

sci-mathematics/scilab: Add PaX mark required for Java binaries on hardened.

 sci-mathematics/scilab/ChangeLog                                    | 6 ++++++
 .../scilab/{scilab-5.5.2.ebuild => scilab-5.5.2-r1.ebuild}          | 3 ++-
 2 files changed, 8 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     81a5abab578b6befdcb6a999e2e3977e487325b3
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Tue Sep  1 07:50:57 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Sep  1 07:50:57 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=81a5abab

Merge branch 'jupyter'

 dev-python/ipykernel/ChangeLog                     |  13 +++
 dev-python/ipykernel/Manifest                      |   1 +
 dev-python/ipykernel/ipykernel-4.0.3.ebuild        |   1 +
 dev-python/ipykernel/ipykernel-9999.ebuild         |  38 ++++++
 dev-python/ipykernel/metadata.xml                  |   8 ++
 dev-python/ipyparallel/ChangeLog                   |  18 +++
 dev-python/ipyparallel/Manifest                    |   1 +
 dev-python/ipyparallel/ipyparallel-4.0.0.ebuild    |   1 +
 dev-python/ipyparallel/ipyparallel-9999.ebuild     |  41 +++++++
 dev-python/ipyparallel/metadata.xml                |   9 ++
 dev-python/ipython/ChangeLog                       |  16 +++
 dev-python/ipython/Manifest                        |   1 +
 .../ipython/files/2.1.0-substitute-files.patch     |  27 +++++
 dev-python/ipython/ipython-4.0.0.ebuild            | 130 +++++++++++++++++++++
 dev-python/ipython/metadata.xml                    |  51 ++++++++
 dev-python/ipython_genutils/ChangeLog              |  14 +++
 dev-python/ipython_genutils/Manifest               |   1 +
 .../ipython_genutils/ipython_genutils-0.1.0.ebuild |   1 +
 .../ipython_genutils/ipython_genutils-9999.ebuild  |  34 ++++++
 dev-python/ipython_genutils/metadata.xml           |  14 +++
 dev-python/ipywidgets/ChangeLog                    |  13 +++
 dev-python/ipywidgets/Manifest                     |   1 +
 dev-python/ipywidgets/ipywidgets-4.0.2.ebuild      |   1 +
 dev-python/ipywidgets/ipywidgets-9999.ebuild       |  39 +++++++
 dev-python/ipywidgets/metadata.xml                 |   9 ++
 dev-python/jupyter_client/ChangeLog                |  18 +++
 dev-python/jupyter_client/Manifest                 |   1 +
 .../jupyter_client/jupyter_client-4.0.0.ebuild     |   1 +
 .../jupyter_client/jupyter_client-9999.ebuild      |  41 +++++++
 dev-python/jupyter_client/metadata.xml             |  11 ++
 dev-python/jupyter_console/ChangeLog               |  18 +++
 dev-python/jupyter_console/Manifest                |   1 +
 .../jupyter_console/jupyter_console-4.0.0.ebuild   |   1 +
 .../jupyter_console/jupyter_console-9999.ebuild    |  39 +++++++
 dev-python/jupyter_console/metadata.xml            |   9 ++
 dev-python/jupyter_core/ChangeLog                  |  10 ++
 dev-python/jupyter_core/Manifest                   |   1 +
 dev-python/jupyter_core/jupyter_core-4.0.2.ebuild  |   1 +
 dev-python/jupyter_core/jupyter_core-9999.ebuild   |  38 ++++++
 dev-python/jupyter_core/metadata.xml               |  10 ++
 dev-python/nbconvert/ChangeLog                     |  16 +++
 dev-python/nbconvert/Manifest                      |   1 +
 dev-python/nbconvert/metadata.xml                  |   9 ++
 dev-python/nbconvert/nbconvert-4.0.0.ebuild        |   1 +
 dev-python/nbconvert/nbconvert-9999.ebuild         |  47 ++++++++
 dev-python/nbformat/ChangeLog                      |  16 +++
 dev-python/nbformat/Manifest                       |   1 +
 dev-python/nbformat/metadata.xml                   |  11 ++
 dev-python/nbformat/nbformat-4.0.0.ebuild          |   1 +
 dev-python/nbformat/nbformat-9999.ebuild           |  43 +++++++
 dev-python/notebook/ChangeLog                      |  16 +++
 dev-python/notebook/Manifest                       |   1 +
 dev-python/notebook/metadata.xml                   |   9 ++
 dev-python/notebook/notebook-4.0.1.ebuild          |   1 +
 dev-python/notebook/notebook-9999.ebuild           |  51 ++++++++
 dev-python/qtconsole/ChangeLog                     |  13 +++
 dev-python/qtconsole/Manifest                      |   1 +
 dev-python/qtconsole/metadata.xml                  |   9 ++
 dev-python/qtconsole/qtconsole-4.0.1.ebuild        |   1 +
 dev-python/qtconsole/qtconsole-9999.ebuild         |  45 +++++++
 dev-python/testpath/ChangeLog                      |  11 ++
 dev-python/testpath/Manifest                       |   1 +
 .../testpath/files/testpath-0.2-setup.py.patch     |  28 +++++
 dev-python/testpath/metadata.xml                   |  11 ++
 dev-python/testpath/testpath-0.2.ebuild            |   1 +
 dev-python/testpath/testpath-9999.ebuild           |  26 +++++
 dev-python/traitlets/ChangeLog                     |  10 ++
 dev-python/traitlets/Manifest                      |   1 +
 dev-python/traitlets/metadata.xml                  |  13 +++
 dev-python/traitlets/traitlets-4.0.0.ebuild        |   1 +
 dev-python/traitlets/traitlets-9999.ebuild         |  33 ++++++
 71 files changed, 1112 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     86ade10a113afece38b9d2f68c82609c81576a3d
Author:     Dongxu Li <dongxuli2011 <AT> gmail <DOT> com>
AuthorDate: Sun Aug 30 19:46:32 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Aug 30 19:46:32 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=86ade10a

Merge pull request #470 from lukash/master

media-gfx/librecad: add a missing dependency with USE="qt5"

 media-gfx/librecad/librecad-2.0.8.ebuild | 1 +
 1 file changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     1843a9f520a11d76ffa3adfa3b8e389d75d6eeff
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Wed Aug 26 14:56:33 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Aug 26 14:56:33 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1843a9f5

Merge branch 'master' into jupyter

 .travis.yml                                        |   7 +-
 app-admin/eselect/ChangeLog                        |  19 +-
 app-admin/eselect/Manifest                         |   2 +-
 ...1.4.4-r102.ebuild => eselect-1.4.5-r101.ebuild} |  14 +-
 app-admin/eselect/eselect-9999.ebuild              |   2 +-
 ...ives.patch => eselect-1.4.5-alternatives.patch} | 260 +++++++++++++++------
 app-benchmarks/btl/ChangeLog                       |   2 +-
 app-benchmarks/btl/btl-9999.ebuild                 |   2 +-
 app-benchmarks/numbench/ChangeLog                  |   2 +-
 app-benchmarks/numbench/numbench-0.2.ebuild        |   2 +-
 app-benchmarks/numbench/numbench-9999.ebuild       |   2 +-
 app-doc/blacs-docs/ChangeLog                       |   2 +-
 app-doc/blacs-docs/blacs-docs-1.1.ebuild           |   2 +-
 app-doc/blas-docs/ChangeLog                        |   2 +-
 app-doc/blas-docs/blas-docs-3.3.ebuild             |   2 +-
 app-doc/lapack-docs/ChangeLog                      |   2 +-
 app-doc/lapack-docs/lapack-docs-3.3-r1.ebuild      |   2 +-
 app-doc/root-docs/ChangeLog                        |   2 +-
 app-doc/root-docs/root-docs-9999.ebuild            |   2 +-
 app-doc/scalapack-docs/ChangeLog                   |   2 +-
 app-doc/scalapack-docs/scalapack-docs-2.0.ebuild   |   2 +-
 app-forensics/vine/ChangeLog                       |   2 +-
 app-forensics/vine/vine-1.0.ebuild                 |   2 +-
 app-portage/g-octave/ChangeLog                     |   2 +-
 app-portage/g-octave/g-octave-9999.ebuild          |   2 +-
 app-text/dgs/ChangeLog                             |   2 +-
 app-text/dgs/dgs-0.5.10-r2.ebuild                  |   2 +-
 app-vim/vim-gromacs/ChangeLog                      |   2 +-
 app-vim/vim-gromacs/vim-gromacs-9999.ebuild        |   2 +-
 dev-cpp/eigen/ChangeLog                            |   2 +-
 dev-cpp/eigen/eigen-9999.ebuild                    |   2 +-
 dev-cpp/growler-arch/ChangeLog                     |   2 +-
 dev-cpp/growler-arch/growler-arch-0.3.7.1.ebuild   |   2 +-
 dev-cpp/growler-core/ChangeLog                     |   2 +-
 dev-cpp/growler-core/growler-core-0.3.7.ebuild     |   2 +-
 dev-cpp/growler-link/ChangeLog                     |   2 +-
 dev-cpp/growler-link/growler-link-0.3.7.ebuild     |   2 +-
 dev-cpp/growler-math/ChangeLog                     |   2 +-
 dev-cpp/growler-math/growler-math-0.3.4.1.ebuild   |   2 +-
 dev-cpp/growler-thread/ChangeLog                   |   2 +-
 dev-cpp/growler-thread/growler-thread-0.3.4.ebuild |   2 +-
 dev-cpp/growler/ChangeLog                          |   2 +-
 dev-cpp/growler/growler-0.3.8.2.ebuild             |   2 +-
 dev-cpp/icnc/ChangeLog                             |   2 +-
 dev-cpp/icnc/icnc-9999.ebuild                      |   2 +-
 dev-java/fits/ChangeLog                            |   2 +-
 dev-java/fits/fits-1.11.0-r1.ebuild                |   2 +-
 dev-java/flexdock/ChangeLog                        |   2 +-
 dev-java/flexdock/flexdock-1.1.1.ebuild            |   2 +-
 dev-java/flexdock/flexdock-1.2.4.ebuild            |   2 +-
 dev-java/gluegen/ChangeLog                         |   2 +-
 dev-java/gluegen/gluegen-1_p20080421.ebuild        |   2 +-
 dev-java/gluegen/gluegen-2.0_rc8.ebuild            |   2 +-
 dev-java/gluegen/gluegen-2.1.4.ebuild              |   2 +-
 dev-java/gluegen/gluegen-2.2.4.ebuild              |   2 +-
 dev-java/hdf-java/ChangeLog                        |   2 +-
 dev-java/hdf-java/hdf-java-2.9.ebuild              |   2 +-
 dev-java/jeuclid-core/ChangeLog                    |   2 +-
 dev-java/jeuclid-core/jeuclid-core-3.1.9-r1.ebuild |   2 +-
 dev-java/jgraphx/ChangeLog                         |   2 +-
 dev-java/jgraphx/jgraphx-1.4.1.0.ebuild            |   2 +-
 dev-java/jgraphx/jgraphx-1.8.0.6.ebuild            |   2 +-
 dev-java/jgraphx/jgraphx-2.5.0.3.ebuild            |   2 +-
 dev-java/jhealpix/ChangeLog                        |   2 +-
 dev-java/jhealpix/jhealpix-3.11.ebuild             |   2 +-
 dev-java/jlatexmath-fop/ChangeLog                  |   2 +-
 .../jlatexmath-fop/jlatexmath-fop-1.0.3.ebuild     |   2 +-
 dev-java/jlatexmath/ChangeLog                      |   2 +-
 dev-java/jlatexmath/jlatexmath-1.0.3.ebuild        |   2 +-
 dev-java/jogl/ChangeLog                            |   2 +-
 dev-java/jogl/jogl-1.1.1a.ebuild                   |   2 +-
 dev-java/jogl/jogl-2.0_rc8-r1.ebuild               |   2 +-
 dev-java/jogl/jogl-2.1.4.ebuild                    |   2 +-
 dev-java/jogl/jogl-2.2.4.ebuild                    |   2 +-
 dev-java/jrosetta/ChangeLog                        |   2 +-
 dev-java/jrosetta/jrosetta-1.0.2.ebuild            |   2 +-
 dev-java/jrosetta/jrosetta-1.0.4.ebuild            |   2 +-
 dev-java/netcdf/ChangeLog                          |   2 +-
 dev-java/netcdf/netcdf-4.2.ebuild                  |   2 +-
 dev-java/scirenderer/ChangeLog                     |   2 +-
 dev-java/scirenderer/scirenderer-1.1.0.ebuild      |   2 +-
 dev-java/vecmath/ChangeLog                         |   2 +-
 dev-java/vecmath/vecmath-1.5.1.ebuild              |   2 +-
 dev-lang/berkeley_upc/ChangeLog                    |   2 +-
 dev-lang/berkeley_upc/berkeley_upc-2.16.2.ebuild   |   2 +-
 dev-lang/berkeley_upc/berkeley_upc-2.18.0.ebuild   |   2 +-
 dev-lang/berkeley_upc/berkeley_upc-2.18.2.ebuild   |   2 +-
 dev-lang/berkeley_upc/berkeley_upc-2.20.0.ebuild   |   2 +-
 dev-lang/berkeley_upc_translator/ChangeLog         |   2 +-
 .../berkeley_upc_translator-2.16.2.ebuild          |   2 +-
 .../berkeley_upc_translator-2.18.0.ebuild          |   2 +-
 .../berkeley_upc_translator-2.18.2.ebuild          |   2 +-
 dev-lang/conceptual/ChangeLog                      |   2 +-
 dev-lang/conceptual/conceptual-1.4.ebuild          |   2 +-
 dev-lang/ispc/ChangeLog                            |   2 +-
 dev-lang/ispc/ispc-9999.ebuild                     |   2 +-
 dev-lang/julia/ChangeLog                           |   2 +-
 dev-lang/julia/julia-9999.ebuild                   |   2 +-
 dev-lang/path64/ChangeLog                          |   2 +-
 dev-lang/path64/path64-9999.ebuild                 |   2 +-
 dev-lang/pgi/pgi-13.5.ebuild                       |   2 +-
 dev-lang/terra/ChangeLog                           |   2 +-
 dev-lang/terra/terra-2015.03.12.ebuild             |   2 +-
 dev-lang/vtune/ChangeLog                           |   2 +-
 dev-lang/vtune/vtune-13.1.10.298370.ebuild         |   2 +-
 dev-lang/vtune/vtune-13.1.12.305106.ebuild         |   2 +-
 dev-lang/vtune/vtune-13.1.13.313935.ebuild         |   2 +-
 dev-lang/vtune/vtune-13.1.17.353306.ebuild         |   2 +-
 dev-lang/vtune/vtune-15.1.380310.ebuild            |   2 +-
 dev-lang/vtune/vtune-15.2.393444.ebuild            |   2 +-
 dev-lang/vtune/vtune-15.3.403110.ebuild            |   2 +-
 dev-libs/asmjit/ChangeLog                          |   2 +-
 dev-libs/asmjit/asmjit-1.0_beta4.ebuild            |   2 +-
 dev-libs/boost-compute/ChangeLog                   |   2 +-
 dev-libs/boost-compute/boost-compute-9999.ebuild   |   2 +-
 dev-libs/boost/ChangeLog                           |   2 +-
 dev-libs/boost/boost-1.56.0-r2.ebuild              |   2 +-
 dev-libs/fortrancl/ChangeLog                       |   2 +-
 dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild     |   2 +-
 dev-libs/libconfig/ChangeLog                       |   2 +-
 dev-libs/libconfig/libconfig-9999.ebuild           |   2 +-
 dev-libs/libcuda/ChangeLog                         |   2 +-
 dev-libs/libcuda/libcuda-9999.ebuild               |   2 +-
 dev-libs/libflatarray/ChangeLog                    |   2 +-
 dev-libs/libflatarray/libflatarray-9999.ebuild     |   2 +-
 dev-libs/libgdev/ChangeLog                         |   2 +-
 dev-libs/libgdev/libgdev-9999.ebuild               |   2 +-
 dev-libs/libunzip/ChangeLog                        |   2 +-
 dev-libs/libunzip/libunzip-5.52.ebuild             |   2 +-
 dev-libs/mxml/mxml-2.9.ebuild                      |   2 +-
 dev-libs/simclist/ChangeLog                        |   2 +-
 dev-libs/simclist/simclist-1.6.ebuild              |   2 +-
 dev-libs/utf8proc/ChangeLog                        |   2 +-
 dev-libs/utf8proc/utf8proc-1.1.6.ebuild            |   2 +-
 dev-libs/utf8proc/utf8proc-1.2-r1.ebuild           |   2 +-
 dev-ml/gsl-ocaml/ChangeLog                         |   2 +-
 dev-ml/gsl-ocaml/gsl-ocaml-1.10.2.ebuild           |   2 +-
 dev-ml/lacaml/ChangeLog                            |   2 +-
 dev-ml/lacaml/lacaml-7.0.3.ebuild                  |   2 +-
 dev-ml/mlgmpidl/ChangeLog                          |   2 +-
 dev-ml/mlgmpidl/mlgmpidl-1.1.ebuild                |   2 +-
 dev-ml/zarith/ChangeLog                            |   2 +-
 dev-ml/zarith/zarith-1.2.1.ebuild                  |   2 +-
 dev-perl/BTLib/BTLib-0.19.ebuild                   |   2 +-
 dev-perl/BTLib/ChangeLog                           |   2 +-
 dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild       |   2 +-
 dev-perl/Bio-BigFile/ChangeLog                     |   2 +-
 .../Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.34.ebuild  |   2 +-
 dev-perl/Bio-DB-Das-Chado/ChangeLog                |   2 +-
 dev-perl/DBIx-DBStag/ChangeLog                     |   2 +-
 dev-perl/DBIx-DBStag/DBIx-DBStag-0.12.ebuild       |   2 +-
 dev-perl/Lab-Instrument/ChangeLog                  |   2 +-
 dev-perl/Lab-Instrument/Lab-Instrument-2.01.ebuild |   2 +-
 dev-perl/Lab-Tools/ChangeLog                       |   2 +-
 dev-perl/Lab-Tools/Lab-Tools-1.4.ebuild            |   2 +-
 dev-perl/Lab-VISA/ChangeLog                        |   2 +-
 dev-perl/Lab-VISA/Lab-VISA-2.06.ebuild             |   2 +-
 dev-perl/Log-Cabin/ChangeLog                       |   2 +-
 dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild           |   2 +-
 dev-perl/Text-ParseWords/ChangeLog                 |   2 +-
 .../Text-ParseWords/Text-ParseWords-3.27.ebuild    |   2 +-
 dev-perl/Time-Progress/ChangeLog                   |   2 +-
 dev-perl/Time-Progress/Time-Progress-1.7.ebuild    |   2 +-
 dev-perl/go-db-perl/ChangeLog                      |   2 +-
 dev-perl/go-db-perl/go-db-perl-0.04.ebuild         |   2 +-
 dev-perl/go-perl/ChangeLog                         |   2 +-
 dev-perl/go-perl/go-perl-0.13.ebuild               |   2 +-
 dev-perl/opal-client/ChangeLog                     |   2 +-
 dev-perl/opal-client/opal-client-1.9.2.ebuild      |   2 +-
 dev-python/Forthon/ChangeLog                       |   2 +-
 dev-python/Forthon/Forthon-0.8.13.ebuild           |   2 +-
 dev-python/GOGrapher/ChangeLog                     |   2 +-
 dev-python/GOGrapher/GOGrapher-9999.ebuild         |   2 +-
 dev-python/RecSQL/ChangeLog                        |   2 +-
 dev-python/RecSQL/RecSQL-9999.ebuild               |   2 +-
 dev-python/astlib/ChangeLog                        |   2 +-
 dev-python/astlib/astlib-0.7.0.ebuild              |   2 +-
 dev-python/astropy-helpers/ChangeLog               |   2 +-
 .../astropy-helpers/astropy-helpers-9999.ebuild    |   2 +-
 dev-python/astropy/ChangeLog                       |   2 +-
 dev-python/astropy/astropy-9999.ebuild             |   2 +-
 dev-python/astropysics/ChangeLog                   |   2 +-
 dev-python/astropysics/astropysics-9999.ebuild     |   2 +-
 dev-python/astroquery/ChangeLog                    |   2 +-
 dev-python/astroquery/astroquery-0.2.ebuild        |   2 +-
 dev-python/astroquery/astroquery-9999.ebuild       |   2 +-
 dev-python/brewer2mpl/ChangeLog                    |   2 +-
 dev-python/brewer2mpl/brewer2mpl-9999.ebuild       |   2 +-
 dev-python/ccdproc/ChangeLog                       |   2 +-
 dev-python/ccdproc/ccdproc-0.2.1.ebuild            |   2 +-
 dev-python/ccdproc/ccdproc-0.2.ebuild              |   2 +-
 dev-python/ccdproc/ccdproc-9999.ebuild             |   2 +-
 dev-python/coards/ChangeLog                        |   2 +-
 dev-python/coards/coards-1.0.5.ebuild              |   2 +-
 dev-python/coords/ChangeLog                        |   2 +-
 dev-python/coords/coords-0.37.ebuild               |   2 +-
 dev-python/cosmocalc/ChangeLog                     |   2 +-
 dev-python/cosmocalc/cosmocalc-0.1.2-r1.ebuild     |   2 +-
 dev-python/dimensionful/ChangeLog                  |   2 +-
 dev-python/dimensionful/dimensionful-9999.ebuild   |   2 +-
 dev-python/emcee/ChangeLog                         |   2 +-
 dev-python/emcee/emcee-1.2.0.ebuild                |   2 +-
 dev-python/emcee/emcee-2.0.0.ebuild                |   2 +-
 dev-python/ffc/ChangeLog                           |   2 +-
 dev-python/ffc/ffc-1.2.0.ebuild                    |   2 +-
 dev-python/ffc/ffc-1.3.0.ebuild                    |   2 +-
 dev-python/ffc/ffc-1.4.0.ebuild                    |   2 +-
 dev-python/ffnet/ChangeLog                         |   2 +-
 dev-python/ffnet/ffnet-0.7.1.ebuild                |   2 +-
 dev-python/fiat/ChangeLog                          |   2 +-
 dev-python/fiat/fiat-1.1.ebuild                    |   2 +-
 dev-python/fiat/fiat-1.3.0.ebuild                  |   2 +-
 dev-python/fiat/fiat-1.4.0.ebuild                  |   2 +-
 dev-python/gammapy/ChangeLog                       |   2 +-
 dev-python/gammapy/gammapy-0.1.ebuild              |   2 +-
 dev-python/gammapy/gammapy-9999.ebuild             |   2 +-
 dev-python/go-parser/ChangeLog                     |   2 +-
 dev-python/go-parser/go-parser-9999.ebuild         |   2 +-
 dev-python/healpy/ChangeLog                        |   2 +-
 dev-python/healpy/healpy-1.7.4.ebuild              |   2 +-
 dev-python/imageutils/ChangeLog                    |   2 +-
 dev-python/imageutils/imageutils-9999.ebuild       |   2 +-
 dev-python/inference/ChangeLog                     |   2 +-
 dev-python/inference/inference-0.4.ebuild          |   2 +-
 dev-python/instant/ChangeLog                       |   2 +-
 dev-python/instant/instant-1.2.0.ebuild            |   2 +-
 dev-python/instant/instant-1.3.0.ebuild            |   2 +-
 dev-python/instant/instant-1.4.0.ebuild            |   2 +-
 dev-python/jupyter-nbgrader/ChangeLog              |   2 +-
 .../jupyter-nbgrader/jupyter-nbgrader-9999.ebuild  |   2 +-
 dev-python/jupyter-nbviewer/ChangeLog              |   2 +-
 .../jupyter-nbviewer/jupyter-nbviewer-9999.ebuild  |   2 +-
 dev-python/line_profiler/ChangeLog                 |  10 +
 dev-python/line_profiler/Manifest                  |   1 +
 dev-python/line_profiler/line_profiler-1.0.ebuild  |   1 +
 dev-python/line_profiler/line_profiler-9999.ebuild |  35 +++
 .../line_profiler}/metadata.xml                    |  10 +-
 dev-python/matlab_wrapper/ChangeLog                |   2 +-
 .../matlab_wrapper/matlab_wrapper-9999.ebuild      |   2 +-
 dev-python/matplotlib2tikz/ChangeLog               |   2 +-
 .../matplotlib2tikz/matplotlib2tikz-9999.ebuild    |   2 +-
 dev-python/meshpy/ChangeLog                        |   2 +-
 dev-python/meshpy/meshpy-2013.1.2.ebuild           |   2 +-
 dev-python/meshpy/meshpy-2014.1.ebuild             |   2 +-
 dev-python/montage-wrapper/ChangeLog               |   2 +-
 .../montage-wrapper/montage-wrapper-0.9.7.ebuild   |   2 +-
 dev-python/newrelic/ChangeLog                      |   2 +-
 dev-python/newrelic/newrelic-2.44.0.36.ebuild      |   2 +-
 dev-python/newrelic/newrelic-2.50.0.39.ebuild      |   2 +-
 dev-python/nvidia-ml-py/ChangeLog                  |   2 +-
 .../nvidia-ml-py/nvidia-ml-py-6.340.0.ebuild       |   2 +-
 .../nvidia-ml-py/nvidia-ml-py-7.346.0.ebuild       |   2 +-
 dev-python/omniorbpy/ChangeLog                     |   2 +-
 dev-python/omniorbpy/omniorbpy-3.4.ebuild          |   2 +-
 dev-python/opal-client/ChangeLog                   |   2 +-
 dev-python/opal-client/opal-client-2.4.1.ebuild    |   2 +-
 dev-python/photutils/ChangeLog                     |   2 +-
 dev-python/photutils/photutils-9999.ebuild         |   2 +-
 dev-python/pickleshare/ChangeLog                   |   2 +-
 dev-python/pickleshare/pickleshare-9999.ebuild     |   2 +-
 dev-python/prettyplotlib/ChangeLog                 |   2 +-
 dev-python/prettyplotlib/prettyplotlib-9999.ebuild |   2 +-
 dev-python/psubprocess/ChangeLog                   |   2 +-
 dev-python/psubprocess/psubprocess-0.1.2.ebuild    |   2 +-
 dev-python/ptyprocess/ChangeLog                    |   2 +-
 dev-python/ptyprocess/ptyprocess-9999.ebuild       |   2 +-
 dev-python/pyfftw/ChangeLog                        |   2 +-
 dev-python/pyfftw/pyfftw-9999.ebuild               |   2 +-
 dev-python/pyhdf/ChangeLog                         |   2 +-
 dev-python/pyhdf/pyhdf-0.8.3.ebuild                |   2 +-
 dev-python/pylibconfig2/ChangeLog                  |   2 +-
 dev-python/pylibconfig2/pylibconfig2-0.2.4.ebuild  |   2 +-
 dev-python/pylibconfig2/pylibconfig2-9999.ebuild   |   2 +-
 dev-python/pymvpa/ChangeLog                        |   2 +-
 dev-python/pymvpa/pymvpa-0.4.4.ebuild              |   2 +-
 dev-python/pynomo/ChangeLog                        |   2 +-
 dev-python/pynomo/pynomo-0.2.2.ebuild              |   2 +-
 dev-python/pysolar/ChangeLog                       |   2 +-
 dev-python/pysolar/pysolar-0.5.ebuild              |   2 +-
 dev-python/pysparse/ChangeLog                      |   2 +-
 dev-python/pysparse/pysparse-1.1.1-r1.ebuild       |   2 +-
 dev-python/python-ivi/ChangeLog                    |   2 +-
 dev-python/python-ivi/python-ivi-9999.ebuild       |   2 +-
 dev-python/python-vxi11/ChangeLog                  |   2 +-
 dev-python/python-vxi11/python-vxi11-9999.ebuild   |   2 +-
 dev-python/pythoncgns/ChangeLog                    |   2 +-
 dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild |   2 +-
 dev-python/pythonocc/ChangeLog                     |   2 +-
 dev-python/pythonocc/pythonocc-0.5.ebuild          |   2 +-
 dev-python/pythonqt/ChangeLog                      |   2 +-
 dev-python/pythonqt/pythonqt-2.1.ebuild            |   2 +-
 dev-python/pythonqt/pythonqt-9999.ebuild           |   2 +-
 dev-python/pywcsgrid2/ChangeLog                    |   2 +-
 dev-python/pywcsgrid2/pywcsgrid2-9999.ebuild       |   2 +-
 dev-python/simplepam/ChangeLog                     |   2 +-
 dev-python/simplepam/simplepam-9999.ebuild         |   2 +-
 dev-python/specutils/ChangeLog                     |   2 +-
 dev-python/specutils/specutils-9999.ebuild         |   2 +-
 dev-python/ufl/ChangeLog                           |   2 +-
 dev-python/ufl/ufl-0.5.4.ebuild                    |   2 +-
 dev-python/ufl/ufl-1.3.0.ebuild                    |   2 +-
 dev-python/ufl/ufl-1.4.0.ebuild                    |   2 +-
 dev-python/viper/ChangeLog                         |   2 +-
 dev-python/viper/viper-1.0.1.ebuild                |   2 +-
 dev-tcltk/img_rotate/ChangeLog                     |   2 +-
 dev-tcltk/img_rotate/img_rotate-1.1.ebuild         |   2 +-
 dev-tcltk/togl/ChangeLog                           |   2 +-
 dev-tcltk/togl/togl-1.7-r1.ebuild                  |   2 +-
 dev-tex/pythontex/ChangeLog                        |   2 +-
 dev-tex/pythontex/pythontex-0.14-r1.ebuild         |   2 +-
 dev-tex/pythontex/pythontex-9999.ebuild            |   2 +-
 dev-util/VampirTrace/ChangeLog                     |   2 +-
 dev-util/VampirTrace/VampirTrace-5.14.3.ebuild     |   2 +-
 dev-util/VampirTrace/VampirTrace-5.14.4.ebuild     |   2 +-
 dev-util/amdapp/ChangeLog                          |   2 +-
 dev-util/amdapp/amdapp-2.9.1.ebuild                |   2 +-
 dev-util/amdapp/amdapp-2.9.ebuild                  |   2 +-
 dev-util/amdapp/amdapp-3.0_beta.ebuild             |   2 +-
 dev-util/f90cache/ChangeLog                        |   2 +-
 dev-util/f90cache/f90cache-0.94.ebuild             |   2 +-
 dev-util/f90cache/f90cache-0.95.ebuild             |   2 +-
 dev-util/ndiff/ChangeLog                           |   2 +-
 dev-util/ndiff/ndiff-2.00.ebuild                   |   2 +-
 dev-util/numdiff/ChangeLog                         |   2 +-
 dev-util/numdiff/numdiff-5.8.1.ebuild              |   2 +-
 dev-util/nvidia-cuda-gdk/ChangeLog                 |   2 +-
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild  |   2 +-
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-346.46.ebuild  |   2 +-
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-352.07.ebuild  |   2 +-
 dev-util/nvidia-cuda-sdk/ChangeLog                 |   2 +-
 .../nvidia-cuda-sdk/nvidia-cuda-sdk-7.5.7.ebuild   |   2 +-
 dev-util/nvidia-cuda-toolkit/ChangeLog             |   2 +-
 .../nvidia-cuda-toolkit-7.5.7.ebuild               |   2 +-
 dev-util/smartgit/ChangeLog                        |   2 +-
 dev-util/smartgit/smartgit-6.5.6.ebuild            |   2 +-
 eclass/alternatives-2.eclass                       |   2 +-
 eclass/fortran-int64.eclass                        |   2 +-
 eclass/intel-sdp.eclass                            |   2 +-
 eclass/mpi.eclass                                  |  25 +-
 eclass/numeric.eclass                              |   2 +-
 media-gfx/PhiloGL/ChangeLog                        |   2 +-
 media-gfx/PhiloGL/PhiloGL-1.4.3.ebuild             |   2 +-
 media-gfx/brlcad/ChangeLog                         |   2 +-
 media-gfx/brlcad/brlcad-7.22.0.ebuild              |   2 +-
 media-gfx/brlcad/brlcad-7.24.0.ebuild              |   2 +-
 media-gfx/brlcad/brlcad-7.24.2.ebuild              |   2 +-
 media-gfx/brlcad/brlcad-9999.ebuild                |   2 +-
 media-gfx/librecad/librecad-1.0.3.ebuild           |   2 +-
 media-gfx/librecad/librecad-1.0.4.ebuild           |   2 +-
 media-gfx/librecad/librecad-2.0.7.ebuild           |   2 +-
 media-gfx/librecad/librecad-9999.ebuild            |   2 +-
 media-libs/OpenMOIV/ChangeLog                      |   2 +-
 media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild         |   2 +-
 media-libs/avbin-bin/ChangeLog                     |   2 +-
 media-libs/avbin-bin/avbin-bin-7.ebuild            |   2 +-
 media-libs/libgfx/ChangeLog                        |   2 +-
 media-libs/libgfx/libgfx-1.1.0.ebuild              |   2 +-
 net-firewall/gcb/ChangeLog                         |   2 +-
 net-firewall/gcb/gcb-1.5.6.ebuild                  |   2 +-
 net-ftp/bbftp-client/ChangeLog                     |   2 +-
 net-ftp/bbftp-client/bbftp-client-3.2.1.ebuild     |   2 +-
 net-ftp/bbftp-server/ChangeLog                     |   2 +-
 net-ftp/bbftp-server/bbftp-server-3.2.1.ebuild     |   2 +-
 net-ftp/bbftp-server/files/bbftpd.init.d           |   2 +-
 net-misc/bbscp/ChangeLog                           |   2 +-
 net-misc/bbscp/bbscp-1.0.6.ebuild                  |   2 +-
 perl-core/encoding-warnings/ChangeLog              |   2 +-
 .../encoding-warnings-0.11.ebuild                  |   2 +-
 profiles/ChangeLog                                 |   2 +-
 profiles/arch/arm/use.mask                         |   2 +-
 profiles/arch/m68k/use.mask                        |   2 +-
 profiles/arch/sparc-fbsd/use.mask                  |   2 +-
 profiles/arch/sparc/use.mask                       |   2 +-
 profiles/arch/x86-fbsd/use.mask                    |   2 +-
 profiles/arch/x86/use.mask                         |   2 +-
 sci-astronomy/astrometry/ChangeLog                 |   2 +-
 sci-astronomy/astrometry/astrometry-0.43.ebuild    |   2 +-
 sci-astronomy/bpz/ChangeLog                        |   2 +-
 sci-astronomy/bpz/bpz-1.99.3.ebuild                |   2 +-
 sci-astronomy/casapy-bin/ChangeLog                 |   2 +-
 .../casapy-bin-4.2.1.29047.001_p1.ebuild           |   2 +-
 .../casapy-bin/casapy-bin-4.2.2.30986_p1.ebuild    |   2 +-
 sci-astronomy/casapy-bin/casapy-bin-4.4.0.ebuild   |   2 +-
 sci-astronomy/chealpix/ChangeLog                   |   2 +-
 sci-astronomy/chealpix/chealpix-3.11.2.ebuild      |   2 +-
 sci-astronomy/eazy/ChangeLog                       |   2 +-
 sci-astronomy/eazy/eazy-1.00.ebuild                |   2 +-
 sci-astronomy/eye/ChangeLog                        |   2 +-
 sci-astronomy/eye/eye-9999.ebuild                  |   2 +-
 sci-astronomy/galfit-bin/ChangeLog                 |   2 +-
 sci-astronomy/galfit-bin/galfit-bin-3.0.5.ebuild   |   2 +-
 sci-astronomy/healpix_cxx/ChangeLog                |   2 +-
 .../healpix_cxx/healpix_cxx-3.11.2.ebuild          |   2 +-
 sci-astronomy/healpix_idl/ChangeLog                |   2 +-
 sci-astronomy/healpix_idl/healpix_idl-3.11.ebuild  |   2 +-
 sci-astronomy/lephare/ChangeLog                    |   2 +-
 sci-astronomy/lephare/lephare-2.2.ebuild           |   2 +-
 sci-astronomy/libthesky/ChangeLog                  |   2 +-
 sci-astronomy/libthesky/libthesky-0.3.2.ebuild     |   2 +-
 sci-astronomy/missfits/ChangeLog                   |   2 +-
 sci-astronomy/missfits/missfits-9999.ebuild        |   2 +-
 sci-astronomy/montage/ChangeLog                    |   2 +-
 sci-astronomy/montage/montage-3.3.ebuild           |   2 +-
 sci-astronomy/mosstack/ChangeLog                   |   2 +-
 sci-astronomy/mosstack/mosstack-0.6.1-r1.ebuild    |   2 +-
 sci-astronomy/mosstack/mosstack-0.6.1.ebuild       |   2 +-
 sci-astronomy/psfex/ChangeLog                      |   2 +-
 sci-astronomy/psfex/psfex-9999.ebuild              |   2 +-
 sci-astronomy/scamp/ChangeLog                      |   2 +-
 sci-astronomy/scamp/scamp-1.7.0-r2.ebuild          |   2 +-
 sci-astronomy/scamp/scamp-9999.ebuild              |   2 +-
 sci-astronomy/sextractor/ChangeLog                 |   2 +-
 .../sextractor/sextractor-2.8.6-r1.ebuild          |   2 +-
 sci-astronomy/sextractor/sextractor-9999.ebuild    |   2 +-
 sci-astronomy/skymaker/ChangeLog                   |   2 +-
 sci-astronomy/skymaker/skymaker-9999.ebuild        |   2 +-
 sci-astronomy/starlink-bin/ChangeLog               |   2 +-
 .../starlink-bin/starlink-bin-20130413.ebuild      |   2 +-
 sci-astronomy/stiff/ChangeLog                      |   2 +-
 sci-astronomy/stiff/stiff-9999.ebuild              |   2 +-
 sci-astronomy/stilts/ChangeLog                     |   2 +-
 sci-astronomy/stilts/stilts-2.5.1.ebuild           |   2 +-
 sci-astronomy/stuff/ChangeLog                      |   2 +-
 sci-astronomy/stuff/stuff-9999.ebuild              |   2 +-
 sci-astronomy/swarp/ChangeLog                      |   2 +-
 sci-astronomy/swarp/swarp-9999.ebuild              |   2 +-
 sci-astronomy/topcat/ChangeLog                     |   2 +-
 sci-astronomy/topcat/topcat-4.0.1.ebuild           |   2 +-
 sci-astronomy/weightwatcher/ChangeLog              |   2 +-
 .../weightwatcher/weightwatcher-9999.ebuild        |   2 +-
 sci-astronomy/zebra/ChangeLog                      |   2 +-
 sci-astronomy/zebra/zebra-1.01.ebuild              |   2 +-
 sci-astronomy/zpeg/ChangeLog                       |   2 +-
 sci-astronomy/zpeg/zpeg-5.23.ebuild                |   2 +-
 sci-biology/AlignGraph/AlignGraph-9999.ebuild      |   2 +-
 sci-biology/AlignGraph/ChangeLog                   |   2 +-
 sci-biology/Atlas-Link/Atlas-Link-0.01.ebuild      |   2 +-
 sci-biology/Atlas-Link/ChangeLog                   |   2 +-
 sci-biology/Atlas/Atlas-2005.ebuild                |   2 +-
 sci-biology/Atlas/ChangeLog                        |   2 +-
 sci-biology/Atlas2/Atlas2-1.4.3.ebuild             |   2 +-
 sci-biology/Atlas2/ChangeLog                       |   2 +-
 sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild |   2 +-
 sci-biology/Atlas_GapFill/ChangeLog                |   2 +-
 sci-biology/BBmap/BBmap-34.56.ebuild               |   2 +-
 sci-biology/BBmap/ChangeLog                        |   2 +-
 sci-biology/BG7/BG7-9999.ebuild                    |   2 +-
 sci-biology/BG7/ChangeLog                          |   2 +-
 sci-biology/BRAKER/BRAKER-20150330.ebuild          |   2 +-
 sci-biology/BRAKER/ChangeLog                       |   2 +-
 sci-biology/BRANCH/BRANCH-9999.ebuild              |   2 +-
 sci-biology/BRANCH/ChangeLog                       |   2 +-
 sci-biology/BamView/BamView-1.2.11.ebuild          |   2 +-
 sci-biology/BamView/ChangeLog                      |   2 +-
 sci-biology/BlastToSam/BlastToSam-9999.ebuild      |   2 +-
 sci-biology/BlastToSam/ChangeLog                   |   2 +-
 sci-biology/CONTIGuator/CONTIGuator-2.7.ebuild     |   2 +-
 sci-biology/CONTIGuator/ChangeLog                  |   2 +-
 sci-biology/EBARDenovo/ChangeLog                   |   2 +-
 sci-biology/EBARDenovo/EBARDenovo-1.2.2.ebuild     |   2 +-
 sci-biology/ESTate/ChangeLog                       |   2 +-
 sci-biology/ESTate/ESTate-0.5.ebuild               |   2 +-
 sci-biology/FLASH/ChangeLog                        |   2 +-
 sci-biology/FLASH/FLASH-1.2.9.ebuild               |   2 +-
 sci-biology/Gambit/ChangeLog                       |   2 +-
 sci-biology/Gambit/Gambit-0.4.145.ebuild           |   2 +-
 sci-biology/HTSeq/ChangeLog                        |   2 +-
 sci-biology/HTSeq/HTSeq-0.6.1.ebuild               |   2 +-
 sci-biology/ICC/ChangeLog                          |   2 +-
 sci-biology/ICC/ICC-2.0.1.ebuild                   |   2 +-
 sci-biology/IMAGE/ChangeLog                        |   2 +-
 sci-biology/IMAGE/IMAGE-2.4.1.ebuild               |   2 +-
 sci-biology/InterMine/ChangeLog                    |   2 +-
 sci-biology/InterMine/InterMine-0.98.ebuild        |   2 +-
 sci-biology/Jannovar-bin/ChangeLog                 |   2 +-
 .../Jannovar-bin/Jannovar-bin-20150503.ebuild      |   2 +-
 sci-biology/KaKs_Calculator/ChangeLog              |   2 +-
 .../KaKs_Calculator/KaKs_Calculator-1.2.ebuild     |   2 +-
 sci-biology/MaSuRCA/ChangeLog                      |   2 +-
 sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild          |   2 +-
 sci-biology/MagicViewer/ChangeLog                  |   2 +-
 sci-biology/MagicViewer/MagicViewer-1.2.1.ebuild   |   2 +-
 sci-biology/MeV/ChangeLog                          |   2 +-
 sci-biology/MeV/MeV-4.8.1.ebuild                   |   2 +-
 sci-biology/MochiView/ChangeLog                    |   2 +-
 sci-biology/MochiView/MochiView-1.45.ebuild        |   2 +-
 sci-biology/NGSTools/ChangeLog                     |   2 +-
 sci-biology/NGSTools/NGSTools-2.0.5.ebuild         |   2 +-
 sci-biology/OBO-Edit/ChangeLog                     |   2 +-
 sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild         |   2 +-
 sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild       |   2 +-
 sci-biology/ONTO-PERL/ChangeLog                    |   2 +-
 sci-biology/ONTO-PERL/ONTO-PERL-1.41.ebuild        |   2 +-
 sci-biology/ORFcor/ChangeLog                       |   2 +-
 sci-biology/ORFcor/ORFcor-20130507.ebuild          |   2 +-
 sci-biology/RADtools/ChangeLog                     |   2 +-
 sci-biology/RADtools/RADtools-1.2.4.ebuild         |   2 +-
 sci-biology/RADtools/RADtools-9999.ebuild          |   2 +-
 sci-biology/RSeQC/ChangeLog                        |   2 +-
 sci-biology/RSeQC/RSeQC-2.6.1.ebuild               |   2 +-
 sci-biology/Ray/ChangeLog                          |   2 +-
 sci-biology/Ray/Ray-2.3.0.ebuild                   |   2 +-
 sci-biology/SEECER/ChangeLog                       |   2 +-
 sci-biology/SEECER/SEECER-0.1.3-r1.ebuild          |   2 +-
 sci-biology/SSAKE/ChangeLog                        |   2 +-
 sci-biology/SSAKE/SSAKE-3.8.2.ebuild               |   2 +-
 sci-biology/STAR/ChangeLog                         |   2 +-
 sci-biology/STAR/STAR-2.4.1c.ebuild                |   2 +-
 sci-biology/STAR/STAR-9999.ebuild                  |   2 +-
 sci-biology/SolexaQA/ChangeLog                     |   2 +-
 sci-biology/SolexaQA/SolexaQA-2.2.ebuild           |   2 +-
 sci-biology/StarORF/ChangeLog                      |   2 +-
 sci-biology/StarORF/StarORF-9999.ebuild            |   2 +-
 sci-biology/TransDecoder/ChangeLog                 |   2 +-
 sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild |   2 +-
 sci-biology/Trinotate/ChangeLog                    |   2 +-
 sci-biology/Trinotate/Trinotate-2.0.1.ebuild       |   2 +-
 sci-biology/VarScan/ChangeLog                      |   2 +-
 sci-biology/VarScan/VarScan-2.3.7.ebuild           |   2 +-
 sci-biology/VelvetOptimiser/ChangeLog              |   2 +-
 .../VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild   |   2 +-
 sci-biology/YASRA/ChangeLog                        |   2 +-
 sci-biology/YASRA/YASRA-2.33.ebuild                |   2 +-
 sci-biology/abacas/ChangeLog                       |   2 +-
 sci-biology/abacas/abacas-1.3.1.ebuild             |   2 +-
 sci-biology/abyss/ChangeLog                        |   2 +-
 sci-biology/abyss/abyss-1.3.3-r1.ebuild            |   2 +-
 sci-biology/abyss/abyss-1.3.4-r1.ebuild            |   2 +-
 sci-biology/abyss/abyss-1.3.6-r1.ebuild            |   2 +-
 sci-biology/aghermann/ChangeLog                    |   2 +-
 sci-biology/aghermann/aghermann-1.0.3-r1.ebuild    |   2 +-
 sci-biology/aghermann/aghermann-1.0.3.ebuild       |   2 +-
 sci-biology/aghermann/aghermann-1.0.4.ebuild       |   2 +-
 sci-biology/aghermann/aghermann-1.0.5.ebuild       |   2 +-
 sci-biology/align_to_scf/align_to_scf-1.06.ebuild  |   2 +-
 sci-biology/amos-short/ChangeLog                   |   2 +-
 sci-biology/amos-short/amos-short-0.9.3.ebuild     |   2 +-
 sci-biology/amos/ChangeLog                         |   2 +-
 sci-biology/amos/amos-3.1.0-r2.ebuild              |   2 +-
 sci-biology/amos/amos-9999.ebuild                  |   2 +-
 sci-biology/ampliconnoise/ChangeLog                |   2 +-
 .../ampliconnoise/ampliconnoise-1.27.ebuild        |   2 +-
 sci-biology/angsd/ChangeLog                        |   2 +-
 sci-biology/angsd/angsd-9999.ebuild                |   2 +-
 sci-biology/ants/ChangeLog                         |   2 +-
 sci-biology/ants/ants-9999.ebuild                  |   2 +-
 sci-biology/apollo/ChangeLog                       |   2 +-
 sci-biology/apollo/apollo-9999.ebuild              |   2 +-
 sci-biology/argo-bin/ChangeLog                     |   2 +-
 sci-biology/argo-bin/argo-bin-1.0.31.ebuild        |   2 +-
 sci-biology/argo-bin/argo-bin-2.0.3.ebuild         |   2 +-
 sci-biology/argo/ChangeLog                         |   2 +-
 sci-biology/argo/argo-1.0.24.ebuild                |   2 +-
 sci-biology/artemis-bin/ChangeLog                  |   2 +-
 sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild |   2 +-
 sci-biology/artemis/ChangeLog                      |   2 +-
 sci-biology/artemis/artemis-9999.ebuild            |   2 +-
 sci-biology/atsas/ChangeLog                        |   2 +-
 sci-biology/atsas/atsas-2.6.0.ebuild               |   2 +-
 sci-biology/augustus/ChangeLog                     |   2 +-
 sci-biology/augustus/augustus-3.1.ebuild           |   2 +-
 sci-biology/autoeditor/ChangeLog                   |   2 +-
 sci-biology/autoeditor/autoeditor-1.20.ebuild      |   2 +-
 sci-biology/bambino/ChangeLog                      |   2 +-
 sci-biology/bambino/bambino-1.02.ebuild            |   2 +-
 sci-biology/bambino/bambino-1.06.ebuild            |   2 +-
 sci-biology/bambus/ChangeLog                       |   2 +-
 sci-biology/bambus/bambus-2.33.ebuild              |   2 +-
 sci-biology/bamtools/ChangeLog                     |   2 +-
 sci-biology/bamtools/bamtools-9999.ebuild          |   2 +-
 sci-biology/barnacle/ChangeLog                     |   2 +-
 sci-biology/barnacle/barnacle-1.0.3.ebuild         |   2 +-
 sci-biology/barrnap/ChangeLog                      |   2 +-
 sci-biology/barrnap/barrnap-0.3.ebuild             |   2 +-
 sci-biology/barrnap/barrnap-0.4.ebuild             |   2 +-
 sci-biology/bcftools/ChangeLog                     |   2 +-
 sci-biology/bcftools/bcftools-1.2.ebuild           |   2 +-
 sci-biology/beagle/ChangeLog                       |   2 +-
 sci-biology/beagle/beagle-4.0.ebuild               |   2 +-
 sci-biology/beaglecall/ChangeLog                   |   2 +-
 sci-biology/beaglecall/beaglecall-20101115.ebuild  |   2 +-
 sci-biology/bedtools/ChangeLog                     |   2 +-
 sci-biology/bedtools/bedtools-2.22.1.ebuild        |   2 +-
 sci-biology/biobambam/ChangeLog                    |   2 +-
 sci-biology/biobambam/biobambam-0.0.183.ebuild     |   2 +-
 sci-biology/biopieces/ChangeLog                    |   2 +-
 sci-biology/biopieces/biopieces-9999.ebuild        |   2 +-
 sci-biology/bismark/bismark-0.13.0.ebuild          |   2 +-
 sci-biology/blasr/ChangeLog                        |   2 +-
 sci-biology/blasr/blasr-9999.ebuild                |   2 +-
 sci-biology/blue/ChangeLog                         |   2 +-
 sci-biology/blue/blue-1.1.2.ebuild                 |   2 +-
 sci-biology/blue/blue-1.1.3.ebuild                 |   2 +-
 sci-biology/bowtie/ChangeLog                       |   2 +-
 sci-biology/bowtie/bowtie-1.1.1.ebuild             |   2 +-
 sci-biology/bowtie/bowtie-2.2.3.ebuild             |   2 +-
 sci-biology/bowtie/bowtie-2.2.5.ebuild             |   2 +-
 sci-biology/brat/ChangeLog                         |   2 +-
 sci-biology/brat/brat-1.2.4.ebuild                 |   2 +-
 sci-biology/breakdancer/ChangeLog                  |   2 +-
 sci-biology/breakdancer/breakdancer-9999.ebuild    |   2 +-
 sci-biology/bx-python/ChangeLog                    |   2 +-
 sci-biology/bx-python/bx-python-0.7.2.ebuild       |   2 +-
 sci-biology/bx-python/bx-python-9999.ebuild        |   2 +-
 sci-biology/caftools/ChangeLog                     |   2 +-
 sci-biology/caftools/caftools-2.0.2.ebuild         |   2 +-
 sci-biology/cap3-bin/cap3-bin-20071221.ebuild      |   2 +-
 sci-biology/cd-hit-auxtools/ChangeLog              |   2 +-
 .../cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild     |   2 +-
 sci-biology/cd-hit/ChangeLog                       |   2 +-
 sci-biology/cd-hit/cd-hit-4.6.1.ebuild             |   2 +-
 sci-biology/cdbfasta/cdbfasta-0.1.ebuild           |   2 +-
 sci-biology/cegma/ChangeLog                        |   2 +-
 sci-biology/cegma/cegma-2.5.ebuild                 |   2 +-
 sci-biology/cgview-bin/ChangeLog                   |   2 +-
 sci-biology/cgview-bin/cgview-bin-20131130.ebuild  |   2 +-
 sci-biology/clover/ChangeLog                       |   2 +-
 sci-biology/clover/clover-2011.10.24.ebuild        |   2 +-
 sci-biology/cluster/ChangeLog                      |   2 +-
 sci-biology/cluster/cluster-1.50-r1.ebuild         |   2 +-
 sci-biology/cluster/cluster-1.50.ebuild            |   2 +-
 sci-biology/clview/ChangeLog                       |   2 +-
 sci-biology/clview/clview-0.1.ebuild               |   2 +-
 sci-biology/cnrun/ChangeLog                        |   2 +-
 sci-biology/cnrun/cnrun-2.0.2.ebuild               |   2 +-
 sci-biology/codonw/ChangeLog                       |   2 +-
 sci-biology/codonw/codonw-1.4.4-r2.ebuild          |   2 +-
 sci-biology/conform-gt/ChangeLog                   |   2 +-
 sci-biology/conform-gt/conform-gt-1174.ebuild      |   2 +-
 sci-biology/conifer/ChangeLog                      |   2 +-
 sci-biology/conifer/conifer-0.2.2.ebuild           |   2 +-
 sci-biology/consed-bin/ChangeLog                   |   2 +-
 sci-biology/consed-bin/consed-bin-20.ebuild        |   2 +-
 sci-biology/consed/ChangeLog                       |   2 +-
 sci-biology/consed/consed-29.ebuild                |   2 +-
 sci-biology/consed2gap/ChangeLog                   |   2 +-
 sci-biology/consed2gap/consed2gap-20050520.ebuild  |   2 +-
 sci-biology/coral/ChangeLog                        |   2 +-
 sci-biology/coral/coral-1.4.ebuild                 |   2 +-
 sci-biology/cortex_var/ChangeLog                   |   2 +-
 sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild  |   2 +-
 sci-biology/cutadapt/ChangeLog                     |   2 +-
 sci-biology/cutadapt/cutadapt-1.2.1.ebuild         |   2 +-
 sci-biology/cutadapt/cutadapt-1.4.1.ebuild         |   2 +-
 sci-biology/cutadapt/cutadapt-1.5.ebuild           |   2 +-
 sci-biology/cutadapt/cutadapt-9999.ebuild          |   2 +-
 sci-biology/dawg/ChangeLog                         |   2 +-
 sci-biology/dawg/dawg-1.1.2.ebuild                 |   2 +-
 sci-biology/dcmstack/ChangeLog                     |   2 +-
 sci-biology/dcmstack/dcmstack-9999.ebuild          |   2 +-
 sci-biology/discrover/ChangeLog                    |   2 +-
 sci-biology/discrover/discrover-1.6.0.ebuild       |   2 +-
 sci-biology/discrover/discrover-9999.ebuild        |   2 +-
 sci-biology/ePCR/ChangeLog                         |   2 +-
 sci-biology/ePCR/ePCR-2.3.12.ebuild                |   2 +-
 sci-biology/edena/ChangeLog                        |   2 +-
 sci-biology/edena/edena-3.131028.ebuild            |   2 +-
 sci-biology/epga/ChangeLog                         |   2 +-
 sci-biology/epga/epga-9999.ebuild                  |   2 +-
 sci-biology/erpin/ChangeLog                        |   2 +-
 sci-biology/erpin/erpin-5.5b.ebuild                |   2 +-
 sci-biology/est2assembly/ChangeLog                 |   2 +-
 sci-biology/est2assembly/est2assembly-1.08.ebuild  |   2 +-
 sci-biology/est2assembly/est2assembly-9999.ebuild  |   2 +-
 sci-biology/est2uni/ChangeLog                      |   2 +-
 sci-biology/est2uni/est2uni-0.27.ebuild            |   2 +-
 sci-biology/est2uni/est2uni-9999.ebuild            |   2 +-
 sci-biology/estscan/ChangeLog                      |   2 +-
 sci-biology/estscan/estscan-3.0.3.ebuild           |   2 +-
 sci-biology/eval/ChangeLog                         |   2 +-
 sci-biology/eval/eval-2.2.8.ebuild                 |   2 +-
 sci-biology/exomiser-bin/ChangeLog                 |   2 +-
 sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild |   2 +-
 sci-biology/exonerate-gff3/ChangeLog               |   2 +-
 .../exonerate-gff3/exonerate-gff3-9999.ebuild      |   2 +-
 sci-biology/fastdnaml/ChangeLog                    |   2 +-
 sci-biology/fastdnaml/fastdnaml-1.2.2_p10.ebuild   |   2 +-
 sci-biology/fastqc/ChangeLog                       |   2 +-
 sci-biology/fastqc/fastqc-0.11.3.ebuild            |   2 +-
 sci-biology/fastx_toolkit/ChangeLog                |   2 +-
 .../fastx_toolkit/fastx_toolkit-0.0.14.ebuild      |   2 +-
 sci-biology/ffindex/ChangeLog                      |   2 +-
 sci-biology/ffindex/ffindex-0.9.9.3.ebuild         |   2 +-
 sci-biology/flexbar/ChangeLog                      |   2 +-
 sci-biology/flexbar/flexbar-2.4.ebuild             |   2 +-
 sci-biology/freebayes/ChangeLog                    |   2 +-
 sci-biology/freebayes/freebayes-9999.ebuild        |   2 +-
 sci-biology/fsa/ChangeLog                          |   2 +-
 sci-biology/fsa/fsa-1.15.7.ebuild                  |   2 +-
 sci-biology/fsl/ChangeLog                          |   2 +-
 sci-biology/fsl/fsl-5.0.6.ebuild                   |   2 +-
 sci-biology/fsl/fsl-5.0.8.ebuild                   |   2 +-
 sci-biology/gap2caf/ChangeLog                      |   2 +-
 sci-biology/gap2caf/gap2caf-2.1.0.ebuild           |   2 +-
 sci-biology/gbench/ChangeLog                       |   2 +-
 sci-biology/gbench/gbench-2.3.2.ebuild             |   2 +-
 sci-biology/gbrowse/ChangeLog                      |   2 +-
 sci-biology/gbrowse/gbrowse-2.39.ebuild            |   2 +-
 sci-biology/gbrowse/gbrowse-2.45.ebuild            |   2 +-
 sci-biology/gbrowse/gbrowse-2.48.ebuild            |   2 +-
 sci-biology/geneid/ChangeLog                       |   2 +-
 sci-biology/geneid/geneid-1.4.4.ebuild             |   2 +-
 sci-biology/genepop/ChangeLog                      |   2 +-
 sci-biology/genepop/genepop-4.2.1.ebuild           |   2 +-
 sci-biology/generecon/ChangeLog                    |   2 +-
 sci-biology/generecon/generecon-1.2.1-r1.ebuild    |   2 +-
 sci-biology/genomeview-bin/ChangeLog               |   2 +-
 .../genomeview-bin/genomeview-bin-2450.ebuild      |   2 +-
 sci-biology/genseed/ChangeLog                      |   2 +-
 sci-biology/genseed/genseed-1.0.22.ebuild          |   2 +-
 sci-biology/gfftools/ChangeLog                     |   2 +-
 sci-biology/gfftools/gfftools-0.98d.ebuild         |   2 +-
 sci-biology/gffutils/ChangeLog                     |   2 +-
 sci-biology/gffutils/gffutils-0.8.3.ebuild         |   2 +-
 sci-biology/glean/ChangeLog                        |   2 +-
 sci-biology/glean/glean-1.0.1.ebuild               |   2 +-
 sci-biology/grappa/ChangeLog                       |   2 +-
 sci-biology/grappa/grappa-2.0.ebuild               |   2 +-
 sci-biology/hexamer/ChangeLog                      |   2 +-
 sci-biology/hexamer/hexamer-19990330.ebuild        |   2 +-
 sci-biology/hydra-sv/ChangeLog                     |   2 +-
 sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild         |   2 +-
 sci-biology/igv/ChangeLog                          |   2 +-
 sci-biology/igv/igv-2.3.47.ebuild                  |   2 +-
 sci-biology/igv/igv-2.3.52.ebuild                  |   2 +-
 sci-biology/inGAP-bin/ChangeLog                    |   2 +-
 sci-biology/inGAP-bin/inGAP-bin-3.0.1.ebuild       |   2 +-
 sci-biology/jellyfish/ChangeLog                    |   2 +-
 sci-biology/jellyfish/jellyfish-1.1.11.ebuild      |   2 +-
 sci-biology/jellyfish/jellyfish-2.1.3.ebuild       |   2 +-
 sci-biology/jellyfish/jellyfish-2.1.4.ebuild       |   2 +-
 sci-biology/jigsaw/ChangeLog                       |   2 +-
 sci-biology/jigsaw/jigsaw-3.2.10.ebuild            |   2 +-
 sci-biology/jtreeview/ChangeLog                    |   2 +-
 sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild     |   2 +-
 sci-biology/kallisto/ChangeLog                     |   2 +-
 sci-biology/kallisto/kallisto-0.42.1.ebuild        |   2 +-
 sci-biology/kallisto/kallisto-9999.ebuild          |   2 +-
 sci-biology/khmer/ChangeLog                        |   2 +-
 sci-biology/khmer/khmer-0.8.ebuild                 |   2 +-
 sci-biology/khmer/khmer-1.0.1.ebuild               |   2 +-
 sci-biology/khmer/khmer-9999.ebuild                |   2 +-
 sci-biology/kmergenie/ChangeLog                    |   2 +-
 sci-biology/kmergenie/kmergenie-1.6971.ebuild      |   2 +-
 sci-biology/lastz/ChangeLog                        |   2 +-
 sci-biology/lastz/lastz-1.03.66.ebuild             |   2 +-
 sci-biology/libgtextutils/ChangeLog                |   2 +-
 .../libgtextutils/libgtextutils-0.6.1.ebuild       |   2 +-
 sci-biology/lighter/ChangeLog                      |   2 +-
 sci-biology/lighter/lighter-9999.ebuild            |   2 +-
 sci-biology/lucy/lucy-1.20.ebuild                  |   2 +-
 sci-biology/maker/ChangeLog                        |   2 +-
 sci-biology/maker/maker-2.31.8.ebuild              |   2 +-
 sci-biology/manatee-igs/ChangeLog                  |   2 +-
 sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild  |   2 +-
 sci-biology/manatee-jcvi/ChangeLog                 |   2 +-
 sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild |   2 +-
 sci-biology/mavid/ChangeLog                        |   2 +-
 sci-biology/mavid/mavid-2.0.4.ebuild               |   2 +-
 sci-biology/merlin/ChangeLog                       |   2 +-
 sci-biology/merlin/merlin-1.1.2.ebuild             |   2 +-
 sci-biology/metaseq/ChangeLog                      |   2 +-
 sci-biology/metaseq/metaseq-0.5.3.ebuild           |   2 +-
 sci-biology/mgblast/ChangeLog                      |   2 +-
 sci-biology/mgblast/mgblast-0.1.ebuild             |   2 +-
 sci-biology/minced/ChangeLog                       |   2 +-
 sci-biology/minced/minced-9999.ebuild              |   2 +-
 sci-biology/mip-scaffolder/ChangeLog               |   2 +-
 .../mip-scaffolder/mip-scaffolder-0.6.ebuild       |   2 +-
 sci-biology/mira/ChangeLog                         |   2 +-
 sci-biology/mira/mira-4.9.5.ebuild                 |   2 +-
 sci-biology/miranda/ChangeLog                      |   2 +-
 sci-biology/miranda/miranda-3.3a.ebuild            |   2 +-
 sci-biology/mne-python/ChangeLog                   |   2 +-
 sci-biology/mne-python/mne-python-0.7.ebuild       |   2 +-
 sci-biology/mne-python/mne-python-9999.ebuild      |   2 +-
 sci-biology/mosaik/ChangeLog                       |   2 +-
 sci-biology/mosaik/mosaik-2.2.3.ebuild             |   2 +-
 sci-biology/mosaik/mosaik-9999.ebuild              |   2 +-
 sci-biology/mreps/ChangeLog                        |   2 +-
 sci-biology/mreps/mreps-2.5.ebuild                 |   2 +-
 sci-biology/mrfast/ChangeLog                       |   2 +-
 sci-biology/mrfast/mrfast-2.6.0.1.ebuild           |   2 +-
 sci-biology/mrsfast/ChangeLog                      |   2 +-
 sci-biology/mrsfast/mrsfast-2.6.0.4.ebuild         |   2 +-
 sci-biology/ncbi-blast+/ChangeLog                  |   2 +-
 sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild  |   2 +-
 sci-biology/ncbi-tools++/ChangeLog                 |   2 +-
 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        |   2 +-
 sci-biology/nesoni/ChangeLog                       |   2 +-
 sci-biology/nesoni/nesoni-0.128.ebuild             |   2 +-
 sci-biology/ngs_backbone/ChangeLog                 |   2 +-
 sci-biology/ngs_backbone/ngs_backbone-9999.ebuild  |   2 +-
 sci-biology/ngsview/ChangeLog                      |   2 +-
 sci-biology/ngsview/ngsview-0.91.ebuild            |   2 +-
 sci-biology/nrcl/ChangeLog                         |   2 +-
 sci-biology/nrcl/nrcl-110625.ebuild                |   2 +-
 sci-biology/pairagon/ChangeLog                     |   2 +-
 sci-biology/pairagon/pairagon-1.1.ebuild           |   2 +-
 sci-biology/parafly/ChangeLog                      |   2 +-
 sci-biology/parafly/parafly-20130121.ebuild        |   2 +-
 sci-biology/pb-honey/ChangeLog                     |   2 +-
 sci-biology/pb-honey/pb-honey-14.1.15.ebuild       |   2 +-
 sci-biology/pb-jelly/ChangeLog                     |   2 +-
 sci-biology/pb-jelly/pb-jelly-14.9.9.ebuild        |   2 +-
 sci-biology/perlprimer/ChangeLog                   |   2 +-
 sci-biology/perlprimer/perlprimer-1.1.21.ebuild    |   2 +-
 sci-biology/phusion/ChangeLog                      |   2 +-
 sci-biology/phusion/phusion-2.1c.ebuild            |   2 +-
 sci-biology/pileup/ChangeLog                       |   2 +-
 sci-biology/pileup/pileup-0.6.ebuild               |   2 +-
 sci-biology/plinkseq/ChangeLog                     |   2 +-
 sci-biology/plinkseq/plinkseq-0.10.ebuild          |   2 +-
 sci-biology/polyphen/ChangeLog                     |   2 +-
 sci-biology/polyphen/polyphen-2.2.2.ebuild         |   2 +-
 sci-biology/primerD/ChangeLog                      |   2 +-
 sci-biology/primerD/primerD-1.0.0.ebuild           |   2 +-
 sci-biology/proda/ChangeLog                        |   2 +-
 sci-biology/proda/proda-1.0.ebuild                 |   2 +-
 sci-biology/prokka/ChangeLog                       |   2 +-
 sci-biology/prokka/prokka-1.11.ebuild              |   2 +-
 sci-biology/prot4EST/ChangeLog                     |   2 +-
 sci-biology/prot4EST/prot4EST-3.1b.ebuild          |   2 +-
 sci-biology/psx/psx-0.1.ebuild                     |   2 +-
 sci-biology/psychopy/ChangeLog                     |   2 +-
 sci-biology/psychopy/psychopy-1.78.00.ebuild       |   2 +-
 sci-biology/psychopy/psychopy-9999.ebuild          |   2 +-
 sci-biology/pvmsx/ChangeLog                        |   2 +-
 sci-biology/pvmsx/pvmsx-0.1.ebuild                 |   2 +-
 sci-biology/pybedtools/ChangeLog                   |   2 +-
 sci-biology/pybedtools/pybedtools-0.6.9.ebuild     |   2 +-
 sci-biology/pybrain/ChangeLog                      |   2 +-
 sci-biology/pybrain/pybrain-9999.ebuild            |   2 +-
 sci-biology/pyfaidx/ChangeLog                      |   2 +-
 sci-biology/pyfaidx/pyfaidx-0.3.8.ebuild           |   2 +-
 sci-biology/pysam/ChangeLog                        |   2 +-
 sci-biology/pysam/pysam-0.6-r2.ebuild              |   2 +-
 sci-biology/pysam/pysam-0.7.5.ebuild               |   2 +-
 sci-biology/pysurfer/ChangeLog                     |   2 +-
 sci-biology/pysurfer/pysurfer-0.4.ebuild           |   2 +-
 sci-biology/pysurfer/pysurfer-9999.ebuild          |   2 +-
 sci-biology/quast/ChangeLog                        |   2 +-
 sci-biology/quast/quast-2.3.ebuild                 |   2 +-
 sci-biology/quicktree/ChangeLog                    |   2 +-
 sci-biology/quicktree/quicktree-1.1-r1.ebuild      |   2 +-
 sci-biology/quorum/ChangeLog                       |   2 +-
 sci-biology/quorum/quorum-0.2.1.ebuild             |   2 +-
 sci-biology/quorum/quorum-1.0.0.ebuild             |   2 +-
 sci-biology/reptile/ChangeLog                      |   2 +-
 sci-biology/reptile/reptile-1.1.ebuild             |   2 +-
 sci-biology/rnaplex/ChangeLog                      |   2 +-
 sci-biology/rnaplex/rnaplex-0.2.ebuild             |   2 +-
 .../roche454ace2caf-20100812.ebuild                |   2 +-
 sci-biology/ruffus/ChangeLog                       |   2 +-
 sci-biology/ruffus/ruffus-9999.ebuild              |   2 +-
 sci-biology/rum/ChangeLog                          |   2 +-
 sci-biology/rum/rum-2.0.5.5.ebuild                 |   2 +-
 sci-biology/sabre/ChangeLog                        |   2 +-
 sci-biology/sabre/sabre-9999.ebuild                |   2 +-
 sci-biology/salmon/ChangeLog                       |   8 +-
 sci-biology/salmon/Manifest                        |   1 +
 sci-biology/salmon/salmon-0.3.2.ebuild             |   6 +-
 .../{salmon-0.3.2.ebuild => salmon-0.4.2.ebuild}   |   6 +-
 sci-biology/salmon/salmon-9999.ebuild              |   6 +-
 sci-biology/samstat/ChangeLog                      |   2 +-
 sci-biology/samstat/samstat-20130708.ebuild        |   2 +-
 sci-biology/samtools/ChangeLog                     |   2 +-
 sci-biology/samtools/samtools-1.0-r2.ebuild        |   2 +-
 sci-biology/samtools/samtools-1.1-r1.ebuild        |   2 +-
 sci-biology/samtools/samtools-1.2-r1.ebuild        |   2 +-
 sci-biology/scaffold_builder/ChangeLog             |   2 +-
 .../scaffold_builder-20131122.ebuild               |   2 +-
 sci-biology/scan_for_matches/ChangeLog             |   2 +-
 .../scan_for_matches-20121220.ebuild               |   2 +-
 sci-biology/sclust/sclust-0.1.ebuild               |   2 +-
 sci-biology/screed/ChangeLog                       |   2 +-
 sci-biology/screed/screed-0.7.1.ebuild             |   2 +-
 sci-biology/scythe/ChangeLog                       |   2 +-
 sci-biology/scythe/scythe-0.992.ebuild             |   2 +-
 sci-biology/seqclean/ChangeLog                     |   2 +-
 sci-biology/seqclean/seqclean-110625.ebuild        |   2 +-
 sci-biology/seqtools/ChangeLog                     |   2 +-
 sci-biology/seqtools/seqtools-4.34.5.ebuild        |   2 +-
 sci-biology/sequin/ChangeLog                       |   2 +-
 sci-biology/sequin/sequin-20121202.ebuild          |   2 +-
 sci-biology/sff_dump/ChangeLog                     |   2 +-
 sci-biology/sff_dump/sff_dump-1.04.ebuild          |   2 +-
 sci-biology/sga/ChangeLog                          |   2 +-
 sci-biology/sga/sga-9999.ebuild                    |   2 +-
 sci-biology/sgp2/ChangeLog                         |   2 +-
 sci-biology/sgp2/sgp2-1.1.ebuild                   |   2 +-
 sci-biology/sickle/ChangeLog                       |   2 +-
 sci-biology/sickle/sickle-1.33.ebuild              |   2 +-
 sci-biology/sickle/sickle-9999.ebuild              |   2 +-
 sci-biology/signalp/ChangeLog                      |   2 +-
 sci-biology/signalp/signalp-3.0.ebuild             |   2 +-
 sci-biology/skewer-bin/ChangeLog                   |   2 +-
 sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild   |   2 +-
 sci-biology/smalt-bin/ChangeLog                    |   2 +-
 sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild       |   2 +-
 sci-biology/snap/ChangeLog                         |   2 +-
 sci-biology/snap/snap-20131129.ebuild              |   2 +-
 sci-biology/snphylo/ChangeLog                      |   2 +-
 sci-biology/snphylo/snphylo-20140701.ebuild        |   2 +-
 sci-biology/spm/ChangeLog                          |   2 +-
 sci-biology/spm/spm-12.ebuild                      |   2 +-
 sci-biology/spm/spm-8.ebuild                       |   2 +-
 sci-biology/sra_sdk/ChangeLog                      |   2 +-
 sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild           |   2 +-
 sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild           |   2 +-
 sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild          |   2 +-
 sci-biology/ssaha2-bin/ChangeLog                   |   2 +-
 sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild     |   2 +-
 sci-biology/stacks/ChangeLog                       |   2 +-
 sci-biology/stacks/stacks-1.16.ebuild              |   2 +-
 sci-biology/staden/ChangeLog                       |   2 +-
 sci-biology/staden/staden-2.0.0_beta9.ebuild       |   2 +-
 sci-biology/staden/staden-9999.ebuild              |   2 +-
 sci-biology/subread/ChangeLog                      |   2 +-
 sci-biology/subread/subread-1.4.6.ebuild           |   2 +-
 sci-biology/swissknife/ChangeLog                   |   2 +-
 sci-biology/swissknife/swissknife-1.70.ebuild      |   2 +-
 sci-biology/symap/ChangeLog                        |   2 +-
 sci-biology/symap/symap-4.0.ebuild                 |   2 +-
 sci-biology/tablet-bin/ChangeLog                   |   2 +-
 .../tablet-bin/tablet-bin-1.14.10.21.ebuild        |   2 +-
 sci-biology/tablet/ChangeLog                       |   2 +-
 sci-biology/tablet/tablet-9999.ebuild              |   2 +-
 sci-biology/tagdust/ChangeLog                      |   2 +-
 sci-biology/tagdust/tagdust-20101028.ebuild        |   2 +-
 sci-biology/tclust/ChangeLog                       |   2 +-
 sci-biology/tclust/tclust-110625.ebuild            |   2 +-
 sci-biology/tgicl/ChangeLog                        |   2 +-
 sci-biology/tgicl/tgicl-2.1.ebuild                 |   2 +-
 sci-biology/tigr-assembler/ChangeLog               |   2 +-
 .../tigr-assembler/tigr-assembler-2.0.ebuild       |   2 +-
 sci-biology/tigr-closure/ChangeLog                 |   2 +-
 .../tigr-closure/tigr-closure-20080106.ebuild      |   2 +-
 sci-biology/tigr-foundation-libs/ChangeLog         |   2 +-
 .../tigr-foundation-libs-2.0-r1.ebuild             |   2 +-
 sci-biology/tmhmm/ChangeLog                        |   2 +-
 sci-biology/tmhmm/tmhmm-2.0c.ebuild                |   2 +-
 sci-biology/tophat/ChangeLog                       |   7 +-
 sci-biology/tophat/Manifest                        |   1 +
 sci-biology/tophat/tophat-2.0.12.ebuild            |   2 +-
 sci-biology/tophat/tophat-2.0.13.ebuild            |   2 +-
 sci-biology/tophat/tophat-2.0.14.ebuild            |   2 +-
 sci-biology/tophat/tophat-2.1.0.ebuild             |  43 ++++
 sci-biology/trans-abyss/ChangeLog                  |   2 +-
 sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild   |   2 +-
 sci-biology/trf/ChangeLog                          |   2 +-
 sci-biology/trf/trf-4.07b.ebuild                   |   2 +-
 sci-biology/trim_galore/ChangeLog                  |   2 +-
 sci-biology/trim_galore/trim_galore-0.4.0.ebuild   |   2 +-
 sci-biology/trimmomatic/ChangeLog                  |   2 +-
 sci-biology/trimmomatic/trimmomatic-0.32.ebuild    |   2 +-
 sci-biology/trinityrnaseq/ChangeLog                |   2 +-
 .../trinityrnaseq/trinityrnaseq-2.0.6.ebuild       |   2 +-
 sci-biology/trowel/ChangeLog                       |   2 +-
 sci-biology/trowel/trowel-0.1.4.1.ebuild           |   2 +-
 sci-biology/twinscan/ChangeLog                     |   2 +-
 sci-biology/twinscan/twinscan-4.1.2-r1.ebuild      |   2 +-
 sci-biology/ugene/ChangeLog                        |   2 +-
 sci-biology/ugene/ugene-1.13.3.ebuild              |   2 +-
 sci-biology/ugene/ugene-1.16.1.ebuild              |   2 +-
 sci-biology/vague-bin/ChangeLog                    |   2 +-
 sci-biology/vague-bin/vague-bin-1.0.5.ebuild       |   2 +-
 sci-biology/velvetk/ChangeLog                      |   2 +-
 sci-biology/velvetk/velvetk-20120606.ebuild        |   2 +-
 sci-biology/wcd/ChangeLog                          |   2 +-
 sci-biology/wcd/wcd-0.6.3.ebuild                   |   2 +-
 sci-biology/wgs-assembler/ChangeLog                |   2 +-
 sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild |   2 +-
 .../wgs-assembler/wgs-assembler-8.3_rc2.ebuild     |   2 +-
 sci-biology/wise/ChangeLog                         |   2 +-
 sci-biology/wise/wise-2.4.1.ebuild                 |   2 +-
 sci-biology/zmsort/ChangeLog                       |   2 +-
 sci-biology/zmsort/zmsort-110625.ebuild            |   2 +-
 sci-chemistry/GromacsWrapper/ChangeLog             |   2 +-
 .../GromacsWrapper/GromacsWrapper-9999.ebuild      |   2 +-
 sci-chemistry/almost/ChangeLog                     |   2 +-
 sci-chemistry/almost/almost-1.0.3-r2.ebuild        |   2 +-
 sci-chemistry/ambertools/ChangeLog                 |   2 +-
 sci-chemistry/ambertools/ambertools-12_p38.ebuild  |   2 +-
 sci-chemistry/avogadro2/ChangeLog                  |   2 +-
 sci-chemistry/avogadro2/avogadro2-0.7.2.ebuild     |   2 +-
 sci-chemistry/ball/ChangeLog                       |   2 +-
 sci-chemistry/ball/ball-9999.ebuild                |   2 +-
 sci-chemistry/bist/ChangeLog                       |   2 +-
 sci-chemistry/bist/bist-0.5.1-r1.ebuild            |   2 +-
 sci-chemistry/burrow-owl/ChangeLog                 |   2 +-
 sci-chemistry/burrow-owl/burrow-owl-9999.ebuild    |   2 +-
 sci-chemistry/camshift/ChangeLog                   |   2 +-
 sci-chemistry/camshift/camshift-1.35.0.ebuild      |   2 +-
 sci-chemistry/chemBuild/ChangeLog                  |   2 +-
 sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild     |   2 +-
 sci-chemistry/chemBuild/chemBuild-1.0.3.ebuild     |   2 +-
 sci-chemistry/chemBuild/chemBuild-1.0.4.ebuild     |   2 +-
 sci-chemistry/chimera-bin/ChangeLog                |   2 +-
 sci-chemistry/chimera-bin/chimera-bin-1.9.ebuild   |   2 +-
 sci-chemistry/chooch/ChangeLog                     |   2 +-
 sci-chemistry/chooch/chooch-5.0.2-r1.ebuild        |   2 +-
 sci-chemistry/cnsface/ChangeLog                    |   2 +-
 sci-chemistry/cnsface/cnsface-0.0.12.ebuild        |   2 +-
 sci-chemistry/concoord/ChangeLog                   |   2 +-
 sci-chemistry/concoord/concoord-2.1.2.ebuild       |   2 +-
 sci-chemistry/concoord/concoord-2.1.ebuild         |   2 +-
 sci-chemistry/coot/ChangeLog                       |   2 +-
 sci-chemistry/coot/coot-9999.ebuild                |   2 +-
 sci-chemistry/cpmgfit/ChangeLog                    |   2 +-
 sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild          |   2 +-
 sci-chemistry/cs-rosetta/ChangeLog                 |   2 +-
 .../cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild |   2 +-
 sci-chemistry/curvefit/ChangeLog                   |   2 +-
 sci-chemistry/curvefit/curvefit-1.40.ebuild        |   2 +-
 sci-chemistry/dl_poly/ChangeLog                    |   2 +-
 sci-chemistry/dl_poly/dl_poly-1.9.ebuild           |   2 +-
 sci-chemistry/dl_poly/dl_poly-4.05.ebuild          |   2 +-
 sci-chemistry/drawxtl/ChangeLog                    |   2 +-
 sci-chemistry/drawxtl/drawxtl-45.ebuild            |   2 +-
 sci-chemistry/drawxtl/drawxtl-55.ebuild            |   2 +-
 sci-chemistry/dssp2pdb/ChangeLog                   |   2 +-
 sci-chemistry/dssp2pdb/dssp2pdb-0.03.ebuild        |   2 +-
 sci-chemistry/erkale/ChangeLog                     |   2 +-
 sci-chemistry/erkale/erkale-9999.ebuild            |   2 +-
 sci-chemistry/freeon/ChangeLog                     |   2 +-
 sci-chemistry/freeon/freeon-9999.ebuild            |   2 +-
 sci-chemistry/gamess/ChangeLog                     |   2 +-
 sci-chemistry/gamess/gamess-20120501.1.ebuild      |   2 +-
 sci-chemistry/gamess/gamess-20130501.1.ebuild      |   2 +-
 sci-chemistry/gnome-chemistry-utils/ChangeLog      |   2 +-
 .../gnome-chemistry-utils-0.14.2-r1.ebuild         |   2 +-
 .../gnome-chemistry-utils-9999.ebuild              |   2 +-
 sci-chemistry/gromacs/ChangeLog                    |   7 +-
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild      |   2 +-
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild      |   2 +-
 ...acs-5.0.9999.ebuild => gromacs-5.1.9999.ebuild} |  37 +--
 sci-chemistry/gromacs/gromacs-9999.ebuild          |   2 +-
 sci-chemistry/hydronmr/ChangeLog                   |   2 +-
 sci-chemistry/hydronmr/hydronmr-7c.ebuild          |   2 +-
 sci-chemistry/jana2000/ChangeLog                   |   2 +-
 sci-chemistry/jana2000/jana2000-20071218.ebuild    |   2 +-
 sci-chemistry/jligand/ChangeLog                    |   2 +-
 sci-chemistry/jligand/jligand-1.0.19.ebuild        |   2 +-
 sci-chemistry/ligplot+/ChangeLog                   |   2 +-
 sci-chemistry/ligplot+/ligplot+-1.4.ebuild         |   2 +-
 sci-chemistry/mage/ChangeLog                       |   2 +-
 sci-chemistry/mage/mage-6.44.060606.ebuild         |   2 +-
 sci-chemistry/mddnmr/ChangeLog                     |   2 +-
 sci-chemistry/mddnmr/mddnmr-2.4-r1.ebuild          |   2 +-
 sci-chemistry/mdsctk/ChangeLog                     |   2 +-
 sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild           |   2 +-
 sci-chemistry/mgltools-autodocktools/ChangeLog     |   2 +-
 .../mgltools-autodocktools-1.5.6.ebuild            |   2 +-
 sci-chemistry/mgltools-bhtree/ChangeLog            |   2 +-
 .../mgltools-bhtree/mgltools-bhtree-1.5.6.ebuild   |   2 +-
 sci-chemistry/mgltools-cadd/ChangeLog              |   2 +-
 .../mgltools-cadd/mgltools-cadd-1.5.6.ebuild       |   2 +-
 sci-chemistry/mgltools-cmolkit/ChangeLog           |   2 +-
 .../mgltools-cmolkit/mgltools-cmolkit-1.5.6.ebuild |   2 +-
 sci-chemistry/mgltools-dejavu/ChangeLog            |   2 +-
 .../mgltools-dejavu-1.5.6-r1.ebuild                |   2 +-
 sci-chemistry/mgltools-geomutils/ChangeLog         |   2 +-
 .../mgltools-geomutils-1.5.6.ebuild                |   2 +-
 sci-chemistry/mgltools-gle/ChangeLog               |   2 +-
 .../mgltools-gle/mgltools-gle-1.5.6.ebuild         |   2 +-
 sci-chemistry/mgltools-mglutil/ChangeLog           |   2 +-
 .../mgltools-mglutil-1.5.6-r1.ebuild               |   2 +-
 sci-chemistry/mgltools-molkit/ChangeLog            |   2 +-
 .../mgltools-molkit/mgltools-molkit-1.5.6.ebuild   |   2 +-
 sci-chemistry/mgltools-networkeditor/ChangeLog     |   2 +-
 .../mgltools-networkeditor-1.5.6.ebuild            |   2 +-
 sci-chemistry/mgltools-opengltk/ChangeLog          |   2 +-
 .../mgltools-opengltk-1.5.6.ebuild                 |   2 +-
 sci-chemistry/mgltools-pmv/ChangeLog               |   2 +-
 .../mgltools-pmv/mgltools-pmv-1.5.6.ebuild         |   2 +-
 sci-chemistry/mgltools-pyautodock/ChangeLog        |   2 +-
 .../mgltools-pyautodock-1.5.6.ebuild               |   2 +-
 sci-chemistry/mgltools-pybabel/ChangeLog           |   2 +-
 .../mgltools-pybabel/mgltools-pybabel-1.5.6.ebuild |   2 +-
 sci-chemistry/mgltools-pyglf/ChangeLog             |   2 +-
 .../mgltools-pyglf/mgltools-pyglf-1.5.6.ebuild     |   2 +-
 sci-chemistry/mgltools-qslimlib/ChangeLog          |   2 +-
 .../mgltools-qslimlib-1.5.6.ebuild                 |   2 +-
 sci-chemistry/mgltools-scenario2/ChangeLog         |   2 +-
 .../mgltools-scenario2-1.5.6.ebuild                |   2 +-
 sci-chemistry/mgltools-sff/ChangeLog               |   2 +-
 .../mgltools-sff/mgltools-sff-1.5.6.ebuild         |   2 +-
 sci-chemistry/mgltools-support/ChangeLog           |   2 +-
 .../mgltools-support/mgltools-support-1.5.6.ebuild |   2 +-
 sci-chemistry/mgltools-symserv/ChangeLog           |   2 +-
 .../mgltools-symserv/mgltools-symserv-1.5.6.ebuild |   2 +-
 sci-chemistry/mgltools-utpackages/ChangeLog        |   2 +-
 .../mgltools-utpackages-1.5.6.ebuild               |   2 +-
 sci-chemistry/mgltools-viewer-framework/ChangeLog  |   2 +-
 .../mgltools-viewer-framework-1.5.6.ebuild         |   2 +-
 sci-chemistry/mgltools-vision/ChangeLog            |   2 +-
 .../mgltools-vision/mgltools-vision-1.5.6.ebuild   |   2 +-
 sci-chemistry/mgltools-visionlib/ChangeLog         |   2 +-
 .../mgltools-visionlib-1.5.6.ebuild                |   2 +-
 sci-chemistry/mgltools-volume/ChangeLog            |   2 +-
 .../mgltools-volume/mgltools-volume-1.5.6.ebuild   |   2 +-
 sci-chemistry/mgltools-webservices/ChangeLog       |   2 +-
 .../mgltools-webservices-1.5.6.ebuild              |   2 +-
 sci-chemistry/mgltools/ChangeLog                   |   2 +-
 sci-chemistry/mgltools/mgltools-1.5.6.ebuild       |   2 +-
 sci-chemistry/mics/ChangeLog                       |   2 +-
 sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild |   2 +-
 sci-chemistry/modelfree/ChangeLog                  |   2 +-
 sci-chemistry/modelfree/modelfree-4.20.ebuild      |   2 +-
 sci-chemistry/modeller/ChangeLog                   |   2 +-
 sci-chemistry/modeller/modeller-9.12-r3.ebuild     |   2 +-
 sci-chemistry/module2/ChangeLog                    |   2 +-
 sci-chemistry/module2/module2-0_pre20140717.ebuild |   2 +-
 sci-chemistry/mtz2hkl/ChangeLog                    |   2 +-
 sci-chemistry/mtz2hkl/mtz2hkl-0.3.ebuild           |   2 +-
 sci-chemistry/mtz2sca/ChangeLog                    |   2 +-
 sci-chemistry/mtz2sca/mtz2sca-0.3.ebuild           |   2 +-
 sci-chemistry/nMOLDYN/ChangeLog                    |   2 +-
 sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild        |   2 +-
 sci-chemistry/nmrpipe/ChangeLog                    |   2 +-
 .../nmrpipe/nmrpipe-8.1.2013.218.23.09-r1.ebuild   |   2 +-
 sci-chemistry/nmrview/ChangeLog                    |   2 +-
 sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild      |   2 +-
 sci-chemistry/nwchem/ChangeLog                     |   2 +-
 sci-chemistry/nwchem/nwchem-6.3_p2-r1.ebuild       |   2 +-
 sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild   |   2 +-
 sci-chemistry/openbabel-java/ChangeLog             |   2 +-
 .../openbabel-java/openbabel-java-9999.ebuild      |   2 +-
 sci-chemistry/openbabel-perl/ChangeLog             |   2 +-
 .../openbabel-perl/openbabel-perl-9999.ebuild      |   2 +-
 sci-chemistry/openbabel-python/ChangeLog           |   2 +-
 .../openbabel-python/openbabel-python-9999.ebuild  |   2 +-
 sci-chemistry/openbabel-ruby/ChangeLog             |   2 +-
 .../openbabel-ruby/openbabel-ruby-9999.ebuild      |   2 +-
 sci-chemistry/openbabel/ChangeLog                  |   2 +-
 sci-chemistry/openbabel/openbabel-9999.ebuild      |   2 +-
 sci-chemistry/pales-bin/ChangeLog                  |   2 +-
 .../pales-bin/pales-bin-0_pre140717.ebuild         |   2 +-
 sci-chemistry/panav/ChangeLog                      |   2 +-
 sci-chemistry/panav/panav-0.20130730.ebuild        |   2 +-
 sci-chemistry/pesto/ChangeLog                      |   2 +-
 sci-chemistry/pesto/pesto-9999.ebuild              |   2 +-
 sci-chemistry/phenix-bin/ChangeLog                 |   2 +-
 .../phenix-bin/phenix-bin-1.9.1692.ebuild          |   2 +-
 sci-chemistry/polygon/ChangeLog                    |   2 +-
 sci-chemistry/polygon/polygon-0612.ebuild          |   2 +-
 sci-chemistry/pymol-apbs-plugin/ChangeLog          |   2 +-
 .../pymol-apbs-plugin-9999.ebuild                  |   2 +-
 sci-chemistry/pymol-plugins-ezviz/ChangeLog        |   2 +-
 .../pymol-plugins-ezviz-1.0.2005-r1.ebuild         |   2 +-
 sci-chemistry/pymol-plugins-psico/ChangeLog        |   2 +-
 .../pymol-plugins-psico-9999.ebuild                |   2 +-
 sci-chemistry/pymol/ChangeLog                      |   2 +-
 sci-chemistry/pymol/pymol-9999.ebuild              |   2 +-
 sci-chemistry/pyquante/ChangeLog                   |   2 +-
 sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild    |   2 +-
 sci-chemistry/pyquante/pyquante-1.6.4.ebuild       |   2 +-
 sci-chemistry/redcat/ChangeLog                     |   2 +-
 sci-chemistry/redcat/redcat-3.ebuild               |   2 +-
 sci-chemistry/rosetta-tools/ChangeLog              |   2 +-
 .../rosetta-tools/rosetta-tools-3.0.ebuild         |   2 +-
 sci-chemistry/rosetta/ChangeLog                    |   2 +-
 sci-chemistry/rosetta/rosetta-3.4.ebuild           |   2 +-
 sci-chemistry/shiftx/ChangeLog                     |   2 +-
 sci-chemistry/shiftx/shiftx-1.1.ebuild             |   2 +-
 sci-chemistry/shiftx2/ChangeLog                    |   2 +-
 .../shiftx2/shiftx2-1.07_p20120106.ebuild          |   2 +-
 sci-chemistry/simpson/ChangeLog                    |   2 +-
 sci-chemistry/simpson/simpson-3.0.1.ebuild         |   2 +-
 sci-chemistry/simpson/simpson-3.1.0.ebuild         |   2 +-
 sci-chemistry/simpson/simpson-3.1.2.ebuild         |   2 +-
 sci-chemistry/smmp/ChangeLog                       |   2 +-
 sci-chemistry/smmp/smmp-3.0.5.ebuild               |   2 +-
 sci-chemistry/specView/ChangeLog                   |   2 +-
 sci-chemistry/specView/specView-1.0.2.ebuild       |   2 +-
 sci-chemistry/specView/specView-1.0.3.ebuild       |   2 +-
 sci-chemistry/specView/specView-1.0.3_p2.ebuild    |   2 +-
 sci-chemistry/specView/specView-1.0.4.ebuild       |   2 +-
 sci-chemistry/ssp/ChangeLog                        |   2 +-
 sci-chemistry/ssp/ssp-09.11.ebuild                 |   2 +-
 sci-chemistry/talosn/ChangeLog                     |   2 +-
 .../talosn/talosn-4.01.2013.148.15.55-r3.ebuild    |   2 +-
 sci-chemistry/trajng/ChangeLog                     |   2 +-
 sci-chemistry/trajng/trajng-0.6.1.ebuild           |   2 +-
 sci-chemistry/unio/ChangeLog                       |   2 +-
 sci-chemistry/unio/unio-2.0.3-r1.ebuild            |   2 +-
 sci-chemistry/usf-tools/ChangeLog                  |   2 +-
 sci-chemistry/usf-tools/usf-tools-9999.ebuild      |   2 +-
 sci-chemistry/votca-csg/ChangeLog                  |   2 +-
 sci-chemistry/votca-csg/votca-csg-9999.ebuild      |   2 +-
 sci-chemistry/votca-csgapps/ChangeLog              |   2 +-
 .../votca-csgapps/votca-csgapps-9999.ebuild        |   2 +-
 sci-chemistry/xplor-nih/ChangeLog                  |   2 +-
 sci-chemistry/xplor-nih/xplor-nih-2.38.ebuild      |   2 +-
 sci-electronics/minipro/ChangeLog                  |   2 +-
 sci-electronics/minipro/minipro-9999.ebuild        |   2 +-
 sci-electronics/player/ChangeLog                   |   2 +-
 sci-electronics/player/player-2.0.4.ebuild         |   2 +-
 sci-electronics/stage/ChangeLog                    |   2 +-
 sci-electronics/stage/stage-2.0.3.ebuild           |   2 +-
 sci-electronics/tnt/ChangeLog                      |   2 +-
 sci-electronics/tnt/tnt-1.2.2.ebuild               |   2 +-
 sci-geosciences/pydap/ChangeLog                    |   2 +-
 sci-geosciences/pydap/pydap-3.1.1.ebuild           |   2 +-
 sci-geosciences/pydap/pydap-3.1.ebuild             |   2 +-
 sci-geosciences/pydap_handlers_cdms/ChangeLog      |   2 +-
 .../pydap_handlers_cdms-0.2.0.1.ebuild             |   2 +-
 sci-geosciences/pydap_handlers_csv/ChangeLog       |   2 +-
 .../pydap_handlers_csv-0.1.1.ebuild                |   2 +-
 sci-geosciences/pydap_handlers_hdf5/ChangeLog      |   2 +-
 .../pydap_handlers_hdf5-0.1.7.ebuild               |   2 +-
 sci-geosciences/pydap_handlers_nca/ChangeLog       |   2 +-
 .../pydap_handlers_nca-0.1.3.ebuild                |   2 +-
 sci-geosciences/pydap_handlers_netcdf/ChangeLog    |   2 +-
 .../pydap_handlers_netcdf-0.6.4.ebuild             |   2 +-
 sci-geosciences/pydap_handlers_proxy/ChangeLog     |   2 +-
 .../pydap_handlers_proxy-0.1.1.ebuild              |   2 +-
 sci-geosciences/pydap_handlers_sql/ChangeLog       |   2 +-
 .../pydap_handlers_sql-0.3.0.ebuild                |   2 +-
 sci-geosciences/pydap_handlers_sqlite/ChangeLog    |   2 +-
 .../pydap_handlers_sqlite-0.1.0.ebuild             |   2 +-
 sci-geosciences/pydap_responses_kml/ChangeLog      |   2 +-
 .../pydap_responses_kml-0.4.6.ebuild               |   2 +-
 sci-geosciences/pydap_responses_matlab/ChangeLog   |   2 +-
 .../pydap_responses_matlab-0.2.1.ebuild            |   2 +-
 sci-geosciences/pydap_responses_netcdf/ChangeLog   |   2 +-
 .../pydap_responses_netcdf-0.1.4.1.ebuild          |   2 +-
 sci-geosciences/pydap_responses_wms/ChangeLog      |   2 +-
 .../pydap_responses_wms-0.5.4.ebuild               |   2 +-
 sci-geosciences/pydap_responses_xls/ChangeLog      |   2 +-
 .../pydap_responses_xls-0.1.2.ebuild               |   2 +-
 sci-geosciences/qgis/ChangeLog                     |   2 +-
 sci-geosciences/qgis/qgis-9999.ebuild              |   2 +-
 sci-libs/Cgraph/Cgraph-2.04.ebuild                 |   2 +-
 sci-libs/Cgraph/ChangeLog                          |   2 +-
 sci-libs/acml/ChangeLog                            |   2 +-
 sci-libs/acml/acml-5.3.1.ebuild                    |   2 +-
 sci-libs/acml/acml-6.1.0.31.ebuild                 |   2 +-
 sci-libs/amber99sb_phipsi/ChangeLog                |   2 +-
 .../amber99sb_phipsi-0_pre130901.ebuild            |   2 +-
 sci-libs/amber99sbnmr-ildn/ChangeLog               |   2 +-
 .../amber99sbnmr-ildn-0_pre130901.ebuild           |   2 +-
 sci-libs/amber99sbnmr/ChangeLog                    |   2 +-
 .../amber99sbnmr/amber99sbnmr-0_pre130901.ebuild   |   2 +-
 sci-libs/amdlibm/ChangeLog                         |   2 +-
 sci-libs/amdlibm/amdlibm-3.1.ebuild                |   2 +-
 sci-libs/armadillo/ChangeLog                       |   2 +-
 sci-libs/armadillo/armadillo-4.650.4.ebuild        |   2 +-
 sci-libs/armadillo/armadillo-5.100.2.ebuild        |   2 +-
 sci-libs/armadillo/armadillo-5.200.2-r1.ebuild     |   2 +-
 sci-libs/arrayfire/ChangeLog                       |   5 +-
 sci-libs/arrayfire/arrayfire-0.9999.ebuild         |   2 +-
 sci-libs/arrayfire/arrayfire-3.0_beta.ebuild       |   2 +-
 sci-libs/arrayfire/arrayfire-9999.ebuild           |   3 +-
 sci-libs/asl/ChangeLog                             |   2 +-
 sci-libs/asl/asl-9999.ebuild                       |   2 +-
 sci-libs/atlas/ChangeLog                           |   2 +-
 sci-libs/atlas/atlas-3.10.1-r1.ebuild              |   2 +-
 sci-libs/atlas/atlas-3.10.1-r2.ebuild              |   2 +-
 sci-libs/bigdft-abi/ChangeLog                      |   2 +-
 sci-libs/bigdft-abi/bigdft-abi-1.0.4-r3.ebuild     |   2 +-
 sci-libs/blas-reference/ChangeLog                  |   2 +-
 .../blas-reference/blas-reference-20131116.ebuild  |   2 +-
 .../blas-reference/blas-reference-99999999.ebuild  |   2 +-
 sci-libs/blastdb/ChangeLog                         |   2 +-
 sci-libs/blastdb/blastdb-9999.ebuild               |   2 +-
 sci-libs/bloom/ChangeLog                           |   2 +-
 sci-libs/bloom/bloom-9999.ebuild                   |   2 +-
 sci-libs/calculix-ccx/ChangeLog                    |   2 +-
 sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild   |   2 +-
 sci-libs/calculix-ccx/calculix-ccx-2.8_p2.ebuild   |   2 +-
 sci-libs/calculix-cgx/ChangeLog                    |   2 +-
 sci-libs/calculix-cgx/calculix-cgx-2.7-r1.ebuild   |   2 +-
 sci-libs/cblas-reference/ChangeLog                 |   2 +-
 .../cblas-reference-20110218-r1.ebuild             |   2 +-
 .../cblas-reference-20110218.ebuild                |   2 +-
 sci-libs/ccif/ChangeLog                            |   2 +-
 sci-libs/ccif/ccif-0.3.20111209.ebuild             |   2 +-
 sci-libs/cgnstools/ChangeLog                       |   2 +-
 sci-libs/cgnstools/cgnstools-2.5.4-r1.ebuild       |   2 +-
 sci-libs/clblas/ChangeLog                          |   2 +-
 sci-libs/clblas/clblas-2.4-r1.ebuild               |   2 +-
 sci-libs/clblas/clblas-9999.ebuild                 |   2 +-
 sci-libs/clfft/ChangeLog                           |   2 +-
 sci-libs/clfft/clfft-0.9999.ebuild                 |   2 +-
 sci-libs/clfft/clfft-2.4-r1.ebuild                 |   2 +-
 sci-libs/clfft/clfft-9999.ebuild                   |   2 +-
 sci-libs/clrng/ChangeLog                           |   2 +-
 sci-libs/clrng/clrng-9999.ebuild                   |   2 +-
 sci-libs/cs-rosetta-db/ChangeLog                   |   2 +-
 .../cs-rosetta-db-1.01.2009.1109.11.ebuild         |   2 +-
 sci-libs/dcmtk/ChangeLog                           |   2 +-
 sci-libs/dcmtk/dcmtk-3.6.0.ebuild                  |   2 +-
 sci-libs/dealii/ChangeLog                          |   2 +-
 sci-libs/dealii/dealii-8.1.0-r2.ebuild             |   2 +-
 sci-libs/dealii/dealii-8.2.1-r1.ebuild             |   2 +-
 sci-libs/dealii/dealii-8.3.0.ebuild                |   2 +-
 sci-libs/dealii/dealii-9999.ebuild                 |   2 +-
 sci-libs/driftwood/ChangeLog                       |   2 +-
 sci-libs/driftwood/driftwood-0.87.ebuild           |   2 +-
 sci-libs/elmer-eio/ChangeLog                       |   2 +-
 sci-libs/elmer-eio/elmer-eio-6.0_p4651.ebuild      |   2 +-
 sci-libs/elmer-eio/elmer-eio-9999.ebuild           |   2 +-
 sci-libs/elmer-hutiter/ChangeLog                   |   2 +-
 .../elmer-hutiter/elmer-hutiter-6.0_p4651.ebuild   |   2 +-
 sci-libs/elmer-hutiter/elmer-hutiter-9999.ebuild   |   2 +-
 sci-libs/etsf_io/ChangeLog                         |   2 +-
 sci-libs/etsf_io/etsf_io-1.0.3-r2.ebuild           |   2 +-
 sci-libs/etsf_io/etsf_io-1.0.4-r1.ebuild           |   2 +-
 sci-libs/factory/ChangeLog                         |   2 +-
 sci-libs/factory/factory-3.1.1-r2.ebuild           |   2 +-
 sci-libs/fdlibm/ChangeLog                          |   2 +-
 sci-libs/fdlibm/fdlibm-5.3.ebuild                  |   2 +-
 sci-libs/fftw/ChangeLog                            |   2 +-
 sci-libs/fftw/fftw-3.3.4-r1.ebuild                 |   2 +-
 sci-libs/fftw/fftw-9999.ebuild                     |   2 +-
 sci-libs/fgsl/ChangeLog                            |   2 +-
 sci-libs/fgsl/fgsl-0.9.3.ebuild                    |   2 +-
 sci-libs/fgsl/fgsl-0.9.4.ebuild                    |   2 +-
 sci-libs/fox/ChangeLog                             |   2 +-
 sci-libs/fox/fox-4.1.2-r2.ebuild                   |   2 +-
 sci-libs/framewave/ChangeLog                       |   2 +-
 sci-libs/framewave/framewave-1.3.1.ebuild          |   2 +-
 sci-libs/geom/ChangeLog                            |   2 +-
 sci-libs/geom/geom-5.1.2.7.ebuild                  |   2 +-
 sci-libs/ghmm/ChangeLog                            |   2 +-
 sci-libs/ghmm/ghmm-9999.ebuild                     |   2 +-
 sci-libs/givaro/ChangeLog                          |   2 +-
 sci-libs/givaro/givaro-3.2.13.ebuild               |   2 +-
 sci-libs/givaro/givaro-3.3.0.ebuild                |   2 +-
 sci-libs/givaro/givaro-3.8.0.ebuild                |   2 +-
 sci-libs/gmsh/ChangeLog                            |   2 +-
 sci-libs/gmsh/gmsh-2.8.5.ebuild                    |   2 +-
 sci-libs/gotoblas2/ChangeLog                       |   2 +-
 sci-libs/gotoblas2/gotoblas2-1.13.ebuild           |   2 +-
 sci-libs/gsl/ChangeLog                             |   2 +-
 sci-libs/gsl/gsl-1.16-r2.ebuild                    |   2 +-
 sci-libs/iml/ChangeLog                             |   2 +-
 sci-libs/iml/iml-1.0.3-r2.ebuild                   |   2 +-
 sci-libs/iml/iml-1.0.4.ebuild                      |   2 +-
 sci-libs/itk/ChangeLog                             |   2 +-
 sci-libs/itk/itk-4.4.2-r1.ebuild                   |   2 +-
 sci-libs/itk/itk-4.4.2.ebuild                      |   2 +-
 sci-libs/itk/itk-4.5.1.ebuild                      |   2 +-
 sci-libs/jhdf5/ChangeLog                           |   2 +-
 sci-libs/jhdf5/jhdf5-14.12.1.ebuild                |   2 +-
 sci-libs/k3match/ChangeLog                         |   2 +-
 sci-libs/k3match/k3match-1.1.ebuild                |   2 +-
 sci-libs/lapack-reference/ChangeLog                |   2 +-
 .../lapack-reference/lapack-reference-9999.ebuild  |   2 +-
 sci-libs/lapacke-reference/ChangeLog               |   2 +-
 .../lapacke-reference-9999.ebuild                  |   2 +-
 sci-libs/lapackpp/ChangeLog                        |   2 +-
 sci-libs/lapackpp/lapackpp-2.5.4.ebuild            |   2 +-
 sci-libs/libcgnsoo/ChangeLog                       |   2 +-
 sci-libs/libcgnsoo/libcgnsoo-1728.ebuild           |   2 +-
 sci-libs/libfac/ChangeLog                          |   2 +-
 sci-libs/libfac/libfac-3.1.1.ebuild                |   2 +-
 sci-libs/libgeodecomp/ChangeLog                    |   2 +-
 sci-libs/libgeodecomp/libgeodecomp-9999.ebuild     |   2 +-
 sci-libs/libmatheval/ChangeLog                     |   2 +-
 sci-libs/libmatheval/libmatheval-1.1.10.ebuild     |   2 +-
 sci-libs/libmaus/ChangeLog                         |   2 +-
 sci-libs/libmaus/libmaus-0.0.185.ebuild            |   2 +-
 sci-libs/libsc/ChangeLog                           |   2 +-
 sci-libs/libsc/libsc-1.0.ebuild                    |   2 +-
 sci-libs/libspatialindex/ChangeLog                 |   2 +-
 .../libspatialindex/libspatialindex-1.8.5.ebuild   |   2 +-
 sci-libs/libsufr/ChangeLog                         |   2 +-
 sci-libs/libsufr/libsufr-0.5.4.ebuild              |   2 +-
 sci-libs/libsufr/libsufr-0.6.3.ebuild              |   2 +-
 sci-libs/libsufr/libsufr-0.6.4.ebuild              |   2 +-
 sci-libs/libxc/ChangeLog                           |   2 +-
 sci-libs/libxc/libxc-2.1.2.ebuild                  |   2 +-
 sci-libs/libxc/libxc-2.2.2.ebuild                  |   2 +-
 sci-libs/lwpr/ChangeLog                            |   2 +-
 sci-libs/lwpr/lwpr-1.2.5.ebuild                    |   2 +-
 sci-libs/matc/ChangeLog                            |   2 +-
 sci-libs/matc/matc-6.0_p4651.ebuild                |   2 +-
 sci-libs/matc/matc-8.0.ebuild                      |   2 +-
 sci-libs/matc/matc-9999.ebuild                     |   2 +-
 sci-libs/med/ChangeLog                             |   2 +-
 sci-libs/med/med-2.3.6.ebuild                      |   2 +-
 sci-libs/mesquite/ChangeLog                        |   2 +-
 sci-libs/mesquite/mesquite-2.1.2.ebuild            |   2 +-
 sci-libs/mkl/ChangeLog                             |   2 +-
 sci-libs/mkl/mkl-11.1.0.080-r1.ebuild              |   2 +-
 sci-libs/mkl/mkl-11.1.1.106.ebuild                 |   2 +-
 sci-libs/mkl/mkl-11.1.2.144.ebuild                 |   2 +-
 sci-libs/mkl/mkl-11.1.3.174.ebuild                 |   2 +-
 sci-libs/mkl/mkl-11.2.0.090.ebuild                 |   2 +-
 sci-libs/mkl/mkl-11.2.1.133.ebuild                 |   2 +-
 sci-libs/mkl/mkl-11.2.2.164.ebuild                 |   2 +-
 sci-libs/mkl/mkl-11.2.3.187.ebuild                 |   2 +-
 sci-libs/mlpack/ChangeLog                          |   2 +-
 sci-libs/mlpack/mlpack-1.0.8.ebuild                |   2 +-
 sci-libs/modglue/ChangeLog                         |   2 +-
 sci-libs/modglue/modglue-1.19.ebuild               |   2 +-
 sci-libs/mpiblacs/ChangeLog                        |   2 +-
 sci-libs/mpiblacs/mpiblacs-1.1-r1.ebuild           |   2 +-
 sci-libs/msms/ChangeLog                            |   2 +-
 sci-libs/msms/msms-1.5.6.ebuild                    |   2 +-
 sci-libs/nexus/nexus-4.3.1.ebuild                  |   2 +-
 sci-libs/ni-visa/ChangeLog                         |   2 +-
 sci-libs/ni-visa/ni-visa-0.0.1.ebuild              |   2 +-
 sci-libs/nibabel/ChangeLog                         |   2 +-
 sci-libs/nibabel/nibabel-1.3.0.ebuild              |   2 +-
 sci-libs/nibabel/nibabel-9999.ebuild               |   2 +-
 sci-libs/nipy/ChangeLog                            |   2 +-
 sci-libs/nipy/nipy-0.3.0.ebuild                    |   2 +-
 sci-libs/nipy/nipy-9999.ebuild                     |   2 +-
 sci-libs/nipype/ChangeLog                          |   2 +-
 sci-libs/nipype/nipype-9999.ebuild                 |   2 +-
 sci-libs/o2scl/ChangeLog                           |   2 +-
 sci-libs/o2scl/o2scl-0.915.ebuild                  |   2 +-
 sci-libs/oasa/ChangeLog                            |   2 +-
 sci-libs/oasa/oasa-0.13.1.ebuild                   |   2 +-
 sci-libs/omalloc/ChangeLog                         |   2 +-
 sci-libs/omalloc/omalloc-0.9.6.ebuild              |   2 +-
 sci-libs/openblas/ChangeLog                        |   2 +-
 sci-libs/openblas/openblas-0.2.11.ebuild           |   2 +-
 sci-libs/openblas/openblas-0.2.8.ebuild            |   2 +-
 sci-libs/openblas/openblas-9999.ebuild             |   2 +-
 sci-libs/openlibm/ChangeLog                        |   2 +-
 sci-libs/openlibm/openlibm-9999.ebuild             |   2 +-
 sci-libs/optpp/ChangeLog                           |   2 +-
 sci-libs/optpp/optpp-2.4.ebuild                    |   2 +-
 sci-libs/p4est/ChangeLog                           |   2 +-
 sci-libs/p4est/p4est-1.0.ebuild                    |   2 +-
 sci-libs/pagmo/ChangeLog                           |   2 +-
 sci-libs/pagmo/pagmo-9999.ebuild                   |   2 +-
 sci-libs/parmetis/ChangeLog                        |   2 +-
 sci-libs/parmetis/parmetis-4.0.3.ebuild            |   2 +-
 sci-libs/pastix/ChangeLog                          |   2 +-
 sci-libs/pastix/pastix-5.2.2_p9.ebuild             |   2 +-
 sci-libs/pfft/ChangeLog                            |   2 +-
 sci-libs/pfft/pfft-1.0.7_alpha.ebuild              |   2 +-
 sci-libs/pfft/pfft-9999.ebuild                     |   2 +-
 sci-libs/pg2plplot/ChangeLog                       |   2 +-
 sci-libs/pg2plplot/pg2plplot-0.2.0.ebuild          |   2 +-
 sci-libs/pg2plplot/pg2plplot-0.3.1.ebuild          |   2 +-
 sci-libs/plasma/ChangeLog                          |   2 +-
 sci-libs/plasma/plasma-2.5.2.ebuild                |   2 +-
 sci-libs/plasma/plasma-2.6.0.ebuild                |   2 +-
 sci-libs/pmx/ChangeLog                             |   2 +-
 sci-libs/pmx/pmx-9999.ebuild                       |   2 +-
 sci-libs/pydicom/ChangeLog                         |   2 +-
 sci-libs/pydicom/pydicom-0.9.8.ebuild              |   2 +-
 sci-libs/pydicom/pydicom-9999.ebuild               |   2 +-
 sci-libs/scalapack/ChangeLog                       |   2 +-
 sci-libs/scalapack/scalapack-2.0.2-r1.ebuild       |   2 +-
 sci-libs/scikits_image/ChangeLog                   |   2 +-
 sci-libs/scikits_image/scikits_image-9999.ebuild   |   2 +-
 sci-libs/spglib/ChangeLog                          |   2 +-
 sci-libs/spglib/spglib-1.6.0.ebuild                |   2 +-
 sci-libs/starparse/ChangeLog                       |   2 +-
 sci-libs/starparse/starparse-9999.ebuild           |   2 +-
 sci-libs/superlu_dist/ChangeLog                    |   2 +-
 sci-libs/superlu_dist/superlu_dist-3.3.ebuild      |   2 +-
 sci-libs/superlu_mt/ChangeLog                      |   2 +-
 sci-libs/superlu_mt/superlu_mt-2.1.ebuild          |   2 +-
 sci-libs/symmetrica/ChangeLog                      |   2 +-
 sci-libs/symmetrica/symmetrica-2.0-r1.ebuild       |   2 +-
 sci-libs/symmetrica/symmetrica-2.0.ebuild          |   2 +-
 sci-libs/tmglib/ChangeLog                          |   2 +-
 sci-libs/tmglib/tmglib-3.4.2.ebuild                |   2 +-
 sci-libs/tmglib/tmglib-3.5.0.ebuild                |   2 +-
 sci-libs/trilinos/ChangeLog                        |   2 +-
 sci-libs/trilinos/trilinos-11.10.2.ebuild          |   2 +-
 sci-libs/trilinos/trilinos-11.12.1-r1.ebuild       |   2 +-
 sci-libs/trilinos/trilinos-11.14.1-r1.ebuild       |   2 +-
 sci-libs/trilinos/trilinos-12.0.1.ebuild           |   2 +-
 sci-libs/votca-tools/ChangeLog                     |   2 +-
 sci-libs/votca-tools/votca-tools-9999.ebuild       |   2 +-
 sci-libs/vxl/ChangeLog                             |   2 +-
 sci-libs/vxl/vxl-9999.ebuild                       |   2 +-
 sci-libs/wannier90/ChangeLog                       |   2 +-
 sci-libs/wannier90/wannier90-1.2-r3.ebuild         |   2 +-
 sci-libs/wannier90/wannier90-2.0.0.ebuild          |   2 +-
 sci-libs/wannier90/wannier90-2.0.1.ebuild          |   2 +-
 sci-libs/xblas/ChangeLog                           |   2 +-
 sci-libs/xblas/xblas-1.0.248-r1.ebuild             |   2 +-
 sci-libs/xblas/xblas-1.0.248.ebuild                |   2 +-
 sci-libs/xraylib/ChangeLog                         |   2 +-
 sci-libs/xraylib/xraylib-2.16.0.ebuild             |   2 +-
 sci-libs/xraylib/xraylib-3.1.0.ebuild              |   2 +-
 sci-libs/zarja/ChangeLog                           |   2 +-
 sci-libs/zarja/zarja-1.1.1.ebuild                  |   2 +-
 sci-mathematics/Macaulay2/ChangeLog                |   2 +-
 sci-mathematics/Macaulay2/Macaulay2-9999.ebuild    |   2 +-
 sci-mathematics/Oid/ChangeLog                      |   2 +-
 sci-mathematics/Oid/Oid-4.0.ebuild                 |   2 +-
 sci-mathematics/acl2/ChangeLog                     |   2 +-
 sci-mathematics/acl2/acl2-7.1.ebuild               |   2 +-
 sci-mathematics/alt-ergo/ChangeLog                 |   2 +-
 sci-mathematics/alt-ergo/alt-ergo-0.95.2.ebuild    |   2 +-
 sci-mathematics/apron/ChangeLog                    |   2 +-
 sci-mathematics/apron/apron-0.9.10-r1.ebuild       |   2 +-
 sci-mathematics/apron/apron-0.9.10.ebuild          |   2 +-
 sci-mathematics/aribas/ChangeLog                   |   2 +-
 sci-mathematics/aribas/aribas-1.63.ebuild          |   2 +-
 sci-mathematics/axiom/ChangeLog                    |   2 +-
 sci-mathematics/axiom/axiom-201009.ebuild          |   2 +-
 sci-mathematics/burrtools/ChangeLog                |   2 +-
 .../burrtools/burrtools-0.5.2-r1.ebuild            |   2 +-
 sci-mathematics/cadabra/ChangeLog                  |   2 +-
 sci-mathematics/cadabra/cadabra-1.33.ebuild        |   2 +-
 sci-mathematics/cadabra/cadabra-1.39.ebuild        |   2 +-
 sci-mathematics/cdfplayer/ChangeLog                |   2 +-
 sci-mathematics/cdfplayer/cdfplayer-10.0.2.ebuild  |   2 +-
 sci-mathematics/cipi/ChangeLog                     |   2 +-
 sci-mathematics/cipi/cipi-1.0.ebuild               |   2 +-
 sci-mathematics/dolfin/ChangeLog                   |   2 +-
 sci-mathematics/dolfin/dolfin-0.9.9.ebuild         |   2 +-
 sci-mathematics/dsfmt/ChangeLog                    |   2 +-
 sci-mathematics/dsfmt/dsfmt-2.2.ebuild             |   2 +-
 sci-mathematics/flocq/ChangeLog                    |   2 +-
 sci-mathematics/flocq/flocq-2.3.0.ebuild           |   2 +-
 sci-mathematics/frama-c/ChangeLog                  |   2 +-
 sci-mathematics/frama-c/frama-c-20140301.ebuild    |   2 +-
 sci-mathematics/freefem++/ChangeLog                |   2 +-
 sci-mathematics/freefem++/freefem++-3.8.ebuild     |   2 +-
 sci-mathematics/gambit/ChangeLog                   |   2 +-
 sci-mathematics/gambit/gambit-0.2010.09.01.ebuild  |   2 +-
 sci-mathematics/gap-guava/ChangeLog                |   2 +-
 sci-mathematics/gap-guava/gap-guava-3.10-r1.ebuild |   2 +-
 sci-mathematics/gap/ChangeLog                      |   2 +-
 sci-mathematics/gap/gap-4.4.12.ebuild              |   2 +-
 sci-mathematics/gappa/ChangeLog                    |   2 +-
 sci-mathematics/gappa/gappa-1.1.1.ebuild           |   2 +-
 sci-mathematics/gappalib-coq/ChangeLog             |   2 +-
 .../gappalib-coq/gappalib-coq-1.0.0.ebuild         |   2 +-
 sci-mathematics/giac/ChangeLog                     |   2 +-
 sci-mathematics/giac/giac-1.1.0.ebuild             |   2 +-
 sci-mathematics/htk/htk-3.4.1.ebuild               |   2 +-
 sci-mathematics/kash-bin/ChangeLog                 |   2 +-
 sci-mathematics/kash-bin/kash-bin-3.ebuild         |   2 +-
 sci-mathematics/kayali/ChangeLog                   |   2 +-
 sci-mathematics/kayali/kayali-0.3.2.ebuild         |   2 +-
 sci-mathematics/lattE-macchiato/ChangeLog          |   2 +-
 .../lattE-macchiato/lattE-macchiato-0.9.3.ebuild   |   2 +-
 sci-mathematics/libsfmt/ChangeLog                  |   2 +-
 sci-mathematics/libsfmt/libsfmt-1.3.0.ebuild       |   2 +-
 sci-mathematics/lie/ChangeLog                      |   2 +-
 sci-mathematics/lie/lie-2.2.2.ebuild               |   2 +-
 sci-mathematics/ltl2ba/ChangeLog                   |   2 +-
 sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild           |   2 +-
 sci-mathematics/mdp/ChangeLog                      |   2 +-
 sci-mathematics/mdp/mdp-3.3.ebuild                 |   2 +-
 sci-mathematics/mdp/mdp-9999.ebuild                |   2 +-
 sci-mathematics/netgen/ChangeLog                   |   2 +-
 sci-mathematics/netgen/netgen-4.9.13.ebuild        |   2 +-
 sci-mathematics/netgen/netgen-5.0.0.ebuild         |   2 +-
 sci-mathematics/open-axiom/ChangeLog               |   2 +-
 sci-mathematics/open-axiom/open-axiom-1.3.0.ebuild |   2 +-
 sci-mathematics/open-axiom/open-axiom-1.4.2.ebuild |   2 +-
 sci-mathematics/pest/ChangeLog                     |   2 +-
 sci-mathematics/pest/pest-12.2.ebuild              |   2 +-
 sci-mathematics/petsc/ChangeLog                    |   2 +-
 sci-mathematics/petsc/petsc-3.4.2.ebuild           |   2 +-
 sci-mathematics/petsc/petsc-3.5.3.ebuild           |   2 +-
 sci-mathematics/petsc/petsc-3.6.0.ebuild           |   2 +-
 sci-mathematics/pff/ChangeLog                      |   2 +-
 sci-mathematics/pff/pff-8.4.ebuild                 |   2 +-
 sci-mathematics/pulp/ChangeLog                     |   2 +-
 sci-mathematics/pulp/pulp-1.5.6.ebuild             |   2 +-
 sci-mathematics/scilab/ChangeLog                   |   2 +-
 sci-mathematics/scilab/scilab-5.5.2.ebuild         |   2 +-
 sci-mathematics/surfer/ChangeLog                   |   2 +-
 sci-mathematics/surfer/surfer-0.0.197.ebuild       |   2 +-
 sci-mathematics/ufc/ChangeLog                      |   2 +-
 sci-mathematics/ufc/ufc-1.4.2.ebuild               |   2 +-
 sci-mathematics/ufc/ufc-2.3.0.ebuild               |   2 +-
 sci-mathematics/why/ChangeLog                      |   2 +-
 sci-mathematics/why/why-2.34.ebuild                |   2 +-
 sci-mathematics/why3/ChangeLog                     |   2 +-
 sci-mathematics/why3/why3-0.83.ebuild              |   2 +-
 sci-mathematics/yorick/ChangeLog                   |   2 +-
 sci-mathematics/yorick/yorick-2.1.06.ebuild        |   2 +-
 sci-mathematics/z3/ChangeLog                       |   2 +-
 sci-mathematics/z3/z3-4.3.1.ebuild                 |   2 +-
 sci-mathematics/z3/z3-9999.ebuild                  |   2 +-
 sci-misc/elmer-elmergrid/ChangeLog                 |   2 +-
 .../elmer-elmergrid-6.0_p4651.ebuild               |   2 +-
 .../elmer-elmergrid/elmer-elmergrid-9999.ebuild    |   2 +-
 sci-misc/elmer-fem/ChangeLog                       |   2 +-
 sci-misc/elmer-fem/elmer-fem-6.0_p4651.ebuild      |   2 +-
 sci-misc/elmer-fem/elmer-fem-9999.ebuild           |   2 +-
 sci-misc/elmer-front/ChangeLog                     |   2 +-
 sci-misc/elmer-front/elmer-front-6.0_p4651.ebuild  |   2 +-
 sci-misc/elmer-front/elmer-front-9999.ebuild       |   2 +-
 sci-misc/elmer-gui/ChangeLog                       |   2 +-
 sci-misc/elmer-gui/elmer-gui-9999.ebuild           |   2 +-
 sci-misc/elmer-meshgen2d/ChangeLog                 |   2 +-
 .../elmer-meshgen2d-6.0_p4651.ebuild               |   2 +-
 .../elmer-meshgen2d/elmer-meshgen2d-9999.ebuild    |   2 +-
 sci-misc/elmer-meta/ChangeLog                      |   2 +-
 sci-misc/elmer-meta/elmer-meta-6.0_p4651.ebuild    |   2 +-
 sci-misc/elmer-meta/elmer-meta-9999.ebuild         |   2 +-
 sci-misc/elmer-post/ChangeLog                      |   2 +-
 sci-misc/elmer-post/elmer-post-6.0_p4651.ebuild    |   2 +-
 sci-misc/elmer-post/elmer-post-9999.ebuild         |   2 +-
 sci-misc/finomaton/ChangeLog                       |   2 +-
 sci-misc/finomaton/finomaton-1.0.ebuild            |   2 +-
 sci-misc/fitscut/ChangeLog                         |   2 +-
 sci-misc/fitscut/fitscut-1.4.4.ebuild              |   2 +-
 sci-misc/foma/ChangeLog                            |   2 +-
 sci-misc/foma/foma-0.9.14_alpha.ebuild             |   2 +-
 sci-misc/foma/foma-0.9.16_alpha.ebuild             |   2 +-
 sci-misc/hfst/ChangeLog                            |   2 +-
 sci-misc/hfst/hfst-2.2.ebuild                      |   2 +-
 sci-misc/hfst/hfst-3.0.2.ebuild                    |   2 +-
 sci-misc/hfst/hfst-3.3.12.ebuild                   |   2 +-
 sci-misc/irstlm/ChangeLog                          |   2 +-
 sci-misc/irstlm/irstlm-5.80.08.ebuild              |   2 +-
 sci-misc/jwnl/ChangeLog                            |   2 +-
 sci-misc/jwnl/jwnl-1.3_rc3.ebuild                  |   2 +-
 sci-misc/kaldi/ChangeLog                           |   2 +-
 sci-misc/kaldi/kaldi-0_p20150709.ebuild            |   2 +-
 sci-misc/kotus-sanalista/ChangeLog                 |   2 +-
 .../kotus-sanalista/kotus-sanalista-1-r1.ebuild    |   2 +-
 sci-misc/mitlm/ChangeLog                           |   2 +-
 sci-misc/mitlm/mitlm-0.4.1.ebuild                  |   2 +-
 sci-misc/nltk/ChangeLog                            |   2 +-
 sci-misc/nltk/nltk-2.0.4.ebuild                    |   2 +-
 sci-misc/omorfi/ChangeLog                          |   2 +-
 sci-misc/omorfi/omorfi-0.1_alpha.ebuild            |   2 +-
 sci-misc/openfst/ChangeLog                         |   2 +-
 sci-misc/openfst/openfst-1.3.4.ebuild              |   2 +-
 sci-misc/openfst/openfst-1.4.1.ebuild              |   2 +-
 sci-misc/opennlp-maxent/ChangeLog                  |   2 +-
 .../opennlp-maxent/opennlp-maxent-2.4.0.ebuild     |   2 +-
 sci-misc/opennlp-tools/ChangeLog                   |   2 +-
 sci-misc/opennlp-tools/opennlp-tools-1.3.0.ebuild  |   2 +-
 sci-misc/praat/ChangeLog                           |   2 +-
 sci-misc/praat/praat-5.1.00.ebuild                 |   2 +-
 sci-misc/praat/praat-5.1.15.ebuild                 |   2 +-
 sci-misc/pywordnet/ChangeLog                       |   2 +-
 sci-misc/pywordnet/pywordnet-2.0.1.ebuild          |   2 +-
 sci-misc/salome-component/ChangeLog                |   2 +-
 .../salome-component/salome-component-5.1.3.ebuild |   2 +-
 .../salome-component/salome-component-5.1.4.ebuild |   2 +-
 sci-misc/salome-geom/ChangeLog                     |   2 +-
 sci-misc/salome-geom/salome-geom-5.1.3.ebuild      |   2 +-
 sci-misc/salome-geom/salome-geom-5.1.4.ebuild      |   2 +-
 sci-misc/salome-gui/ChangeLog                      |   2 +-
 sci-misc/salome-gui/salome-gui-5.1.3.ebuild        |   2 +-
 sci-misc/salome-gui/salome-gui-5.1.4.ebuild        |   2 +-
 sci-misc/salome-kernel/ChangeLog                   |   2 +-
 sci-misc/salome-kernel/salome-kernel-5.1.3.ebuild  |   2 +-
 sci-misc/salome-kernel/salome-kernel-5.1.4.ebuild  |   2 +-
 sci-misc/salome-med/ChangeLog                      |   2 +-
 sci-misc/salome-med/salome-med-5.1.3.ebuild        |   2 +-
 sci-misc/salome-med/salome-med-5.1.4.ebuild        |   2 +-
 sci-misc/salome-meta/ChangeLog                     |   2 +-
 sci-misc/salome-meta/salome-meta-5.1.3.ebuild      |   2 +-
 sci-misc/salome-meta/salome-meta-5.1.4.ebuild      |   2 +-
 sci-misc/salome-pycalculator/ChangeLog             |   2 +-
 .../salome-pycalculator-5.1.3.ebuild               |   2 +-
 .../salome-pycalculator-5.1.4.ebuild               |   2 +-
 sci-misc/salome-smesh/ChangeLog                    |   2 +-
 sci-misc/salome-smesh/salome-smesh-5.1.3.ebuild    |   2 +-
 sci-misc/salome-smesh/salome-smesh-5.1.4.ebuild    |   2 +-
 sci-misc/salome-visu/ChangeLog                     |   2 +-
 sci-misc/salome-visu/salome-visu-5.1.3.ebuild      |   2 +-
 sci-misc/salome-visu/salome-visu-5.1.4.ebuild      |   2 +-
 sci-misc/salome-yacs/ChangeLog                     |   2 +-
 sci-misc/salome-yacs/salome-yacs-5.1.3.ebuild      |   2 +-
 sci-misc/salome-yacs/salome-yacs-5.1.4.ebuild      |   2 +-
 sci-misc/sfst/ChangeLog                            |   2 +-
 sci-misc/sfst/sfst-1.4.2.ebuild                    |   2 +-
 sci-misc/sfst/sfst-1.4.6g.ebuild                   |   2 +-
 sci-misc/simx/ChangeLog                            |   2 +-
 sci-misc/simx/simx-0.2.ebuild                      |   2 +-
 sci-misc/simx/simx-9999.ebuild                     |   2 +-
 sci-misc/stanford-parser/ChangeLog                 |   2 +-
 .../stanford-parser/stanford-parser-1.6.ebuild     |   2 +-
 sci-misc/stanford-tagger/ChangeLog                 |   2 +-
 .../stanford-tagger-20060521.ebuild                |   2 +-
 sci-physics/abinit/ChangeLog                       |   2 +-
 sci-physics/abinit/abinit-7.10.4.ebuild            |   2 +-
 sci-physics/abinit/abinit-7.4.2-r1.ebuild          |   2 +-
 sci-physics/abinit/abinit-7.6.4-r1.ebuild          |   2 +-
 sci-physics/atompaw/ChangeLog                      |   2 +-
 sci-physics/atompaw/atompaw-3.0.1.9-r1.ebuild      |   2 +-
 sci-physics/atompaw/atompaw-4.0.0.10.ebuild        |   2 +-
 sci-physics/atompaw2abinit/ChangeLog               |   2 +-
 .../atompaw2abinit/atompaw2abinit-3.3.0-r1.ebuild  |   2 +-
 sci-physics/bigdft/ChangeLog                       |   2 +-
 sci-physics/bigdft/bigdft-1.7.1.ebuild             |   2 +-
 sci-physics/bigdft/bigdft-1.7.6.ebuild             |   2 +-
 sci-physics/clip/ChangeLog                         |   2 +-
 sci-physics/clip/clip-4.0.0_beta2.ebuild           |   2 +-
 sci-physics/elk/ChangeLog                          |   2 +-
 sci-physics/elk/elk-1.4.22.ebuild                  |   2 +-
 sci-physics/elk/elk-2.1.25.ebuild                  |   2 +-
 sci-physics/espresso++/ChangeLog                   |   2 +-
 sci-physics/espresso++/espresso++-9999.ebuild      |   2 +-
 sci-physics/espresso/ChangeLog                     |   2 +-
 sci-physics/espresso/espresso-9999.ebuild          |   2 +-
 sci-physics/fullprof-bin/ChangeLog                 |   2 +-
 .../fullprof-bin/fullprof-bin-20313.04.ebuild      |   2 +-
 sci-physics/geant-vmc/ChangeLog                    |   2 +-
 sci-physics/geant-vmc/geant-vmc-3.1.15a.ebuild     |   2 +-
 sci-physics/geant-vmc/geant-vmc-4.2.14b.ebuild     |   2 +-
 sci-physics/geant-vmc/geant-vmc-4.2.15.ebuild      |   2 +-
 sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild     |   2 +-
 sci-physics/geant-vmc/geant-vmc-9999.ebuild        |   2 +-
 sci-physics/genfit/ChangeLog                       |   2 +-
 sci-physics/genfit/genfit-9999.ebuild              |   2 +-
 sci-physics/herwig++/ChangeLog                     |   2 +-
 sci-physics/herwig++/herwig++-2.7.0-r1.ebuild      |   2 +-
 sci-physics/herwig++/herwig++-2.7.1.ebuild         |   2 +-
 sci-physics/hoomd-blue/ChangeLog                   |   2 +-
 sci-physics/hoomd-blue/hoomd-blue-9999.ebuild      |   2 +-
 sci-physics/looptools/ChangeLog                    |   2 +-
 sci-physics/looptools/looptools-2.10.ebuild        |   2 +-
 sci-physics/looptools/looptools-2.11.ebuild        |   2 +-
 sci-physics/looptools/looptools-2.12.ebuild        |   2 +-
 sci-physics/looptools/looptools-2.8.ebuild         |   2 +-
 sci-physics/looptools/looptools-2.9.ebuild         |   2 +-
 sci-physics/mc-tester/ChangeLog                    |   2 +-
 sci-physics/mc-tester/mc-tester-1.25.0.ebuild      |   2 +-
 sci-physics/openmx/ChangeLog                       |   2 +-
 sci-physics/openmx/openmx-3.6.ebuild               |   2 +-
 sci-physics/openmx/openmx-3.7.8.ebuild             |   2 +-
 sci-physics/qcl/ChangeLog                          |   2 +-
 sci-physics/qcl/qcl-0.6.3-r1.ebuild                |   2 +-
 sci-physics/qcl/qcl-0.6.4.ebuild                   |   2 +-
 sci-physics/rivet/ChangeLog                        |   9 +-
 sci-physics/rivet/Manifest                         |   1 +
 sci-physics/rivet/rivet-2.1.1.ebuild               |   2 +-
 sci-physics/rivet/rivet-2.1.2.ebuild               |   2 +-
 .../{rivet-2.1.1.ebuild => rivet-2.3.0.ebuild}     |   6 +-
 sci-physics/root/ChangeLog                         |   2 +-
 sci-physics/root/files/proofd.initd                |   2 +-
 sci-physics/root/files/rootd.initd                 |   2 +-
 sci-physics/root/root-9999.ebuild                  |   2 +-
 sci-physics/tauola/ChangeLog                       |   2 +-
 sci-physics/tauola/tauola-1.1.3.ebuild             |   2 +-
 sci-physics/tauola/tauola-1.1.4.ebuild             |   2 +-
 sci-physics/tauola/tauola-1.1.5.ebuild             |   2 +-
 sci-physics/tauola/tauola-9999.ebuild              |   2 +-
 sci-physics/thepeg/ChangeLog                       |   2 +-
 sci-physics/thepeg/thepeg-1.8.3-r1.ebuild          |   2 +-
 sci-physics/thepeg/thepeg-1.9.0-r2.ebuild          |   2 +-
 sci-physics/thepeg/thepeg-1.9.1-r1.ebuild          |   2 +-
 sci-physics/thepeg/thepeg-1.9.2.ebuild             |   2 +-
 sci-physics/vgm/ChangeLog                          |   2 +-
 sci-physics/vgm/vgm-3.06.ebuild                    |   2 +-
 sci-physics/vgm/vgm-9999.ebuild                    |   2 +-
 sci-physics/yoda/ChangeLog                         |   9 +-
 sci-physics/yoda/Manifest                          |   1 +
 sci-physics/yoda/metadata.xml                      |   1 +
 sci-physics/yoda/yoda-1.0.6.ebuild                 |   2 +-
 .../yoda/{yoda-1.0.6.ebuild => yoda-1.4.0.ebuild}  |   7 +-
 sci-visualization/ferret-bin/ChangeLog             |   2 +-
 .../ferret-bin/ferret-bin-6.6.4.ebuild             |   2 +-
 sci-visualization/gnuplot/ChangeLog                |   2 +-
 sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild  |   2 +-
 sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild  |   2 +-
 sci-visualization/mantid/ChangeLog                 |   2 +-
 sci-visualization/mantid/mantid-3.3.0.ebuild       |   2 +-
 sci-visualization/mayavi/ChangeLog                 |   2 +-
 sci-visualization/mayavi/mayavi-4.4.0.ebuild       |   2 +-
 sci-visualization/mayavi/mayavi-4.4.2.ebuild       |   2 +-
 sci-visualization/nodemon/ChangeLog                |   2 +-
 sci-visualization/nodemon/nodemon-0.3.5.ebuild     |   2 +-
 sci-visualization/v_sim/ChangeLog                  |   2 +-
 sci-visualization/v_sim/v_sim-3.6.0.ebuild         |   2 +-
 sci-visualization/vtkPOFFReader/ChangeLog          |   2 +-
 .../vtkPOFFReader/vtkPOFFReader-300.ebuild         |   2 +-
 sci-visualization/yt/yt-2.6.ebuild                 |   2 +-
 sci-visualization/yt/yt-9999.ebuild                |   2 +-
 skel.ChangeLog                                     |   2 +-
 skel.ebuild                                        |   2 +-
 sys-cluster/blcr/ChangeLog                         |   2 +-
 sys-cluster/blcr/blcr-0.8.4.ebuild                 |   2 +-
 sys-cluster/empi/ChangeLog                         |   2 +-
 sys-cluster/empi/empi-0.10.ebuild                  |   2 +-
 .../ganglia_jobmonarch-0.3.1.ebuild                |   2 +-
 sys-cluster/gasnet/ChangeLog                       |   2 +-
 sys-cluster/gasnet/gasnet-1.24.0.ebuild            |   2 +-
 sys-cluster/gasnet/gasnet-9999.ebuild              |   2 +-
 sys-cluster/hpl/ChangeLog                          |   2 +-
 sys-cluster/hpl/hpl-2.0-r1.ebuild                  |   2 +-
 sys-cluster/hpl/hpl-2.1.ebuild                     |   2 +-
 sys-cluster/hpx/ChangeLog                          |   2 +-
 sys-cluster/hpx/hpx-9999.ebuild                    |   2 +-
 sys-cluster/htcondor/ChangeLog                     |   2 +-
 sys-cluster/htcondor/files/condor.initd            |   2 +-
 sys-cluster/htcondor/htcondor-8.0.0.ebuild         |   2 +-
 sys-cluster/htcondor/htcondor-8.3.2.ebuild         |   2 +-
 sys-cluster/libquo/ChangeLog                       |   2 +-
 sys-cluster/libquo/libquo-9999.ebuild              |   2 +-
 sys-cluster/lustre/ChangeLog                       |   2 +-
 sys-cluster/lustre/lustre-9999.ebuild              |   2 +-
 sys-cluster/modules/ChangeLog                      |   2 +-
 sys-cluster/modules/modules-3.2.10-r1.ebuild       |   2 +-
 sys-cluster/modules/modules-3.2.10.ebuild          |   2 +-
 sys-cluster/modules/modules-3.2.9c-r1.ebuild       |   2 +-
 sys-cluster/modules/modules-3.2.9c.ebuild          |   2 +-
 sys-cluster/mpe2/ChangeLog                         |   2 +-
 sys-cluster/mpe2/mpe2-1.3.0.ebuild                 |   2 +-
 sys-cluster/mpich/ChangeLog                        |   2 +-
 sys-cluster/mpich/mpich-3.0.4.ebuild               |   2 +-
 sys-cluster/mpich/mpich-3.1.3-r2.ebuild            |   2 +-
 sys-cluster/mpich/mpich-3.1.3-r99.ebuild           |   2 +-
 sys-cluster/mpich/mpich-3.1.4-r1.ebuild            |   2 +-
 sys-cluster/mpich2/ChangeLog                       |   2 +-
 sys-cluster/mpich2/mpich2-1.5.ebuild               |   2 +-
 sys-cluster/mvapich2/ChangeLog                     |   2 +-
 sys-cluster/mvapich2/mvapich2-1.6-r1.ebuild        |   2 +-
 sys-cluster/nullmpi/ChangeLog                      |   2 +-
 sys-cluster/nullmpi/nullmpi-0.7.ebuild             |   2 +-
 sys-cluster/nullmpi/nullmpi-9999.ebuild            |   2 +-
 sys-cluster/openmpi/ChangeLog                      |   2 +-
 sys-cluster/openmpi/openmpi-1.6.5.ebuild           |   2 +-
 sys-cluster/openmpi/openmpi-1.7.3.ebuild           |   2 +-
 sys-cluster/openmpi/openmpi-1.8.4-r99.ebuild       |   2 +-
 sys-cluster/openmpi/openmpi-1.8.8.ebuild           |   2 +-
 sys-cluster/ovis/ChangeLog                         |   2 +-
 sys-cluster/ovis/ovis-3.0.1.ebuild                 |   2 +-
 sys-cluster/pyslice/ChangeLog                      |   2 +-
 sys-cluster/pyslice/pyslice-1.7.ebuild             |   2 +-
 sys-devel/gdebugger/ChangeLog                      |   2 +-
 sys-devel/gdebugger/gdebugger-6.2.438.ebuild       |   2 +-
 sys-infiniband/librxe/ChangeLog                    |   2 +-
 sys-infiniband/librxe/librxe-1.0.0.ebuild          |   2 +-
 virtual/blacs/ChangeLog                            |   2 +-
 virtual/blacs/blacs-1.1.ebuild                     |   2 +-
 virtual/blas/ChangeLog                             |   2 +-
 virtual/blas/blas-2.1-r1.ebuild                    |   2 +-
 virtual/blas/blas-2.1-r2.ebuild                    |   2 +-
 virtual/blas/blas-2.1-r3.ebuild                    |   2 +-
 virtual/cblas/ChangeLog                            |   2 +-
 virtual/cblas/cblas-2.0-r1.ebuild                  |   2 +-
 virtual/cblas/cblas-2.0-r2.ebuild                  |   2 +-
 virtual/cblas/cblas-2.0-r3.ebuild                  |   2 +-
 virtual/cblas/cblas-2.0.ebuild                     |   2 +-
 virtual/geant/ChangeLog                            |   2 +-
 virtual/geant/geant-3.ebuild                       |   2 +-
 virtual/lapack/ChangeLog                           |   2 +-
 virtual/lapack/lapack-3.4-r1.ebuild                |   2 +-
 virtual/lapack/lapack-3.5-r1.ebuild                |   2 +-
 virtual/lapack/lapack-3.5-r2.ebuild                |   2 +-
 virtual/lapacke/ChangeLog                          |   2 +-
 virtual/lapacke/lapacke-1.0.ebuild                 |   2 +-
 virtual/lapacke/lapacke-3.5.ebuild                 |   2 +-
 virtual/mpi/ChangeLog                              |   2 +-
 virtual/mpi/mpi-2.0-r3.ebuild                      |   2 +-
 virtual/mpi/mpi-2.0-r4.ebuild                      |   2 +-
 virtual/perl-encoding-warnings/ChangeLog           |   2 +-
 .../perl-encoding-warnings-0.11.ebuild             |   2 +-
 virtual/scalapack/ChangeLog                        |   2 +-
 virtual/scalapack/scalapack-2.0.ebuild             |   2 +-
 x11-libs/agg/ChangeLog                             |   2 +-
 x11-libs/agg/agg-2.5-r3.ebuild                     |   2 +-
 x11-libs/tr/ChangeLog                              |   2 +-
 x11-libs/tr/tr-1.3.ebuild                          |   2 +-
 x11-libs/xview-bin/ChangeLog                       |   2 +-
 x11-libs/xview-bin/xview-bin-3.2_p1428.ebuild      |   2 +-
 x11-libs/xview/ChangeLog                           |   2 +-
 x11-libs/xview/xview-3.2-r8.ebuild                 |   2 +-
 x11-misc/envytools/ChangeLog                       |   2 +-
 x11-misc/envytools/envytools-9999.ebuild           |   2 +-
 1867 files changed, 2238 insertions(+), 1984 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6030bf863645978b5fd3077441bad5ff65bd6711
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Aug 28 11:14:23 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Aug 28 11:14:23 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6030bf86

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/trilinos: compilation fixes for 12.2.1

 sci-libs/trilinos/ChangeLog                        |  4 ++
 .../files/trilinos-12.2.1-compilation_fixes.patch  | 43 ++++++++++++++++++++++
 sci-libs/trilinos/trilinos-12.2.1.ebuild           |  5 ++-
 3 files changed, 50 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     93ee0e2aa1b4c22ce96dd3a8f919d4eaf8265fad
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 27 15:01:38 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Aug 27 15:01:38 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=93ee0e2a

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/dealii: update live ebuild
  sci-libs/trilinos: version bump to 12.2.1
  media-gfx/librecad: fixed a building issue
  sci-libs/armadillo: Version bump
  media-gfx/librecad: version bump 2.0.8
  dev-python/line_profiler: New ebuild wirtten by me
  sci-libs/arrayfire: Partitial fix for bug #463: Use system boost-compute

 dev-python/line_profiler/ChangeLog                 | 10 ++++++
 dev-python/line_profiler/Manifest                  |  1 +
 dev-python/line_profiler/line_profiler-1.0.ebuild  |  1 +
 dev-python/line_profiler/line_profiler-9999.ebuild | 35 ++++++++++++++++++
 .../line_profiler}/metadata.xml                    | 10 +++---
 media-gfx/librecad/ChangeLog                       |  8 +++++
 media-gfx/librecad/Manifest                        |  1 +
 ...librecad-2.0.7.ebuild => librecad-2.0.8.ebuild} | 31 +++++++++++++---
 media-gfx/librecad/librecad-9999.ebuild            | 42 +++++++++++++++++-----
 sci-libs/armadillo/ChangeLog                       |  6 ++++
 sci-libs/armadillo/Manifest                        |  1 +
 ...-5.200.2-r1.ebuild => armadillo-5.400.2.ebuild} |  0
 sci-libs/arrayfire/ChangeLog                       |  3 ++
 sci-libs/arrayfire/arrayfire-9999.ebuild           |  1 +
 sci-libs/dealii/ChangeLog                          |  3 ++
 sci-libs/dealii/dealii-9999.ebuild                 |  5 ++-
 sci-libs/trilinos/ChangeLog                        |  5 +++
 sci-libs/trilinos/Manifest                         |  1 +
 ...ilinos-12.0.1.ebuild => trilinos-12.2.1.ebuild} |  2 +-
 19 files changed, 143 insertions(+), 23 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     3a687ca9a14e2c1b9c399cc6ca0aa7895dfbc446
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 20 23:28:52 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Aug 20 23:28:52 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a687ca9

Merge branch 'master' of ssh://github.com/gentoo-science/sci

 eclass/mpi.eclass                                  | 23 ++++++++++++++++++----
 sci-biology/salmon/ChangeLog                       |  6 ++++++
 sci-biology/salmon/Manifest                        |  1 +
 sci-biology/salmon/salmon-0.3.2.ebuild             |  4 ++++
 .../{salmon-0.3.2.ebuild => salmon-0.4.2.ebuild}   |  8 ++++++--
 sci-biology/salmon/salmon-9999.ebuild              |  4 ++++
 6 files changed, 40 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     2cc9a8e0af4ccb684092318978cf22099d6be2b2
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 17 10:52:46 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Aug 17 10:52:46 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2cc9a8e0

Merge pull request #462 from mschubert/salmon

sci-biology/salmon: fix deps & version bump to 0.4.2

 sci-biology/salmon/ChangeLog                                    | 6 ++++++
 sci-biology/salmon/Manifest                                     | 1 +
 sci-biology/salmon/salmon-0.3.2.ebuild                          | 4 ++++
 sci-biology/salmon/{salmon-0.3.2.ebuild => salmon-0.4.2.ebuild} | 8 ++++++--
 sci-biology/salmon/salmon-9999.ebuild                           | 4 ++++
 5 files changed, 21 insertions(+), 2 deletions(-)

diff --cc sci-biology/salmon/ChangeLog
index 9acc5c0,e398b16..478ddfa
--- a/sci-biology/salmon/ChangeLog
+++ b/sci-biology/salmon/ChangeLog
@@@ -1,7 -1,13 +1,13 @@@
  # ChangeLog for sci-biology/salmon
  # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 -# $Header: $
 +# $Id$
  
+ *salmon-0.4.2 (16 Aug 2015)
+ 
+   16 Aug 2015; Michael Schubert <mschu.dev@gmail.com> +salmon-0.4.2.ebuild,
+   salmon-0.3.2.ebuild, salmon-9999.ebuild:
+   sci-biology/salmon: fix deps & version bump to 0.4.2
+ 
    05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
    sci-biology/salmon: Add github to remote-id in metadata.xml
  

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6f4c6bf401ad5865fce15cc89ef71fce7a55bce3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 16 09:13:18 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Aug 16 09:13:18 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6f4c6bf4

Merge remote-tracking branch 'github/master'

* github/master:
  [sci-physics/yoda] fix metadata
  [sci-physics/rivet] version bump
  [sci-physics/yoda] version bump

 sci-physics/rivet/ChangeLog                                  | 7 ++++++-
 sci-physics/rivet/Manifest                                   | 1 +
 sci-physics/rivet/{rivet-2.1.1.ebuild => rivet-2.3.0.ebuild} | 4 +---
 sci-physics/yoda/ChangeLog                                   | 7 ++++++-
 sci-physics/yoda/Manifest                                    | 1 +
 sci-physics/yoda/metadata.xml                                | 1 +
 sci-physics/yoda/{yoda-1.0.6.ebuild => yoda-1.4.0.ebuild}    | 5 +++--
 7 files changed, 19 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     9ddb5ce2ad7a416921674dc82d18961d2a0846a5
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 16 09:12:54 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Aug 16 09:12:54 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9ddb5ce2

Update travis

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index cbe3901..0316560 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,7 +6,7 @@ language: python
 python:
     - pypy
 env:
-    - PORTAGE_VER="2.2.20"
+    - PORTAGE_VER="2.2.20.1"
 before_script:
     - mkdir travis-overlay
     - mv !(travis-overlay) travis-overlay/
@@ -14,7 +14,7 @@ before_script:
     - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/.travis.yml" -O .travis.yml.upstream
     - wget "https://github.com/gentoo/portage/archive/v${PORTAGE_VER}.tar.gz" -O portage-${PORTAGE_VER}.tar.gz
     - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/spinner.sh"
-    - wget "https://github.com/gentoo/gentoo-portage-rsync-mirror/archive/master.tar.gz" -O portage-tree.tar.gz
+    - wget "https://github.com/gentoo-mirror/gentoo/archive/master.tar.gz" -O portage-tree.tar.gz
     - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr spinner.sh
     - chmod a+rwx spinner.sh
     - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
@@ -31,6 +31,3 @@ before_script:
 script:
     - ./../spinner.sh "./../portage-${PORTAGE_VER}/bin/repoman full -d"
 # You can append own scripts after this line
-
-notifications:
-  irc: "chat.freenode.net#gentoo-science"

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     7672a9f4962e4ae9c80622ef78df9bd145780aab
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Aug 15 05:56:44 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Aug 15 05:56:44 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7672a9f4

Merge pull request #461 from mschubert/tophat_2.1.0

sci-biology/tophat: tophat-2.1.0 version bump

 sci-biology/tophat/ChangeLog           |  5 ++++
 sci-biology/tophat/Manifest            |  1 +
 sci-biology/tophat/tophat-2.1.0.ebuild | 43 ++++++++++++++++++++++++++++++++++
 3 files changed, 49 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     fd89b0256af74c5b04de06da92bbad3b52e13119
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Aug 14 07:21:06 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Aug 14 07:21:06 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fd89b025

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/asl: add live ebuild, unify life and release ebuilds.
  sci-libs/asl: remove old version
  sci-libs/asl: version bump
  sci-astronomy/casapy-bin: version bump casapy-bin to 4.4.0
  dev-java/jeuclid-core: Fix src_prepare(); Fixes bug #554558
  Ignore generated manpages
  Import from tree

 .gitignore                                         |  1 +
 dev-java/jeuclid-core/ChangeLog                    |  4 +++
 dev-java/jeuclid-core/jeuclid-core-3.1.9-r1.ebuild |  4 +--
 metadata/layout.conf                               | 41 ++++++++++++----------
 sci-astronomy/casapy-bin/ChangeLog                 |  7 +++-
 sci-astronomy/casapy-bin/Manifest                  |  1 +
 ...2.2.30986_p1.ebuild => casapy-bin-4.4.0.ebuild} |  6 ++--
 sci-libs/asl/ChangeLog                             | 13 +++++++
 sci-libs/asl/Manifest                              |  2 +-
 sci-libs/asl/asl-0.1.5.ebuild                      |  1 +
 sci-libs/asl/{asl-0.1.4.ebuild => asl-9999.ebuild} | 39 ++++++--------------
 11 files changed, 66 insertions(+), 53 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Andrew Savchenko]

commit:     c2efa3013cabfde371b686da113166dcfd6149c1
Author:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
AuthorDate: Mon Aug 10 16:50:23 2015 +0000
Commit:     Andrew Savchenko <bircoph <AT> gentoo <DOT> org>
CommitDate: Mon Aug 10 16:50:23 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c2efa301

Merge remote-tracking branch 'github/master'

 dev-java/jeuclid-core/ChangeLog                                    | 4 ++++
 dev-java/jeuclid-core/jeuclid-core-3.1.9-r1.ebuild                 | 4 ++--
 sci-astronomy/casapy-bin/ChangeLog                                 | 7 ++++++-
 sci-astronomy/casapy-bin/Manifest                                  | 1 +
 .../{casapy-bin-4.2.2.30986_p1.ebuild => casapy-bin-4.4.0.ebuild}  | 6 +++---
 5 files changed, 16 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Andrew Savchenko]

commit:     3b84fdf88d5789a3cf60ac989b9c34b8756a6158
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 10 08:39:57 2015 +0000
Commit:     Andrew Savchenko <bircoph <AT> gentoo <DOT> org>
CommitDate: Mon Aug 10 08:39:57 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3b84fdf8

Merge pull request #460 from sargas/casapy-bin-4.4.0

sci-astronomy/casapy-bin: version bump casapy-bin to 4.4.0

 sci-astronomy/casapy-bin/ChangeLog                                 | 7 ++++++-
 sci-astronomy/casapy-bin/Manifest                                  | 1 +
 .../{casapy-bin-4.2.2.30986_p1.ebuild => casapy-bin-4.4.0.ebuild}  | 6 +++---
 3 files changed, 10 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     60987503b0427d9cfec9a4e2be9fabfa50f9af49
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Aug  9 13:10:25 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Aug  9 13:10:25 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=60987503

Ignore generated manpages

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 14f4f8c..af5f05f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
 .DS_Store
 app-misc/dummy
+eclass/*.5

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     732af598693d9c7fcc4047f5c0bc1cad6fb9ec71
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Aug  9 09:48:20 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Aug  9 09:48:20 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=732af598

Merge remote-tracking branch 'github/master'

* github/master:
  sci-biology/inGAP-bin: Fix CAT move and many more things
  sci-biology/staden: Fix SLOT operators, bug #556946
  sys-cluster/openmpi:  bump 1.8.8 and sync with gx86 (java support)
  sci-chemistry/phenix-bin: Prefix love

 sci-biology/inGAP-bin/ChangeLog                    |  5 ++++-
 sci-biology/inGAP-bin/inGAP-bin-3.0.1.ebuild       | 22 +++++++++---------
 sci-biology/staden/ChangeLog                       |  4 ++++
 sci-biology/staden/staden-2.0.0_beta9.ebuild       |  2 +-
 sci-biology/staden/staden-9999.ebuild              |  2 +-
 sci-chemistry/phenix-bin/ChangeLog                 |  3 +++
 .../phenix-bin/phenix-bin-1.9.1692.ebuild          |  2 +-
 sys-cluster/openmpi/ChangeLog                      |  6 +++++
 sys-cluster/openmpi/Manifest                       |  2 +-
 .../{openmpi-1.8.7.ebuild => openmpi-1.8.8.ebuild} | 26 +++++++++++++++++++---
 10 files changed, 56 insertions(+), 18 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     9ef25a45939d8ebd8aa8f97224885342d4189f33
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Aug  4 09:15:38 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Aug  4 09:15:38 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9ef25a45

Merge pull request #459 from TheChymera/nipy

fixed USE flag requirement

 sci-libs/nipype/ChangeLog          | 6 ++++++
 sci-libs/nipype/nipype-9999.ebuild | 3 ++-
 2 files changed, 8 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     e497404934cd2e0d0331352214139262b5ef5f0e
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Aug  4 09:16:04 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Aug  4 09:16:04 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e4974049

Merge pull request #458 from TheChymera/ants2

New ANTS pull request

 sci-biology/ants/ChangeLog        | 17 +++++++++++++++++
 sci-biology/ants/ants-9999.ebuild | 27 +++++++++++++++++++++++++++
 sci-biology/ants/metadata.xml     | 13 +++++++++++++
 3 files changed, 57 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     9f8d67902ed4263143f32cd86910a96f601052c2
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Aug  3 12:31:26 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Aug  3 12:31:26 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9f8d6790

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/dealii - drop superseded version
  sci-libs/dealii - version bump

 sci-libs/dealii/ChangeLog                                   | 8 ++++++++
 sci-libs/dealii/Manifest                                    | 4 ++--
 sci-libs/dealii/dealii-8.2.0.ebuild                         | 1 -
 sci-libs/dealii/{dealii-9999.ebuild => dealii-8.3.0.ebuild} | 0
 4 files changed, 10 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f8a141859b59dfc501ad5ff81c940b9f8e293a69
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jul 31 10:09:56 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jul 31 10:09:56 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f8a14185

Merge remote-tracking branch 'github/master'

* github/master:
  sci-mathematics/scilab: Fix the conditions under which batik is a dependency.
  sci-mathematics/scilab: Patch to build with new versions of Java dependencies.
  dev-java/jlatexmath-fop: Fix the dependency on xmlgraphics-commons-2.

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     baf77bf4d391ca165649f45a612ba51478844b47
Author:     marbre <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Thu Jul 30 19:10:41 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jul 30 19:10:41 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=baf77bf4

Merge pull request #456 from khumba/scilab

Fix Scilab and jlatexmath-fop to build with new versions of dependencies

 dev-java/jlatexmath-fop/ChangeLog                  |  3 +
 .../jlatexmath-fop/jlatexmath-fop-1.0.3.ebuild     |  2 +-
 sci-mathematics/scilab/ChangeLog                   |  9 ++
 .../scilab/files/scilab-5.5.2-batik-1.8.patch      | 98 ++++++++++++++++++++++
 .../scilab/files/scilab-5.5.2-fop-2.0.patch        | 38 +++++++++
 .../scilab-5.5.2-xmlgraphics-common-2.0.patch      | 91 ++++++++++++++++++++
 sci-mathematics/scilab/scilab-5.5.2.ebuild         | 19 +++--
 7 files changed, 251 insertions(+), 9 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     1af8f7ce8d65eca4c69dd9703e3cfeba1bf6b045
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jul 26 16:40:02 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jul 26 16:40:02 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1af8f7ce

Merge pull request #457 from cjhanks/master

Fixes orphaned Java HDF5 source link in ebuild.

 dev-java/hdf-java/hdf-java-2.9.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     73b68749e35c3619fed69e57257c7b806fe3c4a5
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jul 29 07:52:22 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jul 29 07:52:22 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=73b68749

Merge remote-tracking branch 'github/master'

* github/master:
  Remove git user from github.com URIs
  Use the ${P} variable for filling in URL path.
  Fixes orphaned Java HDF5 source link in ebuild.
  neuro/sci: media-libs/avbin-bin build fixed -- moved source directory determination to pkg_setup
  neuro/sci: media-libs/avbin-bin build fixed -- package S (source directory) depends on architecture

 dev-java/hdf-java/hdf-java-2.9.ebuild            |  2 +-
 dev-python/pylibconfig2/pylibconfig2-9999.ebuild |  2 +-
 dev-python/python-ivi/python-ivi-9999.ebuild     |  2 +-
 dev-python/python-vxi11/python-vxi11-9999.ebuild |  2 +-
 media-libs/avbin-bin/ChangeLog                   | 11 +++++++++--
 media-libs/avbin-bin/Manifest                    |  2 +-
 media-libs/avbin-bin/avbin-bin-7.ebuild          | 11 ++++++-----
 sci-libs/pagmo/pagmo-9999.ebuild                 |  2 +-
 8 files changed, 21 insertions(+), 13 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     442113240d68bf6de868d6acd94a740b8fb858c0
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jul 26 17:14:29 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jul 26 17:14:29 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=44211324

Merge pull request #433 from flagist0/avbin-bin

media-libs/avbin-bin build fixed -- package S (source directory) depends on architecture

 media-libs/avbin-bin/ChangeLog          | 11 +++++++++--
 media-libs/avbin-bin/Manifest           |  2 +-
 media-libs/avbin-bin/avbin-bin-7.ebuild | 11 ++++++-----
 3 files changed, 16 insertions(+), 8 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Andrew Savchenko]

commit:     ccba07d817c43c7c2c492b3d56618584c428ee87
Author:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
AuthorDate: Sat Jul 25 23:39:08 2015 +0000
Commit:     Andrew Savchenko <bircoph <AT> gentoo <DOT> org>
CommitDate: Sat Jul 25 23:39:08 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ccba07d8

Merge remote-tracking branch 'github/master'

 sci-libs/armadillo/ChangeLog                       |  14 +++
 sci-libs/armadillo/Manifest                        |   1 -
 sci-libs/armadillo/armadillo-5.100.2.ebuild        |   4 +-
 ...-5.200.1.ebuild => armadillo-5.200.2-r1.ebuild} |  17 +++-
 sci-libs/armadillo/armadillo-5.200.2.ebuild        | 112 ---------------------
 sci-libs/armadillo/metadata.xml                    |   4 +
 6 files changed, 33 insertions(+), 119 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     64b40f0450b44de9a611187934059715979f5863
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Wed Jul 22 19:27:06 2015 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Wed Jul 22 19:27:06 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=64b40f04

Merge branch 'mirandaconrado-master'

 sci-libs/pagmo/ChangeLog         | 5 ++++-
 sci-libs/pagmo/pagmo-9999.ebuild | 6 +++---
 2 files changed, 7 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     aab8064e34562b92871809dbff25eb2859d1111c
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 23 21:07:27 2015 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Thu Jul 23 21:07:27 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=aab8064e

Merge remote-tracking branch 'gentoo/master'

 sci-biology/consed/ChangeLog                       |  9 +++
 sci-biology/consed/Manifest                        |  2 +
 sci-biology/consed/consed-29.ebuild                | 93 ++++++++++++++++++++++
 .../jhdf5 => sci-biology/consed}/metadata.xml      |  0
 sci-biology/mira/ChangeLog                         |  5 ++
 .../mira-4.9.5-fix-miramer-symlink-error.patch     | 22 +++++
 sci-biology/mira/mira-4.9.5.ebuild                 | 16 +++-
 7 files changed, 146 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     2bae9948de3923c338313ccff085b475742cfade
Author:     Jauhien Piatlicki <piatlicki <AT> gmail <DOT> com>
AuthorDate: Thu Jul 23 06:39:13 2015 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Thu Jul 23 06:39:13 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2bae9948

Merge pull request #449 from akreal/kaldi

sci-misc/kaldi: version bump

 sci-misc/kaldi/ChangeLog                                            | 6 ++++++
 sci-misc/kaldi/Manifest                                             | 1 +
 .../kaldi/{kaldi-0_p20150301.ebuild => kaldi-0_p20150709.ebuild}    | 6 +++---
 3 files changed, 10 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     0b0c5cae7a664141a57a2e7785c3ab1791d29994
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 16 19:41:07 2015 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Thu Jul 16 19:41:07 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0b0c5cae

Merge remote-tracking branch 'gentoo/master'

 .../BTLib => sci-electronics/minipro}/metadata.xml |  2 +-
 sci-electronics/minipro/minipro-9999.ebuild        | 28 ++++++++++++++++++++++
 2 files changed, 29 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     3ba1ad7cd0abd086c399cda14a4cd28d7397405f
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 16 19:44:44 2015 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Thu Jul 16 19:44:44 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3ba1ad7c

Merge remote-tracking branch 'gentoo/master'

 sci-electronics/minipro/minipro-9999.ebuild | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     c687e6ac22b9e55a4465d133b4e2b2bb801e8e81
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 16 19:43:55 2015 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Thu Jul 16 19:43:55 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c687e6ac

Merge remote-tracking branch 'github/master' into gentoo-master

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     2fbef18bf27e0ff61af00809e93de577149ec523
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Fri Jul 10 03:59:07 2015 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gentoo <DOT> org>
CommitDate: Fri Jul 10 03:59:07 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2fbef18b

Merge remote-tracking branch 'gentoo/master'

 dev-lang/vtune/ChangeLog                           |  5 ++++
 dev-lang/vtune/Manifest                            |  1 +
 ...15.2.393444.ebuild => vtune-15.3.403110.ebuild} |  4 +--
 sci-biology/RSeQC/ChangeLog                        |  9 +++++++
 sci-biology/RSeQC/Manifest                         |  2 ++
 sci-biology/RSeQC/RSeQC-2.6.1.ebuild               | 30 ++++++++++++++++++++++
 {sci-libs/jhdf5 => sci-biology/RSeQC}/metadata.xml |  0
 sci-libs/mkl/ChangeLog                             |  5 ++++
 sci-libs/mkl/Manifest                              |  1 +
 ...mkl-11.2.2.164.ebuild => mkl-11.2.3.187.ebuild} |  4 +--
 sys-cluster/openmpi/ChangeLog                      |  5 ++++
 sys-cluster/openmpi/Manifest                       |  1 +
 .../{openmpi-1.8.5.ebuild => openmpi-1.8.6.ebuild} |  0
 13 files changed, 63 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     e9841b74c19d1036053a3f186596fd156772e347
Author:     Jauhien Piatlicki <piatlicki <AT> gmail <DOT> com>
AuthorDate: Mon Jul  6 10:19:30 2015 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gentoo <DOT> org>
CommitDate: Mon Jul  6 10:19:30 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e9841b74

Merge pull request #448 from TheChymera/nipype

need sqlite3 module for sci-libs/nipype

 sci-libs/nipype/ChangeLog          | 3 +++
 sci-libs/nipype/nipype-9999.ebuild | 1 +
 2 files changed, 4 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c026500c60f202d33b5adb7538e25c31be63d0ef
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 24 09:51:52 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 24 09:51:52 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c026500c

Merge remote-tracking branch 'github/master'

* github/master:
  sci-mathematics/petsc: Avoid a sandbox violation, bug #548498
  version bump
  added dep needed at build-time
  pruned deps

 dev-tex/pythontex/ChangeLog                        |  4 ++++
 dev-tex/pythontex/pythontex-0.14-r1.ebuild         |  3 +--
 dev-tex/pythontex/pythontex-9999.ebuild            |  3 +--
 sci-biology/ncbi-tools++/ChangeLog                 |  3 +++
 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        |  1 +
 sci-mathematics/petsc/ChangeLog                    | 12 +++++++++++
 sci-mathematics/petsc/Manifest                     |  2 +-
 ...rpath.patch => petsc-3.6.0-disable-rpath.patch} |  9 ++++----
 .../files/petsc-3.6.0-fix_sandbox_violation.patch  | 15 ++++++++++++++
 sci-mathematics/petsc/petsc-3.5.3.ebuild           |  7 +++++++
 .../{petsc-3.5.1.ebuild => petsc-3.6.0.ebuild}     | 24 +++++++++++++++-------
 11 files changed, 67 insertions(+), 16 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     4d7fced04476d7ddbc02b996651d5f0c06bb069f
Author:     Matthias Maier <tamiko <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 23 17:37:48 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 23 17:37:48 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4d7fced0

Merge remote-tracking branch 'origin/master'

 sci-biology/ncbi-tools++/ChangeLog                  | 3 +++
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 1 +
 2 files changed, 4 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     65b6326a721410fe27d7153b16ff451f036c5382
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 23 16:03:03 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 23 16:03:03 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=65b6326a

Merge pull request #446 from TheChymera/ncbi-tools

sci-biology/ncbi-tools++ added dep needed at build-time

 sci-biology/ncbi-tools++/ChangeLog                  | 3 +++
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 1 +
 2 files changed, 4 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f7bc4f14ddb2e49e221d80cc9957123b2913a6aa
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 22 14:35:50 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 22 14:35:50 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f7bc4f14

Merge pull request #444 from TheChymera/pythontex

pruned deps for dev-tex/pythontex

 dev-tex/pythontex/ChangeLog                | 4 ++++
 dev-tex/pythontex/pythontex-0.14-r1.ebuild | 3 +--
 dev-tex/pythontex/pythontex-9999.ebuild    | 3 +--
 3 files changed, 6 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     2fafef66292df4827f34ae203d28a5ca14c79c7f
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 22 11:49:32 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 22 11:49:32 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2fafef66

Update to latest version

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index cdd8c92..cbe3901 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -24,7 +24,7 @@ before_script:
     - tar xzf portage-tree.tar.gz -C /usr/portage --strip-components=1
     - cp portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/
     - ln -s /usr/portage/profiles/base/ /etc/portage/make.profile
-    - wget "http://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
+    - wget "https://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
     - SIZE=`stat -c %s .travis.yml.upstream`
     - if ! cmp -n $SIZE -s .travis.yml .travis.yml.upstream; then  echo -e "\e[31m !!! .travis.yml outdated! Update available https://github.com/mrueg/repoman-travis \e[0m" > /tmp/update ; fi
     - cd travis-overlay

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     fed021ae3cdd12bbf9bfa092d200358e5e73feb8
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 21 10:38:05 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 21 10:38:05 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fed021ae

Use mrueg/repoman-travis

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 .travis.yml | 34 ++++++++++++++++++++++++----------
 1 file changed, 24 insertions(+), 10 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 043a371..cdd8c92 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,22 +1,36 @@
+#
+# Run repoman via travis
+# See https://github.com/mrueg/repoman-travis
+#
 language: python
 python:
-  - pypy
-
+    - pypy
+env:
+    - PORTAGE_VER="2.2.20"
 before_script:
-    - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr
-    - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
-    - echo "portage::250:portage,travis" >> /etc/group
-    - mkdir -p travis-overlay /etc/portage/ /usr/portage/distfiles
+    - mkdir travis-overlay
     - mv !(travis-overlay) travis-overlay/
     - mv .git travis-overlay/
-    - wget -O - "https://github.com/gentoo/portage/archive/master.tar.gz" | tar -xz
-    - wget -O - "https://github.com/gentoo/gentoo-portage-rsync-mirror/archive/master.tar.gz" | tar xz -C /usr/portage --strip-components=1
-    - cp portage-master/cnf/repos.conf /etc/portage/
+    - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/.travis.yml" -O .travis.yml.upstream
+    - wget "https://github.com/gentoo/portage/archive/v${PORTAGE_VER}.tar.gz" -O portage-${PORTAGE_VER}.tar.gz
+    - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/spinner.sh"
+    - wget "https://github.com/gentoo/gentoo-portage-rsync-mirror/archive/master.tar.gz" -O portage-tree.tar.gz
+    - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr spinner.sh
+    - chmod a+rwx spinner.sh
+    - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
+    - echo "portage::250:portage,travis" >> /etc/group
+    - mkdir -p /etc/portage/ /usr/portage/distfiles
+    - tar xzf portage-${PORTAGE_VER}.tar.gz
+    - tar xzf portage-tree.tar.gz -C /usr/portage --strip-components=1
+    - cp portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/
     - ln -s /usr/portage/profiles/base/ /etc/portage/make.profile
     - wget "http://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
+    - SIZE=`stat -c %s .travis.yml.upstream`
+    - if ! cmp -n $SIZE -s .travis.yml .travis.yml.upstream; then  echo -e "\e[31m !!! .travis.yml outdated! Update available https://github.com/mrueg/repoman-travis \e[0m" > /tmp/update ; fi
     - cd travis-overlay
 script:
-    - python ../portage-master/bin/repoman full -vdx
+    - ./../spinner.sh "./../portage-${PORTAGE_VER}/bin/repoman full -d"
+# You can append own scripts after this line
 
 notifications:
   irc: "chat.freenode.net#gentoo-science"

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b37d54bfcf269261bcebdfb49388fe773aae6c39
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 21 10:14:45 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 21 10:14:45 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b37d54bf

Merge remote-tracking branch 'github/master'

* github/master:
  fixed email address
  fixed trailing whitepace
  dropped emty dep, sorted eclasses
  new ebuild

 sci-libs/vxl/ChangeLog       | 14 ++++++++++++++
 sci-libs/vxl/metadata.xml    | 11 +++++++++++
 sci-libs/vxl/vxl-9999.ebuild | 17 +++++++++++++++++
 3 files changed, 42 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5de174e728fb5fc584788391c6e03921d6f8114b
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 17 07:27:24 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 17 07:27:24 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5de174e7

Merge pull request #428 from TheChymera/vxl

New pull request for sci-libs/vxl

 sci-libs/vxl/ChangeLog       | 14 ++++++++++++++
 sci-libs/vxl/metadata.xml    | 11 +++++++++++
 sci-libs/vxl/vxl-9999.ebuild | 17 +++++++++++++++++
 3 files changed, 42 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     d23a16728d5024f2f91b81e0869adaf3aaab5a5c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 17 05:47:33 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 17 05:47:33 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d23a1672

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

* 'master' of git+ssh://git.gentoo.org/proj/sci:
  Drop unneeded hack

 sci-chemistry/gromacs/ChangeLog           | 3 +++
 sci-chemistry/gromacs/gromacs-9999.ebuild | 7 -------
 2 files changed, 3 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     fd62567376b56296ad8233772aa2099cbe35c3a3
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 17 05:47:05 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 17 05:47:05 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fd625673

Merge pull request #439 from hmmr/master

sci-biology/aghermann: new upstream version

 sci-biology/aghermann/ChangeLog                                        | 3 +++
 sci-biology/aghermann/Manifest                                         | 1 +
 .../aghermann/{aghermann-1.0.3.ebuild => aghermann-1.0.5.ebuild}       | 2 +-
 3 files changed, 5 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     fe50d2a782f3d44551fcbe34b9f91015916fc097
Author:     Andrei Zavada <johnhommer <AT> gmail <DOT> com>
AuthorDate: Tue Jun 16 23:31:45 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 16 23:31:45 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fe50d2a7

Merge branch 'master' of github.com:gentoo-science/sci

 app-admin/eselect/ChangeLog                        |   21 +
 app-admin/eselect/Manifest                         |    6 -
 app-admin/eselect/eselect-1.3.7-r100.ebuild        |   72 -
 app-admin/eselect/eselect-1.3.8-r100.ebuild        |   72 -
 app-admin/eselect/eselect-1.4-r100.ebuild          |   72 -
 app-admin/eselect/eselect-1.4.1-r100.ebuild        |   72 -
 app-admin/eselect/eselect-1.4.2-r100.ebuild        |   72 -
 app-admin/eselect/eselect-1.4.3-r100.ebuild        |   72 -
 app-admin/eselect/eselect-1.4.4-r100.ebuild        |   72 -
 app-admin/eselect/eselect-1.4.4-r102.ebuild        |   72 +
 .../eselect/files/eselect-1.3.8-alternatives.patch |  616 ------
 .../eselect/files/eselect-1.4.2-alternatives.patch |  616 ------
 .../eselect/files/eselect-1.4.4-alternatives.patch | 1496 +++++++++++++
 app-admin/eselect/files/eselect-alternatives.patch |  618 ------
 app-benchmarks/btl/ChangeLog                       |    5 +-
 app-benchmarks/btl/metadata.xml                    |    3 +
 app-benchmarks/numbench/ChangeLog                  |    6 +-
 app-benchmarks/numbench/numbench-0.2.ebuild        |   10 +-
 app-benchmarks/numbench/numbench-9999.ebuild       |   10 +-
 app-doc/root-docs/ChangeLog                        |   36 +-
 app-doc/root-docs/Manifest                         |    3 -
 .../files/root-docs-5.34.01-makehtml.patch         |   51 -
 .../files/root-docs-6.00.01-fillpatterns.patch     |   30 -
 .../root-docs/files/root-docs-6.02.05-jsroot.patch |   11 +
 app-doc/root-docs/metadata.xml                     |    4 +-
 app-doc/root-docs/root-docs-5.34.18-r2.ebuild      |  132 --
 app-doc/root-docs/root-docs-6.00.01-r1.ebuild      |  133 --
 app-doc/root-docs/root-docs-6.00.02.ebuild         |    1 -
 app-doc/root-docs/root-docs-9999.ebuild            |  138 +-
 app-editors/neovim/ChangeLog                       |   19 -
 app-editors/neovim/metadata.xml                    |    5 -
 app-editors/neovim/neovim-9999.ebuild              |   37 -
 app-forensics/vine/ChangeLog                       |    3 +
 app-forensics/vine/vine-1.0.ebuild                 |    2 +-
 app-portage/g-octave/g-octave-9999.ebuild          |    2 +-
 app-text/jabref/ChangeLog                          |  112 -
 app-text/jabref/Manifest                           |    3 -
 app-text/jabref/jabref-2.10.ebuild                 |   70 -
 app-text/jabref/jabref-2.10_beta2-r1.ebuild        |   70 -
 app-text/jabref/jabref-2.9.2-r1.ebuild             |   28 -
 app-text/jabref/metadata.xml                       |    8 -
 app-vim/vim-gromacs/ChangeLog                      |    5 +-
 app-vim/vim-gromacs/metadata.xml                   |    3 +
 dev-cpp/eigen/ChangeLog                            |    6 +
 dev-cpp/eigen/Manifest                             |    6 +-
 dev-cpp/eigen/eigen-3.1.4.ebuild                   |    1 -
 .../{eigen-3.2.1-r2.ebuild => eigen-3.2.4.ebuild}  |    0
 dev-cpp/icnc/ChangeLog                             |    3 +
 dev-cpp/icnc/metadata.xml                          |   11 +-
 dev-java/glazedlists/ChangeLog                     |   12 -
 dev-java/glazedlists/Manifest                      |    1 -
 .../files/glazedlists-1.8.0-build.xml.patch        |   57 -
 dev-java/glazedlists/glazedlists-1.8.0.ebuild      |   50 -
 dev-java/glazedlists/metadata.xml                  |    5 -
 dev-java/gluegen/ChangeLog                         |   16 +-
 dev-java/gluegen/Manifest                          |    1 +
 ...-copy-jars.patch => 2.2.4-dont-copy-jars.patch} |    0
 ...1.4-dont-strip.patch => 2.2.4-dont-strip.patch} |    0
 ...archive.patch => 2.2.4-dont-test-archive.patch} |    0
 dev-java/gluegen/gluegen-2.2.4.ebuild              |   68 +
 dev-java/gluegen/metadata.xml                      |    3 +
 dev-java/hdf-java/hdf-java-2.9.ebuild              |    2 +-
 dev-java/jcip-annotations/ChangeLog                |   20 -
 dev-java/jcip-annotations/Manifest                 |    1 -
 .../jcip-annotations-1.0-r1.ebuild                 |   36 -
 dev-java/jcip-annotations/metadata.xml             |    9 -
 dev-java/jeuclid-core/ChangeLog                    |    3 +
 dev-java/jeuclid-core/metadata.xml                 |    7 +-
 dev-java/jhealpix/ChangeLog                        |    5 +-
 dev-java/jhealpix/metadata.xml                     |    7 +-
 dev-java/jogl/ChangeLog                            |   17 +-
 dev-java/jogl/Manifest                             |    1 +
 dev-java/jogl/jogl-2.2.4.ebuild                    |   70 +
 dev-java/jogl/metadata.xml                         |    3 +
 dev-java/jrosetta/jrosetta-1.0.4.ebuild            |    6 +-
 dev-lang/berkeley_upc/ChangeLog                    |    9 +-
 dev-lang/berkeley_upc/Manifest                     |    1 +
 dev-lang/berkeley_upc/berkeley_upc-2.20.0.ebuild   |   58 +
 dev-lang/conceptual/ChangeLog                      |    3 +
 dev-lang/conceptual/metadata.xml                   |    3 +
 dev-lang/ispc/ChangeLog                            |    5 +-
 dev-lang/ispc/ispc-9999.ebuild                     |    2 +-
 dev-lang/ispc/metadata.xml                         |    3 +
 dev-lang/julia/ChangeLog                           |    5 +-
 dev-lang/julia/julia-9999.ebuild                   |    6 +-
 dev-lang/terra/ChangeLog                           |   12 +
 dev-lang/terra/Manifest                            |    2 +
 dev-lang/terra/metadata.xml                        |   11 +
 dev-lang/terra/terra-2015.03.12.ebuild             |   36 +
 dev-lang/vtune/ChangeLog                           |    4 +-
 dev-libs/boost-compute/ChangeLog                   |   17 +-
 ...pute-0.4.ebuild => boost-compute-0.4-r1.ebuild} |    0
 dev-libs/boost-compute/boost-compute-9999.ebuild   |   10 +-
 .../files/boost-compute-0.4-CMakeLists.patch       |   14 +
 dev-libs/boost-compute/metadata.xml                |    3 +
 dev-libs/boost/ChangeLog                           |   10 +
 dev-libs/boost/boost-1.56.0-r2.ebuild              |    8 +-
 dev-libs/boost/metadata.xml                        |   17 +-
 dev-libs/libcuda/ChangeLog                         |    5 +-
 dev-libs/libcuda/metadata.xml                      |    3 +
 dev-libs/libflatarray/ChangeLog                    |    7 +-
 dev-libs/libflatarray/Manifest                     |    1 -
 dev-libs/libflatarray/libflatarray-0.1.1.ebuild    |   52 -
 dev-libs/libgdev/ChangeLog                         |    5 +-
 dev-libs/libgdev/metadata.xml                      |    3 +
 dev-libs/libpfm/ChangeLog                          |   18 -
 dev-libs/libpfm/Manifest                           |    2 -
 dev-libs/libpfm/libpfm-4.3.0.ebuild                |   35 -
 dev-libs/libpfm/libpfm-4.4.0.ebuild                |   36 -
 dev-libs/libpfm/metadata.xml                       |   17 -
 dev-libs/libunzip/ChangeLog                        |    6 +-
 dev-libs/libunzip/libunzip-5.52.ebuild             |   16 +-
 dev-libs/papi/ChangeLog                            |   12 -
 dev-libs/papi/Manifest                             |    2 -
 dev-libs/papi/metadata.xml                         |   15 -
 dev-libs/papi/papi-5.1.0.2.ebuild                  |   30 -
 dev-libs/papi/papi-5.3.0.ebuild                    |   39 -
 dev-libs/utf8proc/ChangeLog                        |   18 +-
 dev-libs/utf8proc/Manifest                         |    1 +
 .../utf8proc/files/utf8proc-1.2-buildflags.patch   |   40 +
 dev-libs/utf8proc/metadata.xml                     |    7 +-
 dev-libs/utf8proc/utf8proc-1.2-r1.ebuild           |   36 +
 dev-lua/cmsgpack/ChangeLog                         |   13 -
 dev-lua/cmsgpack/Manifest                          |    1 -
 dev-lua/cmsgpack/cmsgpack-0.3.0.ebuild             |    1 -
 dev-lua/cmsgpack/cmsgpack-9999.ebuild              |   48 -
 dev-ml/gsl-ocaml/ChangeLog                         |    9 +-
 dev-ml/gsl-ocaml/gsl-ocaml-1.10.2.ebuild           |    6 +-
 dev-ml/gsl-ocaml/metadata.xml                      |    7 +-
 dev-ml/ocamlgraph/ChangeLog                        |   40 -
 dev-ml/ocamlgraph/Manifest                         |    1 -
 dev-ml/ocamlgraph/files/ocamlgraph-makefile.patch  |   37 -
 dev-ml/ocamlgraph/metadata.xml                     |   23 -
 dev-ml/ocamlgraph/ocamlgraph-1.8.5.ebuild          |   51 -
 dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild       |    4 +-
 dev-perl/Bio-BigFile/ChangeLog                     |    8 +-
 dev-perl/Bio-BigFile/metadata.xml                  |   10 +-
 .../Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.34.ebuild  |    4 +-
 dev-perl/Bio-DB-Das-Chado/ChangeLog                |   10 +-
 dev-perl/Bio-DB-Das-Chado/metadata.xml             |   10 +-
 dev-perl/opal-client/ChangeLog                     |    6 +-
 dev-perl/opal-client/metadata.xml                  |    3 +
 dev-python/Forthon/Forthon-0.8.13.ebuild           |    2 +-
 dev-python/GOGrapher/GOGrapher-9999.ebuild         |    2 +-
 dev-python/RecSQL/ChangeLog                        |    5 +-
 dev-python/RecSQL/RecSQL-9999.ebuild               |    2 +-
 dev-python/RecSQL/metadata.xml                     |    3 +
 dev-python/astlib/ChangeLog                        |    5 +-
 dev-python/astlib/astlib-0.7.0.ebuild              |    2 +-
 dev-python/astlib/metadata.xml                     |    7 +-
 dev-python/astropy-helpers/ChangeLog               |    7 +
 dev-python/astropy-helpers/Manifest                |    1 -
 .../astropy-helpers/astropy-helpers-0.4.1.ebuild   |    1 -
 .../astropy-helpers/astropy-helpers-9999.ebuild    |    2 +-
 dev-python/astropy-helpers/metadata.xml            |    4 +
 dev-python/astropy/astropy-9999.ebuild             |    2 +-
 dev-python/astropysics/ChangeLog                   |    7 +-
 dev-python/astropysics/astropysics-9999.ebuild     |    4 +-
 dev-python/astroquery/ChangeLog                    |    5 +-
 dev-python/astroquery/metadata.xml                 |    8 +-
 dev-python/brewer2mpl/ChangeLog                    |    3 +
 dev-python/brewer2mpl/metadata.xml                 |    4 +
 dev-python/ccdproc/ChangeLog                       |    5 +-
 dev-python/ccdproc/ccdproc-0.2.1.ebuild            |    2 +-
 dev-python/ccdproc/ccdproc-0.2.ebuild              |    2 +-
 dev-python/ccdproc/ccdproc-9999.ebuild             |    2 +-
 dev-python/ccdproc/metadata.xml                    |    8 +-
 dev-python/coards/coards-1.0.5.ebuild              |    2 +-
 dev-python/coards/metadata.xml                     |    3 +
 dev-python/coords/coords-0.37.ebuild               |    2 +-
 dev-python/cosmocalc/cosmocalc-0.1.2-r1.ebuild     |    2 +-
 dev-python/dimensionful/ChangeLog                  |    6 +-
 dev-python/dimensionful/dimensionful-9999.ebuild   |    2 +-
 dev-python/dimensionful/metadata.xml               |    3 +
 dev-python/emcee/emcee-1.2.0.ebuild                |    2 +-
 dev-python/emcee/emcee-2.0.0.ebuild                |    2 +-
 dev-python/emcee/metadata.xml                      |    7 +-
 dev-python/ffc/ChangeLog                           |    5 +-
 dev-python/ffc/ffc-1.2.0.ebuild                    |    2 +-
 dev-python/ffc/ffc-1.3.0.ebuild                    |    2 +-
 dev-python/ffc/ffc-1.4.0.ebuild                    |    2 +-
 dev-python/ffc/metadata.xml                        |    7 +-
 dev-python/ffnet/ChangeLog                         |    8 +-
 dev-python/ffnet/ffnet-0.7.1.ebuild                |    2 +-
 dev-python/ffnet/metadata.xml                      |    3 +
 dev-python/fiat/ChangeLog                          |    5 +-
 dev-python/fiat/fiat-1.1.ebuild                    |    2 +-
 dev-python/fiat/fiat-1.3.0.ebuild                  |    2 +-
 dev-python/fiat/fiat-1.4.0.ebuild                  |    2 +-
 dev-python/fiat/metadata.xml                       |    7 +-
 dev-python/gammapy/ChangeLog                       |    5 +-
 dev-python/gammapy/metadata.xml                    |    8 +-
 dev-python/go-parser/go-parser-9999.ebuild         |    2 +-
 dev-python/healpy/ChangeLog                        |    5 +-
 dev-python/healpy/healpy-1.7.4.ebuild              |    2 +-
 dev-python/healpy/metadata.xml                     |   11 +-
 dev-python/imageutils/ChangeLog                    |    5 +-
 dev-python/imageutils/metadata.xml                 |    8 +-
 dev-python/inference/inference-0.4.ebuild          |    2 +-
 dev-python/instant/ChangeLog                       |    5 +-
 dev-python/instant/instant-1.2.0.ebuild            |    2 +-
 dev-python/instant/instant-1.3.0.ebuild            |    2 +-
 dev-python/instant/instant-1.4.0.ebuild            |    2 +-
 dev-python/instant/metadata.xml                    |    7 +-
 dev-python/jupyter-nbgrader/ChangeLog              |    9 +
 .../jupyter-nbgrader/jupyter-nbgrader-9999.ebuild  |   32 +
 dev-python/jupyter-nbgrader/metadata.xml           |    8 +
 dev-python/jupyter-nbviewer/ChangeLog              |    9 +
 .../jupyter-nbviewer/jupyter-nbviewer-9999.ebuild  |   35 +
 dev-python/jupyter-nbviewer/metadata.xml           |   10 +
 dev-python/matlab_wrapper/ChangeLog                |    3 +
 dev-python/matlab_wrapper/metadata.xml             |    4 +
 dev-python/matplotlib2tikz/ChangeLog               |   13 +
 dev-python/matplotlib2tikz/Manifest                |    1 +
 .../matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild   |    1 +
 .../matplotlib2tikz/matplotlib2tikz-9999.ebuild    |   30 +
 dev-python/matplotlib2tikz/metadata.xml            |   12 +
 dev-python/meshpy/ChangeLog                        |    7 +-
 dev-python/meshpy/Manifest                         |    1 +
 dev-python/meshpy/meshpy-2013.1.2.ebuild           |    2 +-
 dev-python/meshpy/meshpy-2014.1.ebuild             |   46 +
 dev-python/meshpy/metadata.xml                     |    3 +
 dev-python/montage-wrapper/metadata.xml            |    7 +-
 dev-python/newrelic/ChangeLog                      |   15 +
 dev-python/newrelic/Manifest                       |    2 +
 dev-python/newrelic/metadata.xml                   |   12 +
 dev-python/newrelic/newrelic-2.44.0.36.ebuild      |   35 +
 dev-python/newrelic/newrelic-2.50.0.39.ebuild      |   40 +
 dev-python/nvidia-ml-py/ChangeLog                  |    6 +
 dev-python/nvidia-ml-py/Manifest                   |    1 +
 dev-python/nvidia-ml-py/metadata.xml               |    3 +
 ...-6.340.0.ebuild => nvidia-ml-py-7.346.0.ebuild} |    0
 dev-python/omniorbpy/ChangeLog                     |    6 +
 dev-python/omniorbpy/metadata.xml                  |    3 +
 dev-python/omniorbpy/omniorbpy-3.4.ebuild          |    4 +-
 dev-python/opal-client/ChangeLog                   |    6 +-
 dev-python/opal-client/metadata.xml                |    3 +
 dev-python/opal-client/opal-client-2.4.1.ebuild    |    2 +-
 dev-python/photutils/ChangeLog                     |    5 +-
 dev-python/photutils/metadata.xml                  |    8 +-
 dev-python/pickleshare/ChangeLog                   |   13 +
 dev-python/pickleshare/Manifest                    |    1 +
 dev-python/pickleshare/metadata.xml                |   18 +
 dev-python/pickleshare/pickleshare-0.5.ebuild      |    1 +
 dev-python/pickleshare/pickleshare-9999.ebuild     |   39 +
 dev-python/prettyplotlib/metadata.xml              |    3 +
 dev-python/psubprocess/psubprocess-0.1.2.ebuild    |    2 +-
 dev-python/ptyprocess/ChangeLog                    |   18 +
 dev-python/ptyprocess/metadata.xml                 |    8 +
 dev-python/ptyprocess/ptyprocess-9999.ebuild       |   25 +
 dev-python/pyfftw/ChangeLog                        |    3 +
 dev-python/pyfftw/metadata.xml                     |    3 +
 dev-python/pyfftw/pyfftw-9999.ebuild               |    9 +
 dev-python/pyhdf/ChangeLog                         |    6 +-
 dev-python/pyhdf/metadata.xml                      |    3 +
 dev-python/pyhdf/pyhdf-0.8.3.ebuild                |    2 +-
 dev-python/pymvpa/pymvpa-0.4.4.ebuild              |    2 +-
 dev-python/pynomo/ChangeLog                        |    5 +-
 dev-python/pynomo/metadata.xml                     |   11 +-
 dev-python/pyqtgraph/ChangeLog                     |   23 -
 dev-python/pyqtgraph/Manifest                      |    1 -
 dev-python/pyqtgraph/metadata.xml                  |   14 -
 dev-python/pyqtgraph/pyqtgraph-0.9.8.ebuild        |   32 -
 dev-python/pysolar/ChangeLog                       |    5 +-
 dev-python/pysolar/metadata.xml                    |   11 +-
 dev-python/pysolar/pysolar-0.5.ebuild              |    2 +-
 dev-python/pysparse/ChangeLog                      |    6 +-
 dev-python/pysparse/metadata.xml                   |    3 +
 dev-python/pysparse/pysparse-1.1.1-r1.ebuild       |    2 +-
 dev-python/python-ivi/ChangeLog                    |    3 +
 dev-python/python-ivi/metadata.xml                 |    5 +-
 dev-python/python-vxi11/ChangeLog                  |    3 +
 dev-python/python-vxi11/metadata.xml               |    5 +-
 dev-python/pythoncgns/metadata.xml                 |    3 +
 dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild |    2 +-
 dev-python/pythonqt/pythonqt-2.1.ebuild            |    2 +-
 dev-python/pythonqt/pythonqt-9999.ebuild           |    2 +-
 dev-python/simplepam/ChangeLog                     |   13 +
 dev-python/simplepam/Manifest                      |    1 +
 dev-python/simplepam/metadata.xml                  |   15 +
 dev-python/simplepam/simplepam-0.1.5.ebuild        |    1 +
 dev-python/simplepam/simplepam-9999.ebuild         |   22 +
 dev-python/specutils/ChangeLog                     |    5 +-
 dev-python/specutils/metadata.xml                  |    8 +-
 dev-python/specutils/specutils-9999.ebuild         |    2 +-
 dev-python/ufl/ChangeLog                           |    5 +-
 dev-python/ufl/metadata.xml                        |    7 +-
 dev-python/ufl/ufl-0.5.4.ebuild                    |    2 +-
 dev-python/ufl/ufl-1.3.0.ebuild                    |    2 +-
 dev-python/ufl/ufl-1.4.0.ebuild                    |    2 +-
 dev-python/viper/ChangeLog                         |    6 +-
 dev-python/viper/metadata.xml                      |    7 +-
 dev-python/viper/viper-1.0.1.ebuild                |    2 +-
 dev-tcltk/togl/ChangeLog                           |    9 +-
 dev-tcltk/togl/metadata.xml                        |    5 +-
 dev-tcltk/togl/togl-1.7-r1.ebuild                  |   11 +-
 dev-tex/pythontex/ChangeLog                        |   18 +-
 dev-tex/pythontex/Manifest                         |    2 +-
 dev-tex/pythontex/metadata.xml                     |    3 +
 dev-tex/pythontex/pythontex-0.12.ebuild            |   70 -
 dev-tex/pythontex/pythontex-0.14-r1.ebuild         |   57 +
 dev-tex/pythontex/pythontex-9999.ebuild            |   58 +-
 dev-util/VampirTrace/ChangeLog                     |    9 +
 dev-util/VampirTrace/Manifest                      |    1 +
 dev-util/VampirTrace/VampirTrace-5.14.4.ebuild     |   44 +
 dev-util/amdapp/ChangeLog                          |   16 +
 dev-util/amdapp/Manifest                           |    4 +
 dev-util/amdapp/amdapp-2.9.1.ebuild                |   83 +
 dev-util/amdapp/amdapp-2.9.ebuild                  |    4 +-
 dev-util/amdapp/amdapp-3.0_beta.ebuild             |   83 +
 dev-util/f90cache/ChangeLog                        |    7 +-
 dev-util/f90cache/Manifest                         |    1 +
 dev-util/f90cache/f90cache-0.95.ebuild             |   38 +
 dev-util/intel-ocl-sdk/ChangeLog                   |   13 -
 dev-util/intel-ocl-sdk/Manifest                    |    3 -
 .../intel-ocl-sdk/intel-ocl-sdk-3.0.67279.ebuild   |   65 -
 .../intel-ocl-sdk/intel-ocl-sdk-3.1.1.11385.ebuild |   60 -
 .../intel-ocl-sdk/intel-ocl-sdk-3.2.1.16712.ebuild |   60 -
 dev-util/intel-ocl-sdk/metadata.xml                |   17 -
 dev-util/nvidia-cuda-gdk/ChangeLog                 |    6 +
 dev-util/nvidia-cuda-gdk/Manifest                  |    1 +
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-346.46.ebuild  |  121 ++
 dev-util/nvidia-cuda-sdk/ChangeLog                 |    8 -
 dev-util/nvidia-cuda-sdk/Manifest                  |    1 -
 dev-util/nvidia-cuda-sdk/metadata.xml              |   17 -
 .../nvidia-cuda-sdk/nvidia-cuda-sdk-7.0.18.ebuild  |  151 --
 dev-util/nvidia-cuda-toolkit/ChangeLog             |   15 -
 dev-util/nvidia-cuda-toolkit/Manifest              |    1 -
 dev-util/nvidia-cuda-toolkit/files/cuda-config.in  |   28 -
 dev-util/nvidia-cuda-toolkit/metadata.xml          |   18 -
 .../nvidia-cuda-toolkit-7.0.18-r1.ebuild           |  154 --
 dev-util/smartgit/ChangeLog                        |    2 +-
 eclass/alternatives-2.eclass                       |  156 +-
 eclass/emboss-r1.eclass                            |  144 --
 licenses/AMD-APPSDK                                |  267 +++
 licenses/FSL                                       |   94 +
 licenses/NVIDIA-CUDA                               | 2262 --------------------
 licenses/UPennState                                |    7 +
 licenses/hoomd-blue                                |   46 +
 licenses/newmat                                    |   30 +
 licenses/polyphen                                  |    7 +
 media-gfx/brlcad/ChangeLog                         |    8 +
 media-gfx/brlcad/Manifest                          |    3 +-
 media-gfx/brlcad/brlcad-7.20.4.ebuild              |  112 -
 media-gfx/brlcad/brlcad-7.22.0.ebuild              |   15 +-
 media-gfx/brlcad/brlcad-7.24.0.ebuild              |  111 +
 media-gfx/brlcad/brlcad-7.24.2.ebuild              |  110 +
 media-gfx/brlcad/brlcad-9999.ebuild                |   53 +-
 media-gfx/brlcad/files/brlcad-7.24.2-cmake.patch   |   13 +
 media-gfx/librecad/ChangeLog                       |    4 +
 media-gfx/librecad/librecad-2.0.7.ebuild           |    4 +-
 media-gfx/librecad/librecad-9999.ebuild            |    4 +-
 media-libs/OpenMOIV/ChangeLog                      |    6 +
 media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild         |   14 +-
 media-libs/libgfx/ChangeLog                        |    8 +-
 media-libs/libgfx/libgfx-1.1.0.ebuild              |   18 +-
 net-libs/xrootd/ChangeLog                          |  122 --
 net-libs/xrootd/Manifest                           |    1 -
 net-libs/xrootd/files/cmsd.confd                   |    9 -
 net-libs/xrootd/files/cmsd.initd                   |   35 -
 net-libs/xrootd/files/frm_purged.initd             |   35 -
 net-libs/xrootd/files/frm_xfrd.initd               |   35 -
 net-libs/xrootd/files/xrootd-no-werror.patch       |   11 -
 net-libs/xrootd/files/xrootd.confd                 |   21 -
 net-libs/xrootd/files/xrootd.initd                 |   33 -
 net-libs/xrootd/metadata.xml                       |   16 -
 net-libs/xrootd/xrootd-4.0.4.ebuild                |   80 -
 profiles/categories                                |    5 -
 profiles/license_groups                            |    2 +-
 sci-astronomy/bpz/bpz-1.99.3.ebuild                |    2 +-
 sci-astronomy/chealpix/ChangeLog                   |    5 +-
 sci-astronomy/chealpix/metadata.xml                |    7 +-
 sci-astronomy/healpix_cxx/ChangeLog                |    5 +-
 sci-astronomy/healpix_cxx/metadata.xml             |    7 +-
 sci-astronomy/healpix_idl/ChangeLog                |    5 +-
 sci-astronomy/healpix_idl/metadata.xml             |    7 +-
 sci-astronomy/libthesky/ChangeLog                  |   57 +
 sci-astronomy/libthesky/Manifest                   |    2 +
 sci-astronomy/libthesky/libthesky-0.3.2.ebuild     |   36 +
 sci-astronomy/libthesky/metadata.xml               |   12 +
 sci-astronomy/mosstack/mosstack-0.6.1-r1.ebuild    |    2 +-
 sci-astronomy/mosstack/mosstack-0.6.1.ebuild       |    2 +-
 sci-biology/AlignGraph/AlignGraph-9999.ebuild      |   53 +
 sci-biology/AlignGraph/ChangeLog                   |   12 +
 sci-biology/AlignGraph/metadata.xml                |   12 +
 sci-biology/BBmap/BBmap-31.40.ebuild               |   25 -
 sci-biology/BBmap/BBmap-34.56.ebuild               |   41 +
 sci-biology/BBmap/ChangeLog                        |   10 +
 sci-biology/BBmap/Manifest                         |    2 +-
 sci-biology/BRAKER/BRAKER-20150330.ebuild          |   36 +
 sci-biology/BRAKER/ChangeLog                       |   11 +
 sci-biology/BRAKER/Manifest                        |    1 +
 sci-biology/{transdecoder => BRAKER}/metadata.xml  |    0
 sci-biology/BRANCH/ChangeLog                       |    4 +-
 sci-biology/BRANCH/metadata.xml                    |    3 +
 sci-biology/BlastToSam/BlastToSam-9999.ebuild      |   31 +
 sci-biology/BlastToSam/ChangeLog                   |   12 +
 sci-biology/BlastToSam/metadata.xml                |   12 +
 sci-biology/CAutils/CAutils-20120126.ebuild        |   20 -
 sci-biology/CAutils/ChangeLog                      |    7 -
 sci-biology/CAutils/Manifest                       |    1 -
 sci-biology/ESTate/ChangeLog                       |    3 +
 sci-biology/ESTate/ESTate-0.5.ebuild               |    5 +
 sci-biology/Gambit/Manifest                        |    4 +-
 sci-biology/HTSeq/HTSeq-0.6.1.ebuild               |    2 +-
 sci-biology/HTSeq/metadata.xml                     |    3 +
 sci-biology/InterMine/ChangeLog                    |    4 +-
 sci-biology/InterMine/metadata.xml                 |    3 +
 sci-biology/Jannovar-bin/ChangeLog                 |    9 +
 .../Jannovar-bin/Jannovar-bin-20150503.ebuild      |   30 +
 sci-biology/Jannovar-bin/Manifest                  |    3 +
 sci-biology/{MAKER => Jannovar-bin}/metadata.xml   |    0
 sci-biology/KaKs_Calculator/ChangeLog              |   10 +
 .../KaKs_Calculator/KaKs_Calculator-1.2.ebuild     |   38 +
 sci-biology/KaKs_Calculator/Manifest               |    2 +
 .../{CAutils => KaKs_Calculator}/metadata.xml      |    0
 sci-biology/MAKER/MAKER-9999.ebuild                |   21 -
 sci-biology/MaSuRCA/ChangeLog                      |    8 +-
 sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild           |   64 -
 sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild          |   58 +
 sci-biology/MaSuRCA/Manifest                       |    2 +-
 sci-biology/ONTO-PERL/ChangeLog                    |    2 +-
 sci-biology/ORFcor/ChangeLog                       |   13 +
 sci-biology/ORFcor/Manifest                        |    1 +
 sci-biology/ORFcor/ORFcor-20130507.ebuild          |   31 +
 sci-biology/{zmsort => ORFcor}/metadata.xml        |    0
 sci-biology/SEECER/ChangeLog                       |    7 +-
 sci-biology/SEECER/Manifest                        |    2 +-
 sci-biology/SEECER/SEECER-0.1.3-r1.ebuild          |   35 +
 sci-biology/SEECER/SEECER-0.1.3.ebuild             |   34 -
 sci-biology/SEECER/files/replace_ids.cc            |  Bin 0 -> 1006 bytes
 sci-biology/SSAKE/ChangeLog                        |    9 +
 sci-biology/SSAKE/Manifest                         |    1 +
 sci-biology/SSAKE/SSAKE-3.8.2.ebuild               |   29 +
 sci-biology/{zmsort => SSAKE}/metadata.xml         |    0
 sci-biology/STAR/ChangeLog                         |   10 +
 sci-biology/STAR/Manifest                          |    1 +
 sci-biology/STAR/STAR-2.4.1c.ebuild                |   38 +
 sci-biology/STAR/STAR-9999.ebuild                  |   37 +
 sci-biology/{zmsort => STAR}/metadata.xml          |    0
 sci-biology/StarORF/ChangeLog                      |   11 +
 sci-biology/StarORF/StarORF-9999.ebuild            |   32 +
 sci-biology/{zmsort => StarORF}/metadata.xml       |    0
 sci-biology/TransDecoder/ChangeLog                 |   57 +
 sci-biology/TransDecoder/Manifest                  |    1 +
 sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild |   69 +
 .../files/TransDecoder.patch                       |    0
 .../files/pfam_runner.pl.patch                     |    0
 sci-biology/TransDecoder/metadata.xml              |   12 +
 sci-biology/Trinotate/ChangeLog                    |   15 +
 sci-biology/Trinotate/Manifest                     |    1 +
 sci-biology/Trinotate/Trinotate-2.0.1.ebuild       |   45 +
 sci-biology/Trinotate/metadata.xml                 |   12 +
 sci-biology/VarScan/ChangeLog                      |    6 +
 sci-biology/VarScan/Manifest                       |    2 +-
 sci-biology/VarScan/VarScan-2.3.6.ebuild           |   21 -
 sci-biology/VarScan/VarScan-2.3.7.ebuild           |   30 +
 sci-biology/VelvetOptimiser/ChangeLog              |    6 +-
 .../VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild   |   10 +-
 sci-biology/abacas/ChangeLog                       |   12 +
 sci-biology/abacas/Manifest                        |    1 +
 sci-biology/abacas/abacas-1.3.1.ebuild             |   33 +
 sci-biology/{zmsort => abacas}/metadata.xml        |    0
 sci-biology/abyss/ChangeLog                        |   17 +
 sci-biology/abyss/Manifest                         |    3 +
 sci-biology/abyss/abyss-1.3.3-r1.ebuild            |   42 +
 sci-biology/abyss/abyss-1.3.4-r1.ebuild            |   47 +
 sci-biology/abyss/abyss-1.3.6-r1.ebuild            |   48 +
 .../abyss/files/abyss-1.3.3-ac_prog_ar.patch       |   18 +
 sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch  |   15 +
 sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch |   40 +
 sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch  |   15 +
 sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch |   40 +
 .../abyss/files/abyss-1.3.6-ac_prog_ar.patch       |   18 +
 sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch  |   15 +
 sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch |   40 +
 sci-biology/{embassy => abyss}/metadata.xml        |    0
 sci-biology/amos-short/ChangeLog                   |    8 +
 sci-biology/amos-short/amos-short-0.9.3.ebuild     |   14 +-
 sci-biology/amos/ChangeLog                         |   26 +-
 sci-biology/amos/Manifest                          |    1 +
 sci-biology/amos/amos-3.1.0-r2.ebuild              |   60 +
 sci-biology/amos/amos-9999.ebuild                  |   34 +-
 sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch    |   15 +
 ...mos-3.1.0-goBambus2.py-indent-and-cleanup.patch |   25 +
 sci-biology/angsd/ChangeLog                        |   10 +
 sci-biology/angsd/angsd-9999.ebuild                |   49 +
 sci-biology/{zmsort => angsd}/metadata.xml         |    0
 sci-biology/argo-bin/ChangeLog                     |   18 +-
 sci-biology/argo-bin/Manifest                      |    3 +-
 sci-biology/argo-bin/argo-bin-1.0.31.ebuild        |   18 +-
 sci-biology/argo-bin/argo-bin-2.0.3.ebuild         |   30 +
 sci-biology/argo/ChangeLog                         |    9 +
 sci-biology/argo/Manifest                          |    2 +-
 sci-biology/argo/argo-1.0.24.ebuild                |   17 +-
 sci-biology/artemis-bin/ChangeLog                  |    4 +
 sci-biology/artemis-bin/Manifest                   |    2 +
 sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild |   31 +-
 sci-biology/artemis/ChangeLog                      |    5 +
 sci-biology/artemis/Manifest                       |    1 +
 sci-biology/artemis/artemis-9999.ebuild            |   38 +-
 sci-biology/augustus/ChangeLog                     |   90 +
 sci-biology/augustus/Manifest                      |    1 +
 sci-biology/augustus/augustus-3.1.ebuild           |   59 +
 .../{embassy-vienna => augustus}/metadata.xml      |    0
 sci-biology/bambino/ChangeLog                      |    6 +-
 sci-biology/bambino/bambino-1.02.ebuild            |    6 +-
 sci-biology/bambino/bambino-1.06.ebuild            |    6 +-
 sci-biology/bambus/ChangeLog                       |   14 +
 sci-biology/bambus/Manifest                        |    3 +-
 sci-biology/bambus/bambus-2.33.ebuild              |   61 +-
 sci-biology/bamtools/ChangeLog                     |    6 +-
 sci-biology/bamtools/metadata.xml                  |    3 +
 sci-biology/barnacle/ChangeLog                     |    9 +
 sci-biology/barnacle/Manifest                      |    1 +
 sci-biology/barnacle/barnacle-1.0.3.ebuild         |   39 +
 sci-biology/{zmsort => barnacle}/metadata.xml      |    0
 sci-biology/barrnap/ChangeLog                      |    6 +
 sci-biology/barrnap/Manifest                       |    1 +
 sci-biology/barrnap/barrnap-0.3.ebuild             |    2 +-
 sci-biology/barrnap/barrnap-0.4.ebuild             |   43 +
 sci-biology/bcftools/ChangeLog                     |    9 +
 sci-biology/bcftools/Manifest                      |    2 +-
 sci-biology/bcftools/bcftools-1.1.ebuild           |   26 -
 sci-biology/bcftools/bcftools-1.2.ebuild           |   30 +
 sci-biology/bcftools/metadata.xml                  |    3 +
 sci-biology/beagle/ChangeLog                       |   10 +
 sci-biology/beagle/Manifest                        |    4 +
 sci-biology/beagle/beagle-4.0.ebuild               |   24 +
 sci-biology/{zmsort => beagle}/metadata.xml        |    0
 sci-biology/beaglecall/ChangeLog                   |   10 +
 sci-biology/beaglecall/Manifest                    |    3 +
 sci-biology/beaglecall/beaglecall-20101115.ebuild  |   25 +
 sci-biology/{zmsort => beaglecall}/metadata.xml    |    0
 sci-biology/bedtools/ChangeLog                     |    6 +
 sci-biology/bedtools/bedtools-2.22.1.ebuild        |    4 +-
 sci-biology/bedtools/metadata.xml                  |    1 +
 sci-biology/biobambam/ChangeLog                    |    6 +
 sci-biology/biobambam/metadata.xml                 |    7 +-
 sci-biology/biopieces/ChangeLog                    |    3 +
 sci-biology/biopieces/biopieces-9999.ebuild        |    8 +-
 sci-biology/blue/ChangeLog                         |   10 +-
 sci-biology/blue/Manifest                          |    6 +-
 sci-biology/blue/blue-1.1.2.ebuild                 |   16 +-
 sci-biology/blue/blue-1.1.3.ebuild                 |   38 +
 sci-biology/bowtie/ChangeLog                       |   15 +-
 sci-biology/bowtie/Manifest                        |    3 +-
 sci-biology/bowtie/bowtie-1.1.1.ebuild             |    2 +-
 sci-biology/bowtie/bowtie-2.2.3.ebuild             |   52 +
 sci-biology/bowtie/bowtie-2.2.4.ebuild             |   52 -
 sci-biology/bowtie/bowtie-2.2.5.ebuild             |   52 +
 sci-biology/bowtie/metadata.xml                    |    3 +
 sci-biology/breakdancer/ChangeLog                  |   16 +-
 sci-biology/breakdancer/Manifest                   |    1 -
 sci-biology/breakdancer/breakdancer-1.1.2.ebuild   |   20 -
 sci-biology/breakdancer/breakdancer-9999.ebuild    |   33 +
 sci-biology/bwa/Manifest                           |    1 -
 sci-biology/bwa/bwa-0.7.12.ebuild                  |   34 -
 sci-biology/bwa/files/bwa_Makefile.patch           |   27 -
 sci-biology/bwa/metadata.xml                       |    5 -
 sci-biology/bx-python/ChangeLog                    |   17 +
 sci-biology/bx-python/Manifest                     |    1 +
 sci-biology/bx-python/bx-python-0.7.2.ebuild       |   22 +
 sci-biology/bx-python/bx-python-9999.ebuild        |   23 +
 sci-biology/bx-python/metadata.xml                 |   13 +
 sci-biology/caftools/ChangeLog                     |    7 +-
 sci-biology/caftools/caftools-2.0.2.ebuild         |    5 +-
 .../cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild     |    2 +-
 sci-biology/cd-hit/cd-hit-4.6.1.ebuild             |    2 +-
 sci-biology/cegma/ChangeLog                        |    5 +-
 sci-biology/cegma/cegma-2.5.ebuild                 |   22 +-
 sci-biology/cgview-bin/ChangeLog                   |    4 +
 sci-biology/cgview-bin/cgview-bin-20131130.ebuild  |   18 +-
 sci-biology/codonw/ChangeLog                       |   11 +-
 sci-biology/codonw/codonw-1.4.4-r1.ebuild          |   39 -
 sci-biology/codonw/codonw-1.4.4-r2.ebuild          |   41 +
 sci-biology/codonw/metadata.xml                    |   13 +-
 sci-biology/conform-gt/ChangeLog                   |   10 +
 sci-biology/conform-gt/Manifest                    |    1 +
 sci-biology/conform-gt/conform-gt-1174.ebuild      |   22 +
 sci-biology/{zmsort => conform-gt}/metadata.xml    |    0
 sci-biology/coral/ChangeLog                        |    9 +
 sci-biology/coral/Manifest                         |    1 +
 sci-biology/coral/coral-1.4.ebuild                 |   28 +
 sci-biology/{zmsort => coral}/metadata.xml         |    0
 sci-biology/cortex_var/ChangeLog                   |   13 +
 sci-biology/cortex_var/Manifest                    |    2 +
 sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild  |   47 +
 sci-biology/{zmsort => cortex_var}/metadata.xml    |    0
 sci-biology/cutadapt/cutadapt-1.2.1.ebuild         |    2 +-
 sci-biology/cutadapt/cutadapt-1.4.1.ebuild         |    2 +-
 sci-biology/cutadapt/cutadapt-1.5.ebuild           |    2 +-
 sci-biology/cutadapt/cutadapt-9999.ebuild          |    2 +-
 sci-biology/cutadapt/metadata.xml                  |    3 +
 sci-biology/dcmstack/ChangeLog                     |   24 +
 sci-biology/dcmstack/dcmstack-9999.ebuild          |   24 +
 .../labplot => sci-biology/dcmstack}/metadata.xml  |    0
 sci-biology/discrover/ChangeLog                    |    9 +
 sci-biology/discrover/Manifest                     |    2 +-
 sci-biology/discrover/discrover-1.5.2.ebuild       |   93 -
 sci-biology/discrover/discrover-1.6.0.ebuild       |   79 +
 sci-biology/discrover/discrover-9999.ebuild        |   18 +-
 sci-biology/discrover/metadata.xml                 |   26 +-
 sci-biology/embassy-cbstools/ChangeLog             |   61 -
 sci-biology/embassy-cbstools/Manifest              |    1 -
 .../embassy-cbstools-1.0.0.650.ebuild              |   11 -
 ...bassy-cbstools-1.0.0.650_fix-build-system.patch |   97 -
 sci-biology/embassy-cbstools/metadata.xml          |    5 -
 sci-biology/embassy-clustalomega/ChangeLog         |  117 -
 sci-biology/embassy-clustalomega/Manifest          |    1 -
 .../embassy-clustalomega-1.1.0.ebuild              |   13 -
 ...bassy-clustalomega-1.1.0_fix-build-system.patch |   90 -
 sci-biology/embassy-clustalomega/metadata.xml      |    5 -
 sci-biology/embassy-domainatrix/ChangeLog          |  174 --
 sci-biology/embassy-domainatrix/Manifest           |    1 -
 .../embassy-domainatrix-0.1.650.ebuild             |   11 -
 ...assy-domainatrix-0.1.650_fix-build-system.patch |   91 -
 sci-biology/embassy-domainatrix/metadata.xml       |    5 -
 sci-biology/embassy-domalign/ChangeLog             |  118 -
 sci-biology/embassy-domalign/Manifest              |    1 -
 .../embassy-domalign-0.1.650.ebuild                |   11 -
 ...embassy-domalign-0.1.650_fix-build-system.patch |   92 -
 sci-biology/embassy-domalign/metadata.xml          |    5 -
 sci-biology/embassy-domsearch/ChangeLog            |  116 -
 sci-biology/embassy-domsearch/Manifest             |    1 -
 .../embassy-domsearch-0.1.650.ebuild               |   11 -
 ...mbassy-domsearch-0.1.650_fix-build-system.patch |   91 -
 sci-biology/embassy-domsearch/metadata.xml         |    5 -
 sci-biology/embassy-emnu/ChangeLog                 |  157 --
 sci-biology/embassy-emnu/Manifest                  |    1 -
 .../embassy-emnu/embassy-emnu-1.05.650.ebuild      |   15 -
 .../embassy-emnu-1.05.650_fix-build-system.patch   |  127 --
 sci-biology/embassy-emnu/metadata.xml              |    5 -
 sci-biology/embassy-esim4/ChangeLog                |  160 --
 sci-biology/embassy-esim4/Manifest                 |    1 -
 .../embassy-esim4/embassy-esim4-1.0.0.650.ebuild   |   11 -
 .../embassy-esim4-1.0.0.650_fix-build-system.patch |   97 -
 sci-biology/embassy-esim4/metadata.xml             |    5 -
 sci-biology/embassy-hmmer/ChangeLog                |  166 --
 sci-biology/embassy-hmmer/Manifest                 |    1 -
 .../embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild   |   13 -
 .../embassy-hmmer-2.3.2.650_fix-build-system.patch |   90 -
 sci-biology/embassy-hmmer/metadata.xml             |    5 -
 sci-biology/embassy-iprscan/ChangeLog              |   45 -
 sci-biology/embassy-iprscan/Manifest               |    1 -
 .../embassy-iprscan-4.3.1.650.ebuild               |   11 -
 ...mbassy-iprscan-4.3.1.650_fix-build-system.patch |   97 -
 sci-biology/embassy-iprscan/metadata.xml           |    5 -
 sci-biology/embassy-meme/ChangeLog                 |   75 -
 sci-biology/embassy-meme/Manifest                  |    1 -
 .../embassy-meme/embassy-meme-4.7.650.ebuild       |   13 -
 .../embassy-meme-4.7.650_fix-build-system.patch    |   90 -
 sci-biology/embassy-meme/metadata.xml              |    5 -
 sci-biology/embassy-mse/ChangeLog                  |  185 --
 sci-biology/embassy-mse/Manifest                   |    1 -
 .../embassy-mse/embassy-mse-3.0.0.650.ebuild       |   21 -
 .../embassy-mse-3.0.0.650_fix-build-system.patch   |  133 --
 sci-biology/embassy-mse/metadata.xml               |    5 -
 sci-biology/embassy-phylipnew/ChangeLog            |   81 -
 sci-biology/embassy-phylipnew/Manifest             |    1 -
 .../embassy-phylipnew-3.69.650.ebuild              |   13 -
 ...bassy-phylipnew-3.69.650_fix-build-system.patch |   98 -
 sci-biology/embassy-phylipnew/metadata.xml         |    5 -
 sci-biology/embassy-signature/ChangeLog            |  116 -
 sci-biology/embassy-signature/Manifest             |    1 -
 .../embassy-signature-0.1.650.ebuild               |   11 -
 ...mbassy-signature-0.1.650_fix-build-system.patch |   90 -
 sci-biology/embassy-signature/metadata.xml         |    5 -
 sci-biology/embassy-structure/ChangeLog            |  116 -
 sci-biology/embassy-structure/Manifest             |    1 -
 .../embassy-structure-0.1.650.ebuild               |   11 -
 ...mbassy-structure-0.1.650_fix-build-system.patch |   90 -
 sci-biology/embassy-topo/ChangeLog                 |  161 --
 sci-biology/embassy-topo/Manifest                  |    1 -
 .../embassy-topo/embassy-topo-2.0.650.ebuild       |   11 -
 .../embassy-topo-2.0.650_fix-build-system.patch    |   97 -
 sci-biology/embassy-vienna/ChangeLog               |   65 -
 sci-biology/embassy-vienna/Manifest                |    1 -
 .../embassy-vienna/embassy-vienna-1.7.2.650.ebuild |   11 -
 ...embassy-vienna-1.7.2.650_fix-build-system.patch |   98 -
 sci-biology/embassy/ChangeLog                      |  160 --
 sci-biology/embassy/embassy-6.6.0.ebuild           |   30 -
 sci-biology/emboss/ChangeLog                       |  407 ----
 sci-biology/emboss/Manifest                        |    1 -
 sci-biology/emboss/emboss-6.6.0.ebuild             |   57 -
 sci-biology/emboss/files/README.gentoo             |   34 -
 .../files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch    |   11 -
 .../files/emboss-6.6.0_fix-build-system.patch      |  368 ----
 .../files/emboss-6.6.0_plplot-declarations.patch   |   61 -
 .../emboss-6.6.0_qa-implicit-declarations.patch    |   74 -
 sci-biology/emboss/metadata.xml                    |   18 -
 sci-biology/epga/ChangeLog                         |    3 +
 sci-biology/epga/metadata.xml                      |    3 +
 sci-biology/est2assembly/ChangeLog                 |    4 +
 sci-biology/est2assembly/est2assembly-1.08.ebuild  |    4 +-
 sci-biology/est2uni/ChangeLog                      |    6 +-
 sci-biology/est2uni/est2uni-0.27.ebuild            |    4 +-
 sci-biology/eval/ChangeLog                         |    8 +
 sci-biology/eval/eval-2.2.8.ebuild                 |   21 +-
 sci-biology/exomiser-bin/ChangeLog                 |    9 +
 sci-biology/exomiser-bin/Manifest                  |    1 +
 sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild |   23 +
 sci-biology/{zmsort => exomiser-bin}/metadata.xml  |    0
 sci-biology/exonerate-gff3/ChangeLog               |   21 +
 .../exonerate-gff3/exonerate-gff3-9999.ebuild      |   55 +
 .../files/exonerate-gff3-9999-asneeded.patch       |   15 +
 sci-biology/exonerate-gff3/metadata.xml            |   15 +
 sci-biology/fastqc/ChangeLog                       |   28 +-
 sci-biology/fastqc/Manifest                        |    2 +-
 sci-biology/fastqc/fastqc-0.10.1.ebuild            |   30 -
 sci-biology/fastqc/fastqc-0.11.3.ebuild            |   55 +
 sci-biology/fastqc/files/build.xml                 |   59 +
 sci-biology/fastx_toolkit/ChangeLog                |    5 +-
 sci-biology/fastx_toolkit/metadata.xml             |    3 +
 sci-biology/ffindex/ChangeLog                      |    8 +
 sci-biology/ffindex/Manifest                       |    2 +-
 sci-biology/ffindex/ffindex-0.9.9.3.ebuild         |    3 +-
 sci-biology/ffindex/metadata.xml                   |    3 +
 sci-biology/freebayes/ChangeLog                    |   17 +-
 sci-biology/freebayes/freebayes-9999.ebuild        |   23 +-
 sci-biology/freebayes/metadata.xml                 |    3 +
 sci-biology/fsl/ChangeLog                          |   85 +
 sci-biology/fsl/Manifest                           |    2 +
 sci-biology/fsl/files/99fsl                        |    5 +
 sci-biology/fsl/files/fsl-5.0.4-headers.patch      |   32 +
 sci-biology/fsl/files/fsl-5.0.4-setup.patch        |  110 +
 sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch |  456 ++++
 sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch |  452 ++++
 sci-biology/fsl/files/fsl-5.0.8-headers.patch      |   21 +
 sci-biology/fsl/files/fsl-5.0.8-setup.patch        |  113 +
 sci-biology/fsl/fsl-5.0.6.ebuild                   |  130 ++
 sci-biology/fsl/fsl-5.0.8.ebuild                   |  130 ++
 sci-biology/fsl/metadata.xml                       |    8 +
 sci-biology/genepop/ChangeLog                      |    6 +-
 sci-biology/genepop/genepop-4.2.1.ebuild           |    5 +-
 sci-biology/genseed/ChangeLog                      |    7 +-
 sci-biology/genseed/genseed-1.0.22.ebuild          |   10 +-
 sci-biology/gffutils/ChangeLog                     |   15 +
 sci-biology/gffutils/Manifest                      |    1 +
 sci-biology/gffutils/gffutils-0.8.3.ebuild         |   21 +
 sci-biology/gffutils/metadata.xml                  |   12 +
 sci-biology/glean/ChangeLog                        |   13 +
 sci-biology/glean/Manifest                         |    1 +
 sci-biology/glean/glean-1.0.1.ebuild               |   40 +
 sci-biology/{zmsort => glean}/metadata.xml         |    0
 sci-biology/grappa/ChangeLog                       |    6 +-
 sci-biology/grappa/grappa-2.0.ebuild               |    9 +-
 sci-biology/hexamer/ChangeLog                      |    9 +
 sci-biology/hexamer/Manifest                       |    1 +
 sci-biology/hexamer/hexamer-19990330.ebuild        |   30 +
 sci-biology/{zmsort => hexamer}/metadata.xml       |    0
 sci-biology/igv/ChangeLog                          |   43 +
 sci-biology/igv/Manifest                           |    2 +
 .../igv/files/2.3.52-remove-oracle.jdbc.patch      |   21 +
 sci-biology/igv/igv-2.0.35.ebuild                  |  101 -
 sci-biology/igv/igv-2.3.47.ebuild                  |   83 +
 sci-biology/igv/igv-2.3.52.ebuild                  |   83 +
 sci-biology/igv/metadata.xml                       |    3 +
 sci-biology/jellyfish/ChangeLog                    |   33 +
 sci-biology/jellyfish/Manifest                     |    3 +
 sci-biology/jellyfish/jellyfish-1.1.11.ebuild      |   32 +
 sci-biology/jellyfish/jellyfish-2.1.3.ebuild       |   18 +-
 sci-biology/jellyfish/jellyfish-2.1.4.ebuild       |   30 +
 sci-biology/kallisto/ChangeLog                     |   10 +
 sci-biology/kallisto/Manifest                      |    1 +
 sci-biology/kallisto/kallisto-0.42.1.ebuild        |   19 +
 sci-biology/kallisto/kallisto-9999.ebuild          |   20 +
 sci-biology/kallisto/metadata.xml                  |    9 +
 sci-biology/khmer/ChangeLog                        |    7 +-
 sci-biology/khmer/metadata.xml                     |    4 +
 sci-biology/kmergenie/ChangeLog                    |   25 +
 sci-biology/kmergenie/Manifest                     |    1 +
 sci-biology/kmergenie/kmergenie-1.6971.ebuild      |   45 +
 sci-biology/{zmsort => kmergenie}/metadata.xml     |    0
 sci-biology/lastz/ChangeLog                        |   10 +-
 sci-biology/lastz/Manifest                         |    2 +-
 sci-biology/lastz/files/lastz-1.03.34-build.patch  |   43 -
 sci-biology/lastz/files/lastz-1.03.66-build.patch  |   37 +
 sci-biology/lastz/lastz-1.03.34.ebuild             |   33 -
 sci-biology/lastz/lastz-1.03.66.ebuild             |   33 +
 sci-biology/lighter/ChangeLog                      |   13 +
 sci-biology/lighter/lighter-9999.ebuild            |   36 +
 sci-biology/lighter/metadata.xml                   |   12 +
 sci-biology/{MAKER => maker}/ChangeLog             |    0
 sci-biology/maker/Manifest                         |    1 +
 sci-biology/maker/maker-2.31.8.ebuild              |   54 +
 sci-biology/{zmsort => maker}/metadata.xml         |    0
 sci-biology/manatee-igs/ChangeLog                  |    7 +-
 sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild  |   65 +-
 sci-biology/metaseq/ChangeLog                      |   15 +
 sci-biology/metaseq/Manifest                       |    1 +
 sci-biology/metaseq/metadata.xml                   |   12 +
 sci-biology/metaseq/metaseq-0.5.3.ebuild           |   32 +
 sci-biology/minced/ChangeLog                       |   16 +
 sci-biology/minced/metadata.xml                    |   12 +
 sci-biology/minced/minced-9999.ebuild              |   29 +
 sci-biology/mip-scaffolder/ChangeLog               |    5 +
 .../mip-scaffolder/mip-scaffolder-0.6.ebuild       |    2 +-
 sci-biology/mira/ChangeLog                         |  160 +-
 sci-biology/mira/Manifest                          |    3 +-
 sci-biology/mira/files/libtool.m4.patch            |   13 -
 sci-biology/mira/files/mira-3.0.0-asneeded.patch   |   56 -
 sci-biology/mira/files/mira-3.4.0.1-asneeded.patch |   29 -
 sci-biology/mira/files/mira-4.9.5-cout.patch       |   16 +
 .../mira/files/mira_left_clip.readpool.C.patch     |   36 -
 sci-biology/mira/metadata.xml                      |    7 +-
 sci-biology/mira/mira-4.0.2.ebuild                 |   76 -
 sci-biology/mira/mira-4.0_rc4.ebuild               |   76 -
 sci-biology/mira/mira-4.9.5.ebuild                 |   79 +
 sci-biology/mrbayes/ChangeLog                      |   94 -
 sci-biology/mrbayes/Manifest                       |    1 -
 sci-biology/mrbayes/files/mb_readline_312.patch    |   37 -
 sci-biology/mrbayes/metadata.xml                   |   15 -
 sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild        |   50 -
 sci-biology/mrfast/ChangeLog                       |    6 +-
 sci-biology/mrfast/metadata.xml                    |    3 +
 sci-biology/mrsfast/ChangeLog                      |    6 +-
 sci-biology/mrsfast/metadata.xml                   |    3 +
 sci-biology/ncbi-tools++/ChangeLog                 |    9 +
 .../files/ncbi-tools++-12.0.0-bdb6.patch           |  114 +
 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        |    4 +-
 sci-biology/ngs_backbone/ChangeLog                 |    6 +-
 sci-biology/ngs_backbone/ngs_backbone-9999.ebuild  |   16 +-
 sci-biology/ngsview/ChangeLog                      |    6 +
 sci-biology/ngsview/metadata.xml                   |    3 +
 sci-biology/pairagon/ChangeLog                     |   17 +
 sci-biology/pairagon/Manifest                      |    1 +
 sci-biology/{zmsort => pairagon}/metadata.xml      |    0
 sci-biology/pairagon/pairagon-1.1.ebuild           |   41 +
 sci-biology/pb-honey/ChangeLog                     |    5 +-
 sci-biology/pb-honey/pb-honey-14.1.15.ebuild       |    2 +-
 sci-biology/perlprimer/ChangeLog                   |    6 +-
 sci-biology/perlprimer/metadata.xml                |    3 +
 sci-biology/phusion/ChangeLog                      |   10 +
 sci-biology/phusion/Manifest                       |    1 +
 sci-biology/{zmsort => phusion}/metadata.xml       |    0
 sci-biology/phusion/phusion-2.1c.ebuild            |   42 +
 sci-biology/plinkseq/ChangeLog                     |   13 +
 sci-biology/plinkseq/Manifest                      |    1 +
 sci-biology/{zmsort => plinkseq}/metadata.xml      |    0
 sci-biology/plinkseq/plinkseq-0.10.ebuild          |   33 +
 sci-biology/polyphen/ChangeLog                     |    9 +
 sci-biology/polyphen/Manifest                      |    1 +
 sci-biology/{zmsort => polyphen}/metadata.xml      |    0
 sci-biology/polyphen/polyphen-2.2.2.ebuild         |   27 +
 sci-biology/prokka/ChangeLog                       |   15 +
 sci-biology/prokka/Manifest                        |    1 +
 sci-biology/{zmsort => prokka}/metadata.xml        |    0
 sci-biology/prokka/prokka-1.11.ebuild              |   34 +
 sci-biology/psychopy/ChangeLog                     |    3 +
 sci-biology/psychopy/psychopy-1.78.00.ebuild       |    2 +-
 sci-biology/pybedtools/ChangeLog                   |   15 +
 sci-biology/pybedtools/Manifest                    |    1 +
 sci-biology/pybedtools/metadata.xml                |   12 +
 sci-biology/pybedtools/pybedtools-0.6.9.ebuild     |   22 +
 sci-biology/pybrain/pybrain-9999.ebuild            |    2 +-
 sci-biology/pyfaidx/ChangeLog                      |   12 +
 sci-biology/pyfaidx/Manifest                       |    1 +
 sci-biology/pyfaidx/metadata.xml                   |   12 +
 sci-biology/pyfaidx/pyfaidx-0.3.8.ebuild           |   18 +
 sci-biology/pysam/ChangeLog                        |   22 +
 sci-biology/pysam/Manifest                         |    2 +
 sci-biology/pysam/metadata.xml                     |    8 +
 sci-biology/pysam/pysam-0.6-r2.ebuild              |   26 +
 sci-biology/pysam/pysam-0.7.5.ebuild               |   26 +
 sci-biology/quorum/ChangeLog                       |   15 +
 sci-biology/quorum/Manifest                        |    2 +
 sci-biology/{zmsort => quorum}/metadata.xml        |    0
 sci-biology/quorum/quorum-0.2.1.ebuild             |   21 +
 sci-biology/quorum/quorum-1.0.0.ebuild             |   21 +
 sci-biology/reptile/ChangeLog                      |    9 +
 sci-biology/reptile/Manifest                       |    1 +
 sci-biology/{zmsort => reptile}/metadata.xml       |    0
 sci-biology/reptile/reptile-1.1.ebuild             |   41 +
 sci-biology/ruffus/ruffus-9999.ebuild              |    2 +-
 sci-biology/rum/ChangeLog                          |   15 +
 sci-biology/rum/Manifest                           |    1 +
 sci-biology/rum/metadata.xml                       |   12 +
 sci-biology/rum/rum-2.0.5.5.ebuild                 |   38 +
 sci-biology/sabre/ChangeLog                        |    3 +
 sci-biology/sabre/metadata.xml                     |    3 +
 sci-biology/salmon/ChangeLog                       |   22 +
 sci-biology/salmon/Manifest                        |    1 +
 .../files/salmon-0.3.2-no-boost-static.patch       |   20 +
 sci-biology/salmon/metadata.xml                    |   12 +
 sci-biology/salmon/salmon-0.3.2.ebuild             |   18 +
 sci-biology/salmon/salmon-9999.ebuild              |   19 +
 sci-biology/samtools/ChangeLog                     |   20 +
 sci-biology/samtools/Manifest                      |    3 +
 .../samtools/files/samtools-1.0-buildsystem.patch  |   59 +
 .../samtools/files/samtools-1.0-rmdup.patch        |   47 +
 .../samtools/files/samtools-1.1-buildsystem.patch  |  153 ++
 .../samtools/files/samtools-1.1-rmdup.patch        |   47 +
 .../samtools/files/samtools-1.2-buildsystem.patch  |  193 ++
 .../samtools/files/samtools-1.2-rmdup.patch        |   47 +
 sci-biology/samtools/metadata.xml                  |    8 +
 sci-biology/samtools/samtools-1.0-r2.ebuild        |   74 +
 sci-biology/samtools/samtools-1.1-r1.ebuild        |   84 +
 sci-biology/samtools/samtools-1.2-r1.ebuild        |   84 +
 sci-biology/scaffold_builder/ChangeLog             |   10 +
 .../scaffold_builder-20131122.ebuild               |    6 +-
 sci-biology/screed/ChangeLog                       |    5 +-
 sci-biology/screed/metadata.xml                    |    4 +
 sci-biology/scythe/ChangeLog                       |    6 +-
 sci-biology/scythe/metadata.xml                    |    3 +
 sci-biology/seqclean/ChangeLog                     |   11 +-
 sci-biology/seqclean/seqclean-110625.ebuild        |    6 +-
 sci-biology/seqtools/ChangeLog                     |   17 +
 sci-biology/seqtools/Manifest                      |    1 +
 sci-biology/{zmsort => seqtools}/metadata.xml      |    0
 sci-biology/seqtools/seqtools-4.34.5.ebuild        |   22 +
 sci-biology/sga/ChangeLog                          |    4 +-
 sci-biology/sga/metadata.xml                       |    9 +-
 sci-biology/sgp2/ChangeLog                         |    5 +-
 sci-biology/sgp2/sgp2-1.1.ebuild                   |    3 +-
 sci-biology/sickle/ChangeLog                       |    9 +
 sci-biology/sickle/Manifest                        |    1 +
 sci-biology/sickle/metadata.xml                    |    3 +
 sci-biology/sickle/sickle-1.33.ebuild              |   36 +
 sci-biology/sickle/sickle-9999.ebuild              |   17 +-
 sci-biology/signalp/ChangeLog                      |    6 +-
 sci-biology/signalp/signalp-3.0.ebuild             |    6 +-
 sci-biology/skewer-bin/ChangeLog                   |    6 +-
 sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild   |    4 +-
 sci-biology/snap/ChangeLog                         |    9 +
 sci-biology/snap/Manifest                          |    1 +
 sci-biology/{zmsort => snap}/metadata.xml          |    0
 sci-biology/snap/snap-20131129.ebuild              |   35 +
 sci-biology/snphylo/ChangeLog                      |   10 +
 sci-biology/snphylo/Manifest                       |    1 +
 sci-biology/{zmsort => snphylo}/metadata.xml       |    0
 sci-biology/snphylo/snphylo-20140701.ebuild        |   35 +
 sci-biology/spm/ChangeLog                          |   29 +
 sci-biology/spm/Manifest                           |    2 +
 {dev-lua/cmsgpack => sci-biology/spm}/metadata.xml |    0
 sci-biology/spm/spm-12.ebuild                      |   36 +
 sci-biology/spm/spm-8.ebuild                       |   40 +
 sci-biology/stacks/ChangeLog                       |    8 +-
 sci-biology/stacks/stacks-1.16.ebuild              |    7 +-
 sci-biology/staden/ChangeLog                       |   10 +-
 sci-biology/staden/staden-2.0.0_beta9.ebuild       |    4 +-
 sci-biology/staden/staden-9999.ebuild              |    4 +-
 sci-biology/swissknife/ChangeLog                   |    9 +-
 sci-biology/swissknife/swissknife-1.70.ebuild      |    4 +-
 sci-biology/tablet-bin/ChangeLog                   |    9 +-
 sci-biology/tablet-bin/Manifest                    |    3 +-
 .../tablet-bin/tablet-bin-1.13.12.17.ebuild        |   90 -
 .../tablet-bin/tablet-bin-1.14.04.10.ebuild        |   97 -
 .../tablet-bin/tablet-bin-1.14.10.21.ebuild        |   97 +
 sci-biology/tgicl/ChangeLog                        |    7 +-
 sci-biology/tgicl/tgicl-2.1.ebuild                 |    4 +-
 sci-biology/tmhmm/ChangeLog                        |    6 +-
 sci-biology/tmhmm/tmhmm-2.0c.ebuild                |   12 +-
 sci-biology/tophat/ChangeLog                       |   84 +
 sci-biology/tophat/Manifest                        |    3 +
 sci-biology/tophat/files/tophat-2.0.9-flags.patch  |  109 +
 sci-biology/tophat/metadata.xml                    |    8 +
 sci-biology/tophat/tophat-2.0.12.ebuild            |   60 +
 sci-biology/tophat/tophat-2.0.13.ebuild            |   63 +
 sci-biology/tophat/tophat-2.0.14.ebuild            |   64 +
 sci-biology/transdecoder/ChangeLog                 |   25 -
 sci-biology/transdecoder/Manifest                  |    1 -
 .../transdecoder/transdecoder-20140704.ebuild      |   51 -
 sci-biology/trf/trf-4.07b.ebuild                   |    2 +-
 sci-biology/trim_galore/ChangeLog                  |   15 +-
 sci-biology/trim_galore/Manifest                   |    2 +-
 sci-biology/trim_galore/trim_galore-0.3.3.ebuild   |   20 -
 sci-biology/trim_galore/trim_galore-0.4.0.ebuild   |   27 +
 sci-biology/trinityrnaseq/ChangeLog                |   31 +
 sci-biology/trinityrnaseq/Manifest                 |    1 +
 sci-biology/trinityrnaseq/metadata.xml             |   12 +
 .../trinityrnaseq/trinityrnaseq-2.0.6.ebuild       |   66 +
 sci-biology/twinscan/ChangeLog                     |   10 +-
 sci-biology/twinscan/twinscan-4.1.2-r1.ebuild      |   62 +
 sci-biology/twinscan/twinscan-4.1.2.ebuild         |   49 -
 sci-biology/ucsc-genome-browser/Manifest           |    1 -
 sci-biology/ucsc-genome-browser/metadata.xml       |   12 -
 .../ucsc-genome-browser-260.ebuild                 |  106 -
 sci-biology/ugene/ChangeLog                        |    6 +
 sci-biology/ugene/Manifest                         |    1 +
 .../{ugene-1.13.3.ebuild => ugene-1.16.1.ebuild}   |    0
 sci-biology/wgs-assembler/ChangeLog                |   19 +
 sci-biology/wgs-assembler/Manifest                 |    2 +
 .../{embassy-topo => wgs-assembler}/metadata.xml   |    0
 sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild |   78 +
 .../wgs-assembler/wgs-assembler-8.3_rc2.ebuild     |   80 +
 sci-biology/wise/ChangeLog                         |   10 +
 sci-biology/wise/Manifest                          |    1 +
 .../{embassy-structure => wise}/metadata.xml       |    0
 sci-biology/wise/wise-2.4.1.ebuild                 |   74 +
 sci-chemistry/GromacsWrapper/ChangeLog             |    5 +-
 .../GromacsWrapper/GromacsWrapper-9999.ebuild      |    2 +-
 sci-chemistry/GromacsWrapper/metadata.xml          |    3 +
 sci-chemistry/avogadro2/ChangeLog                  |    6 +-
 sci-chemistry/avogadro2/metadata.xml               |    3 +
 sci-chemistry/ball/ball-9999.ebuild                |    2 +-
 sci-chemistry/burrow-owl/ChangeLog                 |    6 +-
 sci-chemistry/burrow-owl/metadata.xml              |    3 +
 sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild     |    2 +-
 sci-chemistry/chemBuild/chemBuild-1.0.3.ebuild     |    2 +-
 sci-chemistry/chemBuild/chemBuild-1.0.4.ebuild     |    2 +-
 sci-chemistry/cnsface/ChangeLog                    |    6 +-
 sci-chemistry/cnsface/cnsface-0.0.12.ebuild        |    2 +-
 sci-chemistry/cnsface/metadata.xml                 |    5 +-
 sci-chemistry/cpmgfit/ChangeLog                    |    6 +-
 sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild          |    4 +-
 sci-chemistry/curvefit/ChangeLog                   |    6 +-
 sci-chemistry/curvefit/curvefit-1.40.ebuild        |    4 +-
 sci-chemistry/dl_poly/ChangeLog                    |    5 +-
 sci-chemistry/dl_poly/dl_poly-4.05.ebuild          |    5 +-
 sci-chemistry/freeon/ChangeLog                     |    5 +-
 sci-chemistry/freeon/freeon-9999.ebuild            |    5 +-
 sci-chemistry/gromacs/ChangeLog                    |    4 +
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild      |   27 +-
 sci-chemistry/gromacs/metadata.xml                 |    1 -
 sci-chemistry/mage/ChangeLog                       |    9 +-
 sci-chemistry/mage/Manifest                        |    2 +-
 sci-chemistry/mage/mage-6.44.060606.ebuild         |   10 +-
 sci-chemistry/mdsctk/ChangeLog                     |    9 +-
 sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild           |    6 +-
 sci-chemistry/mdsctk/metadata.xml                  |   19 +-
 sci-chemistry/mgltools-autodocktools/ChangeLog     |   12 +-
 .../mgltools-autodocktools-1.5.6.ebuild            |   17 +-
 sci-chemistry/mgltools-bhtree/ChangeLog            |    9 +-
 .../mgltools-bhtree/mgltools-bhtree-1.5.6.ebuild   |   12 +-
 sci-chemistry/mgltools-cadd/ChangeLog              |    9 +-
 .../mgltools-cadd/mgltools-cadd-1.5.6.ebuild       |   10 +-
 sci-chemistry/mgltools-cmolkit/ChangeLog           |    9 +-
 .../mgltools-cmolkit/mgltools-cmolkit-1.5.6.ebuild |   10 +-
 sci-chemistry/mgltools-dejavu/ChangeLog            |   10 +-
 .../mgltools-dejavu-1.5.6-r1.ebuild                |   10 +-
 .../mgltools-dejavu/mgltools-dejavu-1.5.6.ebuild   |   48 -
 sci-chemistry/mgltools-geomutils/ChangeLog         |   10 +-
 .../mgltools-geomutils-1.5.6.ebuild                |   12 +-
 sci-chemistry/mgltools-gle/ChangeLog               |   13 +-
 .../files/mgltools-gle-1.5.6-swig.patch            |   43 +
 .../mgltools-gle/mgltools-gle-1.5.6.ebuild         |   11 +-
 sci-chemistry/mgltools-mglutil/ChangeLog           |   16 +-
 .../files/mgltools-mglutil-1.5.6-tcltk86.patch     |  104 +
 .../mgltools-mglutil-1.5.6-r1.ebuild               |   49 +
 .../mgltools-mglutil/mgltools-mglutil-1.5.6.ebuild |   48 -
 sci-chemistry/mgltools-molkit/ChangeLog            |    9 +-
 .../mgltools-molkit/mgltools-molkit-1.5.6.ebuild   |   10 +-
 sci-chemistry/mgltools-networkeditor/ChangeLog     |   12 +-
 .../mgltools-networkeditor-1.5.6.ebuild            |   10 +-
 sci-chemistry/mgltools-opengltk/ChangeLog          |    9 +-
 .../mgltools-opengltk-1.5.6.ebuild                 |   16 +-
 sci-chemistry/mgltools-pmv/ChangeLog               |   18 +-
 .../mgltools-pmv/mgltools-pmv-1.5.6.ebuild         |   19 +-
 sci-chemistry/mgltools-pyautodock/ChangeLog        |   10 +-
 .../mgltools-pyautodock-1.5.6.ebuild               |   10 +-
 sci-chemistry/mgltools-pybabel/ChangeLog           |    9 +-
 .../mgltools-pybabel/mgltools-pybabel-1.5.6.ebuild |   10 +-
 sci-chemistry/mgltools-pyglf/ChangeLog             |    9 +-
 .../mgltools-pyglf/mgltools-pyglf-1.5.6.ebuild     |   12 +-
 sci-chemistry/mgltools-qslimlib/ChangeLog          |    9 +-
 .../mgltools-qslimlib-1.5.6.ebuild                 |   12 +-
 sci-chemistry/mgltools-scenario2/ChangeLog         |   10 +-
 .../mgltools-scenario2-1.5.6.ebuild                |   15 +-
 sci-chemistry/mgltools-sff/ChangeLog               |    9 +-
 .../mgltools-sff/mgltools-sff-1.5.6.ebuild         |   12 +-
 sci-chemistry/mgltools-support/ChangeLog           |    9 +-
 .../mgltools-support/mgltools-support-1.5.6.ebuild |   10 +-
 sci-chemistry/mgltools-symserv/ChangeLog           |    9 +-
 .../mgltools-symserv/mgltools-symserv-1.5.6.ebuild |   10 +-
 sci-chemistry/mgltools-utpackages/ChangeLog        |   10 +-
 .../mgltools-utpackages-1.5.6.ebuild               |   12 +-
 sci-chemistry/mgltools-viewer-framework/ChangeLog  |   12 +-
 .../mgltools-viewer-framework-1.5.6.ebuild         |   10 +-
 sci-chemistry/mgltools-vision/ChangeLog            |    9 +-
 .../mgltools-vision/mgltools-vision-1.5.6.ebuild   |   12 +-
 sci-chemistry/mgltools-visionlib/ChangeLog         |   10 +-
 .../mgltools-visionlib-1.5.6.ebuild                |   10 +-
 sci-chemistry/mgltools-volume/ChangeLog            |    9 +-
 .../mgltools-volume/mgltools-volume-1.5.6.ebuild   |   10 +-
 sci-chemistry/mgltools-webservices/ChangeLog       |   12 +-
 .../mgltools-webservices-1.5.6.ebuild              |   12 +-
 sci-chemistry/mgltools/ChangeLog                   |    6 +-
 sci-chemistry/mgltools/mgltools-1.5.6.ebuild       |   13 +-
 sci-chemistry/modelfree/ChangeLog                  |    6 +-
 sci-chemistry/modelfree/modelfree-4.20.ebuild      |    4 +-
 sci-chemistry/modeller/modeller-9.12-r3.ebuild     |    2 +-
 sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild        |    2 +-
 sci-chemistry/nmrpipe/ChangeLog                    |    6 +-
 .../nmrpipe/nmrpipe-8.1.2013.218.23.09-r1.ebuild   |   11 +-
 sci-chemistry/nwchem/ChangeLog                     |    6 +
 sci-chemistry/nwchem/Manifest                      |    2 +
 sci-chemistry/nwchem/nwchem-6.3_p2-r1.ebuild       |    2 +-
 sci-chemistry/nwchem/nwchem-6.5_p26243-r6.ebuild   |  291 ---
 sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild   |  293 +++
 .../openbabel-python/openbabel-python-9999.ebuild  |    2 +-
 sci-chemistry/pesto/pesto-9999.ebuild              |    2 +-
 .../phenix-bin/phenix-bin-1.8.2.1309.ebuild        |    2 +-
 .../phenix-bin/phenix-bin-1.8.4.1496.ebuild        |    2 +-
 sci-chemistry/pymol-plugins-psico/ChangeLog        |    6 +-
 sci-chemistry/pymol-plugins-psico/metadata.xml     |    3 +
 .../pymol-plugins-psico-9999.ebuild                |    2 +-
 sci-chemistry/pymol/ChangeLog                      |    9 +-
 sci-chemistry/pymol/pymol-9999.ebuild              |   12 +-
 sci-chemistry/pyquante/ChangeLog                   |    5 +-
 sci-chemistry/pyquante/metadata.xml                |    3 +
 sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild    |    2 +-
 sci-chemistry/pyquante/pyquante-1.6.4.ebuild       |    2 +-
 sci-chemistry/smmp/smmp-3.0.5.ebuild               |    2 +-
 sci-chemistry/specView/ChangeLog                   |    4 +-
 sci-chemistry/specView/specView-1.0.2.ebuild       |    2 +-
 sci-chemistry/specView/specView-1.0.3.ebuild       |    2 +-
 sci-chemistry/specView/specView-1.0.3_p2.ebuild    |    2 +-
 sci-chemistry/specView/specView-1.0.4.ebuild       |    2 +-
 sci-chemistry/unio/ChangeLog                       |    5 +-
 sci-chemistry/unio/unio-2.0.3-r1.ebuild            |   11 +-
 sci-chemistry/xplor-nih/ChangeLog                  |    3 +
 sci-chemistry/xplor-nih/xplor-nih-2.38.ebuild      |    5 +-
 sci-electronics/player/ChangeLog                   |    5 +-
 sci-electronics/player/metadata.xml                |    3 +
 sci-electronics/player/player-2.0.4.ebuild         |    2 +-
 sci-electronics/stage/ChangeLog                    |    8 +-
 sci-electronics/stage/Manifest                     |    2 +-
 sci-electronics/stage/metadata.xml                 |    5 +-
 sci-electronics/stage/stage-2.0.3.ebuild           |   16 +-
 sci-electronics/tnt/ChangeLog                      |    5 +-
 sci-electronics/tnt/metadata.xml                   |    3 +
 sci-geosciences/cdat-lite/ChangeLog                |   26 -
 sci-geosciences/cdat-lite/Manifest                 |    2 -
 sci-geosciences/cdat-lite/cdat-lite-5.2.ebuild     |   44 -
 sci-geosciences/cdat-lite/cdat-lite-6.0_rc2.ebuild |   40 -
 sci-geosciences/cdat-lite/files/5.2-impl-dec.patch |   60 -
 .../cdat-lite/files/5.2-shared-lib.patch           |   13 -
 sci-geosciences/cdat-lite/metadata.xml             |   12 -
 sci-geosciences/congen/ChangeLog                   |   11 -
 sci-geosciences/congen/Manifest                    |    1 -
 sci-geosciences/congen/congen-1.6.ebuild           |   17 -
 sci-geosciences/congen/metadata.xml                |    5 -
 .../harmonics-dwf-free-noncomm/ChangeLog           |   48 -
 .../harmonics-dwf-free-noncomm/Manifest            |    1 -
 .../harmonics-dwf-free-noncomm-20110410-r1.ebuild  |   22 -
 .../harmonics-dwf-free-noncomm/metadata.xml        |   13 -
 sci-geosciences/harmonics-dwf-free/ChangeLog       |   50 -
 sci-geosciences/harmonics-dwf-free/Manifest        |    1 -
 .../harmonics-dwf-free-20120302.ebuild             |   23 -
 sci-geosciences/harmonics-dwf-free/metadata.xml    |   12 -
 sci-geosciences/libtcd/ChangeLog                   |   45 -
 sci-geosciences/libtcd/Manifest                    |    1 -
 sci-geosciences/libtcd/libtcd-2.2.5_p2.ebuild      |   29 -
 sci-geosciences/libtcd/metadata.xml                |   12 -
 sci-geosciences/pydap/metadata.xml                 |    3 +
 sci-geosciences/pydap/pydap-3.1.1.ebuild           |    2 +-
 sci-geosciences/pydap/pydap-3.1.ebuild             |    2 +-
 sci-geosciences/pydap_handlers_cdms/metadata.xml   |    3 +
 .../pydap_handlers_cdms-0.2.0.1.ebuild             |    2 +-
 sci-geosciences/pydap_handlers_csv/metadata.xml    |    3 +
 .../pydap_handlers_csv-0.1.1.ebuild                |    2 +-
 sci-geosciences/pydap_handlers_hdf5/metadata.xml   |    3 +
 .../pydap_handlers_hdf5-0.1.7.ebuild               |    2 +-
 sci-geosciences/pydap_handlers_nca/metadata.xml    |    3 +
 .../pydap_handlers_nca-0.1.3.ebuild                |    2 +-
 sci-geosciences/pydap_handlers_netcdf/metadata.xml |    3 +
 .../pydap_handlers_netcdf-0.6.4.ebuild             |    2 +-
 sci-geosciences/pydap_handlers_proxy/metadata.xml  |    3 +
 .../pydap_handlers_proxy-0.1.1.ebuild              |    2 +-
 sci-geosciences/pydap_handlers_sql/metadata.xml    |    3 +
 .../pydap_handlers_sql-0.3.0.ebuild                |    2 +-
 sci-geosciences/pydap_handlers_sqlite/metadata.xml |    3 +
 .../pydap_handlers_sqlite-0.1.0.ebuild             |    2 +-
 sci-geosciences/pydap_responses_kml/metadata.xml   |    3 +
 .../pydap_responses_kml-0.4.6.ebuild               |    2 +-
 .../pydap_responses_matlab/metadata.xml            |    3 +
 .../pydap_responses_matlab-0.2.1.ebuild            |    2 +-
 .../pydap_responses_netcdf/metadata.xml            |    3 +
 .../pydap_responses_netcdf-0.1.4.1.ebuild          |    2 +-
 sci-geosciences/pydap_responses_wms/metadata.xml   |    3 +
 .../pydap_responses_wms-0.5.4.ebuild               |    2 +-
 sci-geosciences/pydap_responses_xls/metadata.xml   |    3 +
 .../pydap_responses_xls-0.1.2.ebuild               |    2 +-
 sci-geosciences/qgis/qgis-9999.ebuild              |    2 +-
 sci-geosciences/swmm/ChangeLog                     |   36 -
 sci-geosciences/swmm/Manifest                      |    1 -
 sci-geosciences/swmm/metadata.xml                  |   12 -
 sci-geosciences/swmm/swmm-5.0.022.ebuild           |   47 -
 sci-geosciences/tappy/ChangeLog                    |   44 -
 sci-geosciences/tappy/Manifest                     |    1 -
 sci-geosciences/tappy/metadata.xml                 |   16 -
 sci-geosciences/tappy/tappy-0.9.0.ebuild           |   21 -
 sci-geosciences/tcd-utils/ChangeLog                |   22 -
 sci-geosciences/tcd-utils/Manifest                 |    1 -
 sci-geosciences/tcd-utils/metadata.xml             |   12 -
 .../tcd-utils/tcd-utils-20080820.ebuild            |   17 -
 sci-geosciences/xtide/ChangeLog                    |   51 -
 sci-geosciences/xtide/Manifest                     |    1 -
 sci-geosciences/xtide/metadata.xml                 |   12 -
 sci-geosciences/xtide/xtide-2.13.ebuild            |   33 -
 sci-libs/acml/ChangeLog                            |    3 +
 sci-libs/acml/acml-6.1.0.31.ebuild                 |    3 +-
 sci-libs/amdlibm/amdlibm-3.1.ebuild                |    4 +-
 sci-libs/armadillo/ChangeLog                       |   54 +
 sci-libs/armadillo/Manifest                        |    8 +-
 sci-libs/armadillo/armadillo-4.200.0.ebuild        |  114 -
 sci-libs/armadillo/armadillo-4.300.8.ebuild        |  114 -
 sci-libs/armadillo/armadillo-4.300.9.ebuild        |  114 -
 sci-libs/armadillo/armadillo-4.600.2.ebuild        |  112 -
 ...llo-4.600.4.ebuild => armadillo-4.650.4.ebuild} |    0
 sci-libs/armadillo/armadillo-5.100.2.ebuild        |  112 +
 sci-libs/armadillo/armadillo-5.200.1.ebuild        |  112 +
 .../files/armadillo-3.820.1-example-makefile.patch |   33 -
 .../armadillo/files/armadillo-4.000.3-hdf5.patch   |   19 -
 sci-libs/armadillo/metadata.xml                    |   23 +-
 sci-libs/arrayfire/ChangeLog                       |   40 +
 sci-libs/arrayfire/arrayfire-0.9999.ebuild         |   96 +-
 sci-libs/arrayfire/arrayfire-3.0_beta.ebuild       |   94 +
 sci-libs/arrayfire/arrayfire-9999.ebuild           |   24 +-
 sci-libs/arrayfire/files/CMakeLists_examples.patch |   15 -
 sci-libs/arrayfire/files/FindBoostCompute.cmake    |   18 +
 .../arrayfire-3.0_beta-FindBoostCompute.patch      |   34 +
 ...AS.patch => arrayfire-3.0_beta-FindCBLAS.patch} |    0
 .../arrayfire-3.0_beta-opencl_CMakeLists.patch     |   26 +
 .../arrayfire/files/arrayfire-9999-FindCBLAS.patch |   52 +
 sci-libs/arrayfire/files/build_gtest.patch         |   55 -
 sci-libs/arrayfire/metadata.xml                    |    3 +
 sci-libs/atlas/ChangeLog                           |    5 +-
 sci-libs/atlas/metadata.xml                        |    3 +
 sci-libs/bliss/ChangeLog                           |   14 -
 sci-libs/bliss/Manifest                            |    1 -
 sci-libs/bliss/bliss-0.72.ebuild                   |   43 -
 sci-libs/bliss/files/bliss-0.72-autotools.patch    |  159 --
 sci-libs/bliss/files/bliss-0.72-fedora.patch       |  648 ------
 sci-libs/bliss/metadata.xml                        |    9 -
 sci-libs/bloom/ChangeLog                           |    9 +
 sci-libs/bloom/bloom-9999.ebuild                   |   28 +
 .../zmsort => sci-libs/bloom}/metadata.xml         |    0
 sci-libs/calculix-ccx/Manifest                     |    3 +
 sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild   |    4 +-
 sci-libs/calculix-ccx/calculix-ccx-2.8_p2.ebuild   |   70 +
 ...2_Makefile_custom_cc_flags_spooles_arpack.patch |   32 +
 sci-libs/ccif/ChangeLog                            |    7 +-
 sci-libs/ccif/ccif-0.3.20111209.ebuild             |    4 +-
 sci-libs/cgnslib/ChangeLog                         |   71 -
 sci-libs/cgnslib/Manifest                          |    2 -
 sci-libs/cgnslib/cgnslib-2.5.4.ebuild              |   57 -
 sci-libs/cgnslib/cgnslib-3.2.1.ebuild              |   49 -
 sci-libs/cgnslib/files/cgnslib-2.5.4.patch         |   71 -
 sci-libs/cgnslib/files/cgnslib-2.5.4_hdf5.patch    |   39 -
 sci-libs/cgnslib/files/cgnslib-3.2.1-cmake.patch   |  149 --
 sci-libs/cgnslib/metadata.xml                      |    8 -
 sci-libs/cgnstools/ChangeLog                       |    4 +-
 sci-libs/cgnstools/metadata.xml                    |    5 +-
 sci-libs/clblas/ChangeLog                          |   51 +
 sci-libs/clblas/Manifest                           |    1 +
 sci-libs/clblas/clblas-2.4-r1.ebuild               |   63 +
 sci-libs/clblas/clblas-9999.ebuild                 |   62 +
 ...l-cmake-configuration-to-lib-cmake-clBLAS.patch |   25 +
 .../clblas/files/clblas-samples_CMakeLists.patch   |   20 +
 .../files/clblas-scripts_perf_CMakeLists.patch     |   11 +
 sci-libs/clblas/metadata.xml                       |   26 +
 sci-libs/clfft/ChangeLog                           |   29 +
 sci-libs/clfft/Manifest                            |    1 -
 sci-libs/clfft/clfft-0.9999.ebuild                 |   53 +
 sci-libs/clfft/clfft-2.2.ebuild                    |    1 -
 sci-libs/clfft/clfft-2.4-r1.ebuild                 |   54 +
 sci-libs/clfft/clfft-2.4.ebuild                    |    1 -
 sci-libs/clfft/clfft-9999.ebuild                   |   20 +-
 .../files/clfft-2.4-fix-cmake-config-install.patch |  128 ++
 ...ll-cmake-configuration-to-lib-cmake-clFFT.patch |   25 +
 sci-libs/clfft/files/clfft-client_CMakeLists.patch |   33 +-
 .../files/clfft-scripts_perf_CMakeLists.patch      |   34 +-
 sci-libs/clfft/metadata.xml                        |    3 +
 sci-libs/clrng/ChangeLog                           |   12 +
 sci-libs/clrng/clrng-9999.ebuild                   |   54 +
 sci-libs/clrng/metadata.xml                        |   13 +
 sci-libs/dcmtk/ChangeLog                           |    6 +-
 sci-libs/dcmtk/dcmtk-3.6.0.ebuild                  |    6 +-
 sci-libs/dealii/ChangeLog                          |   14 +
 sci-libs/dealii/dealii-8.1.0-r2.ebuild             |    4 +-
 sci-libs/dealii/dealii-8.2.0.ebuild                |    2 +-
 sci-libs/dealii/dealii-8.2.1-r1.ebuild             |  127 ++
 sci-libs/dealii/dealii-8.2.1.ebuild                |  129 --
 sci-libs/dealii/dealii-9999.ebuild                 |   14 +-
 sci-libs/dealii/metadata.xml                       |    3 +
 sci-libs/elmer-eio/Manifest                        |    2 +-
 sci-libs/etsf_io/ChangeLog                         |    8 +-
 sci-libs/etsf_io/etsf_io-1.0.4-r1.ebuild           |   36 +
 sci-libs/etsf_io/etsf_io-1.0.4.ebuild              |   35 -
 sci-libs/etsf_io/metadata.xml                      |    8 +-
 sci-libs/fftw/ChangeLog                            |    6 +
 sci-libs/fftw/fftw-3.3.4-r1.ebuild                 |    8 +-
 sci-libs/framewave/ChangeLog                       |    9 +
 sci-libs/framewave/framewave-1.3.1.ebuild          |   10 +-
 sci-libs/framewave/metadata.xml                    |    3 +
 sci-libs/geom/ChangeLog                            |    9 +-
 sci-libs/geom/Manifest                             |    2 +-
 sci-libs/geom/geom-5.1.2.7.ebuild                  |   10 +-
 sci-libs/geom/metadata.xml                         |    5 +-
 sci-libs/ghmm/ghmm-9999.ebuild                     |    2 +-
 sci-libs/gotoblas2/ChangeLog                       |    7 +-
 sci-libs/gotoblas2/gotoblas2-1.13.ebuild           |    4 +-
 sci-libs/gotoblas2/metadata.xml                    |   14 +-
 sci-libs/gsl/ChangeLog                             |    7 +-
 sci-libs/gsl/gsl-1.16-r1.ebuild                    |   60 -
 sci-libs/gsl/gsl-1.16-r2.ebuild                    |    8 +-
 sci-libs/gsl/metadata.xml                          |   10 +-
 sci-libs/iml/ChangeLog                             |   12 +-
 sci-libs/iml/Manifest                              |    1 +
 .../iml-1.0.4-use-any-cblas-implementation.patch   |   22 +
 sci-libs/iml/iml-1.0.3-r2.ebuild                   |    4 +-
 sci-libs/iml/iml-1.0.4.ebuild                      |   35 +
 sci-libs/itk/ChangeLog                             |    3 +
 sci-libs/itk/itk-4.4.2-r1.ebuild                   |    2 +-
 sci-libs/itk/itk-4.4.2.ebuild                      |    2 +-
 sci-libs/itk/itk-4.5.1.ebuild                      |    2 +-
 sci-libs/itk/metadata.xml                          |    3 +
 sci-libs/jhdf5/ChangeLog                           |    9 +
 sci-libs/jhdf5/Manifest                            |    1 +
 sci-libs/jhdf5/jhdf5-14.12.1.ebuild                |   26 +
 .../zmsort => sci-libs/jhdf5}/metadata.xml         |    0
 sci-libs/k3match/k3match-1.1.ebuild                |    2 +-
 sci-libs/lapackpp/ChangeLog                        |    5 +-
 sci-libs/lapackpp/metadata.xml                     |    7 +-
 sci-libs/levmar/ChangeLog                          |   12 -
 sci-libs/levmar/Manifest                           |    1 -
 sci-libs/levmar/files/levmar-2.6-shared.patch      |   12 -
 sci-libs/levmar/levmar-2.6.ebuild                  |   47 -
 sci-libs/levmar/metadata.xml                       |   16 -
 sci-libs/libgeodecomp/ChangeLog                    |    8 +-
 sci-libs/libgeodecomp/Manifest                     |    3 -
 sci-libs/libgeodecomp/libgeodecomp-0.1.0.ebuild    |   26 -
 sci-libs/libgeodecomp/libgeodecomp-0.2.0.ebuild    |   36 -
 sci-libs/libgeodecomp/libgeodecomp-0.3.1.ebuild    |   36 -
 sci-libs/libmaus/ChangeLog                         |    6 +
 sci-libs/libmaus/metadata.xml                      |    7 +-
 sci-libs/libsc/ChangeLog                           |    8 +-
 sci-libs/libsc/libsc-1.0.ebuild                    |   13 +-
 sci-libs/libsc/metadata.xml                        |    3 +
 sci-libs/libsufr/ChangeLog                         |   25 +-
 sci-libs/libsufr/Manifest                          |    4 +-
 .../libsufr/files/libsufr-0.3.0-multilib.patch     |   11 -
 sci-libs/libsufr/libsufr-0.4.1.ebuild              |   28 -
 sci-libs/libsufr/libsufr-0.5.2.ebuild              |   28 -
 sci-libs/libsufr/libsufr-0.6.3.ebuild              |   28 +
 sci-libs/libsufr/libsufr-0.6.4.ebuild              |   28 +
 sci-libs/libsufr/metadata.xml                      |   21 +-
 sci-libs/libxc/ChangeLog                           |    9 +-
 sci-libs/libxc/Manifest                            |    4 +-
 sci-libs/libxc/libxc-2.1.1.ebuild                  |   57 -
 sci-libs/libxc/libxc-2.1.2.ebuild                  |   57 +
 sci-libs/libxc/libxc-2.2.1.ebuild                  |   57 -
 sci-libs/libxc/libxc-2.2.2.ebuild                  |   57 +
 sci-libs/lwpr/ChangeLog                            |    5 +-
 sci-libs/lwpr/metadata.xml                         |   13 +-
 sci-libs/matc/ChangeLog                            |   11 +-
 sci-libs/matc/Manifest                             |    5 +-
 sci-libs/matc/matc-8.0.ebuild                      |   42 +
 sci-libs/matc/matc-9999.ebuild                     |   20 +-
 sci-libs/matio/ChangeLog                           |   43 -
 sci-libs/matio/Manifest                            |    1 -
 sci-libs/matio/files/matio-1.3.4-autotools.patch   |   29 -
 sci-libs/matio/matio-1.3.4.ebuild                  |   43 -
 sci-libs/matio/metadata.xml                        |    9 -
 sci-libs/mkl/ChangeLog                             |    2 +-
 sci-libs/msms/msms-1.5.6.ebuild                    |    2 +-
 sci-libs/nibabel/ChangeLog                         |    6 +-
 sci-libs/nibabel/Manifest                          |    2 +-
 sci-libs/nibabel/nibabel-1.3.0.ebuild              |    4 +-
 sci-libs/nipy/metadata.xml                         |    3 +
 sci-libs/nipype/ChangeLog                          |    6 +-
 sci-libs/nipype/nipype-9999.ebuild                 |    6 +-
 sci-libs/o2scl/ChangeLog                           |    5 +-
 sci-libs/o2scl/metadata.xml                        |    7 +-
 sci-libs/oasa/oasa-0.13.1.ebuild                   |    2 +-
 sci-libs/omalloc/ChangeLog                         |    6 +-
 sci-libs/omalloc/omalloc-0.9.6.ebuild              |    8 +-
 sci-libs/openblas/ChangeLog                        |   17 +-
 sci-libs/openblas/Manifest                         |    1 +
 sci-libs/openblas/metadata.xml                     |    3 +
 sci-libs/openblas/openblas-0.2.11.ebuild           |  228 +-
 ...enblas-0.2.12.ebuild => openblas-0.2.14.ebuild} |    0
 sci-libs/openblas/openblas-0.2.8.ebuild            |    4 +-
 sci-libs/openblas/openblas-9999.ebuild             |    6 +-
 sci-libs/p4est/ChangeLog                           |    8 +-
 sci-libs/p4est/metadata.xml                        |    3 +
 sci-libs/p4est/p4est-1.0.ebuild                    |    4 +-
 sci-libs/pagmo/pagmo-9999.ebuild                   |    2 +-
 sci-libs/pg2plplot/ChangeLog                       |    5 +-
 sci-libs/pg2plplot/metadata.xml                    |   15 +-
 sci-libs/pmx/pmx-9999.ebuild                       |    2 +-
 sci-libs/pydicom/ChangeLog                         |   30 +-
 sci-libs/pydicom/pydicom-0.9.8.ebuild              |    4 +-
 sci-libs/pydicom/pydicom-9999.ebuild               |   21 +
 sci-libs/scikits_image/scikits_image-9999.ebuild   |    2 +-
 sci-libs/silo/Manifest                             |    1 -
 sci-libs/silo/files/silo-4.9.1-qtlibs.patch        |   66 -
 sci-libs/silo/metadata.xml                         |   18 -
 sci-libs/silo/silo-4.9.1.ebuild                    |   38 -
 sci-libs/symmetrica/ChangeLog                      |    9 +-
 sci-libs/symmetrica/Manifest                       |    2 +-
 .../symmetrica/files/symmetrica-2.0-banner.patch   |   11 +
 .../files/symmetrica-2.0-freeing_errors.patch      |   39 +
 .../files/symmetrica-2.0-function_names.patch      |  329 +++
 .../files/symmetrica-2.0-integersize.patch         |   37 +
 sci-libs/symmetrica/symmetrica-2.0-r1.ebuild       |   40 +
 sci-libs/symmetrica/symmetrica-2.0.ebuild          |    2 +-
 sci-libs/trilinos/ChangeLog                        |   23 +-
 sci-libs/trilinos/Manifest                         |    9 +-
 .../files/trilinos-11.12.1-fix-install-paths.patch |    2 +-
 .../files/trilinos-11.14.1-fix-install-paths.patch |   61 +
 ...nos-11.14.1-fix_install_paths_for_destdir.patch |  617 ++++++
 sci-libs/trilinos/metadata.xml                     |   73 +-
 sci-libs/trilinos/trilinos-11.0.3.ebuild           |    6 +-
 sci-libs/trilinos/trilinos-11.10.2.ebuild          |    6 +-
 sci-libs/trilinos/trilinos-11.12.1-r1.ebuild       |  202 ++
 sci-libs/trilinos/trilinos-11.12.1.ebuild          |  202 --
 sci-libs/trilinos/trilinos-11.14.1-r1.ebuild       |  207 ++
 sci-libs/trilinos/trilinos-11.4.2.ebuild           |    6 +-
 sci-libs/wannier90/ChangeLog                       |    9 +-
 sci-libs/wannier90/Manifest                        |    1 +
 sci-libs/wannier90/wannier90-2.0.1.ebuild          |   66 +
 sci-libs/xraylib/ChangeLog                         |   15 +-
 sci-libs/xraylib/Manifest                          |    1 +
 sci-libs/xraylib/metadata.xml                      |    3 +
 sci-libs/xraylib/xraylib-2.16.0.ebuild             |   10 +-
 sci-libs/xraylib/xraylib-3.1.0.ebuild              |   84 +
 sci-libs/zarja/ChangeLog                           |    6 +-
 sci-libs/zarja/metadata.xml                        |    3 +
 sci-mathematics/Macaulay2/Macaulay2-9999.ebuild    |    2 +-
 sci-mathematics/acl2/ChangeLog                     |   19 +-
 sci-mathematics/acl2/Manifest                      |    4 +-
 sci-mathematics/acl2/acl2-6.3.ebuild               |   69 -
 sci-mathematics/acl2/acl2-7.1.ebuild               |   51 +
 sci-mathematics/acl2/files/set-booksdir.patch      |   11 -
 sci-mathematics/acl2/metadata.xml                  |   41 +-
 sci-mathematics/burrtools/ChangeLog                |    6 +-
 sci-mathematics/burrtools/metadata.xml             |    7 +-
 sci-mathematics/cdfplayer/ChangeLog                |    9 +-
 sci-mathematics/cdfplayer/Manifest                 |    2 +-
 sci-mathematics/cdfplayer/cdfplayer-10.0.2.ebuild  |   50 +
 sci-mathematics/cdfplayer/cdfplayer-9.0.1.ebuild   |   54 -
 .../files/cdfplayer-9.0.1-installer.patch          |   19 -
 sci-mathematics/cipi/ChangeLog                     |    6 +-
 sci-mathematics/cipi/metadata.xml                  |    3 +
 sci-mathematics/dolfin/ChangeLog                   |    6 +-
 sci-mathematics/dolfin/dolfin-0.9.9.ebuild         |    2 +-
 sci-mathematics/dolfin/metadata.xml                |    3 +
 sci-mathematics/freefem++/ChangeLog                |    5 +-
 sci-mathematics/freefem++/Manifest                 |    2 +-
 sci-mathematics/freefem++/freefem++-3.8.ebuild     |    6 +-
 sci-mathematics/gambit/ChangeLog                   |    6 +-
 sci-mathematics/gambit/metadata.xml                |    3 +
 sci-mathematics/kayali/ChangeLog                   |    5 +-
 sci-mathematics/kayali/kayali-0.3.2.ebuild         |    2 +-
 sci-mathematics/kayali/metadata.xml                |    3 +
 sci-mathematics/lie/ChangeLog                      |   11 +-
 sci-mathematics/lie/Manifest                       |    2 +-
 sci-mathematics/lie/lie-2.2.2.ebuild               |   20 +-
 sci-mathematics/mdp/mdp-9999.ebuild                |    2 +-
 sci-mathematics/netgen/ChangeLog                   |    9 +-
 sci-mathematics/netgen/Manifest                    |    2 +-
 sci-mathematics/netgen/metadata.xml                |   11 +-
 sci-mathematics/netgen/netgen-5.0.0.ebuild         |   21 +-
 sci-mathematics/open-axiom/ChangeLog               |    6 +-
 sci-mathematics/open-axiom/metadata.xml            |    3 +
 sci-mathematics/petsc/ChangeLog                    |    8 +-
 sci-mathematics/petsc/Manifest                     |    1 +
 .../petsc/files/petsc-3.5.3-disable-rpath.patch    |   18 +
 sci-mathematics/petsc/petsc-3.5.3.ebuild           |  243 +++
 sci-mathematics/pulp/ChangeLog                     |    2 +-
 sci-mathematics/pulp/metadata.xml                  |    3 +
 sci-mathematics/pulp/pulp-1.5.6.ebuild             |    2 +-
 sci-mathematics/scilab/ChangeLog                   |   10 +
 sci-mathematics/scilab/Manifest                    |    1 +
 ...on.patch => scilab-5.5.2-accessviolation.patch} |    0
 ... scilab-5.5.2-fix-random-runtime-failure.patch} |    0
 ...wlinks.patch => scilab-5.5.2-followlinks.patch} |    0
 ....1-gluegen.patch => scilab-5.5.2-gluegen.patch} |    0
 ...ava-heap.patch => scilab-5.5.2-java-heap.patch} |    0
 ...singlib.patch => scilab-5.5.2-missinglib.patch} |    0
 ...-5.5.1-nogui.patch => scilab-5.5.2-nogui.patch} |    0
 sci-mathematics/scilab/scilab-5.5.2.ebuild         |  261 +++
 sci-mathematics/singular/ChangeLog                 |   10 -
 sci-mathematics/singular/Manifest                  |    1 -
 .../singular/files/60singular-gentoo.el            |   10 -
 .../singular-4.0.0-fix-omalloc-ar-detection.patch  |   12 -
 .../singular/files/singular-4.0.0-gentoo.patch     |   65 -
 sci-mathematics/singular/metadata.xml              |   12 -
 sci-mathematics/singular/singular-4.0.0_p2.ebuild  |  147 --
 sci-mathematics/ufc/ChangeLog                      |    5 +-
 sci-mathematics/ufc/metadata.xml                   |    8 +-
 sci-mathematics/yorick/ChangeLog                   |    5 +-
 sci-mathematics/yorick/metadata.xml                |    3 +
 sci-mathematics/z3/ChangeLog                       |    6 +-
 sci-mathematics/z3/z3-4.3.1.ebuild                 |    6 +-
 sci-mathematics/z3/z3-9999.ebuild                  |    6 +-
 sci-misc/elmer-gui/elmer-gui-9999.ebuild           |    2 +-
 sci-misc/hfst/ChangeLog                            |    6 +-
 sci-misc/hfst/metadata.xml                         |   19 +-
 sci-misc/irstlm/ChangeLog                          |   11 +-
 sci-misc/irstlm/Manifest                           |    3 +-
 sci-misc/irstlm/irstlm-5.80.03.ebuild              |   19 -
 sci-misc/irstlm/irstlm-5.80.06.ebuild              |   21 -
 sci-misc/irstlm/irstlm-5.80.08.ebuild              |   21 +
 sci-misc/irstlm/metadata.xml                       |   11 +-
 sci-misc/jwnl/ChangeLog                            |    5 +-
 sci-misc/jwnl/metadata.xml                         |    3 +
 sci-misc/kaldi/ChangeLog                           |    7 +
 sci-misc/kaldi/files/Makefile.patch                |   76 +-
 sci-misc/kaldi/files/configure.patch               |  164 +-
 sci-misc/kaldi/files/default_rules.mk.patch        |   67 +-
 sci-misc/kaldi/kaldi-0_p20150101.ebuild            |   59 -
 sci-misc/kaldi/kaldi-0_p20150301.ebuild            |   58 +
 sci-misc/nltk/ChangeLog                            |    5 +-
 sci-misc/nltk/metadata.xml                         |    3 +
 sci-misc/nltk/nltk-2.0.4.ebuild                    |    2 +-
 sci-misc/openfst/ChangeLog                         |    8 +-
 sci-misc/openfst/Manifest                          |    1 +
 sci-misc/openfst/files/kaldi-openfst-1.4.1.patch   |  269 +++
 sci-misc/openfst/openfst-1.4.1.ebuild              |   19 +
 sci-misc/opennlp-maxent/ChangeLog                  |    5 +-
 sci-misc/opennlp-maxent/metadata.xml               |    3 +
 sci-misc/opennlp-tools/ChangeLog                   |    5 +-
 sci-misc/opennlp-tools/metadata.xml                |    3 +
 sci-misc/pywordnet/ChangeLog                       |    5 +-
 sci-misc/pywordnet/metadata.xml                    |    3 +
 sci-misc/pywordnet/pywordnet-2.0.1.ebuild          |    2 +-
 sci-misc/simx/ChangeLog                            |    5 +-
 sci-misc/simx/metadata.xml                         |    3 +
 sci-misc/simx/simx-0.2.ebuild                      |    2 +-
 sci-misc/simx/simx-9999.ebuild                     |    2 +-
 sci-physics/abinit/ChangeLog                       |   10 +-
 sci-physics/abinit/Manifest                        |    1 +
 sci-physics/abinit/abinit-7.10.4.ebuild            |  390 ++++
 sci-physics/abinit/abinit-7.6.4-r1.ebuild          |    2 +-
 .../abinit/files/7.10.4-libabinit_options.patch    |   82 +
 sci-physics/abinit/files/7.10.4-syntax.patch       |   12 +
 sci-physics/bigdft/ChangeLog                       |   15 +-
 sci-physics/bigdft/Manifest                        |    3 +-
 sci-physics/bigdft/bigdft-1.7.1.ebuild             |  172 ++
 sci-physics/bigdft/bigdft-1.7.5.ebuild             |  178 --
 sci-physics/bigdft/bigdft-1.7.6.ebuild             |  172 ++
 .../bigdft/files/bigdft-1.7.1-longline.patch       |   14 +
 .../bigdft/files/bigdft-1.7.1-pkgconfig.patch      |   10 +
 .../bigdft/files/bigdft-1.7.5-pkgconfig.patch      |   10 -
 sci-physics/bigdft/metadata.xml                    |    3 +
 sci-physics/clip/ChangeLog                         |    6 +
 sci-physics/clip/metadata.xml                      |    5 +-
 sci-physics/elk/ChangeLog                          |    6 +-
 sci-physics/elk/metadata.xml                       |    3 +
 sci-physics/espresso++/ChangeLog                   |   11 +-
 sci-physics/espresso++/espresso++-9999.ebuild      |   12 +-
 sci-physics/espresso++/metadata.xml                |    3 +
 sci-physics/espresso/ChangeLog                     |    5 +-
 sci-physics/espresso/espresso-9999.ebuild          |    6 +-
 sci-physics/geant/ChangeLog                        |  353 ---
 sci-physics/geant/Manifest                         |    2 -
 sci-physics/geant/geant-3.21.14-r4.ebuild          |   70 -
 sci-physics/geant/metadata.xml                     |   14 -
 sci-physics/hoomd-blue/ChangeLog                   |   18 +
 sci-physics/hoomd-blue/hoomd-blue-9999.ebuild      |   61 +
 sci-physics/hoomd-blue/metadata.xml                |   12 +
 sci-physics/looptools/ChangeLog                    |    7 +-
 sci-physics/looptools/Manifest                     |    1 +
 sci-physics/looptools/looptools-2.12.ebuild        |   39 +
 sci-physics/root/ChangeLog                         |   65 +
 sci-physics/root/Manifest                          |    3 -
 sci-physics/root/files/root-5.32.00-chklib64.patch |    1 +
 sci-physics/root/files/root-5.32.00-dotfont.patch  |   58 -
 .../root/files/root-5.32.00-prop-flags.patch       |   15 -
 .../root/files/root-5.34.05-nobyte-compile.patch   |  137 --
 .../root/files/root-5.34.18-tutorials-path.patch   |   94 -
 sci-physics/root/files/root-6.00.01-cling.patch    |   19 -
 .../root/files/root-6.00.01-prop-flags.patch       |   17 -
 .../root/files/root-6.00.01-tutorials-path.patch   |   39 -
 sci-physics/root/files/root-6.00.02-tm_zone.patch  |   22 -
 sci-physics/root/metadata.xml                      |   32 +-
 sci-physics/root/root-5.34.18-r2.ebuild            |  389 ----
 sci-physics/root/root-6.00.01-r1.ebuild            |  442 ----
 sci-physics/root/root-6.00.02.ebuild               |  442 ----
 sci-physics/root/root-9999.ebuild                  |    4 +-
 sci-visualization/gnuplot/ChangeLog                |   10 +-
 sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild  |  194 --
 sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild  |   14 +-
 sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild  |    9 +-
 sci-visualization/gnuplot/metadata.xml             |    4 +-
 sci-visualization/labplot/ChangeLog                |    8 -
 .../labplot/files/labplot-9999-liborigin2.patch    |   12 -
 sci-visualization/labplot/labplot-9999.ebuild      |   37 -
 sci-visualization/mantid/ChangeLog                 |    3 +
 sci-visualization/mantid/metadata.xml              |    3 +
 sci-visualization/mayavi/ChangeLog                 |    3 +
 sci-visualization/mayavi/mayavi-4.4.0.ebuild       |    2 +-
 sci-visualization/mayavi/metadata.xml              |    3 +
 sci-visualization/visit/Manifest                   |    3 -
 .../files/visit-2.7.1-dont_symlink_visit_dir.patch |   18 -
 .../visit/files/visit-2.7.1-findpython.patch       |   19 -
 .../visit/files/visit-2.7.1-findsilo.patch         |   12 -
 .../visit/files/visit-2.7.1-findvtk.patch          |   24 -
 .../visit/files/visit-2.7.1-vtklibs.patch          |  142 --
 .../files/visit-2.7.2-dont_symlink_visit_dir.patch |   18 -
 .../visit/files/visit-2.7.2-findpython.patch       |   19 -
 .../visit/files/visit-2.7.2-findsilo.patch         |   12 -
 .../visit/files/visit-2.7.2-findvtk.patch          |   24 -
 .../visit/files/visit-2.7.2-vtklibs.patch          |  142 --
 .../files/visit-2.7.3-dont_symlink_visit_dir.patch |   18 -
 .../visit/files/visit-2.7.3-findpython.patch       |   19 -
 .../visit/files/visit-2.7.3-findsilo.patch         |   12 -
 .../visit/files/visit-2.7.3-findvtk.patch          |   24 -
 .../visit/files/visit-2.7.3-vtklibs.patch          |  142 --
 sci-visualization/visit/metadata.xml               |   21 -
 sci-visualization/visit/visit-2.7.1.ebuild         |   76 -
 sci-visualization/visit/visit-2.7.2.ebuild         |   82 -
 sci-visualization/visit/visit-2.7.3.ebuild         |   83 -
 sci-visualization/yt/metadata.xml                  |   15 +-
 sys-apps/hwloc/ChangeLog                           |  240 ---
 sys-apps/hwloc/Manifest                            |    1 -
 sys-apps/hwloc/files/hwloc-1.8.1-gl.patch          |   11 -
 sys-apps/hwloc/hwloc-1.10.1.ebuild                 |   69 -
 sys-apps/hwloc/metadata.xml                        |   21 -
 sys-apps/likwid/Manifest                           |    2 -
 sys-apps/likwid/files/likwid-3.0-paths.patch       |   27 -
 sys-apps/likwid/files/likwid-3.1.1-paths.patch     |   22 -
 .../likwid/files/likwid-3.1.1-shared_lib.patch     |   12 -
 sys-apps/likwid/files/use_access_daemon.patch      |   27 -
 sys-apps/likwid/files/use_uncore.patch             |   12 -
 sys-apps/likwid/likwid-3.0.ebuild                  |   33 -
 sys-apps/likwid/likwid-3.1.1.ebuild                |   32 -
 sys-apps/likwid/metadata.xml                       |   22 -
 sys-cluster/charmdebug/ChangeLog                   |   27 -
 sys-cluster/charmdebug/Manifest                    |    1 -
 sys-cluster/charmdebug/charmdebug-6.2.0-r1.ebuild  |   31 -
 sys-cluster/charmdebug/metadata.xml                |    5 -
 sys-cluster/gasnet/ChangeLog                       |   14 +
 sys-cluster/gasnet/Manifest                        |    1 +
 sys-cluster/gasnet/gasnet-1.24.0.ebuild            |   36 +
 sys-cluster/gasnet/gasnet-9999.ebuild              |   44 +
 sys-cluster/{nullmpi => gasnet}/metadata.xml       |    0
 sys-cluster/hpx/hpx-9999.ebuild                    |    2 +-
 sys-cluster/htcondor/ChangeLog                     |    3 +
 sys-cluster/htcondor/metadata.xml                  |    3 +
 sys-cluster/libquo/libquo-9999.ebuild              |    2 +-
 sys-cluster/mpich/ChangeLog                        |   19 +
 sys-cluster/mpich/Manifest                         |    1 +
 sys-cluster/mpich/mpich-3.1.3-r1.ebuild            |  127 --
 sys-cluster/mpich/mpich-3.1.3-r2.ebuild            |  122 ++
 sys-cluster/mpich/mpich-3.1.3-r99.ebuild           |  133 ++
 sys-cluster/mpich/mpich-3.1.4-r1.ebuild            |  122 ++
 sys-cluster/mpich2/ChangeLog                       |    6 +
 sys-cluster/mpich2/mpich2-1.5-r1.ebuild            |  125 --
 sys-cluster/openmpi/ChangeLog                      |   36 +
 sys-cluster/openmpi/Manifest                       |    1 +
 sys-cluster/openmpi/metadata.xml                   |    1 +
 sys-cluster/openmpi/openmpi-1.8.4-r2.ebuild        |  183 --
 sys-cluster/openmpi/openmpi-1.8.4-r4.ebuild        |  169 ++
 sys-cluster/openmpi/openmpi-1.8.4-r99.ebuild       |  191 ++
 sys-cluster/openmpi/openmpi-1.8.5.ebuild           |  164 ++
 sys-cluster/projections/ChangeLog                  |   13 -
 sys-cluster/projections/Manifest                   |    1 -
 sys-cluster/projections/metadata.xml               |    7 -
 sys-cluster/projections/projections-6.2.1.ebuild   |   30 -
 sys-cluster/pyslice/metadata.xml                   |    3 +
 sys-cluster/pyslice/pyslice-1.7.ebuild             |    2 +-
 sys-process/numactl/ChangeLog                      |   10 -
 sys-process/numactl/Manifest                       |    1 -
 .../numactl/files/numactl-2.0.8-cpuid-pic.patch    |   17 -
 sys-process/numactl/metadata.xml                   |    5 -
 sys-process/numactl/numactl-2.0.10-r1.ebuild       |   49 -
 virtual/mpi/ChangeLog                              |    6 +
 virtual/mpi/mpi-2.0-r4.ebuild                      |    8 +-
 .../perl-encoding-warnings-0.11.ebuild             |    2 +-
 x11-misc/envytools/ChangeLog                       |    5 +-
 x11-misc/envytools/metadata.xml                    |    3 +
 1666 files changed, 23173 insertions(+), 25158 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a32f235103241efb9e1f7fe5aa409499c65360a7
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 16 13:32:23 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 16 13:32:23 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a32f2351

Merge remote-tracking branch 'github/master'

* github/master:
  sci-mathematics/acl2: Version bump; Upstream url changes.

 sci-mathematics/acl2/ChangeLog                            | 7 +++++++
 sci-mathematics/acl2/Manifest                             | 2 +-
 sci-mathematics/acl2/{acl2-7.0.ebuild => acl2-7.1.ebuild} | 9 +++++----
 sci-mathematics/acl2/metadata.xml                         | 2 +-
 4 files changed, 14 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     d7d89a86f90ff1cd9766884591c2bfd727e424d9
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 16 07:32:42 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 16 07:32:42 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d7d89a86

Merge pull request #437 from ustcscgy/acl2-7.1

sci-mathematics/acl2: Version bump; Upstream url changes.

 sci-mathematics/acl2/ChangeLog                            | 7 +++++++
 sci-mathematics/acl2/Manifest                             | 2 +-
 sci-mathematics/acl2/{acl2-7.0.ebuild => acl2-7.1.ebuild} | 9 +++++----
 sci-mathematics/acl2/metadata.xml                         | 2 +-
 4 files changed, 14 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c045376d3e989449f1ca08fd9becb58de6dfdb65
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 15 07:23:52 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 15 07:23:52 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c045376d

Merge remote-tracking branch 'github/master'

* github/master:
  downloading tarball instead of zip

 sci-libs/nibabel/ChangeLog            | 6 ++++--
 sci-libs/nibabel/Manifest             | 2 +-
 sci-libs/nibabel/nibabel-1.3.0.ebuild | 4 ++--
 3 files changed, 7 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     cc4abc758fc880aaaf8fba7202e90f7ad6d86b9a
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 15 06:45:36 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 15 06:45:36 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cc4abc75

Merge pull request #434 from TheChymera/nibabel1

sci-lib/nibabel downloading tarball instead of zip

 sci-libs/nibabel/ChangeLog            | 6 ++++--
 sci-libs/nibabel/Manifest             | 2 +-
 sci-libs/nibabel/nibabel-1.3.0.ebuild | 4 ++--
 3 files changed, 7 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     508d33449e86d3721dfe71a599bfd42d59f75fa8
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun  7 18:33:44 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun  7 18:33:44 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=508d3344

Merge remote-tracking branch 'github/master'

* github/master:
  no longer depending on outdated version
  Revert "new ebuild"
  new ebuild

 sci-libs/nipype/ChangeLog          | 6 ++++--
 sci-libs/nipype/nipype-9999.ebuild | 4 ++--
 2 files changed, 6 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     161bbe69d571d57d061dafb8b99b9f20d66dd866
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Sat Jun  6 07:52:44 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun  6 07:52:44 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=161bbe69

Merge branch 'master' of https://github.com/gentoo-science/sci into sci

 app-vim/vim-gromacs/ChangeLog                      |   5 +-
 app-vim/vim-gromacs/metadata.xml                   |   3 +
 dev-libs/boost-compute/ChangeLog                   |  17 ++-
 ...pute-0.4.ebuild => boost-compute-0.4-r1.ebuild} |   0
 dev-libs/boost-compute/boost-compute-9999.ebuild   |  10 +-
 .../files/boost-compute-0.4-CMakeLists.patch       |  14 +++
 dev-libs/boost-compute/metadata.xml                |   3 +
 dev-libs/libcuda/ChangeLog                         |   5 +-
 dev-libs/libcuda/metadata.xml                      |   3 +
 dev-libs/libgdev/ChangeLog                         |   5 +-
 dev-libs/libgdev/metadata.xml                      |   3 +
 dev-python/astropy-helpers/ChangeLog               |   3 +
 dev-python/astropy-helpers/metadata.xml            |   4 +
 dev-python/astroquery/ChangeLog                    |   5 +-
 dev-python/astroquery/metadata.xml                 |   8 +-
 dev-python/brewer2mpl/ChangeLog                    |   3 +
 dev-python/brewer2mpl/metadata.xml                 |   4 +
 dev-python/ccdproc/ChangeLog                       |   5 +-
 dev-python/ccdproc/metadata.xml                    |   8 +-
 dev-python/coards/metadata.xml                     |   3 +
 dev-python/dimensionful/ChangeLog                  |   6 +-
 dev-python/dimensionful/metadata.xml               |   3 +
 dev-python/emcee/metadata.xml                      |   7 +-
 dev-python/gammapy/ChangeLog                       |   5 +-
 dev-python/gammapy/metadata.xml                    |   8 +-
 dev-python/healpy/ChangeLog                        |   5 +-
 dev-python/healpy/metadata.xml                     |  11 +-
 dev-python/imageutils/ChangeLog                    |   5 +-
 dev-python/imageutils/metadata.xml                 |   8 +-
 dev-python/matlab_wrapper/ChangeLog                |   3 +
 dev-python/matlab_wrapper/metadata.xml             |   4 +
 dev-python/matplotlib2tikz/ChangeLog               |  13 +++
 dev-python/matplotlib2tikz/Manifest                |   1 +
 .../matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild   |   1 +
 .../matplotlib2tikz/matplotlib2tikz-9999.ebuild    |  30 +++++
 .../metadata.xml                                   |   8 +-
 dev-python/meshpy/ChangeLog                        |   7 +-
 dev-python/meshpy/Manifest                         |   1 +
 ...meshpy-2013.1.2.ebuild => meshpy-2014.1.ebuild} |  17 ++-
 dev-python/meshpy/metadata.xml                     |   3 +
 dev-python/montage-wrapper/metadata.xml            |   7 +-
 dev-python/newrelic/ChangeLog                      |   6 +
 dev-python/newrelic/Manifest                       |   1 +
 dev-python/newrelic/metadata.xml                   |   3 +
 ...-2.44.0.36.ebuild => newrelic-2.50.0.39.ebuild} |   5 +
 dev-python/nvidia-ml-py/metadata.xml               |   3 +
 dev-python/photutils/ChangeLog                     |   5 +-
 dev-python/photutils/metadata.xml                  |   8 +-
 dev-python/pickleshare/ChangeLog                   |  13 +++
 dev-python/pickleshare/Manifest                    |   1 +
 dev-python/pickleshare/metadata.xml                |  18 +++
 dev-python/pickleshare/pickleshare-0.5.ebuild      |   1 +
 dev-python/pickleshare/pickleshare-9999.ebuild     |  39 +++++++
 dev-python/prettyplotlib/metadata.xml              |   3 +
 dev-python/ptyprocess/ChangeLog                    |  18 +++
 .../pysam => dev-python/ptyprocess}/metadata.xml   |   4 +-
 dev-python/ptyprocess/ptyprocess-9999.ebuild       |  25 ++++
 dev-python/pyfftw/ChangeLog                        |   3 +
 dev-python/pyfftw/metadata.xml                     |   3 +
 dev-python/pyfftw/pyfftw-9999.ebuild               |   9 ++
 dev-python/python-ivi/ChangeLog                    |   3 +
 dev-python/python-ivi/metadata.xml                 |   5 +-
 dev-python/python-vxi11/ChangeLog                  |   3 +
 dev-python/python-vxi11/metadata.xml               |   5 +-
 dev-python/pythoncgns/metadata.xml                 |   3 +
 dev-python/simplepam/ChangeLog                     |   3 +
 dev-python/simplepam/metadata.xml                  |   4 +
 dev-python/specutils/ChangeLog                     |   5 +-
 dev-python/specutils/metadata.xml                  |   8 +-
 dev-tex/pythontex/ChangeLog                        |   3 +
 dev-tex/pythontex/metadata.xml                     |   3 +
 profiles/categories                                |   3 -
 sci-biology/AlignGraph/ChangeLog                   |   3 +
 sci-biology/AlignGraph/metadata.xml                |   3 +
 sci-biology/BRANCH/ChangeLog                       |   4 +-
 sci-biology/BRANCH/metadata.xml                    |   3 +
 sci-biology/BlastToSam/ChangeLog                   |   3 +
 sci-biology/BlastToSam/metadata.xml                |   3 +
 sci-biology/HTSeq/metadata.xml                     |   3 +
 sci-biology/InterMine/ChangeLog                    |   4 +-
 sci-biology/InterMine/metadata.xml                 |   3 +
 sci-biology/argo-bin/ChangeLog                     |  10 ++
 sci-biology/argo-bin/Manifest                      |   1 +
 sci-biology/argo-bin/argo-bin-1.0.31.ebuild        |  16 +--
 ...rgo-bin-1.0.31.ebuild => argo-bin-2.0.3.ebuild} |  20 ++--
 sci-biology/argo/ChangeLog                         |   3 +
 sci-biology/argo/argo-1.0.24.ebuild                |   9 +-
 sci-biology/bamtools/ChangeLog                     |   6 +-
 sci-biology/bamtools/metadata.xml                  |   3 +
 sci-biology/biobambam/ChangeLog                    |   6 +
 sci-biology/biobambam/metadata.xml                 |   7 +-
 sci-biology/blue/ChangeLog                         |   6 +
 sci-biology/blue/Manifest                          |   6 +-
 sci-biology/blue/blue-1.1.2.ebuild                 |  12 +-
 sci-biology/blue/blue-1.1.3.ebuild                 |  38 ++++++
 sci-biology/bx-python/metadata.xml                 |   3 +
 sci-biology/codonw/ChangeLog                       |   8 +-
 ...donw-1.4.4-r1.ebuild => codonw-1.4.4-r2.ebuild} |   8 +-
 sci-biology/codonw/metadata.xml                    |  10 +-
 sci-biology/cutadapt/metadata.xml                  |   3 +
 sci-biology/dcmstack/ChangeLog                     |  13 ++-
 sci-biology/discrover/ChangeLog                    |   3 +
 sci-biology/discrover/metadata.xml                 |   3 +
 sci-biology/epga/ChangeLog                         |   3 +
 sci-biology/epga/metadata.xml                      |   3 +
 sci-biology/exonerate-gff3/ChangeLog               |   3 +
 sci-biology/exonerate-gff3/metadata.xml            |   3 +
 sci-biology/fastqc/ChangeLog                       |   7 ++
 sci-biology/fastqc/Manifest                        |   2 +-
 .../{fastqc-0.11.2.ebuild => fastqc-0.11.3.ebuild} |   8 +-
 sci-biology/freebayes/ChangeLog                    |   3 +
 sci-biology/freebayes/metadata.xml                 |   3 +
 sci-biology/fsl/ChangeLog                          |  53 +++++----
 sci-biology/khmer/ChangeLog                        |   5 +-
 sci-biology/khmer/metadata.xml                     |   4 +
 sci-biology/lighter/ChangeLog                      |   3 +
 sci-biology/lighter/metadata.xml                   |   3 +
 sci-biology/minced/ChangeLog                       |   3 +
 sci-biology/minced/metadata.xml                    |   3 +
 sci-biology/prokka/ChangeLog                       |   3 +
 sci-biology/prokka/prokka-1.11.ebuild              |   2 +-
 sci-biology/pyfaidx/metadata.xml                   |   3 +
 sci-biology/rum/ChangeLog                          |   6 +
 sci-biology/rum/Manifest                           |   2 +-
 sci-biology/rum/metadata.xml                       |   3 +
 sci-biology/rum/rum-2.0.5.5.ebuild                 |  14 +--
 sci-biology/sabre/ChangeLog                        |   3 +
 sci-biology/sabre/metadata.xml                     |   3 +
 sci-biology/salmon/ChangeLog                       |   3 +
 sci-biology/salmon/metadata.xml                    |   3 +
 sci-biology/scaffold_builder/ChangeLog             |  10 ++
 .../scaffold_builder-20131122.ebuild               |   6 +-
 sci-biology/screed/ChangeLog                       |   5 +-
 sci-biology/screed/metadata.xml                    |   4 +
 sci-biology/scythe/ChangeLog                       |   6 +-
 sci-biology/scythe/metadata.xml                    |   3 +
 sci-biology/sga/ChangeLog                          |   4 +-
 sci-biology/sga/metadata.xml                       |   9 +-
 sci-biology/sickle/ChangeLog                       |   3 +
 sci-biology/sickle/metadata.xml                    |   3 +
 sci-biology/spm/ChangeLog                          |  18 +--
 sci-biology/trim_galore/ChangeLog                  |   7 ++
 sci-biology/trim_galore/Manifest                   |   2 +-
 ...alore-0.3.7.ebuild => trim_galore-0.4.0.ebuild} |   5 +-
 sci-chemistry/mdsctk/ChangeLog                     |   3 +
 sci-chemistry/mdsctk/metadata.xml                  |   3 +
 sci-chemistry/pymol-plugins-psico/ChangeLog        |   6 +-
 sci-chemistry/pymol-plugins-psico/metadata.xml     |   3 +
 sci-geosciences/pydap/metadata.xml                 |   3 +
 sci-geosciences/pydap_handlers_cdms/metadata.xml   |   3 +
 sci-geosciences/pydap_handlers_csv/metadata.xml    |   3 +
 sci-geosciences/pydap_handlers_hdf5/metadata.xml   |   3 +
 sci-geosciences/pydap_handlers_nca/metadata.xml    |   3 +
 sci-geosciences/pydap_handlers_netcdf/metadata.xml |   3 +
 sci-geosciences/pydap_handlers_proxy/metadata.xml  |   3 +
 sci-geosciences/pydap_handlers_sql/metadata.xml    |   3 +
 sci-geosciences/pydap_handlers_sqlite/metadata.xml |   3 +
 sci-geosciences/pydap_responses_kml/metadata.xml   |   3 +
 .../pydap_responses_matlab/metadata.xml            |   3 +
 .../pydap_responses_netcdf/metadata.xml            |   3 +
 sci-geosciences/pydap_responses_wms/metadata.xml   |   3 +
 sci-geosciences/pydap_responses_xls/metadata.xml   |   3 +
 sci-libs/clblas/ChangeLog                          |  11 ++
 sci-libs/clblas/clblas-2.2.ebuild                  |  19 ++-
 sci-libs/clblas/clblas-2.4.ebuild                  |  63 +++++++++-
 sci-libs/clblas/clblas-9999.ebuild                 |  18 +--
 sci-libs/clblas/metadata.xml                       |   3 +
 sci-libs/clfft/ChangeLog                           |  15 +++
 sci-libs/clfft/Manifest                            |   1 -
 sci-libs/clfft/clfft-0.9999.ebuild                 |  54 ++++++++-
 sci-libs/clfft/clfft-2.2.ebuild                    |   1 -
 .../{clfft-9999.ebuild => clfft-2.4-r1.ebuild}     |  28 ++---
 sci-libs/clfft/clfft-2.4.ebuild                    |   1 -
 sci-libs/clfft/clfft-9999.ebuild                   |  28 ++---
 .../files/clfft-2.4-fix-cmake-config-install.patch | 128 +++++++++++++++++++++
 ...ll-cmake-configuration-to-lib-cmake-clFFT.patch |  25 ++++
 sci-libs/clfft/metadata.xml                        |   3 +
 sci-libs/clrng/ChangeLog                           |   3 +
 sci-libs/clrng/metadata.xml                        |   3 +
 sci-libs/elmer-eio/Manifest                        |   2 +-
 sci-libs/gotoblas2/ChangeLog                       |   7 +-
 sci-libs/gotoblas2/gotoblas2-1.13.ebuild           |   4 +-
 sci-libs/gotoblas2/metadata.xml                    |  14 +--
 sci-libs/libmaus/ChangeLog                         |   6 +
 sci-libs/libmaus/metadata.xml                      |   7 +-
 sci-libs/matc/ChangeLog                            |  11 +-
 sci-libs/matc/Manifest                             |   5 +-
 .../{matc-6.0_p4651.ebuild => matc-8.0.ebuild}     |  15 +--
 sci-libs/matc/matc-9999.ebuild                     |  20 ++--
 sci-libs/nipy/metadata.xml                         |   3 +
 sci-libs/pydicom/ChangeLog                         |  16 +--
 sci-libs/xraylib/ChangeLog                         |   7 ++
 sci-libs/xraylib/metadata.xml                      |   3 +
 sci-libs/xraylib/xraylib-2.16.0.ebuild             |   8 +-
 sci-libs/xraylib/xraylib-3.1.0.ebuild              |   6 +-
 sci-mathematics/cipi/ChangeLog                     |   6 +-
 sci-mathematics/cipi/metadata.xml                  |   3 +
 sci-mathematics/pulp/metadata.xml                  |   3 +
 sci-misc/simx/ChangeLog                            |   5 +-
 sci-misc/simx/metadata.xml                         |   3 +
 sci-visualization/yt/metadata.xml                  |  15 ++-
 sys-cluster/pyslice/metadata.xml                   |   3 +
 x11-misc/envytools/ChangeLog                       |   5 +-
 x11-misc/envytools/metadata.xml                    |   3 +
 204 files changed, 1291 insertions(+), 292 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     309a9899a61b40b7bb0a2d3afed13256e6aa9c13
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Fri May 29 00:19:06 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri May 29 00:19:06 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=309a9899

Merge branch 'master' of https://github.com/gentoo-science/sci into sci

 dev-libs/utf8proc/ChangeLog                        |   7 +
 .../utf8proc/files/utf8proc-1.2-buildflags.patch   |  40 ++++-
 dev-libs/utf8proc/metadata.xml                     |   4 +-
 ...{utf8proc-1.2.ebuild => utf8proc-1.2-r1.ebuild} |  13 +-
 sci-biology/AlignGraph/AlignGraph-9999.ebuild      |  53 ++++++
 sci-biology/AlignGraph/ChangeLog                   |   9 +
 .../bloom => sci-biology/AlignGraph}/metadata.xml  |   0
 sci-biology/amos/ChangeLog                         |   5 +
 sci-biology/amos/amos-3.1.0-r2.ebuild              |   3 +-
 sci-biology/amos/amos-9999.ebuild                  |   3 +-
 sci-biology/argo-bin/ChangeLog                     |   8 +-
 sci-biology/argo-bin/Manifest                      |   2 +-
 sci-biology/argo-bin/argo-bin-1.0.31.ebuild        |   4 +-
 sci-biology/augustus/ChangeLog                     |   6 +
 sci-biology/augustus/Manifest                      |   2 +-
 .../{augustus-3.0.3.ebuild => augustus-3.1.ebuild} |   0
 sci-biology/est2assembly/ChangeLog                 |   4 +
 sci-biology/est2assembly/est2assembly-1.08.ebuild  |   4 +-
 sci-biology/ffindex/ChangeLog                      |   5 +
 sci-biology/ffindex/Manifest                       |   2 +-
 sci-biology/ffindex/ffindex-0.9.9.3.ebuild         |   3 +-
 sci-biology/plinkseq/ChangeLog                     |   4 +
 sci-biology/plinkseq/plinkseq-0.10.ebuild          |   2 +
 sci-biology/wgs-assembler/ChangeLog                |   6 +
 sci-biology/wgs-assembler/Manifest                 |   2 +-
 sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild |  24 +--
 ...8.3_rc1.ebuild => wgs-assembler-8.3_rc2.ebuild} |  25 ++-
 sci-libs/armadillo/ChangeLog                       |  10 ++
 sci-libs/armadillo/Manifest                        |   3 +-
 sci-libs/armadillo/armadillo-5.000.1.ebuild        | 112 ------------
 ...llo-5.100.1.ebuild => armadillo-5.200.1.ebuild} |   0
 sci-libs/pydicom/ChangeLog                         |  28 ++-
 sci-libs/pydicom/pydicom-0.9.8.ebuild              |   4 +-
 sci-libs/pydicom/pydicom-9999.ebuild               |  21 +++
 sci-visualization/gnuplot/ChangeLog                |  10 +-
 sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild  | 194 ---------------------
 sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild  |  14 +-
 sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild  |   9 +-
 sci-visualization/gnuplot/metadata.xml             |   4 +-
 39 files changed, 273 insertions(+), 376 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     45b12f2821f9dcd078aa44a785d752b660e7f735
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun  7 11:19:03 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun  7 11:19:03 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=45b12f28

Merge pull request #431 from TheChymera/nipype

Nipype - removed outdated dep version

 sci-libs/nipype/ChangeLog          | 6 ++++--
 sci-libs/nipype/nipype-9999.ebuild | 4 ++--
 2 files changed, 6 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     80de9dc8cc9e9dd43c8c9e447be921dc06656769
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun  6 09:46:05 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun  6 09:46:05 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=80de9dc8

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/clblas: Fix installation of cmake configuration
  sci-libs/clblas: Drop old
  dev-libs/boost-compute: Update HOMEPAGE, SRC_URI and github remote-id: project was transfered on from kylelutz to boostorg
  sci-libs/clfft: Drop old; Install cmake configuration
  sci-libs/clfft: Cleanup ebuilds
  sci-libs/clfft: Fork 0.9999 from 9999
  sci-libs/clfft: Fork 2.4 from 9999
  sci-libs/clblas: Cleanup ebuilds
  sci-libs/clblas: Fork 2.4 from 9999

 dev-libs/boost-compute/ChangeLog                   |   5 +
 dev-libs/boost-compute/boost-compute-9999.ebuild   |   6 +-
 dev-libs/boost-compute/metadata.xml                |   2 +-
 sci-libs/clblas/ChangeLog                          |  16 +++
 sci-libs/clblas/Manifest                           |   1 -
 .../{clblas-2.2.ebuild => clblas-2.4-r1.ebuild}    |  16 +--
 sci-libs/clblas/clblas-2.4.ebuild                  |   1 -
 sci-libs/clblas/clblas-9999.ebuild                 |  15 +--
 .../files/clblas-2.2-client_CMakeLists.patch       |  11 --
 .../clblas-2.2-library_tools_tune_CMakeLists.patch |  14 ---
 ...l-cmake-configuration-to-lib-cmake-clBLAS.patch |  25 ++++
 sci-libs/clfft/ChangeLog                           |  12 ++
 sci-libs/clfft/Manifest                            |   1 -
 sci-libs/clfft/clfft-0.9999.ebuild                 |  54 ++++++++-
 sci-libs/clfft/clfft-2.2.ebuild                    |   1 -
 .../{clfft-9999.ebuild => clfft-2.4-r1.ebuild}     |  28 ++---
 sci-libs/clfft/clfft-2.4.ebuild                    |   1 -
 sci-libs/clfft/clfft-9999.ebuild                   |  28 ++---
 .../files/clfft-2.4-fix-cmake-config-install.patch | 128 +++++++++++++++++++++
 ...ll-cmake-configuration-to-lib-cmake-clFFT.patch |  25 ++++
 20 files changed, 291 insertions(+), 99 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Andrew Savchenko]

commit:     2835789d9d3802ed1cd1c6ce36a11fe152a4bf41
Author:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
AuthorDate: Fri Jun  5 07:33:28 2015 +0000
Commit:     Andrew Savchenko <bircoph <AT> gentoo <DOT> org>
CommitDate: Fri Jun  5 07:33:28 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2835789d

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 sci-biology/codonw/ChangeLog                                   |  8 +++++++-
 .../codonw/{codonw-1.4.4-r1.ebuild => codonw-1.4.4-r2.ebuild}  |  8 +++++---
 sci-biology/codonw/metadata.xml                                | 10 +++++-----
 3 files changed, 17 insertions(+), 9 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     8b08de27dcf31ce722b1da0cbfc760f3d498917c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun  4 12:58:00 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun  4 12:58:00 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8b08de27

Merge remote-tracking branch 'github/master'

* github/master:
  sci-physics/pythia:8: version bump

 sci-physics/pythia/ChangeLog            | 286 ++++++++++++++++++++++++++++++++
 sci-physics/pythia/Manifest             |   1 +
 sci-physics/pythia/metadata.xml         |  22 +++
 sci-physics/pythia/pythia-8.2.09.ebuild | 130 +++++++++++++++
 4 files changed, 439 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     4f355a29f7b7f9e40bfb8935bc16754d7db4c310
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun  3 10:21:33 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun  3 10:21:33 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4f355a29

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/arrayfire: Fetch tarball instead of getting src from git
  sci-libs/matc: Version bump
  sci-libs/matc: Source moved from sf.net to github; Fix LICENSE
  dev-python/matplotlib2tikz: New ebuild written by me
  dev-python/meshpy: Version bump; Implement python_test()
  sci-libs/elmer-eio: Update Manifest, fixes Bug #548398
  dev-python/newrelic: Version bump
  dev-python/pickleshare: Initial ebuild (required for >dev-python/ipython-3.1.0)
  dev-python/pyfftw: Copy missing data in python_test() phase
  dev-python/pyfftw: Implement python_test()
  dev-python/ptyprocess: Minor fix

 dev-python/matplotlib2tikz/ChangeLog               | 10 ++++++
 dev-python/matplotlib2tikz/Manifest                |  1 +
 .../matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild   |  1 +
 .../matplotlib2tikz/matplotlib2tikz-9999.ebuild    | 30 +++++++++++++++++
 .../{RecSQL => matplotlib2tikz}/metadata.xml       |  4 +--
 dev-python/meshpy/ChangeLog                        |  7 +++-
 dev-python/meshpy/Manifest                         |  1 +
 ...meshpy-2013.1.2.ebuild => meshpy-2014.1.ebuild} | 17 +++++++---
 dev-python/newrelic/ChangeLog                      |  6 ++++
 dev-python/newrelic/Manifest                       |  1 +
 ...-2.44.0.36.ebuild => newrelic-2.50.0.39.ebuild} |  5 +++
 dev-python/pickleshare/ChangeLog                   | 10 ++++++
 dev-python/pickleshare/Manifest                    |  1 +
 dev-python/pickleshare/metadata.xml                | 14 ++++++++
 dev-python/pickleshare/pickleshare-0.5.ebuild      |  1 +
 dev-python/pickleshare/pickleshare-9999.ebuild     | 39 ++++++++++++++++++++++
 dev-python/ptyprocess/ptyprocess-9999.ebuild       |  2 +-
 dev-python/pyfftw/ChangeLog                        |  3 ++
 dev-python/pyfftw/pyfftw-9999.ebuild               |  9 +++++
 sci-libs/arrayfire/ChangeLog                       |  4 +++
 sci-libs/arrayfire/Manifest                        |  1 +
 sci-libs/arrayfire/arrayfire-3.0_beta.ebuild       | 10 +++---
 sci-libs/elmer-eio/Manifest                        |  2 +-
 sci-libs/matc/ChangeLog                            | 11 ++++--
 sci-libs/matc/Manifest                             |  5 +--
 .../{matc-6.0_p4651.ebuild => matc-8.0.ebuild}     | 15 ++++-----
 sci-libs/matc/matc-9999.ebuild                     | 20 ++++-------
 27 files changed, 189 insertions(+), 41 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     77a867a4004e309acc1ace3a5a8366201f50f342
Author:     marbre <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Sat May 30 19:49:16 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat May 30 19:49:16 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=77a867a4

Merge pull request #430 from marbre/pyfftw

dev-python/pyfftw: Implement python_test()

 dev-python/pyfftw/ChangeLog          | 3 +++
 dev-python/pyfftw/pyfftw-9999.ebuild | 9 +++++++++
 2 files changed, 12 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c1bc1f4edfc2fb6ae3fe00124cf5f4b042d6c4c8
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat May 30 06:03:35 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat May 30 06:03:35 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c1bc1f4e

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/ptyprocess: Initial ebuild
  Correct ChangeLogs

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6222af206350e9426e6bfef413be54c3910a7efb
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue May 26 08:10:00 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue May 26 08:10:00 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6222af20

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/armadillo: Drop old
  sci-libs/armadillo: Version bump

 sci-libs/armadillo/ChangeLog                       |  10 ++
 sci-libs/armadillo/Manifest                        |   3 +-
 sci-libs/armadillo/armadillo-5.000.1.ebuild        | 112 ---------------------
 ...llo-5.100.1.ebuild => armadillo-5.200.1.ebuild} |   0
 4 files changed, 11 insertions(+), 114 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     9945cb28f62d59215ebc4ae6bf074ab2bb281113
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 25 23:29:54 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 25 23:29:54 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9945cb28

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 sci-libs/pydicom/ChangeLog                        |  28 +++-
 sci-libs/pydicom/pydicom-0.9.8.ebuild             |   4 +-
 sci-libs/pydicom/pydicom-9999.ebuild              |  21 +++
 sci-visualization/gnuplot/ChangeLog               |  10 +-
 sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild | 194 ----------------------
 sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild |  14 +-
 sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild |   9 +-
 sci-visualization/gnuplot/metadata.xml            |   4 +-
 8 files changed, 71 insertions(+), 213 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     c3104782a27833b406b7b5cfcae24d1700f74e43
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon May 25 19:40:01 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon May 25 19:40:01 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c3104782

Merge pull request #400 from TheChymera/pydicom

Pydicom live ebuild

 sci-libs/pydicom/ChangeLog            | 28 ++++++++++++++++++++++++++--
 sci-libs/pydicom/pydicom-0.9.8.ebuild |  4 ++--
 sci-libs/pydicom/pydicom-9999.ebuild  | 21 +++++++++++++++++++++
 3 files changed, 49 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     eb99a429362fd32fb9124706b7b6bc954c5ae9c5
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon May 25 23:02:34 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon May 25 23:02:34 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=eb99a429

Merge branch 'master' of ssh://github.com/gentoo-science/sci

 sci-libs/pydicom/ChangeLog            | 28 ++++++++++++++++++++++++++--
 sci-libs/pydicom/pydicom-0.9.8.ebuild |  4 ++--
 sci-libs/pydicom/pydicom-9999.ebuild  | 21 +++++++++++++++++++++
 3 files changed, 49 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     536799dcd824170367fcad85ea72fd30b3734c90
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun May 24 08:12:06 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun May 24 08:12:06 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=536799dc

Merge remote-tracking branch 'github/master'

* github/master:
  dev-java/jrosetta: Fix SRC_URI
  sci-libs/arrayfire: Split ebuilds/Typechange
  sci-biology/salmon: clean patch
  sci-biology/salmon: streamline ebuild
  sci-biology/salmon: add salmon

 dev-java/jrosetta/jrosetta-1.0.4.ebuild            |  4 +-
 sci-biology/salmon/ChangeLog                       | 19 +++++
 sci-biology/salmon/Manifest                        |  1 +
 .../files/salmon-0.3.2-no-boost-static.patch       | 20 +++++
 sci-biology/{pyfaidx => salmon}/metadata.xml       |  0
 sci-biology/salmon/salmon-0.3.2.ebuild             | 18 ++++
 sci-biology/salmon/salmon-9999.ebuild              | 19 +++++
 sci-libs/arrayfire/arrayfire-0.9999.ebuild         | 96 +++++++++++++++++++++-
 sci-libs/arrayfire/arrayfire-3.0_beta.ebuild       | 95 ++++++++++++++++++++-
 9 files changed, 268 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     1550f2e664d1b7a00c1ca9d9165ba1c1c1e8c75b
Author:     marbre <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Sat May 23 22:04:53 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat May 23 22:04:53 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1550f2e6

Merge pull request #425 from mschubert/salmon

sci-biology/salmon: add salmon

 sci-biology/salmon/ChangeLog                         | 19 +++++++++++++++++++
 sci-biology/salmon/Manifest                          |  1 +
 .../salmon/files/salmon-0.3.2-no-boost-static.patch  | 20 ++++++++++++++++++++
 sci-biology/{pyfaidx => salmon}/metadata.xml         |  0
 sci-biology/salmon/salmon-0.3.2.ebuild               | 18 ++++++++++++++++++
 sci-biology/salmon/salmon-9999.ebuild                | 19 +++++++++++++++++++
 6 files changed, 77 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     bbdf78006c7f7d0ced4f29515aed9e7631d71adc
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat May 23 17:10:18 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat May 23 17:10:18 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=bbdf7800

Merge pull request #426 from Fat-Zer/master

sci-libs/calculix-ccx: inherit fortran-2 as well

 sci-libs/calculix-ccx/calculix-ccx-2.8_p2.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     1a930a0faaead47c6d02c2d07c9636f006b5c3e9
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat May 23 15:52:59 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat May 23 15:52:59 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a930a0f

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/arrayfire: Split up ebuilds to fix 9999
  sci-libs/ccif: Bump to EAPI=5
  sci-libs/geom: Bump to EAPI=5
  sci-libs/amdlibm: Add missing die
  app-admin/eselect: Add missing die
  sci-libs/calculix-ccx: Add missing die
  sci-biology/kallisto: add kallisto
  media-gfx/brlcad: fixed deps tcl/tk slots
  sci-libs/calculix-ccx-2.8_p2: several small fixes
  dev-libs/utf8proc: Version bump
  sci-libs/calculix-ccx-2.8_p2 version bump
  dev-util/f90cache: Version bump
  dev-java/jrosetta: switching to fedora mirror because upstream server unavailable

 app-admin/eselect/eselect-1.4.4-r100.ebuild        |  2 +-
 dev-java/jrosetta/jrosetta-1.0.4.ebuild            |  4 +++-
 dev-libs/utf8proc/ChangeLog                        |  8 ++++++-
 dev-libs/utf8proc/Manifest                         |  1 +
 .../utf8proc/files/utf8proc-1.2-buildflags.patch   | 14 ++++++++++++
 .../{utf8proc-1.1.6.ebuild => utf8proc-1.2.ebuild} | 12 +++--------
 dev-util/f90cache/ChangeLog                        |  7 +++++-
 dev-util/f90cache/Manifest                         |  1 +
 .../{f90cache-0.94.ebuild => f90cache-0.95.ebuild} |  2 +-
 media-gfx/brlcad/ChangeLog                         |  4 ++++
 media-gfx/brlcad/brlcad-7.24.2.ebuild              |  4 ++--
 media-gfx/brlcad/brlcad-9999.ebuild                |  4 ++--
 sci-biology/kallisto/ChangeLog                     | 10 +++++++++
 sci-biology/kallisto/Manifest                      |  1 +
 sci-biology/kallisto/kallisto-0.42.1.ebuild        | 19 ++++++++++++++++
 sci-biology/kallisto/kallisto-9999.ebuild          | 20 +++++++++++++++++
 sci-biology/{pyfaidx => kallisto}/metadata.xml     |  0
 sci-libs/amdlibm/amdlibm-3.1.ebuild                |  4 ++--
 sci-libs/arrayfire/ChangeLog                       |  9 ++++++++
 sci-libs/arrayfire/arrayfire-9999.ebuild           | 15 +++++--------
 sci-libs/arrayfire/files/FindBoostCompute.cmake    | 18 ++++++++++++++++
 ...h => arrayfire-3.0_beta-FindBoostCompute.patch} |  0
 ...AS.patch => arrayfire-3.0_beta-FindCBLAS.patch} |  0
 ... => arrayfire-3.0_beta-opencl_CMakeLists.patch} |  0
 ...dCBLAS.patch => arrayfire-9999-FindCBLAS.patch} | 20 ++++++++---------
 sci-libs/calculix-ccx/Manifest                     |  3 +++
 sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild   |  4 ++--
 ...cx-2.7-r1.ebuild => calculix-ccx-2.8_p2.ebuild} | 13 ++++++-----
 ..._Makefile_custom_cc_flags_spooles_arpack.patch} | 25 +++++++++++-----------
 sci-libs/ccif/ChangeLog                            |  7 ++++--
 sci-libs/ccif/ccif-0.3.20111209.ebuild             |  4 ++--
 sci-libs/geom/ChangeLog                            |  6 ++++--
 sci-libs/geom/Manifest                             |  2 +-
 sci-libs/geom/geom-5.1.2.7.ebuild                  | 10 ++++-----
 34 files changed, 180 insertions(+), 73 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     481587b8e17d63cc269260068143ae2f9ee03bac
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu May 21 18:13:24 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu May 21 18:13:24 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=481587b8

Merge pull request #424 from mschubert/kallisto

sci-biology/kallisto: add kallisto

 sci-biology/kallisto/ChangeLog                 | 10 ++++++++++
 sci-biology/kallisto/Manifest                  |  1 +
 sci-biology/kallisto/kallisto-0.42.1.ebuild    | 19 +++++++++++++++++++
 sci-biology/kallisto/kallisto-9999.ebuild      | 20 ++++++++++++++++++++
 sci-biology/{pyfaidx => kallisto}/metadata.xml |  0
 5 files changed, 50 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     9385a068c4f96b5f819bb1315c5c6d44005ef040
Author:     marbre <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Sat May 23 13:04:55 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat May 23 13:04:55 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9385a068

Merge pull request #422 from Fat-Zer/master

sci-libs/calculix-ccx-2.8_p2 version bump

 sci-libs/calculix-ccx/Manifest                     |  3 +++
 ...cx-2.7-r1.ebuild => calculix-ccx-2.8_p2.ebuild} | 13 ++++++-----
 ..._Makefile_custom_cc_flags_spooles_arpack.patch} | 25 +++++++++++-----------
 3 files changed, 22 insertions(+), 19 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ea38a5827160055231ea3bdff57d7d3cd96cec49
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon May 18 19:13:46 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon May 18 19:13:46 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ea38a582

Merge pull request #417 from JohannesBuchner/master

dev-java/jrosetta: switching to fedora mirror because upstream server unavailable

 dev-java/jrosetta/jrosetta-1.0.4.ebuild | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     495779468e642d02b1da726e76822ea3ccbf1c8d
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon May 18 13:04:16 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon May 18 13:04:16 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=49577946

Merge pull request #416 from kiwifb/lie

Updating lie upstream and move to EAPI 5 issue #415

 sci-mathematics/lie/ChangeLog        | 11 +++++++++--
 sci-mathematics/lie/Manifest         |  2 +-
 sci-mathematics/lie/lie-2.2.2.ebuild | 20 ++++++++++----------
 3 files changed, 20 insertions(+), 13 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b3e413fb2c194b76fc2fe6905596b0e5af0f7016
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon May 18 13:05:18 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon May 18 13:05:18 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b3e413fb

Merge remote-tracking branch 'github/master'

* github/master:
  Cosmetic fixes requested by jlec
  signing
  dev-python/nvidia-ml-py: Version bump
  sci-libs/armadillo: Version bump
  Drop NVIDIA-CUDA license
  Move to tree

 dev-python/nvidia-ml-py/ChangeLog                  |    6 +
 dev-python/nvidia-ml-py/Manifest                   |    1 +
 ...-6.340.0.ebuild => nvidia-ml-py-7.346.0.ebuild} |    0
 dev-util/nvidia-cuda-sdk/ChangeLog                 |   14 -
 dev-util/nvidia-cuda-sdk/Manifest                  |    2 -
 dev-util/nvidia-cuda-sdk/metadata.xml              |   17 -
 .../nvidia-cuda-sdk/nvidia-cuda-sdk-7.0.18.ebuild  |  151 --
 .../nvidia-cuda-sdk/nvidia-cuda-sdk-7.0.28.ebuild  |  144 --
 dev-util/nvidia-cuda-toolkit/ChangeLog             |   21 -
 dev-util/nvidia-cuda-toolkit/Manifest              |    2 -
 dev-util/nvidia-cuda-toolkit/files/cuda-config.in  |   28 -
 dev-util/nvidia-cuda-toolkit/metadata.xml          |   18 -
 .../nvidia-cuda-toolkit-7.0.18-r1.ebuild           |  154 --
 .../nvidia-cuda-toolkit-7.0.28.ebuild              |  143 --
 licenses/NVIDIA-CUDA                               | 2262 --------------------
 sci-libs/armadillo/ChangeLog                       |    6 +
 sci-libs/armadillo/Manifest                        |    1 +
 ...llo-5.100.1.ebuild => armadillo-5.100.2.ebuild} |    0
 sci-mathematics/lie/ChangeLog                      |   11 +-
 sci-mathematics/lie/Manifest                       |    2 +-
 sci-mathematics/lie/lie-2.2.2.ebuild               |   20 +-
 21 files changed, 34 insertions(+), 2969 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     546a7e874370525c79f7765c5916381225e4b364
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May 12 17:15:10 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May 12 17:15:10 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=546a7e87

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 dev-tex/pythontex/ChangeLog                        |  6 ++
 ...hontex-0.14.ebuild => pythontex-0.14-r1.ebuild} |  2 +-
 dev-tex/pythontex/pythontex-9999.ebuild            |  8 +--
 licenses/polyphen                                  |  7 +++
 sci-libs/clblas/ChangeLog                          | 12 ++++
 sci-libs/clblas/Manifest                           |  1 +
 sci-libs/clblas/clblas-2.2.ebuild                  | 70 +++++++++++++++++++++-
 .../{clblas-2.2.ebuild => clblas-2.4.ebuild}       |  0
 sci-libs/clblas/clblas-9999.ebuild                 |  2 -
 ...ts.patch => clblas-2.2-client_CMakeLists.patch} |  0
 ...clblas-2.2-library_tools_tune_CMakeLists.patch} |  0
 sci-libs/clfft/ChangeLog                           |  6 ++
 .../{clfft-2.4.ebuild => clfft-0.9999.ebuild}      |  0
 sci-libs/clfft/clfft-9999.ebuild                   | 16 +++--
 sci-libs/clrng/ChangeLog                           |  9 +++
 .../clfft-9999.ebuild => clrng/clrng-9999.ebuild}  | 32 ++++------
 {dev-tex/pythontex => sci-libs/clrng}/metadata.xml |  4 +-
 17 files changed, 142 insertions(+), 33 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c4123fcd7b91c68fa91faee4c4f8a8b386d9de65
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue May 12 11:18:37 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue May 12 11:18:37 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c4123fcd

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/clfft: clfft-9999 points to develop branch
  sci-libs/clrng: Initial ebuild
  sci-libs/clblas: Version bump
  sci-libs/clblas-2.2: Replace symlink by file; New patchset
  sci-libs/clblas: Adjust patchset
  Dummy polyphen license

 licenses/polyphen                                  |  7 +++
 sci-libs/clblas/ChangeLog                          | 12 ++++
 sci-libs/clblas/Manifest                           |  1 +
 sci-libs/clblas/clblas-2.2.ebuild                  | 70 +++++++++++++++++++++-
 .../{clblas-2.2.ebuild => clblas-2.4.ebuild}       |  0
 sci-libs/clblas/clblas-9999.ebuild                 |  2 -
 ...ts.patch => clblas-2.2-client_CMakeLists.patch} |  0
 ...clblas-2.2-library_tools_tune_CMakeLists.patch} |  0
 sci-libs/clfft/ChangeLog                           |  6 ++
 .../{clfft-2.4.ebuild => clfft-0.9999.ebuild}      |  0
 sci-libs/clfft/clfft-9999.ebuild                   | 16 +++--
 sci-libs/clrng/ChangeLog                           |  9 +++
 .../clfft-9999.ebuild => clrng/clrng-9999.ebuild}  | 32 ++++------
 {dev-tex/pythontex => sci-libs/clrng}/metadata.xml |  4 +-
 14 files changed, 131 insertions(+), 28 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     b3c5536dafc95bae5f17da941a8c4bde8eedb968
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May  5 14:02:08 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May  5 14:02:08 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b3c5536d

Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci

 sci-libs/libsufr/ChangeLog                                    | 11 +++++++++--
 sci-libs/libsufr/Manifest                                     |  4 ++--
 .../libsufr/{libsufr-0.5.2.ebuild => libsufr-0.6.2.ebuild}    |  2 +-
 .../libsufr/{libsufr-0.4.1.ebuild => libsufr-0.6.3.ebuild}    |  2 +-
 4 files changed, 13 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     dde51a34e83526e0ee59e617a1fb3e310769acff
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon May  4 09:56:42 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon May  4 09:56:42 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=dde51a34

Merge pull request #409 from apieum/patch-1

add metis dependency #408

 sci-mathematics/netgen/netgen-5.0.0.ebuild | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Andrew Savchenko]

commit:     ccc478083ef4b8085960c74124524eab498b1cf6
Author:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
AuthorDate: Sun May  3 20:43:08 2015 +0000
Commit:     Andrew Savchenko <bircoph <AT> gentoo <DOT> org>
CommitDate: Sun May  3 20:43:08 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ccc47808

Merge remote-tracking branch 'github/master'

 media-gfx/brlcad/ChangeLog                         |   4 +
 media-gfx/brlcad/Manifest                          |   3 +-
 media-gfx/brlcad/brlcad-7.22.0.ebuild              |  15 +-
 .../{brlcad-7.20.4.ebuild => brlcad-7.24.0.ebuild} |  33 ++---
 .../{brlcad-7.20.4.ebuild => brlcad-7.24.2.ebuild} |  60 ++++----
 media-gfx/brlcad/brlcad-9999.ebuild                |  53 +++----
 media-gfx/brlcad/files/brlcad-7.24.2-cmake.patch   |  13 ++
 sci-biology/grappa/ChangeLog                       |   6 +-
 sci-biology/grappa/grappa-2.0.ebuild               |   9 +-
 sci-biology/signalp/ChangeLog                      |   6 +-
 sci-biology/signalp/signalp-3.0.ebuild             |   6 +-
 sci-biology/tmhmm/ChangeLog                        |   6 +-
 sci-biology/tmhmm/tmhmm-2.0c.ebuild                |  12 +-
 sci-chemistry/mage/ChangeLog                       |   9 +-
 sci-chemistry/mage/mage-6.44.060606.ebuild         |  10 +-
 sci-libs/armadillo/ChangeLog                       | 165 +++++++++++++++++++++
 sci-libs/armadillo/Manifest                        |   2 +
 sci-libs/armadillo/armadillo-4.650.4.ebuild        | 112 ++++++++++++++
 sci-libs/armadillo/armadillo-5.000.1.ebuild        | 112 ++++++++++++++
 sci-libs/armadillo/metadata.xml                    |  33 +++++
 sci-mathematics/netgen/ChangeLog                   |   6 +-
 sci-mathematics/netgen/Manifest                    |   2 +-
 sci-mathematics/netgen/netgen-5.0.0.ebuild         |  12 +-
 23 files changed, 567 insertions(+), 122 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Francois Bissey]

commit:     936bdadea119ee5e11e1a0760b97d3689fee0d2f
Author:     François Bissey <francois.bissey <AT> canterbury <DOT> ac <DOT> nz>
AuthorDate: Mon Apr 20 01:10:05 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Mon Apr 20 01:10:05 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=936bdade

Merge pull request #118 from TheChymera/fsl

FSL is in good enough condition to get in the overlay in my opinion. There is still some work to do (splitting some dependencies not currently in the tree) but this can be managed from the overlay.

 sci-biology/fsl/ChangeLog                          |  82 ++++
 sci-biology/fsl/Manifest                           |   2 +
 sci-biology/fsl/files/99fsl                        |   5 +
 sci-biology/fsl/files/fsl-5.0.4-headers.patch      |  32 ++
 sci-biology/fsl/files/fsl-5.0.4-setup.patch        | 110 +++++
 sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch | 456 +++++++++++++++++++++
 sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch | 452 ++++++++++++++++++++
 sci-biology/fsl/files/fsl-5.0.8-headers.patch      |  21 +
 sci-biology/fsl/files/fsl-5.0.8-setup.patch        | 113 +++++
 sci-biology/fsl/fsl-5.0.6.ebuild                   | 130 ++++++
 sci-biology/fsl/fsl-5.0.8.ebuild                   | 130 ++++++
 sci-biology/{OBO-Edit => fsl}/metadata.xml         |   7 +-
 12 files changed, 1536 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Francois Bissey]

commit:     d2a4fc8ebd3532f2bac248c60614979978b4818d
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Wed Mar 25 10:06:13 2015 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Wed Mar 25 10:06:13 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d2a4fc8e

Merge branch 'master' of https://github.com/gentoo-science/sci into fsl

 .travis.yml                                        |    22 +
 CONTRIBUTING.md                                    |   150 +
 README.md                                          |    15 +-
 app-admin/eselect/ChangeLog                        |    39 +-
 app-admin/eselect/Manifest                         |     5 +
 app-admin/eselect/eselect-1.3.7-r100.ebuild        |     2 +-
 app-admin/eselect/eselect-1.3.8-r100.ebuild        |     2 +-
 app-admin/eselect/eselect-1.4-r100.ebuild          |    72 +
 app-admin/eselect/eselect-1.4.1-r100.ebuild        |    72 +
 app-admin/eselect/eselect-1.4.2-r100.ebuild        |    72 +
 app-admin/eselect/eselect-1.4.3-r100.ebuild        |    72 +
 app-admin/eselect/eselect-1.4.4-r100.ebuild        |    72 +
 app-admin/eselect/eselect-9999.ebuild              |    69 +
 .../eselect/files/eselect-1.4.2-alternatives.patch |   616 +
 app-benchmarks/btl/btl-9999.ebuild                 |     2 +-
 app-benchmarks/numbench/ChangeLog                  |     5 +-
 app-benchmarks/numbench/numbench-0.2.ebuild        |     2 +-
 app-benchmarks/numbench/numbench-9999.ebuild       |     4 +-
 app-doc/blacs-docs/ChangeLog                       |     6 +-
 app-doc/blacs-docs/blacs-docs-1.1.ebuild           |     8 +-
 app-doc/blacs-docs/metadata.xml                    |     4 +-
 app-doc/blas-docs/ChangeLog                        |     6 +-
 app-doc/blas-docs/blas-docs-3.3.ebuild             |    12 +-
 app-doc/blas-docs/metadata.xml                     |     4 +-
 app-doc/lapack-docs/lapack-docs-3.3-r1.ebuild      |     2 +-
 app-doc/root-docs/ChangeLog                        |   225 +-
 app-doc/root-docs/Manifest                         |     7 +-
 .../files/root-docs-5.34.01-makehtml.patch         |    51 -
 .../files/root-docs-6.00.01-fillpatterns.patch     |    30 +
 .../files/root-docs-6.00.01-makehtml.patch         |    55 +
 app-doc/root-docs/metadata.xml                     |     9 +-
 app-doc/root-docs/root-docs-5.34.09.ebuild         |    76 -
 app-doc/root-docs/root-docs-6.00.02.ebuild         |   133 +
 app-doc/root-docs/root-docs-9999.ebuild            |    98 +-
 app-doc/scalapack-docs/scalapack-docs-2.0.ebuild   |     2 +-
 app-forensics/vine/ChangeLog                       |     8 +-
 app-forensics/vine/metadata.xml                    |     8 +-
 app-forensics/vine/vine-1.0.ebuild                 |     7 +-
 app-portage/g-octave/ChangeLog                     |     5 +-
 app-portage/g-octave/g-octave-9999.ebuild          |     5 +-
 app-text/dgs/ChangeLog                             |     6 +-
 app-text/dgs/dgs-0.5.10-r2.ebuild                  |    35 +-
 app-text/dgs/metadata.xml                          |     2 +-
 app-text/jabref/ChangeLog                          |    73 +-
 app-text/jabref/Manifest                           |     3 +-
 app-text/jabref/jabref-2.10.ebuild                 |    70 +
 app-text/jabref/jabref-2.10_beta.ebuild            |    35 -
 app-text/jabref/jabref-2.10_beta2-r1.ebuild        |    70 +
 app-text/jabref/jabref-2.9.2-r1.ebuild             |    13 +-
 app-text/jabref/jabref-2.9.2.ebuild                |    28 -
 app-text/jabref/metadata.xml                       |     8 +-
 app-vim/freefem++-syntax/ChangeLog                 |    33 -
 app-vim/freefem++-syntax/Manifest                  |     1 -
 .../freefem++-syntax-20081108-r1.ebuild            |    17 -
 app-vim/freefem++-syntax/metadata.xml              |     9 -
 app-vim/vim-gromacs/ChangeLog                      |    12 +-
 app-vim/vim-gromacs/metadata.xml                   |     4 +-
 app-vim/vim-gromacs/vim-gromacs-9999.ebuild        |    14 +-
 dev-cpp/eigen/ChangeLog                            |    36 +-
 dev-cpp/eigen/Manifest                             |     6 +-
 .../{eigen-3.2.0.ebuild => eigen-3.2.1-r2.ebuild}  |     0
 .../{eigen-3.2.0.ebuild => eigen-3.2.2.ebuild}     |     0
 dev-cpp/eigen/eigen-9999.ebuild                    |    61 +-
 dev-cpp/eigen/metadata.xml                         |    21 +-
 dev-cpp/growler-arch/ChangeLog                     |     6 +-
 dev-cpp/growler-arch/Manifest                      |     1 -
 dev-cpp/growler-arch/growler-arch-0.3.7.1.ebuild   |    34 +-
 dev-cpp/growler-arch/growler-arch-0.3.7.ebuild     |    35 -
 dev-cpp/growler-arch/metadata.xml                  |    10 +-
 dev-cpp/growler-core/ChangeLog                     |     6 +-
 dev-cpp/growler-core/growler-core-0.3.7.ebuild     |    33 +-
 dev-cpp/growler-core/metadata.xml                  |    10 +-
 dev-cpp/growler-link/ChangeLog                     |     6 +-
 dev-cpp/growler-link/growler-link-0.3.7.ebuild     |     7 +-
 dev-cpp/growler-link/metadata.xml                  |    10 +-
 dev-cpp/growler-math/ChangeLog                     |     6 +-
 dev-cpp/growler-math/growler-math-0.3.4.1.ebuild   |    26 +-
 dev-cpp/growler-math/metadata.xml                  |    10 +-
 dev-cpp/growler-thread/ChangeLog                   |     6 +-
 dev-cpp/growler-thread/growler-thread-0.3.4.ebuild |    28 +-
 dev-cpp/growler-thread/metadata.xml                |    10 +-
 dev-cpp/growler/ChangeLog                          |     6 +-
 dev-cpp/growler/growler-0.3.8.2.ebuild             |    26 +-
 dev-cpp/growler/growler-0.3.8.ebuild               |    21 -
 dev-cpp/growler/metadata.xml                       |    10 +-
 dev-cpp/icnc/ChangeLog                             |    36 +
 dev-cpp/icnc/icnc-9999.ebuild                      |    56 +
 {dev-util/f90cache => dev-cpp/icnc}/metadata.xml   |     0
 dev-db/cppdb/ChangeLog                             |    26 -
 dev-db/cppdb/Manifest                              |     1 -
 dev-db/cppdb/cppdb-0.3.1-r1.ebuild                 |    50 -
 dev-db/cppdb/metadata.xml                          |    14 -
 dev-java/fits/ChangeLog                            |    10 +
 dev-java/fits/fits-1.11.0-r1.ebuild                |    69 +
 dev-java/fits/fits-1.11.0.ebuild                   |    54 -
 dev-java/fits/metadata.xml                         |     4 +-
 dev-java/flexdock/ChangeLog                        |     6 +-
 dev-java/flexdock/Manifest                         |     2 +-
 ....3-nodemo.patch => flexdock-1.2.4-nodemo.patch} |     0
 dev-java/flexdock/flexdock-1.1.1.ebuild            |     7 +-
 dev-java/flexdock/flexdock-1.2.3.ebuild            |    45 -
 dev-java/flexdock/flexdock-1.2.4.ebuild            |    45 +
 dev-java/flexdock/metadata.xml                     |     4 +-
 dev-java/glazedlists/ChangeLog                     |    12 +
 dev-java/glazedlists/Manifest                      |     1 +
 .../files/glazedlists-1.8.0-build.xml.patch        |    57 +
 dev-java/glazedlists/glazedlists-1.8.0.ebuild      |    50 +
 dev-java/glazedlists/metadata.xml                  |     5 +
 dev-java/gluegen/ChangeLog                         |    29 +-
 dev-java/gluegen/Manifest                          |     1 +
 dev-java/gluegen/files/2.1.4-dont-copy-jars.patch  |    17 +
 dev-java/gluegen/files/2.1.4-dont-strip.patch      |    22 +
 .../gluegen/files/2.1.4-dont-test-archive.patch    |    16 +
 dev-java/gluegen/gluegen-1_p20080421.ebuild        |    24 +-
 dev-java/gluegen/gluegen-2.0_rc8.ebuild            |    11 +-
 dev-java/gluegen/gluegen-2.1.4.ebuild              |    68 +
 dev-java/hdf-java/ChangeLog                        |     6 +-
 dev-java/hdf-java/hdf-java-2.9.ebuild              |    15 +-
 dev-java/hdf-java/metadata.xml                     |    12 +-
 dev-java/jcip-annotations/ChangeLog                |     5 +-
 dev-java/jcip-annotations/Manifest                 |     2 +-
 .../jcip-annotations-1.0-r1.ebuild                 |    12 +-
 dev-java/jeuclid-core/ChangeLog                    |    14 +-
 .../files/jeuclid-core-cast-issue.patch            |    18 +
 dev-java/jeuclid-core/jeuclid-core-3.1.8.ebuild    |     4 +-
 dev-java/jeuclid-core/jeuclid-core-3.1.9-r1.ebuild |    50 +
 dev-java/jeuclid-core/jeuclid-core-3.1.9.ebuild    |    59 -
 dev-java/jgraphx/ChangeLog                         |     9 +-
 dev-java/jgraphx/Manifest                          |     1 +
 dev-java/jgraphx/jgraphx-1.4.1.0.ebuild            |     2 +-
 dev-java/jgraphx/jgraphx-1.8.0.6.ebuild            |     2 +-
 dev-java/jgraphx/jgraphx-2.5.0.3.ebuild            |    42 +
 dev-java/jhealpix/jhealpix-3.11.ebuild             |     2 +-
 dev-java/jlatexmath-fop/ChangeLog                  |    12 +-
 dev-java/jlatexmath-fop/Manifest                   |     2 +-
 ...s.patch => jlatexmath-fop-1.0.3-fixpaths.patch} |     0
 dev-java/jlatexmath-fop/files/version.xml          |     2 +-
 .../jlatexmath-fop/jlatexmath-fop-1.0.2.ebuild     |    45 -
 .../jlatexmath-fop/jlatexmath-fop-1.0.3.ebuild     |    45 +
 dev-java/jlatexmath/ChangeLog                      |     8 +-
 dev-java/jlatexmath/Manifest                       |     2 +-
 dev-java/jlatexmath/jlatexmath-1.0.2.ebuild        |    32 -
 dev-java/jlatexmath/jlatexmath-1.0.3.ebuild        |    32 +
 dev-java/joda-convert/ChangeLog                    |    10 -
 dev-java/joda-convert/Manifest                     |     1 -
 dev-java/joda-convert/files/1.2-build.xml          |    99 -
 dev-java/joda-convert/joda-convert-1.2.ebuild      |    45 -
 dev-java/joda-convert/metadata.xml                 |     5 -
 dev-java/joda-time/ChangeLog                       |    10 -
 dev-java/joda-time/Manifest                        |     1 -
 dev-java/joda-time/joda-time-2.1.ebuild            |    47 -
 dev-java/joda-time/metadata.xml                    |     5 -
 dev-java/jogl/ChangeLog                            |    22 +-
 dev-java/jogl/Manifest                             |     3 +-
 dev-java/jogl/jogl-1.1.1.ebuild                    |    80 -
 dev-java/jogl/jogl-1.1.1a.ebuild                   |    80 +
 dev-java/jogl/jogl-2.0_rc8-r1.ebuild               |     8 +-
 dev-java/jogl/jogl-2.1.4.ebuild                    |    73 +
 dev-java/jrosetta/jrosetta-1.0.2.ebuild            |     2 +-
 dev-java/jrosetta/jrosetta-1.0.4.ebuild            |     2 +-
 dev-java/netcdf/netcdf-4.2.ebuild                  |     2 +-
 dev-java/scirenderer/scirenderer-1.1.0.ebuild      |     4 +-
 dev-java/vecmath/ChangeLog                         |     6 +-
 dev-java/vecmath/metadata.xml                      |     4 +-
 dev-java/vecmath/vecmath-1.5.1.ebuild              |    32 +-
 dev-lang/berkeley_upc/ChangeLog                    |    14 +-
 dev-lang/berkeley_upc/Manifest                     |     2 +
 dev-lang/berkeley_upc/berkeley_upc-2.16.2.ebuild   |     4 +-
 dev-lang/berkeley_upc/berkeley_upc-2.18.0.ebuild   |    58 +
 dev-lang/berkeley_upc/berkeley_upc-2.18.2.ebuild   |    58 +
 dev-lang/berkeley_upc/metadata.xml                 |     3 +-
 dev-lang/berkeley_upc_translator/ChangeLog         |    17 +-
 dev-lang/berkeley_upc_translator/Manifest          |     2 +
 .../berkeley_upc_translator-2.16.2.ebuild          |     8 +-
 .../berkeley_upc_translator-2.18.0.ebuild          |    31 +
 .../berkeley_upc_translator-2.18.2.ebuild          |    31 +
 .../berkeley_upc_translator-2.16.2-check-abi.patch |    10 +
 dev-lang/berkeley_upc_translator/metadata.xml      |     3 +-
 dev-lang/conceptual/ChangeLog                      |    16 +
 dev-lang/conceptual/Manifest                       |     1 +
 dev-lang/conceptual/conceptual-1.4.ebuild          |    40 +
 dev-lang/conceptual/metadata.xml                   |    11 +
 dev-lang/ispc/ChangeLog                            |    14 +-
 dev-lang/ispc/ispc-9999.ebuild                     |     7 +-
 dev-lang/julia/ChangeLog                           |    36 +-
 dev-lang/julia/files/julia-nopatchelf.patch        |    14 -
 dev-lang/julia/julia-9999.ebuild                   |   163 +-
 dev-lang/julia/metadata.xml                        |     8 +-
 dev-lang/path64/ChangeLog                          |     9 +-
 dev-lang/path64/path64-9999.ebuild                 |    21 +-
 dev-lang/pgi/pgi-13.5.ebuild                       |     2 +-
 dev-lang/vtune/ChangeLog                           |    30 +-
 dev-lang/vtune/Manifest                            |     5 +
 dev-lang/vtune/vtune-13.1.10.298370.ebuild         |     2 +-
 dev-lang/vtune/vtune-13.1.12.305106.ebuild         |    43 +
 dev-lang/vtune/vtune-13.1.13.313935.ebuild         |    43 +
 dev-lang/vtune/vtune-13.1.17.353306.ebuild         |    43 +
 dev-lang/vtune/vtune-15.1.380310.ebuild            |    50 +
 dev-lang/vtune/vtune-15.2.393444.ebuild            |    50 +
 dev-libs/asmjit/ChangeLog                          |     2 +-
 dev-libs/asmjit/asmjit-1.0_beta4.ebuild            |     2 +-
 dev-libs/boost-compute/ChangeLog                   |    10 +
 dev-libs/boost-compute/Manifest                    |     1 +
 dev-libs/boost-compute/boost-compute-0.4.ebuild    |     1 +
 dev-libs/boost-compute/boost-compute-9999.ebuild   |    28 +
 dev-libs/boost-compute/metadata.xml                |    15 +
 dev-libs/boost/ChangeLog                           |    20 +
 dev-libs/boost/Manifest                            |     1 +
 dev-libs/boost/boost-1.56.0-r2.ebuild              |   398 +
 .../files/boost-1.48.0-disable_icu_rpath.patch     |    29 +
 .../boost-1.48.0-disable_libboost_python3.patch    |    62 +
 .../boost-1.48.0-no_strict_aliasing_python2.patch  |    23 +
 .../boost/files/boost-1.48.0-python_linking.patch  |    24 +
 .../boost-1.51.0-respect_python-buildid.patch      |    69 +
 ...ost-1.51.0-support_dots_in_python-buildid.patch |    22 +
 dev-libs/boost/files/boost-1.52.0-threads.patch    |    63 +
 .../boost/files/boost-1.55.0-context-x32.patch     |    42 +
 .../files/boost-1.55.0-tools-c98-compat.patch      |    17 +
 .../files/boost-1.56.0-build-auto_index-tool.patch |    13 +
 dev-libs/boost/metadata.xml                        |    38 +
 dev-libs/double-conversion/ChangeLog               |    18 -
 dev-libs/double-conversion/Manifest                |     1 -
 .../double-conversion-1.1.1.ebuild                 |    46 -
 .../files/double-conversion-1.1.1-scons.patch      |    26 -
 dev-libs/double-conversion/metadata.xml            |    11 -
 dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild     |     2 +-
 dev-libs/libconfig/ChangeLog                       |     7 +
 dev-libs/libconfig/libconfig-9999.ebuild           |    61 +
 dev-libs/libconfig/metadata.xml                    |    12 +
 dev-libs/libcuda/ChangeLog                         |     8 +-
 dev-libs/libcuda/libcuda-9999.ebuild               |    25 +-
 dev-libs/libcuda/metadata.xml                      |     8 +-
 dev-libs/libflatarray/ChangeLog                    |     7 +
 dev-libs/libflatarray/Manifest                     |     1 +
 dev-libs/libflatarray/libflatarray-0.1.1.ebuild    |    52 +
 dev-libs/libflatarray/libflatarray-9999.ebuild     |    52 +
 dev-libs/libflatarray/metadata.xml                 |    19 +
 dev-libs/libgdev/ChangeLog                         |     8 +-
 dev-libs/libgdev/libgdev-9999.ebuild               |    28 +-
 dev-libs/libgdev/metadata.xml                      |     8 +-
 dev-libs/libpfm/ChangeLog                          |     8 +-
 dev-libs/libpfm/Manifest                           |     1 +
 dev-libs/libpfm/libpfm-4.3.0.ebuild                |     2 +-
 dev-libs/libpfm/libpfm-4.4.0.ebuild                |    36 +
 dev-libs/libpfm/metadata.xml                       |    18 +-
 dev-libs/libunzip/libunzip-5.52.ebuild             |     2 +-
 dev-libs/mxml/Manifest                             |     1 +
 dev-libs/mxml/metadata.xml                         |    14 +
 dev-libs/mxml/mxml-2.9.ebuild                      |    19 +
 dev-libs/papi/ChangeLog                            |     5 +-
 dev-libs/papi/Manifest                             |     1 +
 dev-libs/papi/metadata.xml                         |    16 +-
 dev-libs/papi/papi-5.1.0.2.ebuild                  |     2 +-
 dev-libs/papi/papi-5.3.0.ebuild                    |    39 +
 dev-libs/simclist/ChangeLog                        |     8 +-
 dev-libs/simclist/Manifest                         |     2 +-
 dev-libs/simclist/simclist-1.6.ebuild              |     8 +-
 dev-libs/utf8proc/ChangeLog                        |    13 +
 dev-libs/utf8proc/Manifest                         |     1 +
 .../utf8proc/files/utf8proc-1.1.6-buildflags.patch |    11 +
 .../utf8proc/files/utf8proc-1.1.6-soname.patch     |    11 +
 dev-libs/utf8proc/metadata.xml                     |    14 +
 dev-libs/utf8proc/utf8proc-1.1.6.ebuild            |    37 +
 dev-ml/gsl-ocaml/gsl-ocaml-1.10.2.ebuild           |     2 +-
 dev-ml/lacaml/lacaml-7.0.3.ebuild                  |     2 +-
 dev-ml/mlgmpidl/ChangeLog                          |     9 +-
 dev-ml/mlgmpidl/Manifest                           |     2 +-
 dev-ml/mlgmpidl/metadata.xml                       |    10 +-
 dev-ml/mlgmpidl/mlgmpidl-1.1.ebuild                |    52 +-
 dev-ml/ocamlgraph/ChangeLog                        |    26 +-
 dev-ml/ocamlgraph/Manifest                         |     2 +-
 dev-ml/ocamlgraph/ocamlgraph-1.8.2.ebuild          |    47 -
 dev-ml/ocamlgraph/ocamlgraph-1.8.5.ebuild          |    51 +
 dev-ml/zarith/ChangeLog                            |    33 +-
 dev-ml/zarith/Manifest                             |     2 +-
 dev-ml/zarith/metadata.xml                         |     8 +-
 dev-ml/zarith/zarith-1.1.ebuild                    |    41 -
 dev-ml/zarith/zarith-1.2.1.ebuild                  |    53 +
 dev-perl/BTLib/BTLib-0.19.ebuild                   |    12 +-
 dev-perl/BTLib/ChangeLog                           |     5 +-
 dev-perl/BTLib/metadata.xml                        |     2 +-
 dev-perl/Bio-BigFile/Bio-BigFile-1.06.ebuild       |    28 -
 dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild       |    31 +
 dev-perl/Bio-BigFile/ChangeLog                     |     6 +-
 dev-perl/Bio-BigFile/Manifest                      |     2 +-
 dev-perl/Bio-BigFile/metadata.xml                  |    10 +-
 .../Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.32.ebuild  |    22 -
 .../Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.34.ebuild  |    23 +
 dev-perl/Bio-DB-Das-Chado/ChangeLog                |     6 +-
 dev-perl/Bio-DB-Das-Chado/Manifest                 |     2 +-
 dev-perl/Bio-DB-Das-Chado/metadata.xml             |    10 +-
 dev-perl/DBIx-DBStag/DBIx-DBStag-0.12.ebuild       |     2 +-
 dev-perl/Lab-Instrument/ChangeLog                  |    10 +-
 dev-perl/Lab-Instrument/Lab-Instrument-2.01.ebuild |    18 +-
 dev-perl/Lab-Instrument/metadata.xml               |     6 +-
 dev-perl/Lab-Tools/ChangeLog                       |     5 +-
 dev-perl/Lab-Tools/Lab-Tools-1.4.ebuild            |    20 +-
 dev-perl/Lab-VISA/ChangeLog                        |     6 +-
 dev-perl/Lab-VISA/Lab-VISA-2.06.ebuild             |     4 +-
 dev-perl/Lab-VISA/metadata.xml                     |     6 +-
 dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild           |     2 +-
 .../Text-ParseWords/Text-ParseWords-3.27.ebuild    |     2 +-
 dev-perl/Time-Progress/Time-Progress-1.7.ebuild    |     2 +-
 dev-perl/go-db-perl/ChangeLog                      |     8 +
 dev-perl/go-db-perl/go-db-perl-0.04.ebuild         |    13 +-
 dev-perl/go-db-perl/metadata.xml                   |     2 +-
 dev-perl/go-perl/go-perl-0.13.ebuild               |     2 +-
 dev-perl/opal-client/ChangeLog                     |    10 +-
 dev-perl/opal-client/metadata.xml                  |     2 +-
 dev-perl/opal-client/opal-client-1.9.2.ebuild      |    17 +-
 dev-python/Forthon/ChangeLog                       |     8 +-
 dev-python/Forthon/Forthon-0.8.11.ebuild           |    32 -
 dev-python/Forthon/Forthon-0.8.13.ebuild           |    31 +
 dev-python/Forthon/Manifest                        |     2 +-
 .../files/Forthon-0.8.11-fix_options_parser.patch  |    17 -
 dev-python/Forthon/metadata.xml                    |    11 +
 dev-python/GOGrapher/GOGrapher-9999.ebuild         |     2 +-
 dev-python/RecSQL/ChangeLog                        |     5 +-
 dev-python/RecSQL/RecSQL-9999.ebuild               |     4 +-
 dev-python/astlib/astlib-0.7.0.ebuild              |     2 +-
 dev-python/astropy-helpers/ChangeLog               |    13 +
 dev-python/astropy-helpers/Manifest                |     1 +
 .../astropy-helpers/astropy-helpers-0.4.1.ebuild   |     1 +
 .../astropy-helpers/astropy-helpers-9999.ebuild    |    28 +
 dev-python/astropy-helpers/metadata.xml            |     9 +
 dev-python/astropy/ChangeLog                       |    15 +-
 dev-python/astropy/astropy-9999.ebuild             |    54 +-
 dev-python/astropysics/ChangeLog                   |    10 +-
 dev-python/astropysics/astropysics-9999.ebuild     |     6 +-
 dev-python/astroquery/ChangeLog                    |    10 +
 dev-python/astroquery/Manifest                     |     1 +
 dev-python/astroquery/astroquery-0.2.ebuild        |    69 +
 dev-python/astroquery/astroquery-9999.ebuild       |    69 +
 dev-python/astroquery/metadata.xml                 |    10 +
 dev-python/brewer2mpl/ChangeLog                    |     9 +
 dev-python/brewer2mpl/Manifest                     |     1 +
 dev-python/brewer2mpl/brewer2mpl-1.4.1.ebuild      |     1 +
 dev-python/brewer2mpl/brewer2mpl-9999.ebuild       |    25 +
 dev-python/brewer2mpl/metadata.xml                 |    15 +
 dev-python/ccdproc/ChangeLog                       |     9 +
 dev-python/ccdproc/Manifest                        |     2 +
 dev-python/ccdproc/ccdproc-0.2.1.ebuild            |    59 +
 dev-python/ccdproc/ccdproc-0.2.ebuild              |    59 +
 dev-python/ccdproc/ccdproc-9999.ebuild             |    59 +
 dev-python/ccdproc/metadata.xml                    |    10 +
 dev-python/coards/coards-1.0.5.ebuild              |     2 +-
 dev-python/coords/coords-0.37.ebuild               |     2 +-
 dev-python/cosmocalc/cosmocalc-0.1.2-r1.ebuild     |     2 +-
 dev-python/dimensionful/ChangeLog                  |     5 +-
 dev-python/dimensionful/dimensionful-9999.ebuild   |     4 +-
 dev-python/emcee/ChangeLog                         |     7 +-
 dev-python/emcee/Manifest                          |     1 +
 dev-python/emcee/emcee-1.2.0.ebuild                |     2 +-
 dev-python/emcee/emcee-2.0.0.ebuild                |    27 +
 dev-python/emcee/metadata.xml                      |     4 +-
 dev-python/ffc/ChangeLog                           |    17 +-
 dev-python/ffc/Manifest                            |     2 +
 dev-python/ffc/ffc-1.2.0.ebuild                    |     2 +-
 dev-python/ffc/ffc-1.3.0.ebuild                    |    26 +
 dev-python/ffc/ffc-1.4.0.ebuild                    |    26 +
 dev-python/ffnet/ChangeLog                         |     6 +-
 dev-python/ffnet/Manifest                          |     2 +-
 dev-python/ffnet/ffnet-0.6.2.ebuild                |    48 -
 dev-python/ffnet/ffnet-0.7.1.ebuild                |    45 +
 dev-python/ffnet/metadata.xml                      |    10 +-
 dev-python/fiat/ChangeLog                          |    14 +-
 dev-python/fiat/Manifest                           |     2 +
 dev-python/fiat/fiat-1.1.ebuild                    |     2 +-
 dev-python/fiat/fiat-1.3.0.ebuild                  |    24 +
 dev-python/fiat/fiat-1.4.0.ebuild                  |    24 +
 dev-python/gammapy/ChangeLog                       |    15 +
 dev-python/gammapy/Manifest                        |     1 +
 dev-python/gammapy/gammapy-0.1.ebuild              |    76 +
 dev-python/gammapy/gammapy-9999.ebuild             |    76 +
 dev-python/gammapy/metadata.xml                    |    10 +
 dev-python/go-parser/go-parser-9999.ebuild         |     2 +-
 dev-python/healpy/ChangeLog                        |    17 +-
 dev-python/healpy/Manifest                         |     2 +-
 dev-python/healpy/healpy-1.6.2.ebuild              |    34 -
 dev-python/healpy/healpy-1.7.4.ebuild              |    34 +
 dev-python/healpy/metadata.xml                     |     3 +
 dev-python/imageutils/ChangeLog                    |     9 +
 dev-python/imageutils/imageutils-9999.ebuild       |    58 +
 dev-python/imageutils/metadata.xml                 |    10 +
 dev-python/inference/inference-0.4.ebuild          |     2 +-
 dev-python/instant/ChangeLog                       |    10 +-
 dev-python/instant/Manifest                        |     2 +
 dev-python/instant/instant-1.2.0.ebuild            |     2 +-
 dev-python/instant/instant-1.3.0.ebuild            |    21 +
 dev-python/instant/instant-1.4.0.ebuild            |    21 +
 dev-python/jupyter-nbgrader/ChangeLog              |     9 +
 .../jupyter-nbgrader/jupyter-nbgrader-9999.ebuild  |    32 +
 dev-python/jupyter-nbgrader/metadata.xml           |     8 +
 dev-python/jupyter-nbviewer/ChangeLog              |     9 +
 .../jupyter-nbviewer/jupyter-nbviewer-9999.ebuild  |    35 +
 dev-python/jupyter-nbviewer/metadata.xml           |    10 +
 dev-python/matlab_wrapper/ChangeLog                |     9 +
 dev-python/matlab_wrapper/Manifest                 |     1 +
 .../matlab_wrapper/matlab_wrapper-0.9.6.ebuild     |     1 +
 .../matlab_wrapper/matlab_wrapper-9999.ebuild      |    25 +
 dev-python/matlab_wrapper/metadata.xml             |    16 +
 dev-python/meshpy/meshpy-2013.1.2.ebuild           |     2 +-
 dev-python/montage-wrapper/ChangeLog               |    13 +
 dev-python/montage-wrapper/Manifest                |     1 +
 dev-python/montage-wrapper/metadata.xml            |    11 +
 .../montage-wrapper/montage-wrapper-0.9.7.ebuild   |    39 +
 dev-python/newrelic/ChangeLog                      |     9 +
 dev-python/newrelic/Manifest                       |     1 +
 dev-python/newrelic/metadata.xml                   |     9 +
 dev-python/newrelic/newrelic-2.44.0.36.ebuild      |    35 +
 dev-python/numpydoc/ChangeLog                      |    31 -
 dev-python/numpydoc/Manifest                       |     1 -
 dev-python/numpydoc/metadata.xml                   |    11 -
 dev-python/numpydoc/numpydoc-0.4.ebuild            |    25 -
 dev-python/nvidia-ml-py/ChangeLog                  |     8 +
 dev-python/nvidia-ml-py/Manifest                   |     1 +
 dev-python/nvidia-ml-py/metadata.xml               |    13 +
 .../nvidia-ml-py/nvidia-ml-py-6.340.0.ebuild       |    19 +
 dev-python/omniorbpy/ChangeLog                     |     9 +-
 dev-python/omniorbpy/omniorbpy-3.4.ebuild          |    18 +-
 dev-python/opal-client/ChangeLog                   |     6 +-
 dev-python/opal-client/metadata.xml                |     2 +-
 dev-python/opal-client/opal-client-2.4.1.ebuild    |    15 +-
 dev-python/photutils/ChangeLog                     |     9 +
 dev-python/photutils/metadata.xml                  |    10 +
 dev-python/photutils/photutils-9999.ebuild         |    61 +
 dev-python/prettyplotlib/ChangeLog                 |     9 +
 dev-python/prettyplotlib/Manifest                  |     1 +
 dev-python/prettyplotlib/metadata.xml              |    12 +
 .../prettyplotlib/prettyplotlib-0.1.7.ebuild       |     1 +
 dev-python/prettyplotlib/prettyplotlib-9999.ebuild |    30 +
 dev-python/psubprocess/ChangeLog                   |     9 +
 dev-python/psubprocess/Manifest                    |     1 +
 .../wcd => dev-python/psubprocess}/metadata.xml    |     0
 dev-python/psubprocess/psubprocess-0.1.2.ebuild    |    21 +
 dev-python/pyfftw/ChangeLog                        |     9 +
 dev-python/pyfftw/Manifest                         |     1 +
 dev-python/pyfftw/metadata.xml                     |    13 +
 dev-python/pyfftw/pyfftw-0.9.2.ebuild              |     1 +
 dev-python/pyfftw/pyfftw-9999.ebuild               |    32 +
 dev-python/pyhdf/pyhdf-0.8.3.ebuild                |     2 +-
 dev-python/pymvpa/pymvpa-0.4.4.ebuild              |     4 +-
 dev-python/pynomo/ChangeLog                        |     9 +
 dev-python/pynomo/Manifest                         |     1 +
 dev-python/pynomo/metadata.xml                     |    12 +
 dev-python/pynomo/pynomo-0.2.2.ebuild              |    35 +
 dev-python/pyqtgraph/ChangeLog                     |     6 +
 dev-python/pyqtgraph/Manifest                      |     2 +-
 dev-python/pyqtgraph/pyqtgraph-0.9.7.ebuild        |    32 -
 dev-python/pyqtgraph/pyqtgraph-0.9.8.ebuild        |    32 +
 dev-python/pysolar/pysolar-0.5.ebuild              |     2 +-
 dev-python/pysparse/pysparse-1.1.1-r1.ebuild       |     2 +-
 dev-python/python-ivi/ChangeLog                    |     9 +
 dev-python/python-ivi/Manifest                     |     1 +
 dev-python/python-ivi/metadata.xml                 |    15 +
 dev-python/python-ivi/python-ivi-0.14.9.ebuild     |     1 +
 dev-python/python-ivi/python-ivi-9999.ebuild       |    30 +
 dev-python/python-vxi11/ChangeLog                  |     9 +
 dev-python/python-vxi11/Manifest                   |     1 +
 dev-python/python-vxi11/metadata.xml               |    14 +
 dev-python/python-vxi11/python-vxi11-0.7.ebuild    |     1 +
 dev-python/python-vxi11/python-vxi11-9999.ebuild   |    22 +
 dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild |     2 +-
 dev-python/pythonocc/ChangeLog                     |    14 +-
 dev-python/pythonocc/pythonocc-0.5.ebuild          |     6 +-
 dev-python/pythonqt/ChangeLog                      |    16 +
 dev-python/pythonqt/Manifest                       |     1 +
 .../pythonqt/files/pythonqt-2.1-lib_location.patch |    22 +
 .../files/pythonqt-9999-lib_location.patch         |    20 +
 .../pythonqt}/metadata.xml                         |     0
 dev-python/pythonqt/pythonqt-2.1.ebuild            |    33 +
 dev-python/pythonqt/pythonqt-9999.ebuild           |    37 +
 dev-python/pywcsgrid2/ChangeLog                    |    15 +
 dev-python/pywcsgrid2/metadata.xml                 |    11 +
 dev-python/pywcsgrid2/pywcsgrid2-9999.ebuild       |    25 +
 dev-python/simplepam/ChangeLog                     |    10 +
 dev-python/simplepam/Manifest                      |     1 +
 dev-python/simplepam/metadata.xml                  |    11 +
 dev-python/simplepam/simplepam-0.1.5.ebuild        |     1 +
 dev-python/simplepam/simplepam-9999.ebuild         |    22 +
 dev-python/specutils/ChangeLog                     |     9 +
 dev-python/specutils/metadata.xml                  |    10 +
 dev-python/specutils/specutils-9999.ebuild         |    59 +
 dev-python/theano/ChangeLog                        |    12 -
 dev-python/theano/Manifest                         |     1 -
 dev-python/theano/metadata.xml                     |    13 -
 dev-python/theano/theano-0.6.0_rc3.ebuild          |    33 -
 dev-python/ufl/ChangeLog                           |    10 +-
 dev-python/ufl/Manifest                            |     4 +-
 dev-python/ufl/metadata.xml                        |     3 +
 dev-python/ufl/ufl-0.5.4.ebuild                    |     2 +-
 dev-python/ufl/ufl-1.3.0.ebuild                    |    23 +
 dev-python/ufl/ufl-1.4.0.ebuild                    |    23 +
 dev-python/viper/viper-1.0.1.ebuild                |     2 +-
 dev-tcltk/img_rotate/img_rotate-1.1.ebuild         |     2 +-
 dev-tcltk/togl/togl-1.7-r1.ebuild                  |     2 +-
 dev-tex/pythontex/ChangeLog                        |    13 +
 dev-tex/pythontex/Manifest                         |     1 +
 dev-tex/pythontex/metadata.xml                     |     8 +
 dev-tex/pythontex/pythontex-0.14.ebuild            |    57 +
 dev-tex/pythontex/pythontex-9999.ebuild            |    58 +
 dev-util/VampirTrace/ChangeLog                     |     9 +
 dev-util/VampirTrace/Manifest                      |     1 +
 dev-util/VampirTrace/VampirTrace-5.14.3.ebuild     |     2 +-
 dev-util/VampirTrace/VampirTrace-5.14.4.ebuild     |    44 +
 dev-util/amdapp/ChangeLog                          |    32 +
 dev-util/amdapp/Manifest                           |     8 +-
 dev-util/amdapp/amdapp-2.8.ebuild                  |    76 -
 dev-util/amdapp/amdapp-2.9.1.ebuild                |    83 +
 dev-util/amdapp/amdapp-2.9.ebuild                  |    87 +
 dev-util/amdapp/amdapp-3.0_beta.ebuild             |    83 +
 dev-util/amdapp/metadata.xml                       |     4 +-
 dev-util/ccache/ChangeLog                          |    31 -
 dev-util/ccache/Manifest                           |     1 -
 dev-util/ccache/ccache-3.1.9-r2.ebuild             |    64 -
 dev-util/ccache/files/ccache-3.1.7-no-perl.patch   |    15 -
 .../ccache/files/ccache-3.1.9-test-gcc-4.8.patch   |   156 -
 dev-util/ccache/files/ccache-config-2              |    98 -
 dev-util/ccache/metadata.xml                       |    15 -
 dev-util/f90cache/f90cache-0.94.ebuild             |     2 +-
 dev-util/intel-ocl-sdk/ChangeLog                   |    13 +
 dev-util/intel-ocl-sdk/Manifest                    |     2 +
 .../intel-ocl-sdk/intel-ocl-sdk-3.0.67279.ebuild   |     2 +-
 .../intel-ocl-sdk/intel-ocl-sdk-3.1.1.11385.ebuild |    60 +
 .../intel-ocl-sdk/intel-ocl-sdk-3.2.1.16712.ebuild |    60 +
 dev-util/ndiff/ndiff-2.00.ebuild                   |     2 +-
 dev-util/numdiff/ChangeLog                         |    10 +
 dev-util/numdiff/Manifest                          |     1 +
 dev-util/numdiff/metadata.xml                      |    16 +
 dev-util/numdiff/numdiff-5.8.1.ebuild              |    43 +
 dev-util/nvidia-cuda-gdk/ChangeLog                 |    30 +
 dev-util/nvidia-cuda-gdk/Manifest                  |     3 +
 dev-util/nvidia-cuda-gdk/files/nvidia-healthmon    |     9 +
 dev-util/nvidia-cuda-gdk/metadata.xml              |    22 +
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild  |   131 +
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-346.46.ebuild  |   121 +
 dev-util/nvidia-cuda-sdk/ChangeLog                 |    14 +
 dev-util/nvidia-cuda-sdk/Manifest                  |     2 +
 dev-util/nvidia-cuda-sdk/metadata.xml              |    17 +
 .../nvidia-cuda-sdk/nvidia-cuda-sdk-7.0.18.ebuild  |   151 +
 .../nvidia-cuda-sdk/nvidia-cuda-sdk-7.0.28.ebuild  |   144 +
 dev-util/nvidia-cuda-toolkit/ChangeLog             |    21 +
 dev-util/nvidia-cuda-toolkit/Manifest              |     2 +
 dev-util/nvidia-cuda-toolkit/files/cuda-config.in  |    28 +
 dev-util/nvidia-cuda-toolkit/metadata.xml          |    18 +
 .../nvidia-cuda-toolkit-7.0.18-r1.ebuild           |   154 +
 .../nvidia-cuda-toolkit-7.0.28.ebuild              |   143 +
 dev-util/smartgit/ChangeLog                        |    30 +-
 dev-util/smartgit/Manifest                         |     2 +-
 dev-util/smartgit/metadata.xml                     |     2 +-
 dev-util/smartgit/smartgit-1.0.2.ebuild            |    46 -
 dev-util/smartgit/smartgit-6.5.6.ebuild            |    57 +
 docs/meetings/logs/20130130.log                    |   262 +
 eclass/alternatives-2.eclass                       |   151 +-
 eclass/emboss-r1.eclass                            |   144 +
 eclass/emboss.eclass                               |   135 -
 eclass/fortran-int64.eclass                        |   300 +
 eclass/intel-sdp.eclass                            |   112 +-
 licenses/ACML-EULA                                 |   428 +
 licenses/AMD-APPSDK                                |   267 +
 licenses/ATLAS                                     |    48 +
 licenses/BSD-BroadInstitute                        |    17 +
 licenses/CPC                                       |    41 +
 licenses/CeCILL-2.0                                |   505 +
 licenses/CeCILL-2.1                                |   519 +
 licenses/CeCILL-B                                  |   515 +
 licenses/FSL                                       |    94 +
 licenses/HGSC-BCM                                  |     8 +
 licenses/HSL                                       |   222 -
 licenses/MSR-LA                                    |   104 +
 licenses/Montage                                   |    90 +
 licenses/NVIDIA-CUDA                               |  2262 +++
 licenses/NVIDIA-gdk                                |    32 +
 licenses/Non-profit-OSL-3.0                        |    63 +
 licenses/STFC                                      |    67 +
 licenses/Tablet                                    |    38 +-
 licenses/XPLOR-NIH                                 |    37 +
 licenses/atsas                                     |   211 +
 licenses/bambino                                   |    32 +
 licenses/bcca_2010                                 |   453 +
 licenses/hoomd-blue                                |    46 +
 licenses/mgltools                                  |    42 -
 licenses/mpich2                                    |    39 +
 licenses/newmat                                    |    30 +
 licenses/smartgit                                  |   255 +-
 media-gfx/PhiloGL/PhiloGL-1.4.3.ebuild             |     2 +-
 media-gfx/brlcad/Manifest                          |     1 -
 media-gfx/brlcad/brlcad-7.20.4.ebuild              |     4 +-
 media-gfx/brlcad/brlcad-7.22.0.ebuild              |     4 +-
 media-gfx/brlcad/brlcad-9999.ebuild                |     4 +-
 media-gfx/librecad/ChangeLog                       |    32 +-
 media-gfx/librecad/Manifest                        |     4 +-
 media-gfx/librecad/librecad-1.0.3.ebuild           |    24 +-
 media-gfx/librecad/librecad-1.0.4.ebuild           |    37 +
 media-gfx/librecad/librecad-2.0.0_rc1.ebuild       |    45 -
 media-gfx/librecad/librecad-2.0.0_rc2.ebuild       |    45 -
 media-gfx/librecad/librecad-2.0.7.ebuild           |    42 +
 media-gfx/librecad/librecad-9999.ebuild            |     6 +-
 media-gfx/librecad/metadata.xml                    |    21 +-
 media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild         |     2 +-
 media-libs/avbin-bin/ChangeLog                     |     8 +-
 media-libs/avbin-bin/avbin-bin-7.ebuild            |    16 +-
 media-libs/avbin-bin/metadata.xml                  |    12 +-
 media-libs/libgfx/libgfx-1.1.0.ebuild              |     2 +-
 metadata/layout.conf                               |     4 +-
 net-firewall/gcb/gcb-1.5.6.ebuild                  |     2 +-
 net-ftp/bbftp-client/ChangeLog                     |    10 +-
 net-ftp/bbftp-client/Manifest                      |     2 +-
 net-ftp/bbftp-client/bbftp-client-3.2.0.ebuild     |    32 -
 net-ftp/bbftp-client/bbftp-client-3.2.1.ebuild     |    43 +
 net-ftp/bbftp-client/metadata.xml                  |     4 +-
 net-ftp/bbftp-server/ChangeLog                     |    10 +-
 net-ftp/bbftp-server/Manifest                      |     2 +-
 net-ftp/bbftp-server/bbftp-server-3.2.0.ebuild     |    46 -
 net-ftp/bbftp-server/bbftp-server-3.2.1.ebuild     |    54 +
 net-ftp/bbftp-server/metadata.xml                  |     4 +-
 net-misc/bbscp/ChangeLog                           |     6 +-
 net-misc/bbscp/Manifest                            |     2 +-
 net-misc/bbscp/bbscp-1.0.4.ebuild                  |    22 -
 net-misc/bbscp/bbscp-1.0.6.ebuild                  |    24 +
 net-misc/bbscp/metadata.xml                        |     4 +-
 ...cfs-move-mdd-ofd-proc-handling-to-seq_fil.patch |  2082 +++
 patches/07_doxygen.patch                           |  1804 +++
 patches/bigdft-abi-1.0.4-0005.patch                |  5317 +++++++
 perl-core/encoding-warnings/ChangeLog              |     6 +-
 .../encoding-warnings-0.11.ebuild                  |     4 +-
 perl-core/encoding-warnings/metadata.xml           |     6 +-
 profiles/ChangeLog                                 |    20 +-
 profiles/arch/arm/use.mask                         |    10 +
 profiles/arch/m68k/use.mask                        |    10 +
 profiles/arch/sparc-fbsd/use.mask                  |    10 +
 profiles/arch/sparc/use.mask                       |    10 +
 profiles/arch/x86-fbsd/use.mask                    |    10 +
 profiles/arch/x86/use.mask                         |    10 +
 profiles/categories                                |     8 +-
 profiles/license_groups                            |     1 +
 profiles/package.mask                              |    89 +-
 profiles/package.use.mask                          |    24 +-
 profiles/updates/1Q-2014                           |     1 +
 profiles/updates/2Q-2014                           |     2 +
 profiles/updates/4Q-2013                           |     1 +
 sci-astronomy/astrometry/ChangeLog                 |     9 +-
 sci-astronomy/astrometry/astrometry-0.43.ebuild    |    28 +-
 sci-astronomy/astrometry/metadata.xml              |    10 +-
 sci-astronomy/bpz/bpz-1.99.3.ebuild                |     2 +-
 sci-astronomy/casapy-bin/ChangeLog                 |    28 +
 sci-astronomy/casapy-bin/Manifest                  |     2 +
 .../casapy-bin-4.2.1.29047.001_p1.ebuild           |    69 +
 .../casapy-bin/casapy-bin-4.2.2.30986_p1.ebuild    |    69 +
 sci-astronomy/casapy-bin/metadata.xml              |    10 +
 sci-astronomy/chealpix/ChangeLog                   |     8 +-
 sci-astronomy/chealpix/Manifest                    |     2 +-
 sci-astronomy/chealpix/chealpix-3.11.2.ebuild      |    24 +
 sci-astronomy/chealpix/chealpix-3.11.ebuild        |    30 -
 sci-astronomy/eazy/eazy-1.00.ebuild                |     2 +-
 sci-astronomy/eye/ChangeLog                        |     8 +-
 sci-astronomy/eye/Manifest                         |     1 -
 sci-astronomy/eye/eye-1.4.1.ebuild                 |    32 -
 sci-astronomy/eye/eye-9999.ebuild                  |    18 +-
 sci-astronomy/eye/files/eye-1.4.1-configure.patch  |    58 -
 sci-astronomy/eye/metadata.xml                     |     4 +-
 sci-astronomy/galfit-bin/galfit-bin-3.0.5.ebuild   |     2 +-
 sci-astronomy/healpix_cxx/ChangeLog                |     8 +-
 sci-astronomy/healpix_cxx/Manifest                 |     2 +-
 .../healpix_cxx/healpix_cxx-3.11.2.ebuild          |    48 +
 sci-astronomy/healpix_cxx/healpix_cxx-3.11.ebuild  |    54 -
 sci-astronomy/healpix_idl/healpix_idl-3.11.ebuild  |     2 +-
 sci-astronomy/lephare/lephare-2.2.ebuild           |     2 +-
 sci-astronomy/missfits/ChangeLog                   |    14 +-
 sci-astronomy/missfits/Manifest                    |     2 +-
 .../missfits/files/missfits-2.4.0-configure.patch  |   108 -
 sci-astronomy/missfits/missfits-2.4.0.ebuild       |    29 -
 sci-astronomy/missfits/missfits-2.8.0.ebuild       |     1 +
 sci-astronomy/missfits/missfits-9999.ebuild        |    15 +-
 sci-astronomy/montage/ChangeLog                    |    14 +
 sci-astronomy/montage/Manifest                     |     2 +
 .../montage/files/montage-3.3-gcc48.patch          |    97 +
 sci-astronomy/montage/metadata.xml                 |     9 +
 sci-astronomy/montage/montage-3.3.ebuild           |    55 +
 sci-astronomy/mosstack/ChangeLog                   |    15 +
 sci-astronomy/mosstack/Manifest                    |     1 +
 sci-astronomy/mosstack/metadata.xml                |    20 +
 sci-astronomy/mosstack/mosstack-0.6.1-r1.ebuild    |    33 +
 sci-astronomy/mosstack/mosstack-0.6.1.ebuild       |    33 +
 sci-astronomy/psfex/ChangeLog                      |    14 +-
 sci-astronomy/psfex/Manifest                       |     1 +
 sci-astronomy/psfex/metadata.xml                   |    10 +-
 sci-astronomy/psfex/psfex-3.17.0.ebuild            |     1 +
 sci-astronomy/psfex/psfex-3.9.1-r1.ebuild          |    54 -
 sci-astronomy/psfex/psfex-3.9.1.ebuild             |     1 +
 sci-astronomy/psfex/psfex-9999.ebuild              |    32 +-
 sci-astronomy/scamp/ChangeLog                      |     7 +-
 sci-astronomy/scamp/metadata.xml                   |    10 +-
 sci-astronomy/scamp/scamp-1.7.0-r2.ebuild          |    26 +-
 sci-astronomy/scamp/scamp-9999.ebuild              |    28 +-
 sci-astronomy/sextractor/ChangeLog                 |    13 +-
 sci-astronomy/sextractor/Manifest                  |     1 +
 sci-astronomy/sextractor/sextractor-2.19.5.ebuild  |     1 +
 .../sextractor/sextractor-2.8.6-r1.ebuild          |     7 +-
 sci-astronomy/sextractor/sextractor-9999.ebuild    |    30 +-
 sci-astronomy/skymaker/ChangeLog                   |    13 +-
 sci-astronomy/skymaker/Manifest                    |     2 +-
 .../skymaker/files/skymaker-configure.patch        |    40 -
 sci-astronomy/skymaker/skymaker-3.10.5.ebuild      |     1 +
 sci-astronomy/skymaker/skymaker-3.3.3.ebuild       |    27 -
 sci-astronomy/skymaker/skymaker-9999.ebuild        |    19 +-
 .../starlink-bin/starlink-bin-20130413.ebuild      |     2 +-
 sci-astronomy/stiff/ChangeLog                      |    16 +-
 sci-astronomy/stiff/Manifest                       |     1 +
 sci-astronomy/stiff/stiff-2.4.0.ebuild             |     1 +
 sci-astronomy/stiff/stiff-9999.ebuild              |    17 +-
 sci-astronomy/stilts/stilts-2.5.1.ebuild           |     2 +-
 sci-astronomy/stuff/ChangeLog                      |    13 +-
 sci-astronomy/stuff/Manifest                       |     2 +-
 sci-astronomy/stuff/files/stuff-configure.patch    |    65 -
 sci-astronomy/stuff/stuff-1.19.ebuild              |    27 -
 sci-astronomy/stuff/stuff-1.26.0.ebuild            |     1 +
 sci-astronomy/stuff/stuff-9999.ebuild              |    19 +-
 sci-astronomy/swarp/ChangeLog                      |    11 +-
 sci-astronomy/swarp/Manifest                       |     1 +
 sci-astronomy/swarp/swarp-2.38.0.ebuild            |     1 +
 sci-astronomy/swarp/swarp-9999.ebuild              |    23 +-
 sci-astronomy/topcat/topcat-4.0.1.ebuild           |     2 +-
 sci-astronomy/weightwatcher/ChangeLog              |    14 +-
 sci-astronomy/weightwatcher/Manifest               |     2 +-
 .../files/weightwatcher-1.8.10-configure.patch     |    41 -
 .../weightwatcher/weightwatcher-1.12.ebuild        |     1 +
 .../weightwatcher/weightwatcher-1.8.10.ebuild      |    29 -
 .../weightwatcher/weightwatcher-9999.ebuild        |    17 +-
 sci-astronomy/zebra/zebra-1.01.ebuild              |     2 +-
 sci-astronomy/zpeg/zpeg-5.23.ebuild                |     2 +-
 sci-biology/Atlas-Link/Atlas-Link-0.01.ebuild      |    26 +
 sci-biology/Atlas-Link/ChangeLog                   |    10 +
 sci-biology/Atlas-Link/Manifest                    |     1 +
 sci-biology/{wcd => Atlas-Link}/metadata.xml       |     0
 sci-biology/Atlas/Atlas-2005.ebuild                |    18 +
 sci-biology/Atlas/ChangeLog                        |    13 +
 sci-biology/Atlas/Manifest                         |     1 +
 sci-biology/{wcd => Atlas}/metadata.xml            |     0
 sci-biology/Atlas2/Atlas2-1.4.3.ebuild             |    41 +
 sci-biology/Atlas2/ChangeLog                       |    12 +
 sci-biology/Atlas2/Manifest                        |     1 +
 sci-biology/{wcd => Atlas2}/metadata.xml           |     0
 sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild |    25 +
 sci-biology/Atlas_GapFill/ChangeLog                |    15 +
 sci-biology/Atlas_GapFill/Manifest                 |     2 +
 sci-biology/{wcd => Atlas_GapFill}/metadata.xml    |     0
 sci-biology/BBmap/BBmap-34.56.ebuild               |    41 +
 sci-biology/BBmap/ChangeLog                        |    26 +
 sci-biology/BBmap/Manifest                         |     1 +
 sci-biology/{wcd => BBmap}/metadata.xml            |     0
 sci-biology/BG7/BG7-9999.ebuild                    |    22 +-
 sci-biology/BG7/ChangeLog                          |     9 +-
 .../salome-yacs => sci-biology/BG7}/metadata.xml   |     0
 sci-biology/BRANCH/BRANCH-9999.ebuild              |    38 +
 sci-biology/BRANCH/ChangeLog                       |    14 +
 sci-biology/{wcd => BRANCH}/metadata.xml           |     0
 sci-biology/BamView/BamView-1.2.11.ebuild          |    23 +
 sci-biology/BamView/ChangeLog                      |    21 +
 sci-biology/BamView/Manifest                       |     1 +
 sci-biology/BamView/metadata.xml                   |     8 +
 sci-biology/CAutils/CAutils-20120126.ebuild        |    20 +
 sci-biology/CAutils/ChangeLog                      |     7 +
 sci-biology/CAutils/Manifest                       |     1 +
 sci-biology/{wcd => CAutils}/metadata.xml          |     0
 sci-biology/CONTIGuator/CONTIGuator-2.7.ebuild     |    17 +
 sci-biology/CONTIGuator/ChangeLog                  |     6 +
 sci-biology/CONTIGuator/Manifest                   |     1 +
 sci-biology/{wcd => CONTIGuator}/metadata.xml      |     0
 sci-biology/EBARDenovo/ChangeLog                   |    14 +
 sci-biology/EBARDenovo/EBARDenovo-1.2.2.ebuild     |    25 +
 sci-biology/EBARDenovo/Manifest                    |     1 +
 sci-biology/{wcd => EBARDenovo}/metadata.xml       |     0
 sci-biology/ESTate/ChangeLog                       |    25 +
 sci-biology/ESTate/ESTate-0.5.ebuild               |    46 +
 sci-biology/ESTate/Manifest                        |     2 +
 sci-biology/{wcd => ESTate}/metadata.xml           |     0
 sci-biology/FLASH/ChangeLog                        |     9 +
 sci-biology/FLASH/FLASH-1.2.9.ebuild               |    22 +
 sci-biology/FLASH/Manifest                         |     1 +
 sci-biology/{wcd => FLASH}/metadata.xml            |     0
 sci-biology/Gambit/Gambit-0.4.145.ebuild           |     2 +-
 sci-biology/HTSeq/ChangeLog                        |    12 +
 sci-biology/HTSeq/HTSeq-0.6.1.ebuild               |    23 +
 sci-biology/HTSeq/Manifest                         |     1 +
 sci-biology/{wcd => HTSeq}/metadata.xml            |     0
 sci-biology/ICC/ChangeLog                          |    12 +
 sci-biology/ICC/ICC-2.0.1.ebuild                   |    55 +
 sci-biology/ICC/Manifest                           |     1 +
 sci-biology/{wcd => ICC}/metadata.xml              |     0
 sci-biology/IMAGE/ChangeLog                        |    12 +
 sci-biology/IMAGE/IMAGE-2.4.1.ebuild               |    20 +
 sci-biology/IMAGE/Manifest                         |     1 +
 sci-biology/{wcd => IMAGE}/metadata.xml            |     0
 sci-biology/InterMine/ChangeLog                    |    14 +
 sci-biology/InterMine/InterMine-0.98.ebuild        |    24 +
 sci-biology/{wcd => InterMine}/metadata.xml        |     0
 sci-biology/KaKs_Calculator/ChangeLog              |    10 +
 .../KaKs_Calculator/KaKs_Calculator-1.2.ebuild     |    38 +
 sci-biology/KaKs_Calculator/Manifest               |     2 +
 sci-biology/{wcd => KaKs_Calculator}/metadata.xml  |     0
 sci-biology/MAKER/ChangeLog                        |    12 +
 sci-biology/MAKER/MAKER-9999.ebuild                |    21 +
 sci-biology/{wcd => MAKER}/metadata.xml            |     0
 sci-biology/MaSuRCA/ChangeLog                      |    10 +
 sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild           |    64 +
 sci-biology/MaSuRCA/Manifest                       |     2 +
 sci-biology/{wcd => MaSuRCA}/metadata.xml          |     0
 sci-biology/MagicViewer/ChangeLog                  |    10 +
 sci-biology/MagicViewer/MagicViewer-1.2.1.ebuild   |    24 +
 sci-biology/MagicViewer/Manifest                   |     2 +
 sci-biology/{wcd => MagicViewer}/metadata.xml      |     0
 sci-biology/MeV/ChangeLog                          |     7 +
 sci-biology/MeV/Manifest                           |     1 +
 sci-biology/MeV/MeV-4.8.1.ebuild                   |    24 +
 sci-biology/MeV/metadata.xml                       |     8 +
 sci-biology/MochiView/ChangeLog                    |    13 +
 sci-biology/MochiView/MochiView-1.45.ebuild        |    17 +
 sci-biology/{wcd => MochiView}/metadata.xml        |     0
 sci-biology/NGSTools/ChangeLog                     |    10 +
 sci-biology/NGSTools/Manifest                      |     1 +
 sci-biology/NGSTools/NGSTools-2.0.5.ebuild         |    21 +
 sci-biology/{wcd => NGSTools}/metadata.xml         |     0
 sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild         |     2 +-
 sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild       |     2 +-
 sci-biology/ONTO-PERL/ChangeLog                    |     6 +-
 sci-biology/ONTO-PERL/Manifest                     |     2 +-
 sci-biology/ONTO-PERL/ONTO-PERL-1.31.ebuild        |    25 -
 sci-biology/ONTO-PERL/ONTO-PERL-1.41.ebuild        |    27 +
 sci-biology/ONTO-PERL/metadata.xml                 |     2 +-
 sci-biology/ORFcor/ChangeLog                       |     9 +
 sci-biology/ORFcor/Manifest                        |     1 +
 sci-biology/ORFcor/ORFcor-20130507.ebuild          |    27 +
 sci-biology/{wcd => ORFcor}/metadata.xml           |     0
 sci-biology/RADtools/ChangeLog                     |    18 +
 sci-biology/RADtools/Manifest                      |     2 +
 sci-biology/RADtools/RADtools-1.2.4.ebuild         |    40 +
 sci-biology/RADtools/RADtools-9999.ebuild          |    38 +
 sci-biology/{wcd => RADtools}/metadata.xml         |     0
 sci-biology/Ray/ChangeLog                          |    10 +
 sci-biology/Ray/Manifest                           |     1 +
 sci-biology/Ray/Ray-2.3.0.ebuild                   |    28 +
 sci-biology/{zmsort => Ray}/metadata.xml           |     0
 sci-biology/SEECER/ChangeLog                       |    13 +
 sci-biology/SEECER/Manifest                        |     2 +
 sci-biology/SEECER/SEECER-0.1.3.ebuild             |    34 +
 sci-biology/{wcd => SEECER}/metadata.xml           |     0
 sci-biology/SolexaQA/ChangeLog                     |     9 +
 sci-biology/SolexaQA/Manifest                      |     1 +
 sci-biology/SolexaQA/SolexaQA-2.2.ebuild           |    24 +
 sci-biology/{wcd => SolexaQA}/metadata.xml         |     0
 sci-biology/VarScan/ChangeLog                      |    16 +
 sci-biology/VarScan/Manifest                       |     1 +
 sci-biology/VarScan/VarScan-2.3.7.ebuild           |    30 +
 .../VarScan}/metadata.xml                          |     0
 sci-biology/VelvetOptimiser/ChangeLog              |    13 +
 sci-biology/VelvetOptimiser/Manifest               |     1 +
 .../VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild   |    29 +
 sci-biology/{wcd => VelvetOptimiser}/metadata.xml  |     0
 sci-biology/YASRA/ChangeLog                        |    12 +-
 sci-biology/YASRA/Manifest                         |     2 +-
 sci-biology/YASRA/YASRA-2.32.ebuild                |    17 -
 sci-biology/YASRA/YASRA-2.33.ebuild                |    17 +
 sci-biology/aghermann/ChangeLog                    |    12 +
 sci-biology/aghermann/Manifest                     |     1 +
 sci-biology/aghermann/aghermann-1.0.3.ebuild       |    30 +
 sci-biology/aghermann/metadata.xml                 |    16 +
 sci-biology/align_to_scf/align_to_scf-1.06.ebuild  |     2 +-
 sci-biology/amos-short/amos-short-0.9.3.ebuild     |     2 +-
 sci-biology/amos/ChangeLog                         |     6 +
 sci-biology/amos/Manifest                          |     1 -
 sci-biology/amos/amos-3.1.0-r1.ebuild              |    30 -
 sci-biology/amos/amos-9999.ebuild                  |    10 +-
 sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch    |    15 -
 ...mos-3.1.0-goBambus2.py-indent-and-cleanup.patch |    25 -
 sci-biology/amos/files/amos.m4.patch               |    49 -
 sci-biology/ampliconnoise/ChangeLog                |    12 +
 sci-biology/ampliconnoise/Manifest                 |     3 +
 .../ampliconnoise/ampliconnoise-1.27.ebuild        |    17 +
 sci-biology/{wcd => ampliconnoise}/metadata.xml    |     0
 sci-biology/angsd/ChangeLog                        |    10 +
 sci-biology/angsd/angsd-9999.ebuild                |    49 +
 sci-biology/{wcd => angsd}/metadata.xml            |     0
 sci-biology/apollo/ChangeLog                       |     9 +-
 sci-biology/apollo/apollo-9999.ebuild              |    25 +-
 sci-biology/apollo/metadata.xml                    |    10 +-
 sci-biology/argo-bin/argo-bin-1.0.31.ebuild        |     4 +-
 sci-biology/argo/ChangeLog                         |     6 +
 sci-biology/argo/Manifest                          |     2 +-
 sci-biology/argo/argo-1.0.24.ebuild                |    10 +-
 sci-biology/artemis-bin/ChangeLog                  |    19 +-
 sci-biology/artemis-bin/Manifest                   |     3 +-
 sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild |    21 -
 sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild |    31 +
 sci-biology/artemis/ChangeLog                      |    16 +-
 sci-biology/artemis/artemis-9999.ebuild            |    38 +-
 sci-biology/artemis/metadata.xml                   |    10 +-
 sci-biology/atsas/ChangeLog                        |    25 +
 sci-biology/atsas/Manifest                         |     1 +
 sci-biology/atsas/atsas-2.6.0.ebuild               |    76 +
 sci-biology/{biopython => atsas}/metadata.xml      |     0
 sci-biology/autoeditor/autoeditor-1.20.ebuild      |     2 +-
 sci-biology/bambino/ChangeLog                      |    23 +
 sci-biology/bambino/Manifest                       |     4 +
 sci-biology/bambino/bambino-1.02.ebuild            |    37 +
 sci-biology/bambino/bambino-1.06.ebuild            |    37 +
 sci-biology/{zmsort => bambino}/metadata.xml       |     0
 sci-biology/bambus/bambus-2.33.ebuild              |     2 +-
 sci-biology/bamtools/ChangeLog                     |     6 +-
 sci-biology/bamtools/bamtools-9999.ebuild          |    10 +-
 sci-biology/bamtools/metadata.xml                  |    12 +-
 sci-biology/barrnap/ChangeLog                      |    27 +
 sci-biology/barrnap/Manifest                       |     1 +
 sci-biology/barrnap/barrnap-0.3.ebuild             |    41 +
 sci-biology/{wcd => barrnap}/metadata.xml          |     0
 sci-biology/bcftools/ChangeLog                     |    19 +
 sci-biology/bcftools/Manifest                      |     1 +
 sci-biology/bcftools/bcftools-1.2.ebuild           |    30 +
 sci-biology/{wcd => bcftools}/metadata.xml         |     0
 sci-biology/bedtools/ChangeLog                     |    21 +
 sci-biology/bedtools/Manifest                      |     1 +
 sci-biology/bedtools/bedtools-2.22.1.ebuild        |    33 +
 sci-biology/bedtools/metadata.xml                  |    16 +
 sci-biology/biobambam/Manifest                     |     1 +
 sci-biology/biobambam/biobambam-0.0.183.ebuild     |    21 +
 sci-biology/biobambam/metadata.xml                 |    15 +
 sci-biology/biopieces/ChangeLog                    |    21 +
 sci-biology/biopieces/biopieces-0.51.ebuild        |     1 +
 sci-biology/biopieces/biopieces-9999.ebuild        |    72 +
 sci-biology/{wcd => biopieces}/metadata.xml        |     0
 sci-biology/biopython/ChangeLog                    |    10 -
 sci-biology/biopython/biopython-1.62.ebuild        |    49 -
 sci-biology/bismark/Manifest                       |     1 +
 sci-biology/bismark/bismark-0.13.0.ebuild          |    31 +
 sci-biology/bismark/metadata.xml                   |    20 +
 sci-biology/blasr/ChangeLog                        |     5 +-
 sci-biology/blasr/blasr-9999.ebuild                |     8 +-
 sci-biology/blue/ChangeLog                         |    15 +
 sci-biology/blue/Manifest                          |     2 +
 sci-biology/blue/blue-1.1.2.ebuild                 |    34 +
 sci-biology/{wcd => blue}/metadata.xml             |     0
 sci-biology/bowtie/ChangeLog                       |    11 +
 sci-biology/bowtie/Manifest                        |     2 +
 sci-biology/bowtie/bowtie-1.1.1.ebuild             |    53 +
 sci-biology/bowtie/bowtie-2.2.4.ebuild             |    52 +
 sci-biology/{sequin => bowtie}/metadata.xml        |     0
 sci-biology/brat/ChangeLog                         |     8 +-
 sci-biology/brat/Manifest                          |     2 +-
 sci-biology/brat/brat-1.1.13.ebuild                |    22 -
 sci-biology/brat/brat-1.2.4.ebuild                 |    43 +
 sci-biology/brat/metadata.xml                      |    10 +-
 sci-biology/breakdancer/ChangeLog                  |     9 +
 sci-biology/breakdancer/Manifest                   |     1 +
 sci-biology/breakdancer/breakdancer-1.1.2.ebuild   |    20 +
 sci-biology/{zmsort => breakdancer}/metadata.xml   |     0
 sci-biology/caftools/ChangeLog                     |     7 +-
 sci-biology/caftools/caftools-2.0.2.ebuild         |     4 +-
 sci-biology/cap3-bin/cap3-bin-20071221.ebuild      |     2 +-
 sci-biology/cd-hit-auxtools/ChangeLog              |    14 +
 sci-biology/cd-hit-auxtools/Manifest               |     2 +
 .../cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild     |    44 +
 sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch |    47 +
 sci-biology/{wcd => cd-hit-auxtools}/metadata.xml  |     0
 sci-biology/cd-hit/ChangeLog                       |    12 +
 sci-biology/cd-hit/Manifest                        |     1 +
 sci-biology/cd-hit/cd-hit-4.6.1.ebuild             |    44 +
 sci-biology/cd-hit/files/4.6.1-gentoo.patch        |   118 +
 sci-biology/cd-hit/metadata.xml                    |    23 +
 sci-biology/cdbfasta/cdbfasta-0.1.ebuild           |     2 +-
 sci-biology/cegma/ChangeLog                        |    11 +
 sci-biology/cegma/Manifest                         |     1 +
 sci-biology/cegma/cegma-2.5.ebuild                 |    37 +
 sci-biology/{wcd => cegma}/metadata.xml            |     0
 sci-biology/cgview-bin/ChangeLog                   |    13 +
 sci-biology/cgview-bin/Manifest                    |     1 +
 sci-biology/cgview-bin/cgview-bin-20131130.ebuild  |    44 +
 sci-biology/{wcd => cgview-bin}/metadata.xml       |     0
 sci-biology/clover/ChangeLog                       |     2 +-
 sci-biology/clover/clover-2011.10.24.ebuild        |     2 +-
 sci-biology/cluster/cluster-1.50-r1.ebuild         |     2 +-
 sci-biology/cluster/cluster-1.50.ebuild            |     2 +-
 sci-biology/clview/ChangeLog                       |     6 +
 sci-biology/clview/Manifest                        |     4 +-
 sci-biology/clview/clview-0.1.ebuild               |     4 +-
 sci-biology/cnrun/ChangeLog                        |     6 +
 sci-biology/cnrun/Manifest                         |     1 +
 sci-biology/cnrun/cnrun-2.0.2.ebuild               |    23 +
 sci-biology/cnrun/metadata.xml                     |    29 +
 sci-biology/codonw/ChangeLog                       |     6 +-
 sci-biology/codonw/codonw-1.4.4-r1.ebuild          |    12 +-
 sci-biology/conifer/ChangeLog                      |     9 +
 sci-biology/conifer/Manifest                       |     1 +
 sci-biology/conifer/conifer-0.2.2.ebuild           |    25 +
 sci-biology/{wcd => conifer}/metadata.xml          |     0
 sci-biology/consed-bin/consed-bin-20.ebuild        |     4 +-
 sci-biology/consed/ChangeLog                       |     8 -
 sci-biology/consed/Manifest                        |     2 -
 sci-biology/consed/consed-20-r1.ebuild             |    74 -
 sci-biology/consed/files/nLine.h.patch             |    17 -
 .../consed/files/nextPhredPipeline.cpp.patch       |    11 -
 sci-biology/consed/metadata.xml                    |     9 -
 sci-biology/consed2gap/ChangeLog                   |    13 +
 sci-biology/consed2gap/Manifest                    |     1 +
 sci-biology/consed2gap/consed2gap-20050520.ebuild  |    38 +
 sci-biology/{wcd => consed2gap}/metadata.xml       |     0
 sci-biology/coral/ChangeLog                        |     9 +
 sci-biology/coral/Manifest                         |     1 +
 sci-biology/coral/coral-1.4.ebuild                 |    28 +
 sci-biology/{wcd => coral}/metadata.xml            |     0
 sci-biology/cutadapt/ChangeLog                     |    13 +-
 sci-biology/cutadapt/Manifest                      |     2 +
 sci-biology/cutadapt/cutadapt-1.2.1.ebuild         |    13 +-
 sci-biology/cutadapt/cutadapt-1.4.1.ebuild         |    25 +
 sci-biology/cutadapt/cutadapt-1.5.ebuild           |    25 +
 sci-biology/cutadapt/cutadapt-9999.ebuild          |    25 +
 sci-biology/dawg/ChangeLog                         |     7 +-
 sci-biology/dawg/Manifest                          |     2 +-
 sci-biology/dawg/dawg-1.1.1.ebuild                 |    29 -
 sci-biology/dawg/dawg-1.1.2.ebuild                 |    22 +
 ...wg-1.1.1-gcc43.patch => dawg-1.1.2-gcc43.patch} |     0
 sci-biology/discrover/ChangeLog                    |    46 +
 sci-biology/discrover/Manifest                     |     1 +
 sci-biology/discrover/discrover-1.6.0.ebuild       |    79 +
 sci-biology/discrover/discrover-9999.ebuild        |    80 +
 sci-biology/discrover/metadata.xml                 |    25 +
 sci-biology/ePCR/ChangeLog                         |     7 +
 sci-biology/ePCR/Manifest                          |     1 +
 sci-biology/ePCR/ePCR-2.3.12.ebuild                |    34 +
 sci-biology/ePCR/files/config.mk.patch             |    18 +
 sci-biology/{wcd => ePCR}/metadata.xml             |     0
 sci-biology/edena/ChangeLog                        |     9 +
 sci-biology/edena/Manifest                         |     1 +
 sci-biology/edena/edena-3.131028.ebuild            |    35 +
 sci-biology/{wcd => edena}/metadata.xml            |     0
 sci-biology/embassy-cbstools/ChangeLog             |     7 +-
 sci-biology/embassy-cbstools/Manifest              |     2 +-
 .../embassy-cbstools-1.0.0-r3.ebuild               |    11 -
 .../embassy-cbstools-1.0.0.650.ebuild              |    11 +
 .../files/embassy-cbstools-1.0.0-r2.patch          |   347 -
 ...bassy-cbstools-1.0.0.650_fix-build-system.patch |    97 +
 sci-biology/embassy-cbstools/metadata.xml          |     2 +-
 sci-biology/embassy-clustalomega/ChangeLog         |   117 +
 sci-biology/embassy-clustalomega/Manifest          |     1 +
 .../embassy-clustalomega-1.1.0.ebuild              |    13 +
 ...bassy-clustalomega-1.1.0_fix-build-system.patch |    90 +
 .../{sequin => embassy-clustalomega}/metadata.xml  |     0
 sci-biology/embassy-domainatrix/ChangeLog          |     7 +-
 sci-biology/embassy-domainatrix/Manifest           |     2 +-
 .../embassy-domainatrix-0.1.0-r6.ebuild            |    11 -
 .../embassy-domainatrix-0.1.650.ebuild             |    11 +
 .../files/embassy-domainatrix-0.1.0-r5.patch       |   346 -
 ...assy-domainatrix-0.1.650_fix-build-system.patch |    91 +
 sci-biology/embassy-domainatrix/metadata.xml       |     2 +-
 sci-biology/embassy-domalign/ChangeLog             |     7 +-
 sci-biology/embassy-domalign/Manifest              |     2 +-
 .../embassy-domalign-0.1.0-r5.ebuild               |    11 -
 .../embassy-domalign-0.1.650.ebuild                |    11 +
 .../files/embassy-domalign-0.1.0-r5.patch          |   346 -
 ...embassy-domalign-0.1.650_fix-build-system.patch |    92 +
 sci-biology/embassy-domalign/metadata.xml          |     2 +-
 sci-biology/embassy-domsearch/ChangeLog            |     7 +-
 sci-biology/embassy-domsearch/Manifest             |     2 +-
 .../embassy-domsearch-0.1.0-r5.ebuild              |    11 -
 .../embassy-domsearch-0.1.650.ebuild               |    11 +
 .../files/embassy-domsearch-0.1.0-r5.patch         |   346 -
 ...mbassy-domsearch-0.1.650_fix-build-system.patch |    91 +
 sci-biology/embassy-domsearch/metadata.xml         |     2 +-
 sci-biology/embassy-emnu/ChangeLog                 |     7 +-
 sci-biology/embassy-emnu/Manifest                  |     2 +-
 .../embassy-emnu/embassy-emnu-1.05-r7.ebuild       |    15 -
 .../embassy-emnu/embassy-emnu-1.05.650.ebuild      |    15 +
 .../embassy-emnu/files/embassy-emnu-1.05-r7.patch  |   359 -
 .../embassy-emnu-1.05.650_fix-build-system.patch   |   127 +
 sci-biology/embassy-emnu/metadata.xml              |     2 +-
 sci-biology/embassy-esim4/ChangeLog                |     7 +-
 sci-biology/embassy-esim4/Manifest                 |     2 +-
 .../embassy-esim4/embassy-esim4-1.0.0-r7.ebuild    |    11 -
 .../embassy-esim4/embassy-esim4-1.0.0.650.ebuild   |    11 +
 .../files/embassy-esim4-1.0.0-r7.patch             |   345 -
 .../embassy-esim4-1.0.0.650_fix-build-system.patch |    97 +
 sci-biology/embassy-esim4/metadata.xml             |     2 +-
 sci-biology/embassy-hmmer/ChangeLog                |     7 +-
 sci-biology/embassy-hmmer/Manifest                 |     2 +-
 .../embassy-hmmer/embassy-hmmer-2.3.2-r4.ebuild    |    13 -
 .../embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild   |    13 +
 .../files/embassy-hmmer-2.3.2-r4.patch             |   346 -
 .../embassy-hmmer-2.3.2.650_fix-build-system.patch |    90 +
 sci-biology/embassy-hmmer/metadata.xml             |     2 +-
 sci-biology/embassy-iprscan/ChangeLog              |     7 +-
 sci-biology/embassy-iprscan/Manifest               |     2 +-
 .../embassy-iprscan-4.3.1-r2.ebuild                |    11 -
 .../embassy-iprscan-4.3.1.650.ebuild               |    11 +
 .../files/embassy-iprscan-4.3.1-r2.patch           |   349 -
 ...mbassy-iprscan-4.3.1.650_fix-build-system.patch |    97 +
 sci-biology/embassy-iprscan/metadata.xml           |     2 +-
 sci-biology/embassy-meme/ChangeLog                 |    75 +
 sci-biology/embassy-meme/Manifest                  |     1 +
 .../embassy-meme/embassy-meme-4.7.650.ebuild       |    13 +
 .../embassy-meme-4.7.650_fix-build-system.patch    |    90 +
 sci-biology/{sequin => embassy-meme}/metadata.xml  |     0
 sci-biology/embassy-memenew/ChangeLog              |    71 -
 .../files/embassy-memenew-4.0.0-r1.patch           |   346 -
 sci-biology/embassy-memenew/metadata.xml           |     5 -
 sci-biology/embassy-mira/ChangeLog                 |    50 -
 .../embassy-mira/files/embassy-mira-2.8.2-r2.patch |   345 -
 sci-biology/embassy-mira/metadata.xml              |     5 -
 sci-biology/embassy-mse/ChangeLog                  |     6 +-
 sci-biology/embassy-mse/Manifest                   |     2 +-
 .../embassy-mse/embassy-mse-3.0.0.650.ebuild       |    21 +
 sci-biology/embassy-mse/embassy-mse-3.0.0.ebuild   |    23 -
 .../embassy-mse-3.0.0.650_fix-build-system.patch   |   133 +
 .../embassy-mse/files/embassy-mse-3.0.0.patch      |   398 -
 sci-biology/embassy-mse/metadata.xml               |     2 +-
 sci-biology/embassy-phylipnew/ChangeLog            |     7 +-
 sci-biology/embassy-phylipnew/Manifest             |     2 +-
 .../embassy-phylipnew-3.69.650.ebuild              |    13 +
 .../embassy-phylipnew-3.69.ebuild                  |    13 -
 ...bassy-phylipnew-3.69.650_fix-build-system.patch |    98 +
 .../files/embassy-phylipnew-3.69.patch             |   346 -
 sci-biology/embassy-phylipnew/metadata.xml         |     2 +-
 sci-biology/embassy-signature/ChangeLog            |     7 +-
 sci-biology/embassy-signature/Manifest             |     2 +-
 .../embassy-signature-0.1.0-r5.ebuild              |    11 -
 .../embassy-signature-0.1.650.ebuild               |    11 +
 .../files/embassy-signature-0.1.0-r5.patch         |   346 -
 ...mbassy-signature-0.1.650_fix-build-system.patch |    90 +
 sci-biology/embassy-signature/metadata.xml         |     2 +-
 sci-biology/embassy-structure/ChangeLog            |     7 +-
 sci-biology/embassy-structure/Manifest             |     2 +-
 .../embassy-structure-0.1.0-r5.ebuild              |    11 -
 .../embassy-structure-0.1.650.ebuild               |    11 +
 .../files/embassy-structure-0.1.0-r5.patch         |   347 -
 ...mbassy-structure-0.1.650_fix-build-system.patch |    90 +
 sci-biology/embassy-structure/metadata.xml         |     2 +-
 sci-biology/embassy-topo/ChangeLog                 |     6 +-
 sci-biology/embassy-topo/Manifest                  |     2 +-
 sci-biology/embassy-topo/embassy-topo-2.0.0.ebuild |    11 -
 .../embassy-topo/embassy-topo-2.0.650.ebuild       |    11 +
 .../embassy-topo/files/embassy-topo-2.0.0.patch    |   346 -
 .../embassy-topo-2.0.650_fix-build-system.patch    |    97 +
 sci-biology/embassy-topo/metadata.xml              |     2 +-
 sci-biology/embassy-vienna/ChangeLog               |     7 +-
 sci-biology/embassy-vienna/Manifest                |     2 +-
 .../embassy-vienna/embassy-vienna-1.7.2-r2.ebuild  |    11 -
 .../embassy-vienna/embassy-vienna-1.7.2.650.ebuild |    11 +
 .../files/embassy-vienna-1.7.2-r2.patch            |   355 -
 ...embassy-vienna-1.7.2.650_fix-build-system.patch |    98 +
 sci-biology/embassy-vienna/metadata.xml            |     2 +-
 sci-biology/embassy/ChangeLog                      |     6 +-
 sci-biology/embassy/embassy-6.3.1.ebuild           |    43 -
 sci-biology/embassy/embassy-6.6.0.ebuild           |    30 +
 sci-biology/embassy/metadata.xml                   |     2 +-
 sci-biology/emboss/ChangeLog                       |    36 +-
 sci-biology/emboss/Manifest                        |     4 -
 sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild       |    88 -
 sci-biology/emboss/emboss-6.5.7.ebuild             |    79 -
 sci-biology/emboss/emboss-6.6.0.ebuild             |    60 +-
 sci-biology/emboss/files/README.gentoo             |    34 +
 sci-biology/emboss/files/ax_lib_mysql.m4           |   147 -
 .../emboss/files/emboss-6.3.1_p4-r2_Makefile.patch |    47 -
 .../emboss-6.3.1_p4-r2_compilations-paths.patch    |   315 -
 .../emboss/files/emboss-6.3.1_p4-r2_libtool.patch  |    18 -
 .../emboss/files/emboss-6.3.1_p4-r2_plcol.patch    |   112 -
 .../files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch    |    11 +
 .../files/emboss-6.6.0_fix-build-system.patch      |   368 +
 .../files/emboss-6.6.0_plplot-declarations.patch   |    61 +
 .../emboss-6.6.0_qa-implicit-declarations.patch    |    74 +
 sci-biology/emboss/files/emboss-README.Gentoo-2    |    34 -
 sci-biology/emboss/metadata.xml                    |     4 +-
 sci-biology/epga/ChangeLog                         |    15 +
 sci-biology/epga/epga-9999.ebuild                  |    34 +
 sci-biology/{wcd => epga}/metadata.xml             |     0
 sci-biology/erpin/erpin-5.5b.ebuild                |     4 +-
 sci-biology/est2assembly/ChangeLog                 |     8 +
 sci-biology/est2assembly/Manifest                  |     1 +
 sci-biology/est2assembly/est2assembly-1.08.ebuild  |    26 +
 sci-biology/est2assembly/est2assembly-9999.ebuild  |    48 +
 sci-biology/{wcd => est2assembly}/metadata.xml     |     0
 sci-biology/est2uni/ChangeLog                      |    13 +-
 sci-biology/est2uni/est2uni-0.27.ebuild            |     6 +-
 sci-biology/est2uni/est2uni-9999.ebuild            |    23 +-
 sci-biology/est2uni/metadata.xml                   |    10 +-
 sci-biology/estscan/ChangeLog                      |     5 +-
 sci-biology/estscan/estscan-3.0.3.ebuild           |    52 +-
 sci-biology/eval/ChangeLog                         |    24 +
 sci-biology/eval/Manifest                          |     2 +
 sci-biology/eval/eval-2.2.8.ebuild                 |    40 +
 sci-biology/{wcd => eval}/metadata.xml             |     0
 sci-biology/fastdnaml/ChangeLog                    |     8 +-
 sci-biology/fastdnaml/Manifest                     |     4 +-
 sci-biology/fastdnaml/fastdnaml-1.2.2.ebuild       |    33 -
 sci-biology/fastdnaml/fastdnaml-1.2.2_p10.ebuild   |    35 +
 sci-biology/fastdnaml/metadata.xml                 |    10 +-
 sci-biology/fastqc/ChangeLog                       |    29 +
 sci-biology/fastqc/Manifest                        |     1 +
 sci-biology/fastqc/fastqc-0.11.2.ebuild            |    37 +
 sci-biology/fastqc/files/build.xml                 |    59 +
 sci-biology/{zmsort => fastqc}/metadata.xml        |     0
 sci-biology/fastx_toolkit/ChangeLog                |    17 +-
 sci-biology/fastx_toolkit/Manifest                 |     2 +-
 .../fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild    |    26 -
 .../fastx_toolkit/fastx_toolkit-0.0.14.ebuild      |    33 +
 .../fastx_toolkit}/metadata.xml                    |     0
 sci-biology/ffindex/ChangeLog                      |     9 +
 sci-biology/ffindex/Manifest                       |     1 +
 sci-biology/ffindex/ffindex-0.9.9.3.ebuild         |    43 +
 sci-biology/{wcd => ffindex}/metadata.xml          |     0
 sci-biology/flexbar/ChangeLog                      |    10 +
 sci-biology/flexbar/Manifest                       |     1 +
 sci-biology/flexbar/flexbar-2.4.ebuild             |    23 +
 sci-biology/{zmsort => flexbar}/metadata.xml       |     0
 sci-biology/freebayes/ChangeLog                    |    24 +
 sci-biology/freebayes/freebayes-9999.ebuild        |    41 +
 sci-biology/{wcd => freebayes}/metadata.xml        |     0
 sci-biology/fsa/ChangeLog                          |    10 +
 sci-biology/fsa/Manifest                           |     1 +
 sci-biology/fsa/fsa-1.15.7.ebuild                  |    19 +
 sci-biology/{wcd => fsa}/metadata.xml              |     0
 sci-biology/gap2caf/ChangeLog                      |     7 +-
 sci-biology/gap2caf/gap2caf-2.1.0.ebuild           |     3 +-
 sci-biology/gbench/gbench-2.3.2.ebuild             |     2 +-
 sci-biology/gbrowse/ChangeLog                      |    10 +-
 sci-biology/gbrowse/gbrowse-2.39.ebuild            |    12 +-
 sci-biology/gbrowse/gbrowse-2.45.ebuild            |    12 +-
 sci-biology/gbrowse/gbrowse-2.48.ebuild            |    12 +-
 sci-biology/gbrowse/metadata.xml                   |    14 +-
 sci-biology/geneid/ChangeLog                       |    12 +
 sci-biology/geneid/Manifest                        |     1 +
 sci-biology/geneid/files/Makefile.patch            |    11 +
 sci-biology/geneid/geneid-1.4.4.ebuild             |    32 +
 sci-biology/{wcd => geneid}/metadata.xml           |     0
 sci-biology/genepop/ChangeLog                      |     6 +-
 sci-biology/genepop/Manifest                       |     2 +-
 sci-biology/genepop/genepop-4.0.10.ebuild          |    39 -
 sci-biology/genepop/genepop-4.2.1.ebuild           |    34 +
 sci-biology/genepop/metadata.xml                   |    10 +-
 sci-biology/generecon/generecon-1.2.1-r1.ebuild    |     2 +-
 sci-biology/genomeview-bin/ChangeLog               |    14 +
 sci-biology/genomeview-bin/Manifest                |     1 +
 .../genomeview-bin/genomeview-bin-2450.ebuild      |    22 +
 .../{zmsort => genomeview-bin}/metadata.xml        |     0
 sci-biology/genseed/ChangeLog                      |     6 +-
 sci-biology/genseed/Manifest                       |     2 +-
 sci-biology/genseed/genseed-1.0.22.ebuild          |    21 +-
 sci-biology/genseed/metadata.xml                   |    10 +-
 sci-biology/gfftools/ChangeLog                     |     9 +
 sci-biology/gfftools/Manifest                      |     2 +
 sci-biology/gfftools/gfftools-0.98d.ebuild         |    26 +
 sci-biology/{wcd => gfftools}/metadata.xml         |     0
 sci-biology/grappa/grappa-2.0.ebuild               |     2 +-
 sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild         |     4 +-
 sci-biology/igv/ChangeLog                          |    46 +-
 sci-biology/igv/Manifest                           |     1 +
 sci-biology/igv/igv-2.0.32.ebuild                  |    35 -
 sci-biology/igv/igv-2.3.44.ebuild                  |    81 +
 sci-biology/igv/metadata.xml                       |    10 +-
 sci-biology/inGAP-bin/ChangeLog                    |     9 +
 sci-biology/inGAP-bin/Manifest                     |     1 +
 sci-biology/inGAP-bin/inGAP-bin-3.0.1.ebuild       |    39 +
 sci-biology/{wcd => inGAP-bin}/metadata.xml        |     0
 sci-biology/jalview/ChangeLog                      |    15 -
 sci-biology/jalview/Manifest                       |     1 -
 sci-biology/jalview/jalview-2.6.1.ebuild           |    62 -
 sci-biology/jalview/metadata.xml                   |     9 -
 sci-biology/jellyfish/ChangeLog                    |    13 +
 sci-biology/jellyfish/Manifest                     |     2 +
 sci-biology/jellyfish/jellyfish-2.1.3.ebuild       |    20 +
 sci-biology/{wcd => jellyfish}/metadata.xml        |     0
 sci-biology/jigsaw/ChangeLog                       |    13 +
 sci-biology/jigsaw/Manifest                        |     1 +
 sci-biology/jigsaw/jigsaw-3.2.10.ebuild            |    14 +
 sci-biology/{wcd => jigsaw}/metadata.xml           |     0
 sci-biology/jtreeview/ChangeLog                    |     6 +
 sci-biology/jtreeview/Manifest                     |     2 +
 sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild     |    25 +
 sci-biology/{wcd => jtreeview}/metadata.xml        |     0
 sci-biology/khmer/ChangeLog                        |    36 +
 sci-biology/khmer/Manifest                         |     2 +
 sci-biology/khmer/khmer-0.8.ebuild                 |    40 +
 sci-biology/khmer/khmer-1.0.1.ebuild               |    63 +
 sci-biology/khmer/khmer-9999.ebuild                |    41 +
 sci-biology/{wcd => khmer}/metadata.xml            |     0
 sci-biology/kmergenie/ChangeLog                    |    15 +
 sci-biology/kmergenie/Manifest                     |     1 +
 sci-biology/kmergenie/kmergenie-1.6950.ebuild      |    43 +
 sci-biology/{wcd => kmergenie}/metadata.xml        |     0
 sci-biology/lastz/ChangeLog                        |     4 +-
 sci-biology/lastz/lastz-1.03.34.ebuild             |     2 +-
 .../libgtextutils/libgtextutils-0.6.1.ebuild       |     2 +-
 sci-biology/lucy/lucy-1.20.ebuild                  |     2 +-
 sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild  |     2 +-
 sci-biology/manatee-jcvi/ChangeLog                 |    10 +-
 sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild |    28 +-
 sci-biology/manatee-jcvi/metadata.xml              |    10 +-
 sci-biology/mavid/ChangeLog                        |     6 +-
 sci-biology/mavid/Manifest                         |     2 +-
 sci-biology/mavid/mavid-2.0.4.ebuild               |    33 +-
 sci-biology/mavid/metadata.xml                     |    10 +-
 sci-biology/merlin/ChangeLog                       |     6 +-
 sci-biology/merlin/merlin-1.1.2.ebuild             |    10 +-
 sci-biology/mgblast/ChangeLog                      |    13 +
 sci-biology/mgblast/Manifest                       |     1 +
 sci-biology/{zmsort => mgblast}/metadata.xml       |     0
 sci-biology/mgblast/mgblast-0.1.ebuild             |    46 +
 sci-biology/mip-scaffolder/ChangeLog               |    12 +
 sci-biology/mip-scaffolder/Manifest                |     1 +
 sci-biology/{wcd => mip-scaffolder}/metadata.xml   |     0
 .../mip-scaffolder/mip-scaffolder-0.6.ebuild       |    32 +
 sci-biology/mira/ChangeLog                         |    28 +-
 sci-biology/mira/Manifest                          |     7 +-
 sci-biology/mira/metadata.xml                      |    10 +-
 sci-biology/mira/mira-3.4.0.1.ebuild               |    62 -
 sci-biology/mira/mira-3.4.1.1.ebuild               |    61 -
 sci-biology/mira/mira-3.9.15.ebuild                |    64 -
 sci-biology/mira/mira-3.9.9.ebuild                 |    61 -
 sci-biology/mira/mira-4.0.2.ebuild                 |    76 +
 sci-biology/mira/mira-4.0_rc4.ebuild               |    76 +
 sci-biology/miranda/ChangeLog                      |     6 +-
 sci-biology/miranda/metadata.xml                   |    10 +-
 sci-biology/miranda/miranda-3.3a.ebuild            |     6 +-
 sci-biology/mne-python/ChangeLog                   |     8 +
 sci-biology/mne-python/Manifest                    |     1 +
 .../mne-python}/metadata.xml                       |     0
 sci-biology/mne-python/mne-python-0.7.ebuild       |    57 +
 sci-biology/mne-python/mne-python-9999.ebuild      |    55 +
 sci-biology/mosaik/ChangeLog                       |    15 +-
 sci-biology/mosaik/Manifest                        |     3 +-
 sci-biology/mosaik/metadata.xml                    |    10 +-
 sci-biology/mosaik/mosaik-1.1.0021.ebuild          |    40 -
 sci-biology/mosaik/mosaik-2.1.33.ebuild            |    46 -
 sci-biology/mosaik/mosaik-2.2.3.ebuild             |    30 +
 sci-biology/mosaik/mosaik-9999.ebuild              |    38 +-
 sci-biology/mrbayes/ChangeLog                      |    10 +-
 sci-biology/mrbayes/metadata.xml                   |     4 +-
 sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild        |    16 +-
 sci-biology/mreps/ChangeLog                        |     5 +-
 sci-biology/mreps/Manifest                         |     2 +-
 sci-biology/mreps/metadata.xml                     |    10 +-
 sci-biology/mreps/mreps-2.5.ebuild                 |    18 +-
 sci-biology/mrfast/ChangeLog                       |     9 +
 sci-biology/mrfast/Manifest                        |     2 +-
 .../mrfast-2.1.0.3-disc_buffer_overflow.patch      |    52 -
 sci-biology/mrfast/metadata.xml                    |    10 +-
 sci-biology/mrfast/mrfast-2.1.0.3.ebuild           |    30 -
 sci-biology/mrfast/mrfast-2.6.0.1.ebuild           |    31 +
 sci-biology/mrsfast/ChangeLog                      |     8 +
 sci-biology/mrsfast/Manifest                       |     2 +-
 sci-biology/mrsfast/metadata.xml                   |    10 +-
 sci-biology/mrsfast/mrsfast-2.3.0.2.ebuild         |    30 -
 sci-biology/mrsfast/mrsfast-2.6.0.4.ebuild         |    29 +
 sci-biology/ncbi-blast+/ChangeLog                  |    16 +
 sci-biology/ncbi-blast+/Manifest                   |     1 +
 .../files/disable-testsuite-compilation.txt        |     0
 sci-biology/ncbi-blast+/files/fix_lib_deps.patch   |   668 +
 sci-biology/ncbi-blast+/metadata.xml               |    36 +
 sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild  |   355 +
 sci-biology/ncbi-tools++/ChangeLog                 |   108 +-
 sci-biology/ncbi-tools++/Manifest                  |     2 +-
 .../files/ncbi-tools++-12.0.0-conf-opts.patch      |    64 +
 .../files/ncbi-tools++-12.0.0-configure.patch      |   216 +
 .../ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch |    44 +
 .../ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch |    19 +
 .../ncbi-tools++-12.0.0-fix-creaders-linking.patch |    11 +
 .../files/ncbi-tools++-12.0.0-fix-install.patch    |    11 +
 .../ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch |    10 +
 ...cbi-tools++-12.0.0-linkage-tuneups-addons.patch |    13 +
 .../ncbi-tools++-12.0.0-linkage-tuneups.patch      |   421 +
 .../files/ncbi-tools++-12.0.0-more-patches.patch   |   136 +
 ...ncbi-tools++-12.0.0-support-autoconf-2.60.patch |   296 +
 .../files/ncbi-tools++-9.0.0-as-needed.patch       |  1864 ---
 .../files/ncbi-tools++-9.0.0-conf-opts.patch       |   213 -
 .../ncbi-tools++-9.0.0-disable_test_compress.patch |    15 -
 .../ncbi-tools++-9.0.0-fix-order-of-libs.patch     |    24 -
 sci-biology/ncbi-tools++/metadata.xml              |     3 -
 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        |   355 +
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |   301 -
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild |   308 -
 sci-biology/nesoni/ChangeLog                       |    16 +
 sci-biology/nesoni/Manifest                        |     1 +
 sci-biology/{wcd => nesoni}/metadata.xml           |     0
 sci-biology/nesoni/nesoni-0.128.ebuild             |    33 +
 sci-biology/ngs_backbone/ChangeLog                 |    13 +
 sci-biology/ngs_backbone/Manifest                  |     1 +
 sci-biology/{zmsort => ngs_backbone}/metadata.xml  |     0
 sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild |     1 +
 sci-biology/ngs_backbone/ngs_backbone-9999.ebuild  |   156 +
 sci-biology/ngsview/ChangeLog                      |    15 +
 sci-biology/ngsview/Manifest                       |     1 +
 sci-biology/{wcd => ngsview}/metadata.xml          |     0
 sci-biology/ngsview/ngsview-0.91.ebuild            |    34 +
 sci-biology/nrcl/nrcl-110625.ebuild                |     2 +-
 sci-biology/pairagon/ChangeLog                     |    14 +
 sci-biology/pairagon/Manifest                      |     1 +
 sci-biology/{wcd => pairagon}/metadata.xml         |     0
 sci-biology/pairagon/pairagon-1.1.ebuild           |    42 +
 sci-biology/parafly/ChangeLog                      |     9 +
 sci-biology/parafly/Manifest                       |     1 +
 sci-biology/{wcd => parafly}/metadata.xml          |     0
 sci-biology/parafly/parafly-20130121.ebuild        |    23 +
 sci-biology/pb-honey/ChangeLog                     |     7 +
 sci-biology/pb-honey/Manifest                      |     1 +
 sci-biology/{wcd => pb-honey}/metadata.xml         |     0
 sci-biology/pb-honey/pb-honey-14.1.15.ebuild       |    26 +
 sci-biology/pb-jelly/ChangeLog                     |    13 +
 sci-biology/pb-jelly/Manifest                      |     1 +
 sci-biology/{wcd => pb-jelly}/metadata.xml         |     0
 sci-biology/pb-jelly/pb-jelly-14.9.9.ebuild        |    23 +
 sci-biology/perlprimer/ChangeLog                   |     6 +-
 sci-biology/perlprimer/Manifest                    |     2 +-
 sci-biology/perlprimer/metadata.xml                |     2 +-
 sci-biology/perlprimer/perlprimer-1.1.17.ebuild    |    35 -
 sci-biology/perlprimer/perlprimer-1.1.21.ebuild    |    36 +
 sci-biology/pileup/ChangeLog                       |    16 +
 sci-biology/pileup/Manifest                        |     1 +
 sci-biology/{zmsort => pileup}/metadata.xml        |     0
 sci-biology/pileup/pileup-0.6.ebuild               |    66 +
 sci-biology/primerD/ChangeLog                      |    16 +
 sci-biology/primerD/Manifest                       |     1 +
 sci-biology/{wcd => primerD}/metadata.xml          |     0
 sci-biology/primerD/primerD-1.0.0.ebuild           |    27 +
 sci-biology/proda/ChangeLog                        |     6 +-
 sci-biology/proda/Manifest                         |     2 +-
 .../proda/files/proda-1.0-buildsystem.patch        |    35 +
 sci-biology/proda/files/proda-1.0-newgcc.patch     |   136 +
 sci-biology/proda/proda-1.0.ebuild                 |    29 +-
 sci-biology/prot4EST/ChangeLog                     |    12 +
 sci-biology/prot4EST/Manifest                      |     1 +
 sci-biology/{wcd => prot4EST}/metadata.xml         |     0
 sci-biology/prot4EST/prot4EST-3.1b.ebuild          |    39 +
 sci-biology/psx/psx-0.1.ebuild                     |     2 +-
 sci-biology/psychopy/ChangeLog                     |    10 +-
 sci-biology/psychopy/Manifest                      |     2 -
 sci-biology/psychopy/psychopy-1.75.01.ebuild       |    56 -
 sci-biology/psychopy/psychopy-1.77.02.ebuild       |    56 -
 sci-biology/psychopy/psychopy-1.78.00.ebuild       |     4 +-
 sci-biology/psychopy/psychopy-9999.ebuild          |    12 +-
 sci-biology/pvmsx/ChangeLog                        |     7 +
 sci-biology/pvmsx/Manifest                         |     2 +
 sci-biology/{wcd => pvmsx}/metadata.xml            |     0
 sci-biology/pvmsx/pvmsx-0.1.ebuild                 |    44 +
 sci-biology/pybrain/ChangeLog                      |     5 +-
 sci-biology/pybrain/pybrain-9999.ebuild            |     7 +-
 sci-biology/pysurfer/ChangeLog                     |     8 +
 sci-biology/pysurfer/Manifest                      |     1 +
 .../pysurfer/files/0.4-headless_build.patch        |    22 +
 .../pysurfer}/metadata.xml                         |     0
 sci-biology/pysurfer/pysurfer-0.4.ebuild           |    29 +
 sci-biology/pysurfer/pysurfer-9999.ebuild          |    27 +
 sci-biology/quast/ChangeLog                        |    21 +
 sci-biology/quast/Manifest                         |     1 +
 sci-biology/{wcd => quast}/metadata.xml            |     0
 sci-biology/quast/quast-2.3.ebuild                 |    39 +
 sci-biology/quicktree/quicktree-1.1-r1.ebuild      |     4 +-
 sci-biology/rnaplex/ChangeLog                      |     6 +-
 sci-biology/rnaplex/Manifest                       |     2 +-
 sci-biology/rnaplex/rnaplex-0.2.ebuild             |    14 +-
 .../roche454ace2caf-20100812.ebuild                |     2 +-
 sci-biology/ruffus/ChangeLog                       |    10 +
 sci-biology/{wcd => ruffus}/metadata.xml           |     0
 sci-biology/ruffus/ruffus-9999.ebuild              |    24 +
 sci-biology/sabre/ChangeLog                        |    12 +
 sci-biology/{wcd => sabre}/metadata.xml            |     0
 sci-biology/sabre/sabre-9999.ebuild                |    36 +
 sci-biology/samstat/ChangeLog                      |    12 +
 sci-biology/samstat/Manifest                       |     1 +
 sci-biology/{wcd => samstat}/metadata.xml          |     0
 sci-biology/samstat/samstat-20130708.ebuild        |    29 +
 sci-biology/scaffold_builder/ChangeLog             |    19 +
 sci-biology/scaffold_builder/Manifest              |     3 +
 sci-biology/{wcd => scaffold_builder}/metadata.xml |     0
 .../scaffold_builder-20131122.ebuild               |    33 +
 sci-biology/scan_for_matches/ChangeLog             |    10 +
 sci-biology/scan_for_matches/Manifest              |     1 +
 sci-biology/{wcd => scan_for_matches}/metadata.xml |     0
 .../scan_for_matches-20121220.ebuild               |    26 +
 sci-biology/sclust/sclust-0.1.ebuild               |     2 +-
 sci-biology/screed/ChangeLog                       |    12 +
 sci-biology/screed/Manifest                        |     1 +
 sci-biology/{sequin => screed}/metadata.xml        |     0
 sci-biology/screed/screed-0.7.1.ebuild             |    18 +
 sci-biology/scythe/ChangeLog                       |    10 +
 sci-biology/{wcd => scythe}/metadata.xml           |     0
 sci-biology/scythe/scythe-0.992.ebuild             |    26 +
 sci-biology/seqclean/seqclean-110625.ebuild        |     2 +-
 sci-biology/sequin/ChangeLog                       |     2 +-
 sci-biology/sequin/sequin-20121202.ebuild          |     4 +-
 sci-biology/sff_dump/sff_dump-1.04.ebuild          |     2 +-
 sci-biology/sga/ChangeLog                          |    13 +
 sci-biology/sga/metadata.xml                       |    12 +
 sci-biology/sga/sga-9999.ebuild                    |    45 +
 sci-biology/sgp2/ChangeLog                         |     9 +
 sci-biology/sgp2/Manifest                          |     1 +
 sci-biology/sgp2/files/Makefile.patch              |    88 +
 sci-biology/{wcd => sgp2}/metadata.xml             |     0
 sci-biology/sgp2/sgp2-1.1.ebuild                   |    34 +
 sci-biology/sickle/ChangeLog                       |    19 +
 sci-biology/sickle/Manifest                        |     1 +
 sci-biology/{wcd => sickle}/metadata.xml           |     0
 sci-biology/sickle/sickle-1.33.ebuild              |    36 +
 sci-biology/sickle/sickle-9999.ebuild              |    36 +
 sci-biology/signalp/signalp-3.0.ebuild             |     4 +-
 sci-biology/skewer-bin/ChangeLog                   |     9 +
 sci-biology/skewer-bin/Manifest                    |     2 +
 sci-biology/{wcd => skewer-bin}/metadata.xml       |     0
 sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild   |    25 +
 sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild       |     2 +-
 sci-biology/spm/ChangeLog                          |    27 +
 sci-biology/spm/Manifest                           |     2 +
 .../salome-yacs => sci-biology/spm}/metadata.xml   |     0
 sci-biology/spm/spm-12.ebuild                      |    36 +
 sci-biology/spm/spm-8.ebuild                       |    40 +
 sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild           |     2 +-
 sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild           |     2 +-
 sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild          |     2 +-
 sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild     |     2 +-
 sci-biology/stacks/ChangeLog                       |    13 +
 sci-biology/stacks/Manifest                        |     1 +
 sci-biology/{wcd => stacks}/metadata.xml           |     0
 sci-biology/stacks/stacks-1.16.ebuild              |    48 +
 sci-biology/staden/ChangeLog                       |    11 +-
 sci-biology/staden/metadata.xml                    |    10 +-
 sci-biology/staden/staden-2.0.0_beta9.ebuild       |     4 +-
 sci-biology/staden/staden-9999.ebuild              |    68 +-
 sci-biology/subread/ChangeLog                      |    13 +
 sci-biology/subread/Manifest                       |     1 +
 sci-biology/{wcd => subread}/metadata.xml          |     0
 sci-biology/subread/subread-1.4.6.ebuild           |    42 +
 sci-biology/swissknife/ChangeLog                   |     8 +
 sci-biology/swissknife/Manifest                    |     2 +-
 sci-biology/swissknife/metadata.xml                |     2 +-
 sci-biology/swissknife/swissknife-1.67.ebuild      |    26 -
 sci-biology/swissknife/swissknife-1.70.ebuild      |    26 +
 sci-biology/symap/ChangeLog                        |     5 +-
 .../salome-yacs => sci-biology/symap}/metadata.xml |     0
 sci-biology/symap/symap-4.0.ebuild                 |    19 +-
 sci-biology/tablet-bin/ChangeLog                   |    30 +-
 sci-biology/tablet-bin/Manifest                    |     2 +-
 .../tablet-bin/tablet-bin-1.13.05.17.ebuild        |    89 -
 .../tablet-bin/tablet-bin-1.14.10.21.ebuild        |    97 +
 sci-biology/tablet/ChangeLog                       |    28 +
 .../{tablet-bin => tablet}/files/response.varfile  |     0
 sci-biology/{wcd => tablet}/metadata.xml           |     0
 sci-biology/tablet/tablet-1.14.04.10.ebuild        |     1 +
 sci-biology/tablet/tablet-9999.ebuild              |    49 +
 sci-biology/tagdust/ChangeLog                      |     9 +
 sci-biology/tagdust/Manifest                       |     1 +
 sci-biology/{wcd => tagdust}/metadata.xml          |     0
 sci-biology/tagdust/tagdust-20101028.ebuild        |    33 +
 sci-biology/tclust/tclust-110625.ebuild            |     2 +-
 sci-biology/tgicl/ChangeLog                        |     7 +
 sci-biology/tgicl/metadata.xml                     |    10 +-
 sci-biology/tgicl/tgicl-2.1.ebuild                 |    28 +-
 .../tigr-assembler/tigr-assembler-2.0.ebuild       |     2 +-
 sci-biology/tigr-closure/ChangeLog                 |    13 +
 sci-biology/tigr-closure/Manifest                  |     1 +
 sci-biology/{wcd => tigr-closure}/metadata.xml     |     0
 .../tigr-closure/tigr-closure-20080106.ebuild      |    65 +
 .../tigr-foundation-libs-2.0-r1.ebuild             |     2 +-
 sci-biology/tmhmm/tmhmm-2.0c.ebuild                |     2 +-
 sci-biology/trans-abyss/ChangeLog                  |    13 +
 sci-biology/trans-abyss/Manifest                   |     1 +
 sci-biology/{wcd => trans-abyss}/metadata.xml      |     0
 sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild   |    25 +
 sci-biology/transdecoder/ChangeLog                 |    38 +
 sci-biology/transdecoder/Manifest                  |     2 +
 sci-biology/transdecoder/files/TransDecoder.patch  |   136 +
 .../transdecoder/files/pfam_runner.pl.patch        |    20 +
 sci-biology/{wcd => transdecoder}/metadata.xml     |     0
 sci-biology/transdecoder/transdecoder-2.0.1.ebuild |    57 +
 .../transdecoder/transdecoder-20140704.ebuild      |    51 +
 sci-biology/trf/ChangeLog                          |     9 +
 sci-biology/trf/Manifest                           |     4 +
 sci-biology/{sequin => trf}/metadata.xml           |     0
 sci-biology/trf/trf-4.07b.ebuild                   |    43 +
 sci-biology/trim_galore/ChangeLog                  |    16 +
 sci-biology/trim_galore/Manifest                   |     1 +
 sci-biology/{zmsort => trim_galore}/metadata.xml   |     0
 sci-biology/trim_galore/trim_galore-0.3.7.ebuild   |    28 +
 sci-biology/trimmomatic/ChangeLog                  |    12 +
 sci-biology/trimmomatic/Manifest                   |     2 +
 sci-biology/{wcd => trimmomatic}/metadata.xml      |     0
 sci-biology/trimmomatic/trimmomatic-0.32.ebuild    |    36 +
 sci-biology/trowel/ChangeLog                       |     9 +
 sci-biology/trowel/Manifest                        |     1 +
 sci-biology/{wcd => trowel}/metadata.xml           |     0
 sci-biology/trowel/trowel-0.1.4.1.ebuild           |    20 +
 sci-biology/twinscan/twinscan-4.1.2.ebuild         |     2 +-
 sci-biology/ucsc-genome-browser/Manifest           |     1 +
 sci-biology/ucsc-genome-browser/metadata.xml       |    12 +
 .../ucsc-genome-browser-260.ebuild                 |   106 +
 sci-biology/ugene/ChangeLog                        |    13 +
 sci-biology/ugene/Manifest                         |     1 +
 {dev-libs/papi => sci-biology/ugene}/metadata.xml  |     0
 sci-biology/ugene/ugene-1.13.3.ebuild              |    35 +
 sci-biology/vague-bin/ChangeLog                    |    15 +
 sci-biology/vague-bin/Manifest                     |     1 +
 sci-biology/vague-bin/files/vague.patch            |     8 +
 sci-biology/{wcd => vague-bin}/metadata.xml        |     0
 sci-biology/vague-bin/vague-bin-1.0.5.ebuild       |    40 +
 sci-biology/vcftools/ChangeLog                     |    20 +
 sci-biology/vcftools/Manifest                      |     1 +
 sci-biology/{sequin => vcftools}/metadata.xml      |     0
 sci-biology/vcftools/vcftools-0.1.12b.ebuild       |    48 +
 sci-biology/velvetk/ChangeLog                      |    16 +
 sci-biology/velvetk/Manifest                       |     1 +
 sci-biology/{wcd => velvetk}/metadata.xml          |     0
 sci-biology/velvetk/velvetk-20120606.ebuild        |    25 +
 sci-biology/wcd/ChangeLog                          |    10 +-
 sci-biology/wcd/Manifest                           |     2 +-
 sci-biology/wcd/wcd-0.6.0.ebuild                   |    45 -
 sci-biology/wcd/wcd-0.6.3.ebuild                   |    51 +
 sci-biology/zmsort/ChangeLog                       |     6 +-
 sci-biology/zmsort/metadata.xml                    |    10 +-
 sci-biology/zmsort/zmsort-110625.ebuild            |     4 +-
 sci-chemistry/GromacsWrapper/ChangeLog             |     5 +-
 .../GromacsWrapper/GromacsWrapper-9999.ebuild      |    10 +-
 sci-chemistry/almost/ChangeLog                     |     5 +-
 sci-chemistry/almost/almost-1.0.3-r2.ebuild        |    39 +-
 sci-chemistry/ambertools/ChangeLog                 |    11 +-
 sci-chemistry/ambertools/Manifest                  |     2 +-
 sci-chemistry/ambertools/ambertools-1.5-r4.ebuild  |   159 -
 sci-chemistry/ambertools/ambertools-12.ebuild      |   153 -
 sci-chemistry/ambertools/ambertools-12_p38.ebuild  |   165 +
 .../files/ambertools-1.5-bugfix_1-21.patch         |  5330 -------
 .../files/ambertools-1.5-bugfix_22-27.patch        |  3343 -----
 .../files/ambertools-1.5-bugfix_28.patch           |    23 -
 .../ambertools/files/ambertools-1.5-gentoo2.patch  |  1068 --
 .../ambertools/files/ambertools-1.5-overflow.patch |    30 -
 .../files/ambertools-12-bugfix_14-26.patch         | 14856 -------------------
 .../ambertools/files/ambertools-12-gentoo.patch    |    55 +-
 sci-chemistry/avogadro2/ChangeLog                  |    13 +
 sci-chemistry/avogadro2/Manifest                   |     1 +
 sci-chemistry/avogadro2/avogadro2-0.7.2.ebuild     |    48 +
 sci-chemistry/avogadro2/metadata.xml               |    11 +
 sci-chemistry/ball/ChangeLog                       |     8 +-
 sci-chemistry/ball/ball-9999.ebuild                |    35 +-
 sci-chemistry/ball/files/ball-9999-libsvm.patch    |    24 -
 sci-chemistry/bist/ChangeLog                       |     6 +-
 sci-chemistry/bist/bist-0.5.1-r1.ebuild            |     6 +-
 sci-chemistry/bist/metadata.xml                    |     8 +-
 sci-chemistry/burrow-owl/ChangeLog                 |     4 +
 sci-chemistry/burrow-owl/burrow-owl-9999.ebuild    |    11 +-
 sci-chemistry/burrow-owl/metadata.xml              |     2 +-
 sci-chemistry/camshift/ChangeLog                   |     6 +-
 sci-chemistry/camshift/camshift-1.35.0.ebuild      |     6 +-
 sci-chemistry/chemBuild/ChangeLog                  |    10 +-
 sci-chemistry/chemBuild/Manifest                   |     1 +
 sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild     |     2 +-
 sci-chemistry/chemBuild/chemBuild-1.0.3.ebuild     |     4 +-
 sci-chemistry/chemBuild/chemBuild-1.0.4.ebuild     |    57 +
 sci-chemistry/chimera-bin/ChangeLog                |    19 +-
 sci-chemistry/chimera-bin/Manifest                 |     6 +-
 sci-chemistry/chimera-bin/chimera-bin-1.6.2.ebuild |    94 -
 sci-chemistry/chimera-bin/chimera-bin-1.8.ebuild   |    94 -
 sci-chemistry/chimera-bin/chimera-bin-1.9.ebuild   |    93 +
 sci-chemistry/chooch/chooch-5.0.2-r1.ebuild        |     2 +-
 sci-chemistry/cnsface/cnsface-0.0.12.ebuild        |     2 +-
 sci-chemistry/concoord/concoord-2.1.2.ebuild       |     4 +-
 sci-chemistry/concoord/concoord-2.1.ebuild         |     4 +-
 sci-chemistry/coot/ChangeLog                       |    25 +-
 sci-chemistry/coot/Manifest                        |     2 +-
 sci-chemistry/coot/coot-9999.ebuild                |    24 +-
 sci-chemistry/coot/files/9999-pc.patch             |   101 +-
 .../coot/files/coot-9999-sandbox-icons.patch       |    16 +
 sci-chemistry/cpmgfit/ChangeLog                    |    13 +
 sci-chemistry/cpmgfit/Manifest                     |     1 +
 sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild          |    49 +
 sci-chemistry/{ucsf-tools => cpmgfit}/metadata.xml |     0
 sci-chemistry/cs-rosetta/ChangeLog                 |    15 +-
 .../cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild |     6 +-
 sci-chemistry/curvefit/ChangeLog                   |     8 +-
 sci-chemistry/curvefit/curvefit-1.40.ebuild        |     6 +-
 sci-chemistry/direx/ChangeLog                      |    16 -
 sci-chemistry/direx/Manifest                       |     1 -
 sci-chemistry/direx/direx-0.2.ebuild               |    42 -
 sci-chemistry/direx/metadata.xml                   |     5 -
 sci-chemistry/dl_poly/ChangeLog                    |     9 +-
 sci-chemistry/dl_poly/dl_poly-1.9.ebuild           |     4 +-
 sci-chemistry/dl_poly/dl_poly-4.05.ebuild          |     7 +-
 sci-chemistry/drawxtl/ChangeLog                    |     9 +-
 sci-chemistry/drawxtl/Manifest                     |     4 +-
 sci-chemistry/drawxtl/drawxtl-44.ebuild            |    81 -
 sci-chemistry/drawxtl/drawxtl-45.ebuild            |    77 +
 sci-chemistry/drawxtl/drawxtl-54.ebuild            |    59 -
 sci-chemistry/drawxtl/drawxtl-55.ebuild            |    59 +
 sci-chemistry/drawxtl/files/44-gentoo.patch        |   128 -
 sci-chemistry/drawxtl/files/54-gcc44.patch         |    11 -
 sci-chemistry/drawxtl/files/54-gentoo.patch        |    73 -
 sci-chemistry/drawxtl/files/54-ldflags.patch       |    11 -
 .../drawxtl/files/drawxtl-45-gentoo.patch          |   132 +
 .../drawxtl/files/drawxtl-55-gentoo.patch          |    78 +
 sci-chemistry/drawxtl/metadata.xml                 |     4 +-
 sci-chemistry/dssp2pdb/ChangeLog                   |     9 +-
 sci-chemistry/dssp2pdb/Manifest                    |     2 +-
 sci-chemistry/dssp2pdb/dssp2pdb-0.03.ebuild        |     8 +-
 sci-chemistry/dssp2pdb/metadata.xml                |     2 +-
 sci-chemistry/erkale/ChangeLog                     |    10 +
 sci-chemistry/erkale/erkale-9999.ebuild            |    70 +
 sci-chemistry/erkale/metadata.xml                  |    18 +
 sci-chemistry/freeon/ChangeLog                     |   140 +-
 sci-chemistry/freeon/Manifest                      |     1 -
 .../files/freeon-2012.05.03-no_internal_hdf5.patch |    30 -
 .../files/freeon-9999-no_internal_hdf5.patch       |    25 -
 sci-chemistry/freeon/freeon-2012.05.03.ebuild      |    50 -
 sci-chemistry/freeon/freeon-9999.ebuild            |    41 +-
 sci-chemistry/freeon/metadata.xml                  |     2 +-
 sci-chemistry/gamess/ChangeLog                     |     6 +
 sci-chemistry/gamess/Manifest                      |     1 +
 .../gamess/files/gamess-20130501.1.gentoo.patch    |   206 +
 sci-chemistry/gamess/gamess-20120501.1.ebuild      |     2 +-
 sci-chemistry/gamess/gamess-20130501.1.ebuild      |   338 +
 .../gnome-chemistry-utils-0.14.2-r1.ebuild         |     2 +-
 .../gnome-chemistry-utils-9999.ebuild              |     2 +-
 sci-chemistry/gromacs/ChangeLog                    |   114 +-
 sci-chemistry/gromacs/Manifest                     |     2 -
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild      |   242 -
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild      |    68 +-
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild      |   279 +
 sci-chemistry/gromacs/gromacs-9999.ebuild          |   299 +-
 sci-chemistry/gromacs/metadata.xml                 |    34 +-
 sci-chemistry/hydronmr/ChangeLog                   |     8 +-
 sci-chemistry/hydronmr/hydronmr-7c.ebuild          |     5 +-
 sci-chemistry/jana2000/jana2000-20071218.ebuild    |     2 +-
 sci-chemistry/jligand/jligand-1.0.19.ebuild        |     2 +-
 sci-chemistry/ligplot+/ligplot+-1.4.ebuild         |     2 +-
 sci-chemistry/mage/mage-6.44.060606.ebuild         |     2 +-
 sci-chemistry/mddnmr/ChangeLog                     |    25 +-
 sci-chemistry/mddnmr/Manifest                      |     3 +-
 sci-chemistry/mddnmr/mddnmr-2.1.ebuild             |    59 -
 sci-chemistry/mddnmr/mddnmr-2.2.ebuild             |    59 -
 sci-chemistry/mddnmr/mddnmr-2.4-r1.ebuild          |    66 +
 sci-chemistry/mddnmr/metadata.xml                  |     2 +-
 sci-chemistry/mdsctk/ChangeLog                     |    15 +-
 sci-chemistry/mdsctk/Manifest                      |     2 +-
 sci-chemistry/mdsctk/mdsctk-1.1.0.ebuild           |    46 -
 sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild           |    44 +
 sci-chemistry/mdsctk/metadata.xml                  |    16 +-
 .../mgltools-autodocktools-1.5.6.ebuild            |     2 +-
 .../mgltools-bhtree/mgltools-bhtree-1.5.6.ebuild   |     2 +-
 .../mgltools-cadd/mgltools-cadd-1.5.6.ebuild       |     2 +-
 .../mgltools-cmolkit/mgltools-cmolkit-1.5.6.ebuild |     2 +-
 sci-chemistry/mgltools-dejavu/ChangeLog            |     8 +-
 .../files/mgltools-dejavu-1.5.6-pil.patch          |    43 +
 .../mgltools-dejavu-1.5.6-r1.ebuild                |    50 +
 .../mgltools-dejavu/mgltools-dejavu-1.5.6.ebuild   |     2 +-
 .../mgltools-geomutils-1.5.6.ebuild                |     2 +-
 .../mgltools-gle/mgltools-gle-1.5.6.ebuild         |     2 +-
 .../mgltools-mglutil/mgltools-mglutil-1.5.6.ebuild |     2 +-
 .../mgltools-molkit/mgltools-molkit-1.5.6.ebuild   |     2 +-
 .../mgltools-networkeditor-1.5.6.ebuild            |     2 +-
 .../mgltools-opengltk-1.5.6.ebuild                 |     2 +-
 .../mgltools-pmv/mgltools-pmv-1.5.6.ebuild         |     2 +-
 .../mgltools-pyautodock-1.5.6.ebuild               |     2 +-
 .../mgltools-pybabel/mgltools-pybabel-1.5.6.ebuild |     2 +-
 .../mgltools-pyglf/mgltools-pyglf-1.5.6.ebuild     |     2 +-
 .../mgltools-qslimlib-1.5.6.ebuild                 |     2 +-
 .../mgltools-scenario2-1.5.6.ebuild                |     2 +-
 .../mgltools-sff/mgltools-sff-1.5.6.ebuild         |     2 +-
 .../mgltools-support/mgltools-support-1.5.6.ebuild |     2 +-
 .../mgltools-symserv/mgltools-symserv-1.5.6.ebuild |     2 +-
 .../mgltools-utpackages-1.5.6.ebuild               |     2 +-
 .../mgltools-viewer-framework-1.5.6.ebuild         |     2 +-
 .../mgltools-vision/mgltools-vision-1.5.6.ebuild   |     2 +-
 .../mgltools-visionlib-1.5.6.ebuild                |     2 +-
 .../mgltools-volume/mgltools-volume-1.5.6.ebuild   |     2 +-
 .../mgltools-webservices-1.5.6.ebuild              |     2 +-
 sci-chemistry/mgltools/ChangeLog                   |     3 +
 sci-chemistry/mgltools/mgltools-1.5.6.ebuild       |     5 +-
 sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild |     2 +-
 sci-chemistry/modelfree/ChangeLog                  |     5 +-
 sci-chemistry/modelfree/modelfree-4.20.ebuild      |     4 +-
 sci-chemistry/modeller/ChangeLog                   |     6 +-
 sci-chemistry/modeller/modeller-9.12-r2.ebuild     |   142 -
 sci-chemistry/modeller/modeller-9.12-r3.ebuild     |   149 +
 sci-chemistry/module2/ChangeLog                    |    19 +
 sci-chemistry/module2/Manifest                     |     1 +
 sci-chemistry/{ssp => module2}/metadata.xml        |     0
 sci-chemistry/module2/module2-0_pre20140717.ebuild |    51 +
 sci-chemistry/mtz2hkl/ChangeLog                    |     6 +-
 sci-chemistry/mtz2hkl/metadata.xml                 |     2 +-
 sci-chemistry/mtz2hkl/mtz2hkl-0.3.ebuild           |    17 +-
 sci-chemistry/mtz2sca/ChangeLog                    |     6 +-
 sci-chemistry/mtz2sca/metadata.xml                 |     2 +-
 sci-chemistry/mtz2sca/mtz2sca-0.3.ebuild           |    17 +-
 sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild        |     2 +-
 sci-chemistry/nmrpipe/ChangeLog                    |    42 +-
 sci-chemistry/nmrpipe/files/extract.M              |    37 +
 .../nmrpipe/nmrpipe-8.1.2013.218.23.09-r1.ebuild   |   217 +
 .../nmrpipe/nmrpipe-8.1.2013.218.23.09.ebuild      |   211 -
 sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild      |     2 +-
 sci-chemistry/nwchem/ChangeLog                     |    86 +-
 sci-chemistry/nwchem/Manifest                      |    18 +-
 .../files/nwchem-6.5-icosahedron_zcoord.patch      |    12 +
 .../nwchem/files/nwchem-6.5-python_makefile.patch  |    15 +
 sci-chemistry/nwchem/metadata.xml                  |    31 +
 sci-chemistry/nwchem/nwchem-6.3-r1.ebuild          |   150 -
 sci-chemistry/nwchem/nwchem-6.3_p2-r1.ebuild       |   207 +
 sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild   |   293 +
 sci-chemistry/openbabel-java/ChangeLog             |    16 +
 sci-chemistry/openbabel-java/metadata.xml          |    12 +
 .../openbabel-java/openbabel-java-9999.ebuild      |    65 +
 sci-chemistry/openbabel-perl/ChangeLog             |    19 +
 sci-chemistry/openbabel-perl/metadata.xml          |    12 +
 .../openbabel-perl/openbabel-perl-9999.ebuild      |    63 +
 sci-chemistry/openbabel-python/ChangeLog           |    25 +
 sci-chemistry/openbabel-python/metadata.xml        |    12 +
 .../openbabel-python/openbabel-python-9999.ebuild  |    83 +
 sci-chemistry/openbabel-ruby/ChangeLog             |    22 +
 sci-chemistry/openbabel-ruby/metadata.xml          |    12 +
 .../openbabel-ruby/openbabel-ruby-9999.ebuild      |    82 +
 sci-chemistry/openbabel/ChangeLog                  |    20 +
 sci-chemistry/openbabel/metadata.xml               |    20 +
 sci-chemistry/openbabel/openbabel-9999.ebuild      |    88 +
 sci-chemistry/pales-bin/ChangeLog                  |    13 +
 sci-chemistry/pales-bin/Manifest                   |     1 +
 sci-chemistry/{ssp => pales-bin}/metadata.xml      |     0
 .../pales-bin/pales-bin-0_pre140717.ebuild         |    26 +
 sci-chemistry/panav/panav-0.20130730.ebuild        |     2 +-
 sci-chemistry/pesto/ChangeLog                      |    12 +
 .../msms => sci-chemistry/pesto}/metadata.xml      |     0
 sci-chemistry/pesto/pesto-9999.ebuild              |    38 +
 sci-chemistry/phenix-bin/ChangeLog                 |    24 +-
 sci-chemistry/phenix-bin/Manifest                  |     4 +
 .../phenix-bin/phenix-bin-1.8.2.1309.ebuild        |     2 +-
 .../phenix-bin/phenix-bin-1.8.4.1496.ebuild        |   115 +
 .../phenix-bin/phenix-bin-1.9.1692.ebuild          |   115 +
 sci-chemistry/polygon/ChangeLog                    |     2 +-
 sci-chemistry/polygon/polygon-0612.ebuild          |     2 +-
 .../pymol-apbs-plugin-9999.ebuild                  |     2 +-
 sci-chemistry/pymol-plugins-ezviz/ChangeLog        |     4 +
 .../pymol-plugins-ezviz-1.0.2005-r1.ebuild         |    10 +-
 sci-chemistry/pymol-plugins-psico/ChangeLog        |     3 +
 .../pymol-plugins-psico-9999.ebuild                |     4 +-
 sci-chemistry/pymol/ChangeLog                      |    50 +-
 sci-chemistry/pymol/Manifest                       |     2 +-
 sci-chemistry/pymol/pymol-9999.ebuild              |    55 +-
 sci-chemistry/pyquante/ChangeLog                   |     6 +-
 sci-chemistry/pyquante/Manifest                    |     1 +
 sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild    |     2 +-
 sci-chemistry/pyquante/pyquante-1.6.4.ebuild       |    23 +
 sci-chemistry/redcat/ChangeLog                     |    17 +
 sci-chemistry/redcat/Manifest                      |     1 +
 sci-chemistry/redcat/files/CMakeLists.txt          |    13 +
 sci-chemistry/{ssp => redcat}/metadata.xml         |     0
 sci-chemistry/redcat/redcat-3.ebuild               |    64 +
 sci-chemistry/rosetta-tools/ChangeLog              |     6 +-
 sci-chemistry/rosetta-tools/metadata.xml           |     2 +-
 .../rosetta-tools/rosetta-tools-3.0.ebuild         |    11 +-
 sci-chemistry/rosetta/rosetta-3.4.ebuild           |     2 +-
 sci-chemistry/shiftx/ChangeLog                     |     5 +-
 sci-chemistry/shiftx/shiftx-1.1.ebuild             |    16 +-
 sci-chemistry/shiftx2/ChangeLog                    |    11 +-
 .../shiftx2/shiftx2-1.07_p20120106.ebuild          |     9 +-
 sci-chemistry/simpson/ChangeLog                    |     2 +-
 sci-chemistry/simpson/simpson-3.0.1.ebuild         |     2 +-
 sci-chemistry/simpson/simpson-3.1.0.ebuild         |     2 +-
 sci-chemistry/simpson/simpson-3.1.2.ebuild         |     2 +-
 sci-chemistry/smmp/ChangeLog                       |     3 +
 sci-chemistry/smmp/metadata.xml                    |     2 +-
 sci-chemistry/smmp/smmp-3.0.5.ebuild               |    19 +-
 sci-chemistry/specView/ChangeLog                   |    17 +-
 sci-chemistry/specView/Manifest                    |     2 +
 sci-chemistry/specView/specView-1.0.2.ebuild       |     2 +-
 sci-chemistry/specView/specView-1.0.3.ebuild       |     4 +-
 sci-chemistry/specView/specView-1.0.3_p2.ebuild    |    88 +
 sci-chemistry/specView/specView-1.0.4.ebuild       |    89 +
 sci-chemistry/ssp/ssp-09.11.ebuild                 |     2 +-
 sci-chemistry/talosn/ChangeLog                     |     6 +-
 sci-chemistry/talosn/Manifest                      |     2 +-
 .../talosn/talosn-4.01.2013.148.15.55-r2.ebuild    |    68 -
 .../talosn/talosn-4.01.2013.148.15.55-r3.ebuild    |    68 +
 sci-chemistry/trajng/ChangeLog                     |     5 +-
 sci-chemistry/trajng/trajng-0.6.1.ebuild           |     6 +-
 sci-chemistry/ucsf-tools/ChangeLog                 |    11 -
 sci-chemistry/ucsf-tools/Manifest                  |     2 -
 sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild    |    43 -
 sci-chemistry/unio/ChangeLog                       |    30 +-
 sci-chemistry/unio/Manifest                        |     2 +-
 sci-chemistry/unio/unio-2.0.2-r1.ebuild            |    62 -
 sci-chemistry/unio/unio-2.0.3-r1.ebuild            |    72 +
 sci-chemistry/usf-tools/usf-tools-9999.ebuild      |     4 +-
 sci-chemistry/votca-csg/ChangeLog                  |    11 +-
 sci-chemistry/votca-csg/votca-csg-9999.ebuild      |    57 +-
 sci-chemistry/votca-csgapps/ChangeLog              |     5 +-
 .../votca-csgapps/votca-csgapps-9999.ebuild        |    14 +-
 sci-chemistry/wxmacmolplt/ChangeLog                |    14 -
 sci-chemistry/wxmacmolplt/Manifest                 |     1 -
 .../wxmacmolplt/files/wxmacmolplt-7.4.3-glew.patch |    12 -
 sci-chemistry/wxmacmolplt/metadata.xml             |    11 -
 sci-chemistry/wxmacmolplt/wxmacmolplt-7.4.3.ebuild |    44 -
 sci-chemistry/xdrfile/ChangeLog                    |    21 -
 sci-chemistry/xdrfile/Manifest                     |     1 -
 sci-chemistry/xdrfile/metadata.xml                 |     9 -
 sci-chemistry/xdrfile/xdrfile-1.1.1.ebuild         |    23 -
 sci-chemistry/xplor-nih/ChangeLog                  |    12 +
 sci-chemistry/xplor-nih/Manifest                   |     2 +
 sci-chemistry/xplor-nih/metadata.xml               |     8 +
 sci-chemistry/xplor-nih/xplor-nih-2.38.ebuild      |    52 +
 sci-electronics/player/ChangeLog                   |    11 +-
 sci-electronics/player/player-2.0.4.ebuild         |    57 +-
 sci-electronics/stage/stage-2.0.3.ebuild           |     2 +-
 sci-electronics/tnt/ChangeLog                      |     6 +-
 sci-electronics/tnt/Manifest                       |     2 +-
 .../tnt/files/tnt-1.2.2-autotools.patch            |   277 +
 sci-electronics/tnt/metadata.xml                   |     2 +-
 sci-electronics/tnt/tnt-1.2.2.ebuild               |    40 +-
 sci-geosciences/cdat-lite/ChangeLog                |     6 +-
 sci-geosciences/cdat-lite/Manifest                 |     2 +-
 sci-geosciences/cdat-lite/cdat-lite-5.2.ebuild     |    38 +-
 sci-geosciences/cdat-lite/cdat-lite-6.0_rc2.ebuild |    31 +-
 sci-geosciences/cdat-lite/metadata.xml             |    12 +-
 sci-geosciences/congen/ChangeLog                   |     5 +-
 sci-geosciences/congen/congen-1.6.ebuild           |    12 +-
 sci-geosciences/congen/metadata.xml                |     2 +-
 sci-geosciences/fullprof-bin/ChangeLog             |    10 -
 sci-geosciences/fullprof-bin/Manifest              |     1 -
 .../fullprof-bin/fullprof-bin-2012.11.ebuild       |    66 -
 .../harmonics-dwf-free-noncomm/ChangeLog           |     6 +-
 .../harmonics-dwf-free-noncomm-20110410-r1.ebuild  |    11 +-
 .../harmonics-dwf-free-noncomm/metadata.xml        |    12 +-
 sci-geosciences/harmonics-dwf-free/ChangeLog       |     7 +-
 sci-geosciences/harmonics-dwf-free/Manifest        |     1 -
 .../harmonics-dwf-free-20110410-r1.ebuild          |    22 -
 .../harmonics-dwf-free-20120302.ebuild             |     9 +-
 sci-geosciences/harmonics-dwf-free/metadata.xml    |    12 +-
 sci-geosciences/libtcd/ChangeLog                   |     9 +-
 sci-geosciences/libtcd/Manifest                    |     1 -
 sci-geosciences/libtcd/libtcd-2.2.5-r1.ebuild      |    24 -
 sci-geosciences/libtcd/libtcd-2.2.5_p2.ebuild      |    10 +-
 sci-geosciences/libtcd/metadata.xml                |    18 +-
 sci-geosciences/pydap/ChangeLog                    |     5 +
 sci-geosciences/pydap/Manifest                     |     1 +
 sci-geosciences/pydap/pydap-3.1.1.ebuild           |    38 +
 sci-geosciences/pydap/pydap-3.1.ebuild             |     2 +-
 sci-geosciences/pydap_handlers_cdms/ChangeLog      |     6 +-
 sci-geosciences/pydap_handlers_cdms/metadata.xml   |    12 +-
 .../pydap_handlers_cdms-0.2.0.1.ebuild             |    19 +-
 sci-geosciences/pydap_handlers_csv/ChangeLog       |     6 +-
 sci-geosciences/pydap_handlers_csv/metadata.xml    |    12 +-
 .../pydap_handlers_csv-0.1.1.ebuild                |    14 +-
 sci-geosciences/pydap_handlers_hdf5/ChangeLog      |     7 +-
 sci-geosciences/pydap_handlers_hdf5/Manifest       |     2 +-
 sci-geosciences/pydap_handlers_hdf5/metadata.xml   |    12 +-
 .../pydap_handlers_hdf5-0.1.5.ebuild               |    39 -
 .../pydap_handlers_hdf5-0.1.7.ebuild               |    37 +
 sci-geosciences/pydap_handlers_nca/ChangeLog       |     6 +-
 sci-geosciences/pydap_handlers_nca/metadata.xml    |    12 +-
 .../pydap_handlers_nca-0.1.3.ebuild                |    18 +-
 sci-geosciences/pydap_handlers_netcdf/ChangeLog    |     7 +-
 sci-geosciences/pydap_handlers_netcdf/Manifest     |     2 +-
 sci-geosciences/pydap_handlers_netcdf/metadata.xml |    12 +-
 .../pydap_handlers_netcdf-0.6.1.ebuild             |    38 -
 .../pydap_handlers_netcdf-0.6.4.ebuild             |    36 +
 sci-geosciences/pydap_handlers_proxy/ChangeLog     |     6 +-
 sci-geosciences/pydap_handlers_proxy/metadata.xml  |    12 +-
 .../pydap_handlers_proxy-0.1.1.ebuild              |    19 +-
 sci-geosciences/pydap_handlers_sql/ChangeLog       |     7 +-
 sci-geosciences/pydap_handlers_sql/Manifest        |     2 +-
 sci-geosciences/pydap_handlers_sql/metadata.xml    |    12 +-
 .../pydap_handlers_sql-0.2.1.ebuild                |    45 -
 .../pydap_handlers_sql-0.3.0.ebuild                |    44 +
 sci-geosciences/pydap_handlers_sqlite/ChangeLog    |     6 +-
 sci-geosciences/pydap_handlers_sqlite/metadata.xml |    12 +-
 .../pydap_handlers_sqlite-0.1.0.ebuild             |    18 +-
 sci-geosciences/pydap_responses_kml/ChangeLog      |     7 +-
 sci-geosciences/pydap_responses_kml/Manifest       |     2 +-
 sci-geosciences/pydap_responses_kml/metadata.xml   |    12 +-
 .../pydap_responses_kml-0.4.5.ebuild               |    28 -
 .../pydap_responses_kml-0.4.6.ebuild               |    26 +
 sci-geosciences/pydap_responses_matlab/ChangeLog   |     9 +-
 sci-geosciences/pydap_responses_matlab/Manifest    |     2 +-
 .../pydap_responses_matlab/metadata.xml            |    12 +-
 .../pydap_responses_matlab-0.2.1.ebuild            |    35 +
 .../pydap_responses_matlab-0.2.ebuild              |    35 -
 sci-geosciences/pydap_responses_netcdf/ChangeLog   |     9 +-
 sci-geosciences/pydap_responses_netcdf/Manifest    |     2 +-
 .../pydap_responses_netcdf/metadata.xml            |    12 +-
 .../pydap_responses_netcdf-0.1.4.1.ebuild          |    35 +
 .../pydap_responses_netcdf-0.1.4.ebuild            |    36 -
 sci-geosciences/pydap_responses_wms/ChangeLog      |     9 +-
 sci-geosciences/pydap_responses_wms/Manifest       |     2 +-
 sci-geosciences/pydap_responses_wms/metadata.xml   |    12 +-
 .../pydap_responses_wms-0.4.6.ebuild               |    30 -
 .../pydap_responses_wms-0.5.4.ebuild               |    29 +
 sci-geosciences/pydap_responses_xls/ChangeLog      |     6 +-
 sci-geosciences/pydap_responses_xls/metadata.xml   |    12 +-
 .../pydap_responses_xls-0.1.2.ebuild               |    19 +-
 sci-geosciences/qgis/ChangeLog                     |     6 +
 sci-geosciences/qgis/qgis-9999.ebuild              |    48 +-
 sci-geosciences/seawater/ChangeLog                 |    35 -
 sci-geosciences/seawater/Manifest                  |     1 -
 sci-geosciences/seawater/metadata.xml              |    12 -
 sci-geosciences/seawater/seawater-2.0.1.ebuild     |    22 -
 sci-geosciences/swmm/ChangeLog                     |     6 +-
 sci-geosciences/swmm/metadata.xml                  |    12 +-
 sci-geosciences/swmm/swmm-5.0.022.ebuild           |    24 +-
 sci-geosciences/tappy/ChangeLog                    |     6 +-
 sci-geosciences/tappy/Manifest                     |     2 +-
 sci-geosciences/tappy/metadata.xml                 |    12 +-
 sci-geosciences/tappy/tappy-0.9.0.ebuild           |    18 +-
 sci-geosciences/tcd-utils/ChangeLog                |     6 +-
 sci-geosciences/tcd-utils/Manifest                 |     1 -
 sci-geosciences/tcd-utils/metadata.xml             |    12 +-
 .../tcd-utils/tcd-utils-20061127.ebuild            |    19 -
 .../tcd-utils/tcd-utils-20080820.ebuild            |     8 +-
 sci-geosciences/xtide/ChangeLog                    |     6 +-
 sci-geosciences/xtide/Manifest                     |     1 -
 sci-geosciences/xtide/metadata.xml                 |    18 +-
 sci-geosciences/xtide/xtide-2.12-r1.ebuild         |    30 -
 sci-geosciences/xtide/xtide-2.13.ebuild            |    13 +-
 sci-libs/Cgraph/Cgraph-2.04.ebuild                 |     2 +-
 sci-libs/acml/ChangeLog                            |    21 +-
 sci-libs/acml/Manifest                             |     1 +
 sci-libs/acml/acml-5.3.1.ebuild                    |    12 +-
 sci-libs/acml/acml-6.1.0.31.ebuild                 |    99 +
 sci-libs/acml/metadata.xml                         |     1 -
 sci-libs/amber99sb_phipsi/ChangeLog                |    13 +
 sci-libs/amber99sb_phipsi/Manifest                 |     1 +
 .../amber99sb_phipsi-0_pre130901.ebuild            |    23 +
 sci-libs/{msms => amber99sb_phipsi}/metadata.xml   |     0
 sci-libs/amber99sbnmr-ildn/ChangeLog               |    20 +
 sci-libs/amber99sbnmr-ildn/Manifest                |     1 +
 .../amber99sbnmr-ildn-0_pre130901.ebuild           |    25 +
 sci-libs/{msms => amber99sbnmr-ildn}/metadata.xml  |     0
 sci-libs/amber99sbnmr/ChangeLog                    |    10 +
 sci-libs/amber99sbnmr/Manifest                     |     1 +
 .../amber99sbnmr/amber99sbnmr-0_pre130901.ebuild   |    25 +
 sci-libs/{msms => amber99sbnmr}/metadata.xml       |     0
 sci-libs/amdlibm/ChangeLog                         |     8 +-
 sci-libs/amdlibm/Manifest                          |     2 +-
 sci-libs/amdlibm/amdlibm-3.0.2.ebuild              |    72 -
 sci-libs/amdlibm/amdlibm-3.1.ebuild                |    73 +
 sci-libs/amdlibm/metadata.xml                      |     4 +-
 sci-libs/armadillo/ChangeLog                       |    88 +-
 sci-libs/armadillo/Manifest                        |     5 +-
 sci-libs/armadillo/armadillo-3.910.0.ebuild        |    91 -
 sci-libs/armadillo/armadillo-4.600.2.ebuild        |   112 +
 sci-libs/armadillo/armadillo-4.600.4.ebuild        |   112 +
 sci-libs/armadillo/armadillo-4.650.2.ebuild        |   112 +
 sci-libs/armadillo/armadillo-4.650.4.ebuild        |   112 +
 .../files/armadillo-3.820.1-example-makefile.patch |    33 -
 .../armadillo/files/armadillo-3.820.1-hdf5.patch   |    19 -
 sci-libs/armadillo/metadata.xml                    |     7 +-
 sci-libs/arrayfire/ChangeLog                       |    47 +
 sci-libs/arrayfire/Manifest                        |     1 +
 sci-libs/arrayfire/arrayfire-0.9999.ebuild         |     1 +
 sci-libs/arrayfire/arrayfire-3.0_beta.ebuild       |     1 +
 sci-libs/arrayfire/arrayfire-9999.ebuild           |   100 +
 sci-libs/arrayfire/files/FindBoostCompute.patch    |    34 +
 sci-libs/arrayfire/files/FindCBLAS.patch           |    52 +
 sci-libs/arrayfire/files/opencl_CMakeLists.patch   |    26 +
 sci-libs/arrayfire/metadata.xml                    |    27 +
 sci-libs/atlas/ChangeLog                           |    13 +-
 sci-libs/atlas/Manifest                            |     1 +
 sci-libs/atlas/atlas-3.10.1-r1.ebuild              |    31 +-
 sci-libs/atlas/atlas-3.10.1-r2.ebuild              |   270 +
 sci-libs/atlas/metadata.xml                        |    10 +-
 sci-libs/avogadro-libs/ChangeLog                   |    18 -
 sci-libs/avogadro-libs/Manifest                    |     1 -
 sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild  |    46 -
 .../files/avogadro-libs-0.6.0-underlinking.patch   |    14 -
 sci-libs/avogadro-libs/metadata.xml                |    14 -
 sci-libs/bigdft-abi/ChangeLog                      |    26 +-
 sci-libs/bigdft-abi/Manifest                       |     1 +
 sci-libs/bigdft-abi/bigdft-abi-1.0.4-r1.ebuild     |   168 -
 sci-libs/bigdft-abi/bigdft-abi-1.0.4-r3.ebuild     |   182 +
 .../bigdft-abi/files/bigdft-abi-1.0.4-0002.patch   |    37 +
 .../bigdft-abi/files/bigdft-abi-1.0.4-0003.patch   |    49 +
 .../bigdft-abi/files/bigdft-abi-1.0.4-0004.patch   |    20 +
 .../bigdft-abi/files/bigdft-abi-1.0.4-0006.patch   |    43 +
 .../bigdft-abi/files/bigdft-abi-1.0.4-0007.patch   |   344 +
 .../files/bigdft-abi-1.0.4-tests.tar.bz2           |   Bin 402968 -> 0 bytes
 sci-libs/bigdft-abi/metadata.xml                   |    34 +
 sci-libs/bigdft/ChangeLog                          |   139 -
 sci-libs/bigdft/Manifest                           |     2 -
 sci-libs/bigdft/bigdft-1.6.0-r2.ebuild             |   122 -
 sci-libs/bigdft/bigdft-1.7_pre12.ebuild            |   147 -
 .../bigdft/files/bigdft-1.6-tuto.1-GPUlibs-1.patch |    26 -
 .../files/bigdft-1.6-tuto.1-bigdft.pc-1.patch      |   207 -
 .../bigdft/files/bigdft-1.6-tuto.1-gcc-4.6.patch   |    67 -
 .../bigdft-1.6-tuto.1-libxc_dir_include.patch      |    50 -
 .../files/bigdft-1.6.0-libxc_dir_include.patch     |    50 -
 .../bigdft/files/bigdft-1.7-dev.12-GPUlink.patch   |    12 -
 .../bigdft-1.7-dev.12-libxc_dir_include.patch      |    50 -
 .../files/bigdft-1.7-dev.12-nolib_mods.patch       |    25 -
 .../bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2   |   Bin 22103 -> 0 bytes
 sci-libs/bigdft/metadata.xml                       |    10 -
 sci-libs/blas-reference/ChangeLog                  |    16 +-
 sci-libs/blas-reference/Manifest                   |     2 +-
 ...25.ebuild => blas-reference-20131116-r1.ebuild} |     0
 .../blas-reference/blas-reference-20131116.ebuild  |    78 +
 .../blas-reference/blas-reference-99999999.ebuild  |    96 +-
 sci-libs/blas-reference/metadata.xml               |     3 +
 sci-libs/blastdb/blastdb-9999.ebuild               |     4 +-
 sci-libs/bliss/ChangeLog                           |    14 -
 sci-libs/bliss/Manifest                            |     1 -
 sci-libs/bliss/bliss-0.72.ebuild                   |    43 -
 sci-libs/bliss/files/bliss-0.72-autotools.patch    |   159 -
 sci-libs/bliss/files/bliss-0.72-fedora.patch       |   648 -
 sci-libs/calculix-ccx/ChangeLog                    |    23 +-
 sci-libs/calculix-ccx/Manifest                     |     6 +-
 sci-libs/calculix-ccx/calculix-ccx-2.2.ebuild      |    71 -
 sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild   |    71 +
 .../calculix-ccx/files/01_ccx_2.2_Makefile.patch   |    23 -
 .../calculix-ccx/files/01_ccx_2.2_lapack.patch     |    21 -
 ...7_Makefile_custom_cc_flags_spooles_arpack.patch |    31 +
 .../calculix-ccx/files/01_ccx_2.7_lapack.patch     |    11 +
 sci-libs/calculix-cgx/ChangeLog                    |    16 +-
 sci-libs/calculix-cgx/Manifest                     |     4 +-
 sci-libs/calculix-cgx/calculix-cgx-2.2.ebuild      |    53 -
 sci-libs/calculix-cgx/calculix-cgx-2.7-r1.ebuild   |    58 +
 .../calculix-cgx/files/01_cgx_2.2_Makefile.patch   |    55 -
 .../01_cgx_2.7_Makefile_custom_cxx_flags.patch     |    76 +
 .../files/02_cgx_2.7_menu_fix-freeglut_2.8.1.patch |    73 +
 sci-libs/cblas-reference/ChangeLog                 |    29 +-
 .../cblas-reference-20110218-r1.ebuild             |   157 +
 .../cblas-reference-20110218.ebuild                |    23 +-
 sci-libs/cblas-reference/metadata.xml              |     7 +-
 sci-libs/ccif/ccif-0.3.20111209.ebuild             |     2 +-
 sci-libs/cgnsfoam/ChangeLog                        |    17 -
 sci-libs/cgnsfoam/Manifest                         |     1 -
 sci-libs/cgnsfoam/cgnsfoam-1732.ebuild             |    39 -
 sci-libs/cgnsfoam/files/cgnsfoam-compile.patch     |    51 -
 sci-libs/cgnsfoam/metadata.xml                     |     5 -
 sci-libs/cgnslib/ChangeLog                         |     8 +-
 sci-libs/cgnslib/Manifest                          |     3 +-
 sci-libs/cgnslib/cgnslib-2.5.4.ebuild              |     2 +-
 sci-libs/cgnslib/cgnslib-3.2.1.ebuild              |    49 +
 sci-libs/cgnslib/files/cgnslib-3.2.1-cmake.patch   |   149 +
 sci-libs/cgnslib/metadata.xml                      |     5 +-
 sci-libs/cgnstools/ChangeLog                       |     6 +-
 sci-libs/cgnstools/cgnstools-2.5.4-r1.ebuild       |    17 +-
 sci-libs/chemkit/ChangeLog                         |    10 -
 sci-libs/chemkit/Manifest                          |     1 -
 sci-libs/chemkit/chemkit-0.1.ebuild                |    55 -
 sci-libs/chemkit/metadata.xml                      |    11 -
 sci-libs/clblas/ChangeLog                          |    16 +
 sci-libs/clblas/Manifest                           |     1 +
 sci-libs/clblas/clblas-2.2.ebuild                  |     1 +
 sci-libs/clblas/clblas-9999.ebuild                 |    69 +
 .../clblas/files/clblas-client_CMakeLists.patch    |    11 +
 .../clblas-library_tools_tune_CMakeLists.patch     |    14 +
 .../clblas/files/clblas-samples_CMakeLists.patch   |    20 +
 .../files/clblas-scripts_perf_CMakeLists.patch     |    11 +
 sci-libs/clblas/metadata.xml                       |    23 +
 sci-libs/clfft/ChangeLog                           |    19 +
 sci-libs/clfft/Manifest                            |     2 +
 sci-libs/clfft/clfft-2.2.ebuild                    |     1 +
 sci-libs/clfft/clfft-2.4.ebuild                    |     1 +
 sci-libs/clfft/clfft-9999.ebuild                   |    60 +
 sci-libs/clfft/files/clfft-client_CMakeLists.patch |    26 +
 .../files/clfft-scripts_perf_CMakeLists.patch      |    13 +
 sci-libs/clfft/metadata.xml                        |    17 +
 sci-libs/cnsface-scripts/ChangeLog                 |    10 -
 sci-libs/cnsface-scripts/Manifest                  |     1 -
 .../cnsface-scripts/cnsface-scripts-0.1.ebuild     |    22 -
 sci-libs/cnsface-scripts/metadata.xml              |     5 -
 sci-libs/coinhsl/ChangeLog                         |    18 -
 sci-libs/coinhsl/Manifest                          |     2 -
 sci-libs/coinhsl/coinhsl-2012.12.21.ebuild         |    36 -
 sci-libs/coinhsl/coinhsl-2013.06.18.ebuild         |    32 -
 sci-libs/coinhsl/metadata.xml                      |    12 -
 sci-libs/coinor-alps/ChangeLog                     |    24 -
 sci-libs/coinor-alps/Manifest                      |     1 -
 sci-libs/coinor-alps/coinor-alps-1.4.4.ebuild      |    67 -
 sci-libs/coinor-alps/metadata.xml                  |    13 -
 sci-libs/coinor-bcp/ChangeLog                      |    15 -
 sci-libs/coinor-bcp/Manifest                       |     1 -
 sci-libs/coinor-bcp/coinor-bcp-1.3.5.ebuild        |    56 -
 sci-libs/coinor-bcp/metadata.xml                   |    13 -
 sci-libs/coinor-bcps/ChangeLog                     |    15 -
 sci-libs/coinor-bcps/Manifest                      |     1 -
 sci-libs/coinor-bcps/coinor-bcps-0.93.5.ebuild     |    67 -
 sci-libs/coinor-bcps/metadata.xml                  |    13 -
 sci-libs/coinor-blis/ChangeLog                     |    24 -
 sci-libs/coinor-blis/Manifest                      |     1 -
 sci-libs/coinor-blis/coinor-blis-0.93.5.ebuild     |    65 -
 sci-libs/coinor-blis/metadata.xml                  |    12 -
 sci-libs/coinor-bonmin/ChangeLog                   |    18 -
 sci-libs/coinor-bonmin/Manifest                    |     1 -
 sci-libs/coinor-bonmin/coinor-bonmin-1.7.0.ebuild  |    65 -
 sci-libs/coinor-bonmin/metadata.xml                |    13 -
 sci-libs/coinor-buildtools/ChangeLog               |     9 -
 .../coinor-buildtools-0.7.4.ebuild                 |    38 -
 sci-libs/coinor-buildtools/metadata.xml            |     9 -
 sci-libs/coinor-cbc/ChangeLog                      |    33 -
 sci-libs/coinor-cbc/Manifest                       |     1 -
 sci-libs/coinor-cbc/coinor-cbc-2.8.3.ebuild        |    83 -
 sci-libs/coinor-cbc/metadata.xml                   |    11 -
 sci-libs/coinor-cgl/ChangeLog                      |    30 -
 sci-libs/coinor-cgl/Manifest                       |     1 -
 sci-libs/coinor-cgl/coinor-cgl-0.58.1.ebuild       |    73 -
 sci-libs/coinor-cgl/metadata.xml                   |    12 -
 sci-libs/coinor-clp/ChangeLog                      |    37 -
 sci-libs/coinor-clp/Manifest                       |     1 -
 sci-libs/coinor-clp/coinor-clp-1.15.2.ebuild       |   112 -
 .../files/coinor-clp-1.15.1-mpi-header.patch       |    12 -
 sci-libs/coinor-clp/metadata.xml                   |    20 -
 sci-libs/coinor-couenne/ChangeLog                  |    15 -
 sci-libs/coinor-couenne/Manifest                   |     1 -
 .../coinor-couenne/coinor-couenne-0.4.3.ebuild     |    65 -
 sci-libs/coinor-couenne/metadata.xml               |    12 -
 sci-libs/coinor-cppad/ChangeLog                    |    31 -
 sci-libs/coinor-cppad/Manifest                     |     1 -
 sci-libs/coinor-cppad/coinor-cppad-20130717.ebuild |    54 -
 sci-libs/coinor-cppad/metadata.xml                 |    14 -
 sci-libs/coinor-csdp/ChangeLog                     |    12 -
 sci-libs/coinor-csdp/Manifest                      |     1 -
 sci-libs/coinor-csdp/coinor-csdp-6.1.1.ebuild      |   100 -
 sci-libs/coinor-csdp/metadata.xml                  |    16 -
 sci-libs/coinor-dip/ChangeLog                      |     9 -
 sci-libs/coinor-dip/Manifest                       |     1 -
 sci-libs/coinor-dip/coinor-dip-0.83.2.ebuild       |    62 -
 sci-libs/coinor-dip/metadata.xml                   |    14 -
 sci-libs/coinor-dylp/ChangeLog                     |    15 -
 sci-libs/coinor-dylp/Manifest                      |     1 -
 sci-libs/coinor-dylp/coinor-dylp-1.9.0.ebuild      |    66 -
 sci-libs/coinor-dylp/metadata.xml                  |    12 -
 sci-libs/coinor-flopcpp/ChangeLog                  |    15 -
 sci-libs/coinor-flopcpp/Manifest                   |     1 -
 .../coinor-flopcpp/coinor-flopcpp-1.1.3.ebuild     |    67 -
 sci-libs/coinor-flopcpp/metadata.xml               |    14 -
 sci-libs/coinor-mp/ChangeLog                       |    18 -
 sci-libs/coinor-mp/Manifest                        |     1 -
 sci-libs/coinor-mp/coinor-mp-1.7.0.ebuild          |    55 -
 sci-libs/coinor-mp/metadata.xml                    |    11 -
 sci-libs/coinor-netlib/ChangeLog                   |    19 -
 sci-libs/coinor-netlib/Manifest                    |     1 -
 sci-libs/coinor-netlib/coinor-netlib-1.2.4.ebuild  |    23 -
 sci-libs/coinor-netlib/metadata.xml                |     9 -
 sci-libs/coinor-os/ChangeLog                       |     9 -
 sci-libs/coinor-os/Manifest                        |     1 -
 sci-libs/coinor-os/coinor-os-2.6.0.ebuild          |    69 -
 sci-libs/coinor-os/metadata.xml                    |    11 -
 sci-libs/coinor-osi/ChangeLog                      |    27 -
 sci-libs/coinor-osi/Manifest                       |     1 -
 sci-libs/coinor-osi/coinor-osi-0.106.1.ebuild      |    76 -
 sci-libs/coinor-osi/metadata.xml                   |    15 -
 sci-libs/coinor-sample/ChangeLog                   |    37 -
 sci-libs/coinor-sample/Manifest                    |     1 -
 sci-libs/coinor-sample/coinor-sample-1.2.6.ebuild  |    23 -
 sci-libs/coinor-sample/metadata.xml                |     9 -
 sci-libs/coinor-symphony/ChangeLog                 |    27 -
 sci-libs/coinor-symphony/Manifest                  |     1 -
 .../coinor-symphony/coinor-symphony-5.5.0.ebuild   |    89 -
 sci-libs/coinor-symphony/metadata.xml              |    18 -
 sci-libs/coinor-utils/ChangeLog                    |    33 -
 sci-libs/coinor-utils/Manifest                     |     1 -
 sci-libs/coinor-utils/coinor-utils-2.9.3.ebuild    |    85 -
 sci-libs/coinor-utils/metadata.xml                 |    15 -
 sci-libs/coinor-vol/ChangeLog                      |    18 -
 sci-libs/coinor-vol/Manifest                       |     1 -
 sci-libs/coinor-vol/coinor-vol-1.4.0.ebuild        |    71 -
 sci-libs/coinor-vol/metadata.xml                   |    10 -
 .../cs-rosetta-db-1.01.2009.1109.11.ebuild         |     2 +-
 sci-libs/dcmtk/ChangeLog                           |    22 +-
 sci-libs/dcmtk/Manifest                            |     5 +-
 sci-libs/dcmtk/dcmtk-3.5.4-r3.ebuild               |    71 -
 sci-libs/dcmtk/dcmtk-3.5.5_pre20101008.ebuild      |    79 -
 sci-libs/dcmtk/dcmtk-3.6.0.ebuild                  |    75 +
 sci-libs/dcmtk/files/02_dcmtk_3.6.0-1.patch        |    89 +
 sci-libs/dcmtk/files/bug674361.patch               |  1015 ++
 sci-libs/dcmtk/files/dcmtk-asneeded.patch          |    16 +
 sci-libs/dcmtk/files/dcmtk_version_number.patch    |   131 +
 sci-libs/dcmtk/files/doubledes.patch               |    31 +
 sci-libs/dcmtk/files/fixnull.patch                 |    36 +
 sci-libs/dcmtk/files/noleak.patch                  |    36 +
 sci-libs/dcmtk/files/nothrow.patch                 |    76 +
 sci-libs/dcmtk/files/prefs.patch                   |    26 +
 .../files/regression_stacksequenceisodd.patch      |    98 +
 .../dcmtk/files/use_correct_number_of_TS.patch     |    19 +
 sci-libs/dcmtk/metadata.xml                        |    30 +-
 sci-libs/dealii/ChangeLog                          |    56 +
 sci-libs/dealii/Manifest                           |     8 +-
 sci-libs/dealii/dealii-8.0.0.ebuild                |     1 -
 sci-libs/dealii/dealii-8.1.0-r2.ebuild             |   116 +
 sci-libs/dealii/dealii-8.2.0.ebuild                |     1 +
 sci-libs/dealii/dealii-8.2.1.ebuild                |   129 +
 sci-libs/dealii/dealii-9999.ebuild                 |   126 +-
 .../files/dealii-8.1.0-p4est1.0-support.patch      |   271 +
 sci-libs/dealii/metadata.xml                       |    54 +-
 sci-libs/driftwood/ChangeLog                       |     6 +-
 sci-libs/driftwood/driftwood-0.87.ebuild           |     4 +-
 sci-libs/driftwood/metadata.xml                    |     2 +-
 sci-libs/elmer-eio/ChangeLog                       |    28 +
 sci-libs/elmer-eio/Manifest                        |     1 +
 sci-libs/elmer-eio/elmer-eio-6.0_p4651.ebuild      |    33 +
 sci-libs/elmer-eio/elmer-eio-9999.ebuild           |    40 +
 .../files/elmer-eio-6.0_p4651-shared.patch         |    37 +
 .../elmer-eio}/metadata.xml                        |     0
 sci-libs/elmer-hutiter/ChangeLog                   |    18 +
 sci-libs/elmer-hutiter/Manifest                    |     1 +
 .../elmer-hutiter/elmer-hutiter-6.0_p4651.ebuild   |    38 +
 sci-libs/elmer-hutiter/elmer-hutiter-9999.ebuild   |    45 +
 .../files/elmer-hutiter-6.0_p4651-shared.patch     |    33 +
 .../elmer-hutiter}/metadata.xml                    |     0
 sci-libs/etsf_io/ChangeLog                         |    13 +-
 sci-libs/etsf_io/Manifest                          |     1 +
 sci-libs/etsf_io/etsf_io-1.0.3-r2.ebuild           |     2 +-
 sci-libs/etsf_io/etsf_io-1.0.4.ebuild              |    35 +
 sci-libs/factory/ChangeLog                         |    13 +-
 sci-libs/factory/factory-3.1.1-r1.ebuild           |    42 -
 sci-libs/factory/factory-3.1.1-r2.ebuild           |    46 +
 sci-libs/factory/factory-3.1.1.ebuild              |    44 -
 sci-libs/fdlibm/fdlibm-5.3.ebuild                  |     4 +-
 sci-libs/fftw/ChangeLog                            |    24 +-
 sci-libs/fftw/Manifest                             |     2 +-
 sci-libs/fftw/fftw-3.3.3-r3.ebuild                 |   187 -
 sci-libs/fftw/fftw-3.3.4-r1.ebuild                 |   162 +
 sci-libs/fftw/fftw-9999.ebuild                     |    23 +-
 sci-libs/fftw/metadata.xml                         |     2 -
 sci-libs/fgsl/ChangeLog                            |     6 +-
 sci-libs/fgsl/fgsl-0.9.3.ebuild                    |    30 +-
 sci-libs/fgsl/fgsl-0.9.4.ebuild                    |    29 +-
 sci-libs/fgsl/metadata.xml                         |    12 +-
 sci-libs/fox/fox-4.1.2-r2.ebuild                   |     2 +-
 sci-libs/framewave/framewave-1.3.1.ebuild          |     2 +-
 sci-libs/geom/geom-5.1.2.7.ebuild                  |     2 +-
 sci-libs/ghmm/ChangeLog                            |    12 +-
 sci-libs/ghmm/files/ghmm-9999-clapack.patch        |    11 +
 sci-libs/ghmm/files/ghmm-9999-link.patch           |    24 +
 sci-libs/ghmm/files/ghmm-9999-obsolete.patch       |    13 +
 sci-libs/ghmm/files/ghmm-9999-out-of-source.patch  |    40 +
 sci-libs/ghmm/files/ghmm-9999-respect.patch        |    10 +
 sci-libs/ghmm/ghmm-9999.ebuild                     |    58 +-
 sci-libs/givaro/ChangeLog                          |    12 +-
 sci-libs/givaro/Manifest                           |     5 +-
 sci-libs/givaro/givaro-3.2.13.ebuild               |    13 +-
 sci-libs/givaro/givaro-3.3.0.ebuild                |    20 +-
 sci-libs/givaro/givaro-3.8.0.ebuild                |    21 +
 sci-libs/gmsh/ChangeLog                            |    19 +-
 sci-libs/gmsh/Manifest                             |     2 +-
 sci-libs/gmsh/files/gmsh-2.5.0-libpng-1.5.patch    |    10 -
 sci-libs/gmsh/files/gmsh-2.5.0-link.patch          |    16 -
 sci-libs/gmsh/gmsh-2.5.0-r1.ebuild                 |    91 -
 sci-libs/gmsh/gmsh-2.5.0.ebuild                    |    92 -
 sci-libs/gmsh/gmsh-2.8.5.ebuild                    |    92 +
 sci-libs/gmsh/gmsh-9999.ebuild                     |    87 -
 sci-libs/gotoblas2/gotoblas2-1.13.ebuild           |     2 +-
 sci-libs/gsl/ChangeLog                             |    11 +-
 sci-libs/gsl/files/gsl-1.16-cblas-external.patch   |    13 +
 sci-libs/gsl/gsl-1.16-r1.ebuild                    |     4 +-
 sci-libs/gsl/gsl-1.16-r2.ebuild                    |    60 +
 sci-libs/iml/iml-1.0.3-r2.ebuild                   |     2 +-
 sci-libs/ipopt/ChangeLog                           |    34 -
 sci-libs/ipopt/Manifest                            |     1 -
 sci-libs/ipopt/files/ipopt-3.11.2-mpi-header.patch |    14 -
 sci-libs/ipopt/ipopt-3.11.2.ebuild                 |   100 -
 sci-libs/ipopt/metadata.xml                        |    18 -
 sci-libs/itk/ChangeLog                             |    21 +-
 sci-libs/itk/Manifest                              |     3 +
 ...p-TransformFileReader-TransformFileWriter.patch |    50 +
 ...itkQuasiNewtonOptimizerv4-wrapping-warnin.patch |    28 +
 ...itkGradientDescentOptimizerv4-wrapping-wa.patch |    73 +
 ...OptimizerParameterScalesEstimatorTemplate.patch |    30 +
 .../0005-make-gdcm-helper-library-static.patch     |    11 +
 sci-libs/itk/files/nrrdio-linking.patch            |    15 +
 sci-libs/itk/itk-4.4.2-r1.ebuild                   |   134 +
 sci-libs/itk/itk-4.4.2.ebuild                      |     6 +-
 sci-libs/itk/itk-4.5.1.ebuild                      |   154 +
 sci-libs/itk/metadata.xml                          |    20 +-
 sci-libs/k3match/ChangeLog                         |     6 +-
 sci-libs/k3match/k3match-1.1.ebuild                |    14 +-
 sci-libs/k3match/metadata.xml                      |    16 +-
 sci-libs/lapack-reference/ChangeLog                |    67 +-
 sci-libs/lapack-reference/Manifest                 |     1 +
 ...-3.4.2.ebuild => lapack-reference-3.5.0.ebuild} |     0
 .../lapack-reference/lapack-reference-9999.ebuild  |   113 +-
 sci-libs/lapack-reference/metadata.xml             |    11 +-
 sci-libs/lapacke-reference/ChangeLog               |     6 +
 sci-libs/lapacke-reference/Manifest                |     1 +
 ...3.4.2.ebuild => lapacke-reference-3.5.0.ebuild} |     0
 .../lapacke-reference-9999.ebuild                  |     6 +-
 sci-libs/lapackpp/lapackpp-2.5.4.ebuild            |     2 +-
 sci-libs/lemon/ChangeLog                           |    24 -
 sci-libs/lemon/Manifest                            |     1 -
 sci-libs/lemon/files/lemon-1.2.3-gcc47.patch       |    59 -
 sci-libs/lemon/lemon-1.2.3.ebuild                  |    39 -
 sci-libs/lemon/metadata.xml                        |    20 -
 sci-libs/levmar/levmar-2.6.ebuild                  |     4 +-
 sci-libs/libcgnsoo/libcgnsoo-1728.ebuild           |     2 +-
 sci-libs/libfac/ChangeLog                          |    11 +-
 sci-libs/libfac/Manifest                           |     1 -
 sci-libs/libfac/libfac-3.1.0.ebuild                |    31 -
 sci-libs/libfac/libfac-3.1.1.ebuild                |    10 +-
 sci-libs/libgeodecomp/ChangeLog                    |     8 +
 sci-libs/libgeodecomp/Manifest                     |     1 +
 sci-libs/libgeodecomp/libgeodecomp-0.1.0.ebuild    |     2 +-
 sci-libs/libgeodecomp/libgeodecomp-0.2.0.ebuild    |     2 +-
 sci-libs/libgeodecomp/libgeodecomp-0.3.1.ebuild    |    36 +
 sci-libs/libgeodecomp/libgeodecomp-9999.ebuild     |    47 +-
 sci-libs/libgeodecomp/metadata.xml                 |    26 +-
 sci-libs/libmatheval/libmatheval-1.1.10.ebuild     |     2 +-
 sci-libs/libmaus/Manifest                          |     1 +
 sci-libs/libmaus/libmaus-0.0.185.ebuild            |    18 +
 sci-libs/libmaus/metadata.xml                      |    14 +
 sci-libs/libsc/ChangeLog                           |    21 +
 sci-libs/libsc/Manifest                            |     2 +
 sci-libs/libsc/libsc-1.0.ebuild                    |    72 +
 sci-libs/libsc/libsc-1.1.ebuild                    |     1 +
 sci-libs/libsc/metadata.xml                        |    16 +
 sci-libs/libspatialindex/ChangeLog                 |     7 +-
 sci-libs/libspatialindex/Manifest                  |     2 +-
 .../files/libspatialindex-1.8.1-QA.patch           |    15 +
 .../libspatialindex/libspatialindex-1.6.1.ebuild   |    19 -
 .../libspatialindex/libspatialindex-1.8.5.ebuild   |    32 +
 sci-libs/libspatialindex/metadata.xml              |     4 +
 sci-libs/libsufr/ChangeLog                         |     6 +
 sci-libs/libsufr/Manifest                          |     3 +-
 sci-libs/libsufr/libsufr-0.3.3.ebuild              |    28 -
 sci-libs/libsufr/libsufr-0.4.1.ebuild              |     4 +-
 sci-libs/libsufr/libsufr-0.5.2.ebuild              |     4 +-
 sci-libs/libsufr/libsufr-0.5.4.ebuild              |    28 +
 sci-libs/libxc/ChangeLog                           |    31 +-
 sci-libs/libxc/Manifest                            |     4 +-
 sci-libs/libxc/libxc-1.2.0-r1.ebuild               |    55 -
 sci-libs/libxc/libxc-2.0.1.ebuild                  |    54 -
 sci-libs/libxc/libxc-2.1.1.ebuild                  |    57 +
 sci-libs/libxc/libxc-2.2.1.ebuild                  |    57 +
 sci-libs/libxc/libxc-9999.ebuild                   |    51 -
 sci-libs/libxc/metadata.xml                        |     2 +-
 sci-libs/lwpr/lwpr-1.2.5.ebuild                    |     2 +-
 sci-libs/m4ri/ChangeLog                            |    24 -
 sci-libs/m4ri/Manifest                             |     2 -
 sci-libs/m4ri/m4ri-20090512.ebuild                 |    18 -
 sci-libs/m4ri/m4ri-20100221.ebuild                 |    38 -
 sci-libs/m4ri/metadata.xml                         |     6 -
 sci-libs/magma/ChangeLog                           |    42 -
 sci-libs/magma/Manifest                            |     1 -
 .../magma/files/magma-1.2.1-no-cuda-driver.patch   |    38 -
 sci-libs/magma/magma-1.3.0.ebuild                  |   142 -
 sci-libs/magma/metadata.xml                        |    15 -
 sci-libs/matc/ChangeLog                            |    17 +
 sci-libs/matc/Manifest                             |     2 +
 sci-libs/matc/files/matc-6.0_p4651-shared.patch    |    32 +
 sci-libs/matc/matc-6.0_p4651.ebuild                |    45 +
 sci-libs/matc/matc-9999.ebuild                     |    50 +
 .../salome-yacs => sci-libs/matc}/metadata.xml     |     0
 sci-libs/matio/ChangeLog                           |     6 +-
 sci-libs/matio/matio-1.3.4.ebuild                  |    32 +-
 sci-libs/med/ChangeLog                             |     6 +-
 sci-libs/med/med-2.3.6.ebuild                      |     4 +-
 sci-libs/mesquite/mesquite-2.1.2.ebuild            |     2 +-
 sci-libs/mkl/ChangeLog                             |    44 +-
 sci-libs/mkl/Manifest                              |    13 +-
 sci-libs/mkl/mkl-11.0.3.163.ebuild                 |   131 -
 sci-libs/mkl/mkl-11.0.5.192.ebuild                 |   131 -
 sci-libs/mkl/mkl-11.1.0.080-r1.ebuild              |   141 +
 sci-libs/mkl/mkl-11.1.1.106.ebuild                 |   141 +
 sci-libs/mkl/mkl-11.1.2.144.ebuild                 |   141 +
 sci-libs/mkl/mkl-11.1.3.174.ebuild                 |   141 +
 sci-libs/mkl/mkl-11.2.0.090.ebuild                 |   141 +
 sci-libs/mkl/mkl-11.2.1.133.ebuild                 |   143 +
 sci-libs/mkl/mkl-11.2.2.164.ebuild                 |   143 +
 sci-libs/mlpack/ChangeLog                          |    24 +-
 sci-libs/mlpack/Manifest                           |     2 +-
 sci-libs/mlpack/files/mlpack-1.0.8-uint32_t.patch  |    16 +
 sci-libs/mlpack/mlpack-1.0.6.ebuild                |    51 -
 sci-libs/mlpack/mlpack-1.0.8.ebuild                |    57 +
 sci-libs/modglue/ChangeLog                         |    14 +
 sci-libs/modglue/Manifest                          |     2 +-
 sci-libs/modglue/files/modglue-1.16-ldflags.patch  |    13 -
 sci-libs/modglue/files/modglue-1.16-lib64.patch    |    61 -
 .../modglue/files/modglue-1.16-parallelmake.patch  |    53 -
 .../modglue/files/modglue-1.19-Makefiles.patch     |   113 +
 sci-libs/modglue/modglue-1.16.ebuild               |    45 -
 sci-libs/modglue/modglue-1.19.ebuild               |    40 +
 sci-libs/mpiblacs/ChangeLog                        |     5 +-
 sci-libs/mpiblacs/mpiblacs-1.1-r1.ebuild           |    10 +-
 sci-libs/msms/ChangeLog                            |     4 +-
 sci-libs/msms/msms-1.5.6.ebuild                    |     2 +-
 sci-libs/mumps/ChangeLog                           |    43 -
 sci-libs/mumps/Manifest                            |     1 -
 sci-libs/mumps/metadata.xml                        |    18 -
 sci-libs/mumps/mumps-4.10.0-r2.ebuild              |   184 -
 sci-libs/nexus/Manifest                            |     1 +
 sci-libs/nexus/metadata.xml                        |    26 +
 sci-libs/nexus/nexus-4.3.1.ebuild                  |    54 +
 sci-libs/ni-visa/ChangeLog                         |     6 +-
 sci-libs/ni-visa/metadata.xml                      |     6 +-
 sci-libs/ni-visa/ni-visa-0.0.1.ebuild              |    20 +-
 sci-libs/nibabel/ChangeLog                         |     8 +
 sci-libs/nibabel/Manifest                          |     1 +
 sci-libs/nibabel/metadata.xml                      |    18 +-
 sci-libs/nibabel/nibabel-1.3.0.ebuild              |    42 +
 sci-libs/nibabel/nibabel-9999.ebuild               |     8 +-
 sci-libs/nipy/ChangeLog                            |     8 +
 sci-libs/nipy/metadata.xml                         |    12 +-
 sci-libs/nipy/nipy-0.3.0.ebuild                    |    10 +-
 sci-libs/nipy/nipy-9999.ebuild                     |    12 +-
 sci-libs/nipype/ChangeLog                          |     8 +
 sci-libs/nipype/metadata.xml                       |    12 +-
 sci-libs/nipype/nipype-9999.ebuild                 |    14 +-
 sci-libs/o2scl/ChangeLog                           |    14 +-
 sci-libs/o2scl/Manifest                            |     2 +-
 sci-libs/o2scl/o2scl-0.913.ebuild                  |    47 -
 sci-libs/o2scl/o2scl-0.915.ebuild                  |    47 +
 sci-libs/oasa/ChangeLog                            |     6 +-
 sci-libs/oasa/Manifest                             |     2 +-
 sci-libs/oasa/metadata.xml                         |    10 +-
 sci-libs/oasa/oasa-0.13.1.ebuild                   |    12 +-
 sci-libs/omalloc/omalloc-0.9.6.ebuild              |     2 +-
 sci-libs/openblas/ChangeLog                        |    70 +-
 sci-libs/openblas/Manifest                         |     4 +-
 .../openblas/files/openblas-0.2.11-cpuid_x86.patch |    27 +
 ...-openblas_config_header_same_between_ABIs.patch |    21 +
 sci-libs/openblas/metadata.xml                     |    12 +-
 sci-libs/openblas/openblas-0.2.11.ebuild           |     1 +
 sci-libs/openblas/openblas-0.2.12.ebuild           |     1 +
 sci-libs/openblas/openblas-0.2.8.ebuild            |     2 +-
 sci-libs/openblas/openblas-9999.ebuild             |   280 +-
 sci-libs/openlibm/ChangeLog                        |    10 +-
 .../openlibm/files/openlibm-extras-soname.patch    |    11 -
 sci-libs/openlibm/files/openlibm-soname.patch      |    11 -
 sci-libs/openlibm/metadata.xml                     |     4 +-
 sci-libs/openlibm/openlibm-9999.ebuild             |    23 +-
 sci-libs/optpp/optpp-2.4.ebuild                    |     2 +-
 sci-libs/p4est/ChangeLog                           |    32 +
 sci-libs/p4est/Manifest                            |     5 +-
 sci-libs/p4est/files/p4est-libtool-fix.patch       |    59 -
 sci-libs/p4est/metadata.xml                        |    26 +-
 sci-libs/p4est/p4est-0.3.4.1.ebuild                |    71 -
 sci-libs/p4est/p4est-1.0.ebuild                    |    99 +
 sci-libs/p4est/p4est-1.1.ebuild                    |     1 +
 sci-libs/pagmo/ChangeLog                           |     8 +-
 sci-libs/pagmo/metadata.xml                        |    10 +-
 sci-libs/pagmo/pagmo-9999.ebuild                   |    22 +-
 sci-libs/parmetis/parmetis-4.0.3.ebuild            |     2 +-
 sci-libs/pastix/ChangeLog                          |     9 +
 sci-libs/pastix/Manifest                           |     1 +
 sci-libs/pastix/metadata.xml                       |    20 +
 sci-libs/pastix/pastix-5.2.2_p9.ebuild             |   113 +
 sci-libs/pfft/ChangeLog                            |    36 +
 sci-libs/pfft/Manifest                             |     1 +
 sci-libs/{bliss => pfft}/metadata.xml              |     0
 sci-libs/pfft/pfft-1.0.7_alpha.ebuild              |    54 +
 sci-libs/pfft/pfft-9999.ebuild                     |    54 +
 sci-libs/pg2plplot/ChangeLog                       |     9 +-
 sci-libs/pg2plplot/Manifest                        |     1 +
 sci-libs/pg2plplot/metadata.xml                    |    14 +-
 sci-libs/pg2plplot/pg2plplot-0.2.0.ebuild          |     2 +-
 sci-libs/pg2plplot/pg2plplot-0.3.1.ebuild          |    40 +
 sci-libs/plasma/ChangeLog                          |    10 +-
 sci-libs/plasma/Manifest                           |     4 +-
 sci-libs/plasma/plasma-2.4.6.ebuild                |   125 -
 sci-libs/plasma/plasma-2.5.1.ebuild                |   134 -
 sci-libs/plasma/plasma-2.5.2.ebuild                |   141 +
 sci-libs/plasma/plasma-2.6.0.ebuild                |   142 +
 sci-libs/pmx/ChangeLog                             |    13 +
 sci-libs/pmx/metadata.xml                          |    13 +
 sci-libs/pmx/pmx-9999.ebuild                       |    24 +
 sci-libs/pydicom/ChangeLog                         |     8 +
 .../salome-yacs => sci-libs/pydicom}/metadata.xml  |     0
 sci-libs/pydicom/pydicom-0.9.8.ebuild              |     6 +-
 sci-libs/scalapack/ChangeLog                       |     8 +-
 sci-libs/scalapack/scalapack-2.0.2-r1.ebuild       |    72 +
 sci-libs/scalapack/scalapack-2.0.2.ebuild          |    72 -
 sci-libs/scikits_image/ChangeLog                   |    12 +
 sci-libs/scikits_image/metadata.xml                |    17 +
 sci-libs/scikits_image/scikits_image-9999.ebuild   |    28 +-
 sci-libs/silo/Manifest                             |     1 +
 sci-libs/silo/files/silo-4.9.1-qtlibs.patch        |    66 +
 sci-libs/silo/metadata.xml                         |    18 +
 sci-libs/silo/silo-4.9.1.ebuild                    |    38 +
 sci-libs/spglib/ChangeLog                          |    14 +
 sci-libs/spglib/Manifest                           |     1 +
 sci-libs/spglib/files/spglib-openmp.patch          |    22 +
 sci-libs/spglib/metadata.xml                       |    12 +
 sci-libs/spglib/spglib-1.6.0.ebuild                |    34 +
 sci-libs/starparse/ChangeLog                       |    14 +
 sci-libs/starparse/Manifest                        |     1 -
 .../starparse/files/starparse-9999-guile1.8.patch  |    60 +
 sci-libs/starparse/metadata.xml                    |     2 +-
 sci-libs/starparse/starparse-1.0.ebuild            |    28 -
 sci-libs/starparse/starparse-9999.ebuild           |    20 +-
 sci-libs/starparse/starparse-9999_pre10.ebuild     |    27 -
 sci-libs/superlu_dist/superlu_dist-3.3.ebuild      |     4 +-
 sci-libs/superlu_mt/superlu_mt-2.1.ebuild          |     4 +-
 sci-libs/symmetrica/ChangeLog                      |    13 +-
 sci-libs/symmetrica/Manifest                       |     2 +-
 .../symmetrica/files/symmetrica-2.0-banner.patch   |    11 +
 .../files/symmetrica-2.0-freeing_errors.patch      |    39 +
 .../files/symmetrica-2.0-function_names.patch      |   329 +
 .../files/symmetrica-2.0-integersize.patch         |    37 +
 sci-libs/symmetrica/symmetrica-2.0-r1.ebuild       |    40 +
 sci-libs/symmetrica/symmetrica-2.0.ebuild          |    28 +-
 sci-libs/tmglib/ChangeLog                          |     5 +
 sci-libs/tmglib/Manifest                           |     1 +
 sci-libs/tmglib/tmglib-3.4.2.ebuild                |     2 +-
 sci-libs/tmglib/tmglib-3.5.0.ebuild                |    61 +
 sci-libs/trilinos/ChangeLog                        |    42 +-
 sci-libs/trilinos/Manifest                         |     6 +-
 .../files/trilinos-11.12.1-fix-install-paths.patch |    61 +
 .../files/trilinos-11.14.1-fix-install-paths.patch |    61 +
 ...nos-11.14.1-fix_install_paths_for_destdir.patch |   617 +
 .../files/trilinos-11.2.3-fix-install-paths.patch  |    62 +
 .../files/trilinos-11.4.2-fix-install-paths.patch  |    60 +
 sci-libs/trilinos/metadata.xml                     |    67 +-
 sci-libs/trilinos/trilinos-11.0.3.ebuild           |    15 +-
 sci-libs/trilinos/trilinos-11.10.2.ebuild          |   202 +
 sci-libs/trilinos/trilinos-11.12.1-r1.ebuild       |   202 +
 sci-libs/trilinos/trilinos-11.14.1-r1.ebuild       |   207 +
 sci-libs/trilinos/trilinos-11.2.3-r1.ebuild        |     1 +
 sci-libs/trilinos/trilinos-11.2.3.ebuild           |   186 -
 sci-libs/trilinos/trilinos-11.4.2.ebuild           |   202 +
 sci-libs/votca-tools/ChangeLog                     |     8 +-
 sci-libs/votca-tools/votca-tools-9999.ebuild       |    16 +-
 sci-libs/wannier90/ChangeLog                       |    21 +-
 sci-libs/wannier90/Manifest                        |     1 +
 sci-libs/wannier90/wannier90-1.2-r1.ebuild         |    73 -
 sci-libs/wannier90/wannier90-1.2-r3.ebuild         |    72 +
 sci-libs/wannier90/wannier90-2.0.0.ebuild          |    65 +
 sci-libs/xblas/ChangeLog                           |    14 +-
 sci-libs/xblas/metadata.xml                        |     3 +
 sci-libs/xblas/xblas-1.0.248-r1.ebuild             |   122 +
 sci-libs/xblas/xblas-1.0.248.ebuild                |     2 +-
 sci-libs/xraylib/ChangeLog                         |     7 +
 sci-libs/xraylib/Manifest                          |     1 +
 sci-libs/xraylib/metadata.xml                      |    38 +
 sci-libs/xraylib/xraylib-2.16.0.ebuild             |    84 +
 sci-libs/zarja/zarja-1.1.1.ebuild                  |     2 +-
 sci-mathematics/Macaulay2/ChangeLog                |    17 +-
 sci-mathematics/Macaulay2/Macaulay2-9999.ebuild    |    76 +-
 sci-mathematics/Macaulay2/Manifest                 |     8 +-
 sci-mathematics/Oid/Oid-4.0.ebuild                 |     2 +-
 sci-mathematics/acl2/ChangeLog                     |     9 +-
 sci-mathematics/acl2/Manifest                      |     4 +-
 sci-mathematics/acl2/acl2-4.2.ebuild               |    54 -
 sci-mathematics/acl2/acl2-4.3.ebuild               |    54 -
 sci-mathematics/acl2/acl2-6.3.ebuild               |    69 +
 sci-mathematics/acl2/metadata.xml                  |    32 +-
 sci-mathematics/alt-ergo/ChangeLog                 |    20 +-
 sci-mathematics/alt-ergo/Manifest                  |     2 +-
 sci-mathematics/alt-ergo/alt-ergo-0.95.1.ebuild    |    37 -
 sci-mathematics/alt-ergo/alt-ergo-0.95.2.ebuild    |    40 +
 sci-mathematics/alt-ergo/metadata.xml              |     3 +-
 sci-mathematics/apron/ChangeLog                    |    18 +-
 sci-mathematics/apron/Manifest                     |     2 +-
 sci-mathematics/apron/apron-0.9.10-r1.ebuild       |    67 +
 sci-mathematics/apron/apron-0.9.10.ebuild          |    10 +-
 sci-mathematics/apron/metadata.xml                 |     2 +-
 sci-mathematics/aribas/aribas-1.63.ebuild          |     2 +-
 sci-mathematics/axiom/ChangeLog                    |     6 +-
 sci-mathematics/axiom/axiom-201009.ebuild          |    35 +-
 sci-mathematics/axiom/metadata.xml                 |     2 +-
 .../burrtools/burrtools-0.5.2-r1.ebuild            |     2 +-
 sci-mathematics/cadabra/ChangeLog                  |    16 +-
 sci-mathematics/cadabra/Manifest                   |     3 +-
 sci-mathematics/cadabra/cadabra-1.31.ebuild        |    83 -
 sci-mathematics/cadabra/cadabra-1.33.ebuild        |    88 +
 sci-mathematics/cadabra/cadabra-1.39.ebuild        |    88 +
 .../cadabra/files/cadabra-1.21-no-stripping.patch  |    30 -
 .../files/cadabra-1.25-xcadabra-flags.patch        |    11 -
 .../cadabra/files/cadabra-1.33-FLAGS.patch         |   171 +
 .../cadabra/files/cadabra-1.39-FLAGS.patch         |   171 +
 sci-mathematics/cdfplayer/ChangeLog                |     9 +-
 sci-mathematics/cdfplayer/Manifest                 |     2 +-
 sci-mathematics/cdfplayer/cdfplayer-10.0.2.ebuild  |    50 +
 sci-mathematics/cdfplayer/cdfplayer-9.0.1.ebuild   |    54 -
 .../files/cdfplayer-9.0.1-installer.patch          |    19 -
 sci-mathematics/cipi/ChangeLog                     |     5 +-
 sci-mathematics/cipi/Manifest                      |     1 +
 sci-mathematics/cipi/cipi-1.0.ebuild               |     9 +-
 sci-mathematics/cipi/metadata.xml                  |    12 +-
 sci-mathematics/dolfin/ChangeLog                   |     6 +-
 sci-mathematics/dolfin/dolfin-0.9.9.ebuild         |    24 +-
 sci-mathematics/dolfin/metadata.xml                |    18 +-
 sci-mathematics/dsfmt/dsfmt-2.2.ebuild             |     2 +-
 sci-mathematics/flocq/ChangeLog                    |    23 +-
 sci-mathematics/flocq/Manifest                     |     2 +-
 sci-mathematics/flocq/flocq-2.1.0.ebuild           |    21 -
 sci-mathematics/flocq/flocq-2.3.0.ebuild           |    36 +
 sci-mathematics/frama-c/ChangeLog                  |    28 +-
 sci-mathematics/frama-c/Manifest                   |     2 +-
 .../frama-c/files/ocamlgraph185_compat.patch       |   254 +
 sci-mathematics/frama-c/frama-c-20120901.ebuild    |    63 -
 sci-mathematics/frama-c/frama-c-20140301.ebuild    |    68 +
 sci-mathematics/freefem++/ChangeLog                |    11 +-
 sci-mathematics/freefem++/Manifest                 |     2 +-
 sci-mathematics/freefem++/freefem++-3.8.ebuild     |    45 +-
 sci-mathematics/gambit/gambit-0.2010.09.01.ebuild  |     2 +-
 sci-mathematics/gap-guava/gap-guava-3.10-r1.ebuild |     2 +-
 sci-mathematics/gap/gap-4.4.12.ebuild              |     2 +-
 sci-mathematics/gappa/ChangeLog                    |    37 +-
 sci-mathematics/gappa/Manifest                     |     2 +-
 sci-mathematics/gappa/gappa-1.0.0.ebuild           |    37 -
 sci-mathematics/gappa/gappa-1.1.1.ebuild           |    39 +
 sci-mathematics/gappalib-coq/ChangeLog             |    34 +-
 sci-mathematics/gappalib-coq/Manifest              |     2 +-
 .../gappalib-coq/files/gappalib-coq-coq84.patch    |    71 -
 .../gappalib-coq/gappalib-coq-0.18.0.ebuild        |    35 -
 .../gappalib-coq/gappalib-coq-1.0.0.ebuild         |    34 +
 sci-mathematics/giac/ChangeLog                     |    21 +-
 sci-mathematics/giac/Manifest                      |     2 +-
 sci-mathematics/giac/giac-1.0.0.ebuild             |    59 -
 sci-mathematics/giac/giac-1.1.0.ebuild             |    75 +
 sci-mathematics/giac/metadata.xml                  |     2 +-
 sci-mathematics/htk/htk-3.4.1.ebuild               |     2 +-
 sci-mathematics/kash-bin/kash-bin-3.ebuild         |     2 +-
 sci-mathematics/kayali/ChangeLog                   |     6 +-
 sci-mathematics/kayali/kayali-0.3.2.ebuild         |    43 +-
 sci-mathematics/kayali/metadata.xml                |     4 +-
 .../lattE-macchiato/lattE-macchiato-0.9.3.ebuild   |     2 +-
 sci-mathematics/libsfmt/ChangeLog                  |    10 +-
 sci-mathematics/libsfmt/libsfmt-1.3.0.ebuild       |    16 +-
 sci-mathematics/libsfmt/metadata.xml               |     2 +-
 sci-mathematics/lie/lie-2.2.2.ebuild               |     2 +-
 sci-mathematics/ltl2ba/Manifest                    |     2 +-
 sci-mathematics/ltl2ba/ltl2ba-1.1.ebuild           |     6 +-
 sci-mathematics/mdp/ChangeLog                      |     4 +
 sci-mathematics/mdp/Manifest                       |     2 +-
 sci-mathematics/mdp/mdp-3.2.ebuild                 |    35 -
 sci-mathematics/mdp/mdp-3.3.ebuild                 |    36 +
 sci-mathematics/mdp/mdp-9999.ebuild                |    29 +-
 sci-mathematics/netgen/Manifest                    |     3 +-
 .../netgen-5.x-compile-against-occ-6.5.x.patch     |    28 +
 .../netgen/files/netgen-5.x-missing-define.patch   |    38 +
 sci-mathematics/netgen/files/netgen.desktop        |     5 +-
 sci-mathematics/netgen/netgen-4.9.13.ebuild        |     4 +-
 sci-mathematics/netgen/netgen-5.0.0.ebuild         |    88 +
 sci-mathematics/open-axiom/ChangeLog               |     6 +-
 sci-mathematics/open-axiom/Manifest                |     1 +
 sci-mathematics/open-axiom/metadata.xml            |     4 +-
 sci-mathematics/open-axiom/open-axiom-1.3.0.ebuild |     2 +-
 sci-mathematics/open-axiom/open-axiom-1.4.2.ebuild |    37 +
 sci-mathematics/pest/pest-12.2.ebuild              |     2 +-
 sci-mathematics/petsc/ChangeLog                    |    24 +-
 sci-mathematics/petsc/Manifest                     |     4 +-
 .../petsc/files/petsc-3.4.2-disable-rpath.patch    |    16 +
 .../petsc/files/petsc-3.5.1-disable-rpath.patch    |    16 +
 .../petsc/files/petsc-3.5.3-disable-rpath.patch    |    18 +
 sci-mathematics/petsc/metadata.xml                 |     6 +-
 sci-mathematics/petsc/petsc-3.3_p5.ebuild          |   223 -
 sci-mathematics/petsc/petsc-3.4.2.ebuild           |   247 +
 sci-mathematics/petsc/petsc-3.5.1.ebuild           |   243 +
 sci-mathematics/petsc/petsc-3.5.3.ebuild           |   243 +
 sci-mathematics/pff/ChangeLog                      |    23 +-
 sci-mathematics/pff/metadata.xml                   |     1 +
 sci-mathematics/pff/pff-8.4.ebuild                 |    17 +-
 sci-mathematics/polymake/ChangeLog                 |     8 -
 sci-mathematics/polymake/Manifest                  |     1 -
 sci-mathematics/polymake/files/2.10-soname.patch   |    11 -
 .../files/polymake-2.11-drop-jreality.patch        |    25 -
 sci-mathematics/polymake/metadata.xml              |    17 -
 sci-mathematics/polymake/polymake-2.11-r1.ebuild   |    82 -
 sci-mathematics/pulp/ChangeLog                     |     6 +-
 sci-mathematics/pulp/Manifest                      |     2 +-
 sci-mathematics/pulp/pulp-1.5.3.ebuild             |    43 -
 sci-mathematics/pulp/pulp-1.5.6.ebuild             |    43 +
 sci-mathematics/scilab/ChangeLog                   |    38 +-
 sci-mathematics/scilab/Manifest                    |     4 +-
 .../scilab/files/scilab-5.3.3-as-needed.patch      |    42 -
 .../scilab/files/scilab-5.3.3-blas-libs.patch      |    12 -
 .../files/scilab-5.3.3-disable-build-help.patch    |    12 -
 .../scilab-5.3.3-fix-random-runtime-failures.patch |    98 -
 .../scilab/files/scilab-5.3.3-fortran-link.patch   |    23 -
 .../scilab/files/scilab-5.3.3-gui-no-xcos.patch    |    26 -
 .../scilab/files/scilab-5.3.3-hdf18.patch          |    13 -
 .../scilab/files/scilab-5.3.3-java-heap.patch      |    11 -
 .../scilab/files/scilab-5.3.3-javadoc-utf8.patch   |    25 -
 .../scilab/files/scilab-5.3.3-jgrapx-min.patch     |     0
 .../scilab/files/scilab-5.3.3-jvm-detection.patch  |    44 -
 .../scilab/files/scilab-5.3.3-matio15.patch        |    25 -
 .../scilab/files/scilab-5.3.3-no-lhpi.patch        |    22 -
 .../scilab/files/scilab-5.3.3-no-xcos-deps.patch   |    90 -
 .../scilab/files/scilab-5.4.1-followlinks.patch    |    12 -
 .../scilab/files/scilab-5.4.1-gluegen.patch        |    12 -
 .../scilab/files/scilab-5.4.1-java-heap.patch      |    14 -
 .../files/scilab-5.5.0-accessviolation.patch       |    21 +
 ... scilab-5.5.0-fix-random-runtime-failure.patch} |     0
 .../scilab/files/scilab-5.5.0-followlinks.patch    |    11 +
 .../scilab/files/scilab-5.5.0-gluegen.patch        |    11 +
 .../scilab/files/scilab-5.5.0-java-heap.patch      |    11 +
 .../scilab/files/scilab-5.5.0-jdk1.8.patch         |    76 +
 .../scilab/files/scilab-5.5.0-nogui.patch          |    13 +
 .../files/scilab-5.5.1-accessviolation.patch       |    21 +
 ... scilab-5.5.1-fix-random-runtime-failure.patch} |     0
 .../scilab/files/scilab-5.5.1-followlinks.patch    |    11 +
 .../scilab/files/scilab-5.5.1-gluegen.patch        |    11 +
 .../scilab/files/scilab-5.5.1-java-heap.patch      |    11 +
 .../scilab/files/scilab-5.5.1-missinglib.patch     |    11 +
 .../scilab/files/scilab-5.5.1-nogui.patch          |    13 +
 sci-mathematics/scilab/metadata.xml                |    17 +-
 sci-mathematics/scilab/scilab-5.3.3-r1.ebuild      |   251 -
 sci-mathematics/scilab/scilab-5.4.1.ebuild         |   242 -
 sci-mathematics/scilab/scilab-5.5.0.ebuild         |   252 +
 sci-mathematics/scilab/scilab-5.5.1.ebuild         |   264 +
 sci-mathematics/singular/ChangeLog                 |    10 +
 sci-mathematics/singular/Manifest                  |     1 +
 .../singular/files/60singular-gentoo.el            |    10 +
 .../singular-4.0.0-fix-omalloc-ar-detection.patch  |    12 +
 .../singular/files/singular-4.0.0-gentoo.patch     |    65 +
 sci-mathematics/singular/metadata.xml              |    12 +
 sci-mathematics/singular/singular-4.0.0_p2.ebuild  |   147 +
 sci-mathematics/surfer/surfer-0.0.197.ebuild       |     2 +-
 sci-mathematics/ufc/ChangeLog                      |    10 +-
 sci-mathematics/ufc/Manifest                       |     3 +-
 sci-mathematics/ufc/ufc-1.4.2.ebuild               |     2 +-
 sci-mathematics/ufc/ufc-2.3.0.ebuild               |    19 +
 sci-mathematics/why/ChangeLog                      |    25 +-
 sci-mathematics/why/Manifest                       |     2 +-
 sci-mathematics/why/files/why-2.30.patch           |    36 -
 sci-mathematics/why/files/why-flocq23.patch        |    11 +
 sci-mathematics/why/metadata.xml                   |    17 +-
 sci-mathematics/why/why-2.30.ebuild                |    73 -
 sci-mathematics/why/why-2.34.ebuild                |    70 +
 sci-mathematics/why3/ChangeLog                     |    14 +
 sci-mathematics/why3/Manifest                      |     1 +
 sci-mathematics/why3/metadata.xml                  |    21 +
 sci-mathematics/why3/why3-0.83.ebuild              |    60 +
 sci-mathematics/yorick/yorick-2.1.06.ebuild        |     2 +-
 sci-mathematics/z3/ChangeLog                       |    16 +
 sci-mathematics/z3/Manifest                        |     1 +
 .../z3}/metadata.xml                               |     0
 sci-mathematics/z3/z3-4.3.1.ebuild                 |    75 +
 sci-mathematics/z3/z3-9999.ebuild                  |    80 +
 sci-misc/elmer-elmergrid/ChangeLog                 |    12 +
 sci-misc/elmer-elmergrid/Manifest                  |     1 +
 .../elmer-elmergrid-6.0_p4651.ebuild               |    37 +
 .../elmer-elmergrid/elmer-elmergrid-9999.ebuild    |    44 +
 .../{salome-yacs => elmer-elmergrid}/metadata.xml  |     0
 sci-misc/elmer-fem/ChangeLog                       |    12 +
 sci-misc/elmer-fem/Manifest                        |     1 +
 sci-misc/elmer-fem/elmer-fem-6.0_p4651.ebuild      |    54 +
 sci-misc/elmer-fem/elmer-fem-9999.ebuild           |    56 +
 .../elmer-fem/files/elmer-fem-6.0_p4651-oos.patch  |    75 +
 .../files/elmer-fem-6.0_p4651-underlinking.patch   |    23 +
 .../files/elmer-fem-Makefile-install.patch         |    13 +
 sci-misc/{salome-yacs => elmer-fem}/metadata.xml   |     0
 sci-misc/elmer-front/ChangeLog                     |    14 +
 sci-misc/elmer-front/Manifest                      |     1 +
 sci-misc/elmer-front/elmer-front-6.0_p4651.ebuild  |    44 +
 sci-misc/elmer-front/elmer-front-9999.ebuild       |    51 +
 .../elmer-front-6.0_p4651-out-of-source.patch      |    30 +
 .../files/elmer-front-6.0_p4651-tcltk8.6.patch     |    55 +
 .../files/elmer-front-6.0_p4651-underlinking.patch |    16 +
 .../files/elmer-front-Makefile-install.patch       |    18 +
 sci-misc/{salome-yacs => elmer-front}/metadata.xml |     0
 sci-misc/elmer-gui/ChangeLog                       |    13 +
 sci-misc/elmer-gui/elmer-gui-9999.ebuild           |   151 +
 .../elmer-gui/files/elmer-gui-netgen-fixes.patch   |    11 +
 sci-misc/elmer-gui/metadata.xml                    |    13 +
 sci-misc/elmer-meshgen2d/ChangeLog                 |    13 +
 sci-misc/elmer-meshgen2d/Manifest                  |     1 +
 .../elmer-meshgen2d-6.0_p4651.ebuild               |    34 +
 .../elmer-meshgen2d/elmer-meshgen2d-9999.ebuild    |    41 +
 .../files/elmer-meshgen2d-6.0_p4651-oof.patch      |    17 +
 .../{salome-yacs => elmer-meshgen2d}/metadata.xml  |     0
 sci-misc/elmer-meta/ChangeLog                      |    14 +
 sci-misc/elmer-meta/elmer-meta-6.0_p4651.ebuild    |    27 +
 sci-misc/elmer-meta/elmer-meta-9999.ebuild         |    27 +
 sci-misc/{salome-yacs => elmer-meta}/metadata.xml  |     0
 sci-misc/elmer-post/ChangeLog                      |    16 +
 sci-misc/elmer-post/Manifest                       |     1 +
 sci-misc/elmer-post/elmer-post-6.0_p4651.ebuild    |    60 +
 sci-misc/elmer-post/elmer-post-9999.ebuild         |    62 +
 .../files/elmer-post-6.0_p4651-bfr-overflow.patch  |    16 +
 .../files/elmer-post-6.0_p4651-impl-dec.patch      |    15 +
 .../files/elmer-post-6.0_p4651-oof.patch           |   181 +
 .../files/elmer-post-6.0_p4651-tcltk8.6.patch      |   355 +
 .../files/elmer-post-6.0_p4651-underlinking.patch  |    20 +
 sci-misc/{salome-yacs => elmer-post}/metadata.xml  |     0
 sci-misc/finomaton/ChangeLog                       |     6 +-
 sci-misc/finomaton/finomaton-1.0.ebuild            |     9 +-
 sci-misc/finomaton/metadata.xml                    |     6 +-
 sci-misc/fitscut/ChangeLog                         |     7 +-
 sci-misc/fitscut/Manifest                          |     2 +-
 sci-misc/fitscut/fitscut-1.4.4.ebuild              |    27 +-
 sci-misc/fitscut/metadata.xml                      |     2 +-
 sci-misc/foma/foma-0.9.14_alpha.ebuild             |     2 +-
 sci-misc/foma/foma-0.9.16_alpha.ebuild             |     2 +-
 sci-misc/hfst/hfst-2.2.ebuild                      |     2 +-
 sci-misc/hfst/hfst-3.0.2.ebuild                    |     2 +-
 sci-misc/hfst/hfst-3.3.12.ebuild                   |     2 +-
 sci-misc/irstlm/ChangeLog                          |    21 +
 sci-misc/irstlm/Manifest                           |     1 +
 sci-misc/irstlm/irstlm-5.80.08.ebuild              |    21 +
 sci-misc/irstlm/metadata.xml                       |    14 +
 sci-misc/jwnl/ChangeLog                            |     6 +-
 sci-misc/jwnl/jwnl-1.3_rc3.ebuild                  |    13 +-
 sci-misc/jwnl/metadata.xml                         |     8 +-
 sci-misc/kaldi/ChangeLog                           |    17 +
 sci-misc/kaldi/files/Makefile.patch                |    57 +
 sci-misc/kaldi/files/configure.patch               |    93 +
 sci-misc/kaldi/files/default_rules.mk.patch        |    47 +
 sci-misc/kaldi/kaldi-0_p20150301.ebuild            |    58 +
 sci-misc/kaldi/metadata.xml                        |    12 +
 sci-misc/kotus-sanalista/ChangeLog                 |     8 +-
 .../kotus-sanalista/kotus-sanalista-1-r1.ebuild    |     9 +-
 sci-misc/kotus-sanalista/metadata.xml              |     8 +-
 sci-misc/mitlm/ChangeLog                           |     9 +
 sci-misc/mitlm/Manifest                            |     1 +
 sci-misc/mitlm/metadata.xml                        |    14 +
 sci-misc/mitlm/mitlm-0.4.1.ebuild                  |    20 +
 sci-misc/nltk/ChangeLog                            |     6 +-
 sci-misc/nltk/Manifest                             |     2 +-
 sci-misc/nltk/metadata.xml                         |     8 +-
 sci-misc/nltk/nltk-2.0.1_rc1.ebuild                |    32 -
 sci-misc/nltk/nltk-2.0.4.ebuild                    |    29 +
 sci-misc/omorfi/ChangeLog                          |     6 +-
 sci-misc/omorfi/metadata.xml                       |     8 +-
 sci-misc/omorfi/omorfi-0.1_alpha.ebuild            |    17 +-
 sci-misc/openfst/ChangeLog                         |    17 +-
 sci-misc/openfst/Manifest                          |     4 +-
 sci-misc/openfst/files/kaldi-openfst-1.4.1.patch   |   269 +
 sci-misc/openfst/files/kaldi.patch                 |   599 +
 sci-misc/openfst/openfst-1.2.7.ebuild              |    34 -
 sci-misc/openfst/openfst-1.3.2.ebuild              |    30 -
 sci-misc/openfst/openfst-1.3.4.ebuild              |    24 +
 sci-misc/openfst/openfst-1.4.1.ebuild              |    19 +
 sci-misc/opennlp-maxent/ChangeLog                  |     6 +-
 sci-misc/opennlp-maxent/metadata.xml               |     8 +-
 .../opennlp-maxent/opennlp-maxent-2.4.0.ebuild     |    14 +-
 sci-misc/opennlp-tools/ChangeLog                   |     6 +-
 sci-misc/opennlp-tools/metadata.xml                |    14 +-
 sci-misc/opennlp-tools/opennlp-tools-1.3.0.ebuild  |     9 +-
 sci-misc/praat/praat-5.1.00.ebuild                 |     2 +-
 sci-misc/praat/praat-5.1.15.ebuild                 |     2 +-
 sci-misc/pywordnet/ChangeLog                       |     6 +-
 sci-misc/pywordnet/Manifest                        |     2 +-
 sci-misc/pywordnet/metadata.xml                    |     8 +-
 sci-misc/pywordnet/pywordnet-2.0.1.ebuild          |    13 +-
 .../salome-component/salome-component-5.1.3.ebuild |     4 +-
 .../salome-component/salome-component-5.1.4.ebuild |     4 +-
 sci-misc/salome-geom/salome-geom-5.1.3.ebuild      |     4 +-
 sci-misc/salome-geom/salome-geom-5.1.4.ebuild      |     4 +-
 sci-misc/salome-gui/salome-gui-5.1.3.ebuild        |     4 +-
 sci-misc/salome-gui/salome-gui-5.1.4.ebuild        |     4 +-
 sci-misc/salome-kernel/salome-kernel-5.1.3.ebuild  |     4 +-
 sci-misc/salome-kernel/salome-kernel-5.1.4.ebuild  |     4 +-
 sci-misc/salome-med/salome-med-5.1.3.ebuild        |     4 +-
 sci-misc/salome-med/salome-med-5.1.4.ebuild        |     4 +-
 sci-misc/salome-meta/salome-meta-5.1.3.ebuild      |     4 +-
 sci-misc/salome-meta/salome-meta-5.1.4.ebuild      |     4 +-
 .../salome-pycalculator-5.1.3.ebuild               |     4 +-
 .../salome-pycalculator-5.1.4.ebuild               |     4 +-
 sci-misc/salome-smesh/salome-smesh-5.1.3.ebuild    |     4 +-
 sci-misc/salome-smesh/salome-smesh-5.1.4.ebuild    |     4 +-
 sci-misc/salome-visu/salome-visu-5.1.3.ebuild      |     4 +-
 sci-misc/salome-visu/salome-visu-5.1.4.ebuild      |     4 +-
 sci-misc/salome-yacs/salome-yacs-5.1.3.ebuild      |     4 +-
 sci-misc/salome-yacs/salome-yacs-5.1.4.ebuild      |     4 +-
 sci-misc/sfst/sfst-1.4.2.ebuild                    |     2 +-
 sci-misc/sfst/sfst-1.4.6g.ebuild                   |     2 +-
 sci-misc/simx/ChangeLog                            |    32 +
 sci-misc/simx/Manifest                             |     1 +
 sci-misc/{salome-yacs => simx}/metadata.xml        |     0
 sci-misc/simx/simx-0.2.ebuild                      |    37 +
 sci-misc/simx/simx-9999.ebuild                     |    37 +
 sci-misc/stanford-parser/ChangeLog                 |     6 +-
 sci-misc/stanford-parser/metadata.xml              |     8 +-
 .../stanford-parser/stanford-parser-1.6.ebuild     |    14 +-
 sci-misc/stanford-tagger/ChangeLog                 |     6 +-
 sci-misc/stanford-tagger/metadata.xml              |     8 +-
 .../stanford-tagger-20060521.ebuild                |    34 +-
 sci-physics/LoopTools/ChangeLog                    |    28 -
 sci-physics/LoopTools/LoopTools-2.8.ebuild         |    25 -
 sci-physics/LoopTools/Manifest                     |     1 -
 .../LoopTools/files/LoopTools-2.8-makefile.patch   |    96 -
 sci-physics/LoopTools/metadata.xml                 |    15 -
 sci-physics/abinit/ChangeLog                       |    56 +-
 sci-physics/abinit/Manifest                        |     3 +-
 sci-physics/abinit/abinit-7.2.2.ebuild             |   381 -
 sci-physics/abinit/abinit-7.4.2-r1.ebuild          |   353 +
 sci-physics/abinit/abinit-7.6.4-r1.ebuild          |   391 +
 .../abinit/files/7.4.2-cuda_link_stdc++.patch      |    21 +
 .../abinit/files/7.4.2-levmar_diag_scaling.patch   |    21 +
 sci-physics/abinit/files/7.4.2-syntax.patch        |    21 +
 .../abinit/files/7.6.3-libabinit_options.patch     |    80 +
 sci-physics/abinit/files/7.6.4-cuda_header.patch   |    11 +
 .../abinit/files/7.6.4-libxc_versions.patch        |    40 +
 sci-physics/abinit/metadata.xml                    |    47 +-
 sci-physics/atompaw/ChangeLog                      |     8 +-
 sci-physics/atompaw/Manifest                       |     1 +
 sci-physics/atompaw/atompaw-3.0.1.9-r1.ebuild      |     2 +-
 sci-physics/atompaw/atompaw-4.0.0.10.ebuild        |    69 +
 sci-physics/atompaw/files/4.0-longplot.patch       |    42 +
 sci-physics/atompaw/metadata.xml                   |    18 +-
 .../atompaw2abinit/atompaw2abinit-3.3.0-r1.ebuild  |     2 +-
 sci-physics/bigdft/ChangeLog                       |    15 +-
 sci-physics/bigdft/Manifest                        |     2 +-
 sci-physics/bigdft/bigdft-1.7.5.ebuild             |   178 +
 sci-physics/bigdft/bigdft-1.7_pre24.ebuild         |   142 -
 .../files/bigdft-1.7-dev.24-nolib_mods.patch       |    25 -
 .../bigdft/files/bigdft-1.7.5-dynamic_memory.patch |   106 +
 .../bigdft/files/bigdft-1.7.5-pkgconfig.patch      |    10 +
 sci-physics/bigdft/metadata.xml                    |    30 +
 sci-physics/clip/Manifest                          |     1 +
 sci-physics/clip/clip-4.0.0_beta2.ebuild           |    39 +
 sci-physics/clip/metadata.xml                      |     9 +
 sci-physics/elk/elk-1.4.22.ebuild                  |     2 +-
 sci-physics/elk/elk-2.1.25.ebuild                  |     2 +-
 sci-physics/espresso++/ChangeLog                   |    36 +-
 sci-physics/espresso++/espresso++-9999.ebuild      |    41 +-
 sci-physics/espresso++/metadata.xml                |     3 -
 sci-physics/espresso/ChangeLog                     |    15 +-
 sci-physics/espresso/espresso-9999.ebuild          |    48 +-
 sci-physics/espresso/metadata.xml                  |     1 +
 sci-physics/fullprof-bin/ChangeLog                 |    14 +
 sci-physics/fullprof-bin/Manifest                  |     1 +
 .../fullprof-bin/fullprof-bin-20313.04.ebuild      |    66 +
 .../fullprof-bin/metadata.xml                      |     0
 sci-physics/geant-vmc/ChangeLog                    |    56 +-
 sci-physics/geant-vmc/Manifest                     |     4 +-
 sci-physics/geant-vmc/geant-vmc-3.1.15a.ebuild     |     4 +-
 sci-physics/geant-vmc/geant-vmc-4.2.14a.ebuild     |    60 -
 sci-physics/geant-vmc/geant-vmc-4.2.14b.ebuild     |    62 +
 sci-physics/geant-vmc/geant-vmc-4.2.15.ebuild      |    61 +
 sci-physics/geant-vmc/geant-vmc-4.2.15a.ebuild     |    61 +
 sci-physics/geant-vmc/geant-vmc-9999.ebuild        |    70 +
 sci-physics/geant-vmc/metadata.xml                 |    13 +-
 sci-physics/geant/geant-3.21.14-r4.ebuild          |     4 +-
 sci-physics/genfit/ChangeLog                       |    39 +
 sci-physics/genfit/Manifest                        |     1 +
 sci-physics/genfit/genfit-02.00.00.ebuild          |     1 +
 sci-physics/genfit/genfit-9999.ebuild              |    59 +
 sci-physics/genfit/metadata.xml                    |    31 +
 sci-physics/herwig++/ChangeLog                     |    24 +-
 sci-physics/herwig++/Manifest                      |     3 +-
 sci-physics/herwig++/herwig++-2.6.3.ebuild         |    50 -
 sci-physics/herwig++/herwig++-2.7.0-r1.ebuild      |    57 +
 sci-physics/herwig++/herwig++-2.7.1.ebuild         |    57 +
 sci-physics/herwig++/metadata.xml                  |     4 +-
 sci-physics/hoomd-blue/ChangeLog                   |    18 +
 sci-physics/hoomd-blue/hoomd-blue-9999.ebuild      |    61 +
 sci-physics/hoomd-blue/metadata.xml                |    12 +
 sci-physics/lammps/ChangeLog                       |    36 -
 sci-physics/lammps/Manifest                        |     5 -
 sci-physics/lammps/lammps-20130701.ebuild          |   105 -
 sci-physics/lammps/lammps-20130708.ebuild          |   115 -
 sci-physics/lammps/lammps-20130711.ebuild          |   115 -
 sci-physics/lammps/lammps-20130816.ebuild          |   115 -
 sci-physics/lammps/lammps-20130830.ebuild          |   115 -
 sci-physics/lammps/metadata.xml                    |    31 -
 sci-physics/looptools/ChangeLog                    |    40 +
 sci-physics/looptools/Manifest                     |     4 +
 .../looptools/files/looptools-2.10-makefile.patch  |    98 +
 .../looptools/files/looptools-2.8-makefile.patch   |    96 +
 sci-physics/looptools/looptools-2.10.ebuild        |    39 +
 sci-physics/looptools/looptools-2.11.ebuild        |    39 +
 sci-physics/looptools/looptools-2.8.ebuild         |    39 +
 sci-physics/looptools/looptools-2.9.ebuild         |    39 +
 sci-physics/looptools/metadata.xml                 |    12 +
 sci-physics/mc-tester/ChangeLog                    |    11 +
 sci-physics/mc-tester/Manifest                     |     1 +
 .../files/mc-tester-1.25.0-compare.sh.patch        |    30 +
 sci-physics/mc-tester/mc-tester-1.25.0.ebuild      |    65 +
 sci-physics/mc-tester/metadata.xml                 |    16 +
 sci-physics/openmx/ChangeLog                       |    14 +-
 sci-physics/openmx/Manifest                        |     2 +-
 sci-physics/openmx/openmx-3.6.ebuild               |     2 +-
 sci-physics/openmx/openmx-3.7.4.ebuild             |   163 -
 sci-physics/openmx/openmx-3.7.8.ebuild             |   171 +
 sci-physics/qcl/ChangeLog                          |    12 +-
 sci-physics/qcl/Manifest                           |     9 +-
 sci-physics/qcl/files/qcl-0.6.4-makefile.patch     |    22 +
 sci-physics/qcl/qcl-0.6.3-r1.ebuild                |    19 +-
 sci-physics/qcl/qcl-0.6.4.ebuild                   |    42 +
 sci-physics/rivet/ChangeLog                        |    14 +
 sci-physics/rivet/Manifest                         |     2 +
 sci-physics/rivet/metadata.xml                     |    16 +
 sci-physics/rivet/rivet-2.1.1.ebuild               |    62 +
 sci-physics/rivet/rivet-2.1.2.ebuild               |    62 +
 sci-physics/root/ChangeLog                         |   194 +-
 sci-physics/root/Manifest                          |    10 +-
 sci-physics/root/files/root-5.28.00b-unuran.patch  |    39 -
 sci-physics/root/files/root-5.32.00-chklib64.patch |     1 +
 sci-physics/root/files/root-5.32.00-dotfont.patch  |    58 -
 sci-physics/root/files/root-5.32.00-htmldoc.patch  |    12 -
 .../root/files/root-5.32.00-nobyte-compile.patch   |   137 -
 .../root/files/root-5.32.00-prop-flags.patch       |    15 -
 .../root/files/root-5.34.05-nobyte-compile.patch   |   137 -
 sci-physics/root/files/root-5.34.13-desktop.patch  |    12 +
 sci-physics/root/files/root-5.34.13-unuran.patch   |    40 +
 ...99-dotfont.patch => root-6.00.01-dotfont.patch} |     0
 sci-physics/root/files/root-6.00.01-geocad.patch   |    15 +
 sci-physics/root/files/root-6.00.01-llvm.patch     |    13 +
 .../root/files/root-6.00.01-nobyte-compile.patch   |    33 +
 .../root/files/root-6.00.01-prop-flags.patch       |    17 +
 .../root/files/root-6.00.01-tutorials-path.patch   |    39 +
 sci-physics/root/files/root-6.00.02-tm_zone.patch  |    22 +
 sci-physics/root/files/root-9999-cling.patch       |    13 -
 sci-physics/root/metadata.xml                      |    35 +-
 sci-physics/root/root-5.34.09.ebuild               |   385 -
 sci-physics/root/root-6.00.02.ebuild               |   442 +
 sci-physics/root/root-9999.ebuild                  |   557 +-
 sci-physics/tauola/ChangeLog                       |    31 +
 sci-physics/tauola/Manifest                        |     3 +
 .../tauola/files/tauola-1.1.3-makefile.patch       |    12 +
 .../files/tauola-1.1.3-tau-spinner-makefile.patch  |    11 +
 .../tauola/files/tauola-1.1.4-makefile.patch       |    12 +
 sci-physics/tauola/files/tauola-1.1.5-doc.patch    |    11 +
 sci-physics/tauola/metadata.xml                    |    15 +
 sci-physics/tauola/tauola-1.1.3.ebuild             |    71 +
 sci-physics/tauola/tauola-1.1.4.ebuild             |    71 +
 sci-physics/tauola/tauola-1.1.5.ebuild             |    72 +
 sci-physics/tauola/tauola-9999.ebuild              |    76 +
 sci-physics/thepeg/ChangeLog                       |    37 +-
 sci-physics/thepeg/Manifest                        |     3 +
 sci-physics/thepeg/metadata.xml                    |     6 +-
 sci-physics/thepeg/thepeg-1.8.3-r1.ebuild          |    97 +
 sci-physics/thepeg/thepeg-1.8.3.ebuild             |    92 -
 sci-physics/thepeg/thepeg-1.9.0-r2.ebuild          |    99 +
 sci-physics/thepeg/thepeg-1.9.1-r1.ebuild          |    96 +
 sci-physics/thepeg/thepeg-1.9.2.ebuild             |    97 +
 sci-physics/vgm/ChangeLog                          |    25 +-
 sci-physics/vgm/Manifest                           |     1 +
 sci-physics/vgm/vgm-3.06.ebuild                    |    25 +-
 sci-physics/vgm/vgm-9999.ebuild                    |    68 +
 sci-physics/yoda/ChangeLog                         |     9 +
 sci-physics/yoda/Manifest                          |     1 +
 sci-physics/yoda/metadata.xml                      |    15 +
 sci-physics/yoda/yoda-1.0.6.ebuild                 |    50 +
 .../ferret-bin/ferret-bin-6.6.4.ebuild             |     2 +-
 sci-visualization/gnuplot/ChangeLog                |    33 +-
 sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild  |    68 +-
 sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild  |   224 -
 sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild  |   195 +
 sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild  |   195 +
 sci-visualization/gnuplot/metadata.xml             |    19 +-
 sci-visualization/labplot/ChangeLog                |     8 +
 sci-visualization/labplot/labplot-9999.ebuild      |     5 +-
 sci-visualization/labplot/metadata.xml             |     2 +-
 sci-visualization/mantid/ChangeLog                 |     7 +
 sci-visualization/mantid/Manifest                  |     1 +
 .../mantid/files/mantid-3.3.0-minigzip-OF.patch    |    28 +
 sci-visualization/mantid/mantid-3.3.0.ebuild       |    99 +
 sci-visualization/mantid/metadata.xml              |    23 +
 sci-visualization/mayavi/ChangeLog                 |    12 +
 sci-visualization/mayavi/Manifest                  |     1 +
 sci-visualization/mayavi/mayavi-4.4.0.ebuild       |    69 +
 sci-visualization/mayavi/metadata.xml              |    24 +
 sci-visualization/nodemon/nodemon-0.3.5.ebuild     |     2 +-
 sci-visualization/v_sim/v_sim-3.6.0.ebuild         |     2 +-
 sci-visualization/visit/Manifest                   |     3 +
 .../files/visit-2.7.1-dont_symlink_visit_dir.patch |    18 +
 .../visit/files/visit-2.7.1-findpython.patch       |    19 +
 .../visit/files/visit-2.7.1-findsilo.patch         |    12 +
 .../visit/files/visit-2.7.1-findvtk.patch          |    24 +
 .../visit/files/visit-2.7.1-vtklibs.patch          |   142 +
 .../files/visit-2.7.2-dont_symlink_visit_dir.patch |    18 +
 .../visit/files/visit-2.7.2-findpython.patch       |    19 +
 .../visit/files/visit-2.7.2-findsilo.patch         |    12 +
 .../visit/files/visit-2.7.2-findvtk.patch          |    24 +
 .../visit/files/visit-2.7.2-vtklibs.patch          |   142 +
 .../files/visit-2.7.3-dont_symlink_visit_dir.patch |    18 +
 .../visit/files/visit-2.7.3-findpython.patch       |    19 +
 .../visit/files/visit-2.7.3-findsilo.patch         |    12 +
 .../visit/files/visit-2.7.3-findvtk.patch          |    24 +
 .../visit/files/visit-2.7.3-vtklibs.patch          |   142 +
 sci-visualization/visit/metadata.xml               |    21 +
 sci-visualization/visit/visit-2.7.1.ebuild         |    76 +
 sci-visualization/visit/visit-2.7.2.ebuild         |    82 +
 sci-visualization/visit/visit-2.7.3.ebuild         |    83 +
 .../vtkPOFFReader/vtkPOFFReader-300.ebuild         |     2 +-
 sci-visualization/yt/Manifest                      |     1 +
 sci-visualization/yt/yt-2.6.ebuild                 |    51 +
 sci-visualization/yt/yt-9999.ebuild                |    25 +-
 scripts/merge-dualHEAD                             |    64 +
 skel.ChangeLog                                     |     2 +-
 skel.ebuild                                        |     2 +-
 skel.metadata.xml                                  |     1 -
 sys-apps/likwid/Manifest                           |     1 +
 .../files/{likwid.patch => likwid-3.0-paths.patch} |     0
 sys-apps/likwid/files/likwid-3.1.1-paths.patch     |    22 +
 .../likwid/files/likwid-3.1.1-shared_lib.patch     |    12 +
 sys-apps/likwid/likwid-3.0.ebuild                  |     4 +-
 sys-apps/likwid/likwid-3.1.1.ebuild                |    32 +
 sys-cluster/blcr/ChangeLog                         |     6 +-
 sys-cluster/blcr/Manifest                          |     1 -
 sys-cluster/blcr/blcr-0.8.2.ebuild                 |    57 -
 sys-cluster/blcr/blcr-0.8.4.ebuild                 |    21 +-
 sys-cluster/charm/ChangeLog                        |    51 -
 sys-cluster/charm/Manifest                         |     1 -
 sys-cluster/charm/charm-6.5.1-r1.ebuild            |   195 -
 sys-cluster/charm/charm-6.5.1.ebuild               |   193 -
 .../charm/files/charm-6.5.0-charmc-gentoo.patch    |    25 -
 .../charm/files/charm-6.5.1-CkReductionMgr.patch   |    34 -
 .../charm/files/charm-6.5.1-cleanup-config.patch   |    58 -
 .../files/charm-6.5.1-fix-string-parsing.patch     |    51 -
 sys-cluster/charm/metadata.xml                     |    18 -
 sys-cluster/charmdebug/charmdebug-6.2.0-r1.ebuild  |     2 +-
 sys-cluster/empi/empi-0.10.ebuild                  |     2 +-
 .../ganglia_jobmonarch-0.3.1.ebuild                |     2 +-
 sys-cluster/gasnet/ChangeLog                       |    14 +
 sys-cluster/gasnet/Manifest                        |     1 +
 sys-cluster/gasnet/gasnet-1.24.0.ebuild            |    36 +
 sys-cluster/gasnet/gasnet-9999.ebuild              |    44 +
 sys-cluster/{nullmpi => gasnet}/metadata.xml       |     0
 sys-cluster/hpl/ChangeLog                          |    16 +
 sys-cluster/hpl/hpl-2.0-r1.ebuild                  |     4 +-
 sys-cluster/hpl/hpl-2.1.ebuild                     |     7 +-
 sys-cluster/hpx/ChangeLog                          |    21 +
 sys-cluster/hpx/Manifest                           |     2 -
 .../hpx/files/hpx-0.9.7-move-boost-include.patch   |    18 +
 sys-cluster/hpx/files/hpx-0.9.8-cmake_dir.patch    |    27 +
 sys-cluster/hpx/files/hpx-0.9.8-install-path.patch |    69 +
 sys-cluster/hpx/files/hpx-0.9.8-multilib.patch     |   163 +
 sys-cluster/hpx/hpx-0.9.5.ebuild                   |    29 -
 sys-cluster/hpx/hpx-0.9.6.ebuild                   |    29 -
 sys-cluster/hpx/hpx-9999.ebuild                    |    88 +
 sys-cluster/hpx/metadata.xml                       |    34 +-
 sys-cluster/htcondor/ChangeLog                     |    17 +-
 sys-cluster/htcondor/Manifest                      |     1 +
 ...sers-condor_config-last-rather-than-first.patch |    29 +
 .../htcondor-8.3.2-condor_config.generic.patch     |    47 +
 .../htcondor-8.3.2-packaging_directories.patch     |    36 +
 .../files/htcondor-8.3.2-shadow_dlopen.patch       |    14 +
 sys-cluster/htcondor/htcondor-8.0.0.ebuild         |    26 +-
 sys-cluster/htcondor/htcondor-8.3.2.ebuild         |   114 +
 sys-cluster/libquo/ChangeLog                       |     9 +
 sys-cluster/libquo/libquo-9999.ebuild              |    35 +
 .../bliss => sys-cluster/libquo}/metadata.xml      |     0
 sys-cluster/lustre/ChangeLog                       |   303 +-
 sys-cluster/lustre/Manifest                        |     1 +
 ...ld-make-AC-check-for-linux-arch-sandbox-f.patch |    95 -
 ...cfs-update-zfs-proc-handling-to-seq_files.patch |   204 +
 ...6-kernel-Kernel-update-for-3.7.2-201.fc18.patch |   169 -
 ...rnel-3.9-hlist_for_each_entry-uses-3-args.patch |   117 -
 ...m-Backport-shrinker-changes-from-upstream.patch |   753 +
 ...79-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch |    82 -
 .../lustre/files/lustre-readline6.3_fix.patch      |    13 +
 sys-cluster/lustre/lustre-9999.ebuild              |    43 +-
 sys-cluster/modules/ChangeLog                      |    11 +-
 sys-cluster/modules/files/modules.new.sh.in        |     8 +
 sys-cluster/modules/metadata.xml                   |     2 +-
 sys-cluster/modules/modules-3.2.10-r1.ebuild       |     2 +-
 sys-cluster/modules/modules-3.2.10.ebuild          |     2 +-
 sys-cluster/modules/modules-3.2.9c-r1.ebuild       |     4 +-
 sys-cluster/modules/modules-3.2.9c.ebuild          |     4 +-
 sys-cluster/mpe2/ChangeLog                         |     9 +
 sys-cluster/mpe2/Manifest                          |     1 +
 sys-cluster/mpe2/metadata.xml                      |     5 +
 sys-cluster/mpe2/mpe2-1.3.0.ebuild                 |   142 +
 sys-cluster/mpich/ChangeLog                        |    14 +-
 sys-cluster/mpich/Manifest                         |     1 +
 sys-cluster/mpich/mpich-3.0.4.ebuild               |     2 +-
 sys-cluster/mpich/mpich-3.1.3-r1.ebuild            |   133 +
 sys-cluster/mpich2/ChangeLog                       |    18 +-
 sys-cluster/mpich2/Manifest                        |     2 -
 sys-cluster/mpich2/metadata.xml                    |    28 +-
 sys-cluster/mpich2/mpich2-1.2.1_p1-r2.ebuild       |   202 -
 sys-cluster/mpich2/mpich2-1.4.1_p1.ebuild          |   179 -
 sys-cluster/mpich2/mpich2-1.5.ebuild               |     4 +-
 sys-cluster/mvapich2/ChangeLog                     |     9 +-
 sys-cluster/mvapich2/mvapich2-1.6-r1.ebuild        |    26 +-
 sys-cluster/nullmpi/ChangeLog                      |     5 +-
 sys-cluster/nullmpi/nullmpi-0.7.ebuild             |     2 +-
 sys-cluster/nullmpi/nullmpi-9999.ebuild            |     8 +-
 sys-cluster/openmpi/ChangeLog                      |    44 +-
 sys-cluster/openmpi/Manifest                       |     4 +
 sys-cluster/openmpi/files/openmpi-ltdl.patch       |    78 +
 sys-cluster/openmpi/metadata.xml                   |    23 +-
 sys-cluster/openmpi/openmpi-1.6.5.ebuild           |    12 +-
 sys-cluster/openmpi/openmpi-1.7.3.ebuild           |   159 +
 sys-cluster/openmpi/openmpi-1.8.1.ebuild           |   167 +
 sys-cluster/openmpi/openmpi-1.8.3.ebuild           |   167 +
 sys-cluster/openmpi/openmpi-1.8.4-r3.ebuild        |   191 +
 sys-cluster/ovis/ovis-3.0.1.ebuild                 |     2 +-
 sys-cluster/projections/projections-6.2.1.ebuild   |     2 +-
 sys-cluster/pyslice/ChangeLog                      |     8 +-
 sys-cluster/pyslice/Manifest                       |     2 +-
 sys-cluster/pyslice/metadata.xml                   |     4 +-
 sys-cluster/pyslice/pyslice-1.6.4-r1.ebuild        |    24 -
 sys-cluster/pyslice/pyslice-1.7.ebuild             |    21 +
 sys-devel/gdebugger/gdebugger-6.2.438.ebuild       |     2 +-
 sys-infiniband/librxe/librxe-1.0.0.ebuild          |     4 +-
 virtual/blacs/ChangeLog                            |     5 +-
 virtual/blacs/blacs-1.1.ebuild                     |     4 +-
 virtual/blacs/metadata.xml                         |     4 +-
 virtual/blas/ChangeLog                             |    17 +-
 virtual/blas/blas-2.1-r1.ebuild                    |    38 +
 virtual/blas/blas-2.1-r2.ebuild                    |    41 +
 virtual/blas/blas-2.1-r3.ebuild                    |    44 +
 virtual/blas/blas-2.1.ebuild                       |    25 -
 virtual/blas/metadata.xml                          |     4 +
 virtual/cblas/ChangeLog                            |    21 +-
 virtual/cblas/cblas-2.0-r1.ebuild                  |    28 +
 virtual/cblas/cblas-2.0-r2.ebuild                  |    31 +
 virtual/cblas/cblas-2.0-r3.ebuild                  |    35 +
 virtual/cblas/cblas-2.0.ebuild                     |     4 +-
 virtual/cblas/metadata.xml                         |     4 +
 virtual/geant/ChangeLog                            |     5 +-
 virtual/geant/geant-3.ebuild                       |     4 +-
 virtual/lapack/ChangeLog                           |    20 +-
 virtual/lapack/lapack-3.4-r1.ebuild                |    35 +
 virtual/lapack/lapack-3.4.ebuild                   |    23 -
 virtual/lapack/lapack-3.5-r1.ebuild                |    33 +
 virtual/lapack/lapack-3.5-r2.ebuild                |    34 +
 virtual/lapack/metadata.xml                        |     8 +-
 virtual/lapacke/ChangeLog                          |    12 +-
 virtual/lapacke/lapacke-1.0.ebuild                 |     4 +-
 virtual/lapacke/lapacke-3.5.ebuild                 |    19 +
 virtual/lapacke/metadata.xml                       |     4 +-
 virtual/mpi/ChangeLog                              |    16 +-
 virtual/mpi/mpi-2.0-r3.ebuild                      |     6 +-
 virtual/mpi/mpi-2.0-r4.ebuild                      |    25 +
 virtual/perl-encoding-warnings/ChangeLog           |    10 +
 .../perl-encoding-warnings}/metadata.xml           |     0
 .../perl-encoding-warnings-0.11.ebuild             |    16 +
 virtual/scalapack/ChangeLog                        |     6 +-
 virtual/scalapack/metadata.xml                     |     4 +-
 virtual/scalapack/scalapack-2.0.ebuild             |     4 +-
 www-apps/py-swish-e/ChangeLog                      |    14 -
 www-apps/py-swish-e/Manifest                       |     1 -
 www-apps/py-swish-e/metadata.xml                   |     5 -
 www-apps/py-swish-e/py-swish-e-0.5.ebuild          |    23 -
 x11-libs/agg/ChangeLog                             |     5 +-
 x11-libs/agg/agg-2.5-r3.ebuild                     |     7 +-
 x11-libs/agg/metadata.xml                          |    10 +-
 x11-libs/tr/ChangeLog                              |     5 +-
 x11-libs/tr/Manifest                               |     2 +-
 x11-libs/tr/metadata.xml                           |     2 +-
 x11-libs/tr/tr-1.3.ebuild                          |    17 +-
 x11-libs/xview-bin/xview-bin-3.2_p1428.ebuild      |     2 +-
 x11-libs/xview/ChangeLog                           |     7 +-
 x11-libs/xview/Manifest                            |     3 -
 x11-libs/xview/files/CAN-2005-0076.patch           |    29 -
 x11-libs/xview/files/lseek.diff                    |    26 -
 x11-libs/xview/files/lseek2.diff                   |    22 -
 x11-libs/xview/xview-3.2-r6.ebuild                 |   105 -
 x11-libs/xview/xview-3.2-r7.ebuild                 |   108 -
 x11-libs/xview/xview-3.2-r8.ebuild                 |     6 +-
 x11-misc/envytools/ChangeLog                       |     8 +-
 x11-misc/envytools/envytools-9999.ebuild           |     8 +-
 3325 files changed, 81894 insertions(+), 62000 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     f9aa6e6a2e33e4f4a8bdb37ceadc1ec0c7c648c0
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Apr 18 16:27:31 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Apr 18 16:27:31 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f9aa6e6a

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci

 licenses/UPennState                                |  7 ++
 sci-biology/cortex_var/ChangeLog                   | 13 ++++
 sci-biology/cortex_var/Manifest                    |  2 +
 sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild  | 47 +++++++++++++
 sci-biology/{zmsort => cortex_var}/metadata.xml    |  0
 sci-biology/rum/ChangeLog                          |  9 +++
 sci-biology/rum/Manifest                           |  1 +
 sci-biology/{zmsort => rum}/metadata.xml           |  0
 sci-biology/rum/rum-2.0.5.5.ebuild                 | 40 +++++++++++
 sci-biology/wgs-assembler/ChangeLog                | 13 ++++
 sci-biology/wgs-assembler/Manifest                 |  2 +
 sci-biology/{trf => wgs-assembler}/metadata.xml    |  0
 sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild | 78 +++++++++++++++++++++
 .../wgs-assembler/wgs-assembler-8.3_rc1.ebuild     | 81 ++++++++++++++++++++++
 14 files changed, 293 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     fdfc5d969ffddee97dd512cd0a5e38e5f225bf7d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 13 06:25:04 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Apr 13 06:25:04 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fdfc5d96

Merge remote-tracking branch 'github/master'

* github/master:
  sci-physics/root: 6.02.05-r2 moved to the tree
  app-doc/root-docs: 6.02.05 moved to the tree
  sci-physics/root: fix pg_config QA

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     e027dab25a2646d3d9634839b66ba4e8bc79522a
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Apr 10 07:04:39 2015 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gentoo <DOT> org>
CommitDate: Fri Apr 10 07:04:39 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e027dab2

Merge pull request #403 from hmmr/master

sci-biology/aghermann: new upstream version

 sci-biology/aghermann/ChangeLog                                        | 3 +++
 sci-biology/aghermann/Manifest                                         | 1 +
 .../aghermann/{aghermann-1.0.3-r1.ebuild => aghermann-1.0.4.ebuild}    | 0
 3 files changed, 4 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     23f108119bb1f093e257db47be42a20d6e1e6cd2
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Apr  7 08:56:24 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Apr  7 08:56:24 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=23f10811

Merge remote-tracking branch 'github/master'

* github/master:
  dev-java/hdf-java: Fix SRC_URI
  media-gfx/librecad fixed doc/appdata
  sci-libs/clfft: Replace patches by upstream patches
  gentoo does not support python 2_6
  corrected python compatibilities
  added python 3.3 compatibility
  removed unneeded bits, sorted eclasses
  updated deps
  new package, initial draft

 dev-java/hdf-java/hdf-java-2.9.ebuild              |  2 +-
 media-gfx/librecad/ChangeLog                       |  4 +++
 media-gfx/librecad/librecad-2.0.7.ebuild           |  4 ++-
 media-gfx/librecad/librecad-9999.ebuild            |  4 ++-
 sci-biology/dcmstack/ChangeLog                     | 23 +++++++++++++++
 sci-biology/dcmstack/dcmstack-9999.ebuild          | 25 ++++++++++++++++
 {x11-libs/tr => sci-biology/dcmstack}/metadata.xml |  0
 sci-libs/clfft/ChangeLog                           |  5 ++++
 sci-libs/clfft/files/clfft-client_CMakeLists.patch | 33 +++++++++++++++------
 .../files/clfft-scripts_perf_CMakeLists.patch      | 34 +++++++++++++++++-----
 10 files changed, 115 insertions(+), 19 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     e97096d09d4fabe86a748c4a7735b7da4f80d502
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Apr  6 08:54:46 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Apr  6 08:54:46 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e97096d0

Merge pull request #398 from TheChymera/dcmstack

Dcmstack

 sci-biology/dcmstack/ChangeLog                     | 23 ++++++++++++++++++++
 sci-biology/dcmstack/dcmstack-9999.ebuild          | 25 ++++++++++++++++++++++
 {x11-libs/tr => sci-biology/dcmstack}/metadata.xml |  0
 3 files changed, 48 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Guillaume Horel]

commit:     971f94094ae884ecb5393c25ff72e0a36e3ab2aa
Author:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
AuthorDate: Fri Apr  3 17:52:16 2015 +0000
Commit:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
CommitDate: Fri Apr  3 17:52:16 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=971f9409

Merge branch 'master' of github.com:gentoo-science/sci

 dev-lang/berkeley_upc/ChangeLog                    |   9 +-
 dev-lang/berkeley_upc/Manifest                     |   1 +
 ...pc-2.18.0.ebuild => berkeley_upc-2.20.0.ebuild} |   2 +-
 dev-libs/libunzip/ChangeLog                        |   6 +-
 dev-libs/libunzip/libunzip-5.52.ebuild             |  16 +--
 dev-tcltk/togl/ChangeLog                           |   6 +-
 dev-tcltk/togl/togl-1.7-r1.ebuild                  |   8 +-
 media-libs/OpenMOIV/ChangeLog                      |   6 ++
 media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild         |  14 +--
 media-libs/libgfx/ChangeLog                        |   8 +-
 media-libs/libgfx/libgfx-1.1.0.ebuild              |  18 ++--
 sci-biology/amos-short/ChangeLog                   |   8 ++
 sci-biology/amos-short/amos-short-0.9.3.ebuild     |  14 ++-
 sci-electronics/stage/ChangeLog                    |   5 +-
 sci-electronics/stage/Manifest                     |   2 +-
 sci-electronics/stage/stage-2.0.3.ebuild           |  16 +--
 sci-libs/armadillo/ChangeLog                       |   5 +
 sci-libs/armadillo/Manifest                        |   3 -
 sci-libs/armadillo/armadillo-4.600.2.ebuild        | 112 ---------------------
 sci-libs/armadillo/armadillo-4.600.4.ebuild        | 112 ---------------------
 sci-libs/armadillo/armadillo-4.650.2.ebuild        | 112 ---------------------
 sci-libs/framewave/ChangeLog                       |   6 ++
 sci-libs/framewave/framewave-1.3.1.ebuild          |  10 +-
 sci-libs/iml/ChangeLog                             |  12 ++-
 sci-libs/iml/Manifest                              |   1 +
 .../iml-1.0.4-use-any-cblas-implementation.patch   |  22 ++++
 sci-libs/iml/iml-1.0.3-r2.ebuild                   |   4 +-
 .../iml/{iml-1.0.3-r2.ebuild => iml-1.0.4.ebuild}  |   8 +-
 sci-libs/omalloc/ChangeLog                         |   6 +-
 sci-libs/omalloc/omalloc-0.9.6.ebuild              |   8 +-
 sci-libs/xraylib/ChangeLog                         |   8 +-
 sci-libs/xraylib/Manifest                          |   1 +
 ...{xraylib-2.16.0.ebuild => xraylib-3.1.0.ebuild} |   2 +-
 33 files changed, 149 insertions(+), 422 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     44d77ebaa8b120a2680c3c09b6a0ea2921536780
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Apr  2 10:15:38 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Apr  2 10:15:38 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=44d77eba

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/openblas: Cleanup symlinks and files
  sci-libs/openblas: Fix Bug 528974

 sci-libs/openblas/ChangeLog              |   3 +
 sci-libs/openblas/openblas-0.2.11.ebuild | 228 ++++++++++++++++++++++++++++++-
 sci-libs/openblas/openblas-0.2.14.ebuild | 228 +------------------------------
 sci-libs/openblas/openblas-9999.ebuild   |   4 +-
 4 files changed, 233 insertions(+), 230 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     51c14c78b2eaefa76cb7e5bf9aa347e93dfaf453
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 29 10:09:27 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar 29 10:09:27 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=51c14c78

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/dealii: Ebuild maintenance, remove wrong avx2 use flag
  sci-mathematics/acl2: Version bump, drop old; USE flags change.

 sci-libs/dealii/ChangeLog                          |  7 +++
 sci-libs/dealii/dealii-8.1.0-r2.ebuild             |  2 +-
 sci-libs/dealii/dealii-8.2.0.ebuild                |  2 +-
 ...{dealii-8.2.1.ebuild => dealii-8.2.1-r1.ebuild} | 10 ++--
 sci-libs/dealii/dealii-9999.ebuild                 | 10 ++--
 sci-mathematics/acl2/ChangeLog                     |  9 ++-
 sci-mathematics/acl2/Manifest                      |  4 +-
 sci-mathematics/acl2/acl2-6.3.ebuild               | 69 ----------------------
 sci-mathematics/acl2/acl2-7.0.ebuild               | 50 ++++++++++++++++
 sci-mathematics/acl2/files/set-booksdir.patch      | 11 ----
 sci-mathematics/acl2/metadata.xml                  | 20 ++-----
 11 files changed, 81 insertions(+), 113 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a1571ed130883b1fc810955b23fa418285245e9d
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 29 09:27:11 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar 29 09:27:11 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a1571ed1

Merge pull request #382 from ustcscgy/acl2

sci-mathematics/acl2: Version bump; USE flags change.

 sci-mathematics/acl2/ChangeLog                |  9 +++-
 sci-mathematics/acl2/Manifest                 |  4 +-
 sci-mathematics/acl2/acl2-6.3.ebuild          | 69 ---------------------------
 sci-mathematics/acl2/acl2-7.0.ebuild          | 50 +++++++++++++++++++
 sci-mathematics/acl2/files/set-booksdir.patch | 11 -----
 sci-mathematics/acl2/metadata.xml             | 20 +++-----
 6 files changed, 64 insertions(+), 99 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     9aa7e57931b32f77ea8ee5343c2835c51edf2837
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 28 16:40:10 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Mar 28 16:40:10 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9aa7e579

Merge pull request #393 from SoapZaNet/emboss

Updated emboss-r1.eclass and all embassy/emboss packages to confirm to QA

 eclass/emboss-r1.eclass                               | 19 ++++---------------
 .../embassy-cbstools-1.0.0.650.ebuild                 |  2 ++
 .../embassy-clustalomega-1.1.0.ebuild                 |  2 ++
 .../embassy-domainatrix-0.1.650.ebuild                |  2 ++
 .../embassy-domalign/embassy-domalign-0.1.650.ebuild  |  2 ++
 .../embassy-domsearch-0.1.650.ebuild                  |  2 ++
 sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild |  2 ++
 .../embassy-esim4/embassy-esim4-1.0.0.650.ebuild      |  2 ++
 .../embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild      |  2 ++
 .../embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild  |  2 ++
 sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild  |  2 ++
 sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild  |  2 ++
 .../embassy-phylipnew-3.69.650.ebuild                 |  2 ++
 .../embassy-signature-0.1.650.ebuild                  |  2 ++
 .../embassy-structure-0.1.650.ebuild                  |  2 ++
 sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild  |  2 ++
 .../embassy-vienna/embassy-vienna-1.7.2.650.ebuild    |  2 ++
 sci-biology/emboss/emboss-6.6.0.ebuild                |  2 ++
 18 files changed, 38 insertions(+), 15 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a6cdd47a7b3ac13d3a10e70139206d9ed57a9dd7
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 28 09:55:25 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Mar 28 09:55:25 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a6cdd47a

Merge pull request #392 from hmmr/master

install binaries in /usr/bin not /bin

 sci-biology/aghermann/ChangeLog                                        | 3 +++
 .../aghermann/{aghermann-1.0.3.ebuild => aghermann-1.0.3-r1.ebuild}    | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6d7ea7b0c0da5ee464838a3e10262c2f712eaa59
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Mar 25 17:34:15 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Mar 25 17:34:15 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6d7ea7b0

Merge remote-tracking branch 'github/master'

* github/master: (55 commits)
  sci-libs/arrayfire: Drop patch, fixed upstream
  sci-libs/arrayfire: Enable OpenCL backend
  sci-libs/armadillo: Version bump
  sci-libs/arrayfire: Add ~amd64 keyword to 3.0_beta
  sci-libs/clblas: Fix homepage
  dev-util/amdapp: Add 3.0_beta
  sci-libs/clblas: Fix client installation
  sci-libs/clblas: New package
  sci-libs/arrayfire: Add 3.0_beta
  sci-libs/arrayfire: Drop patches, fix ebuild
  sci-biology/est2uni: Drop keywords (php:5.3 is hardmasked)
  installing into octave M subdirectory
  installing ALL the things
  typo
  fixed doins path
  removed slots, added new version
  added quotation marks, removed ori file
  added metadata
  inlined URI_BASE
  Minor improvements + added metadata.xml
  ...

 dev-util/amdapp/ChangeLog                          |  6 +++
 dev-util/amdapp/Manifest                           |  2 +
 ...{amdapp-2.9.1.ebuild => amdapp-3.0_beta.ebuild} | 10 ++--
 sci-biology/est2uni/ChangeLog                      |  6 ++-
 sci-biology/est2uni/est2uni-0.27.ebuild            |  4 +-
 sci-biology/spm/ChangeLog                          | 27 +++++++++++
 sci-biology/spm/Manifest                           |  2 +
 {x11-libs/tr => sci-biology/spm}/metadata.xml      |  0
 sci-biology/spm/spm-12.ebuild                      | 36 ++++++++++++++
 sci-biology/spm/spm-8.ebuild                       | 40 ++++++++++++++++
 sci-libs/armadillo/ChangeLog                       |  6 +++
 sci-libs/armadillo/Manifest                        |  1 +
 ...llo-4.650.2.ebuild => armadillo-4.650.4.ebuild} |  0
 sci-libs/arrayfire/ChangeLog                       | 20 ++++++++
 ...ire-0.9999.ebuild => arrayfire-3.0_beta.ebuild} |  0
 sci-libs/arrayfire/arrayfire-9999.ebuild           | 20 +++++---
 sci-libs/arrayfire/files/FindBoostCompute.patch    | 34 +++++++++++++
 .../arrayfire-0.9999-CMakeLists_examples.patch     | 15 ------
 .../files/arrayfire-0.9999-build_gtest.patch       | 55 ----------------------
 .../files/arrayfire-9999-CMakeLists_examples.patch | 14 ------
 sci-libs/arrayfire/files/opencl_CMakeLists.patch   | 26 ++++++++++
 sci-libs/arrayfire/metadata.xml                    |  3 ++
 sci-libs/clblas/ChangeLog                          | 16 +++++++
 sci-libs/clblas/Manifest                           |  1 +
 sci-libs/clblas/clblas-2.2.ebuild                  |  1 +
 .../clblas-9999.ebuild}                            | 29 ++++++++----
 .../clblas/files/clblas-client_CMakeLists.patch    | 11 +++++
 .../clblas-library_tools_tune_CMakeLists.patch     | 14 ++++++
 .../clblas/files/clblas-samples_CMakeLists.patch   | 20 ++++++++
 .../files/clblas-scripts_perf_CMakeLists.patch}    |  6 +--
 sci-libs/clblas/metadata.xml                       | 23 +++++++++
 31 files changed, 334 insertions(+), 114 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b351b4895ebb6d3c93b1339170bd6fee08532baf
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Mar 23 08:10:18 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Mar 23 08:10:18 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b351b489

Merge remote-tracking branch 'github/master'

* github/master:
  app-forensics/vine: Drop keywords, since gmetadom is hardmasked

 app-forensics/vine/ChangeLog       | 3 +++
 app-forensics/vine/vine-1.0.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     e563f4cbbde41c690dc1cb47489e638faebba9cf
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Mar 23 08:10:07 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Mar 23 08:10:07 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e563f4cb

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/acml: Fix #543740 (drop fma4)
  Fixed upstream bug https://github.com/broadinstitute/IGV/issues/114 as requested by Martin Mokrejŝ (note: i've excluded the test code by passing -Dnotests=true to ant so it may break at some point).

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/igv/ChangeLog          |  10 ++++
 sci-biology/igv/Manifest           |   2 +-
 sci-biology/igv/igv-2.3.44.ebuild  | 109 +++++++++++++------------------------
 sci-libs/acml/ChangeLog            |   3 +
 sci-libs/acml/acml-6.1.0.31.ebuild |   3 +-
 5 files changed, 53 insertions(+), 74 deletions(-)

diff --cc sci-biology/igv/ChangeLog
index bb4f3a0,9eb94ff..57365d0
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@@ -2,9 -2,16 +2,19 @@@
  # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
  # $Header: $
  
+   21 Mar 2015; Johann Schmitz <ercpe@gentoo.org> igv-2.3.44.ebuild:
+   Fixed upstream bug https://github.com/broadinstitute/IGV/issues/114 as
+   requested by Martin Mokrejŝ (note: i've excluded the test code by passing
+   -Dnotests=true to ant so it may break at some point).  Also improved the
+   ebuild by unbundling stuff we already have in portage. There are quite a
+   number of libraries which aren't used for compilation which may be needed at
+   runtime. I haven't tested the program in depth: it started at didn't throw
+   errors when i clicked around - everything else is way beyond my knowledge.
+   Improved the ebuild for sci-biology/igv
+ 
 +  21 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.3.44.ebuild:
 +  sci-biology/igv: fix inherit to git-r3
 +
    17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.3.44.ebuild:
    fix inherit to use git instead of previously used subversion
  

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     2eb12e45698dbaaac4a2b54489da343fddef0f2d
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 21 18:19:22 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Mar 21 18:19:22 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2eb12e45

Merge pull request #391 from ercpe/igv

Updated ebuild for sci-biology/igv

 sci-biology/igv/ChangeLog         |  10 ++++
 sci-biology/igv/Manifest          |   2 +-
 sci-biology/igv/igv-2.3.44.ebuild | 109 +++++++++++++-------------------------
 3 files changed, 49 insertions(+), 72 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     5c153b90ea7100f963694354b245fa628263999f
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 20 04:31:22 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Mar 20 04:31:22 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5c153b90

Merge branch 'master' of ssh://github.com/gentoo-science/sci

 dev-util/nvidia-cuda-gdk/ChangeLog                 |  6 +++++
 dev-util/nvidia-cuda-gdk/Manifest                  |  1 +
 ...340.29.ebuild => nvidia-cuda-gdk-346.46.ebuild} | 30 ++++++++--------------
 dev-util/nvidia-cuda-sdk/ChangeLog                 |  6 +++++
 dev-util/nvidia-cuda-sdk/Manifest                  |  1 +
 ...7.0.18.ebuild => nvidia-cuda-sdk-7.0.28.ebuild} | 15 +++--------
 dev-util/nvidia-cuda-toolkit/ChangeLog             |  8 +++++-
 dev-util/nvidia-cuda-toolkit/Manifest              |  1 +
 ...r1.ebuild => nvidia-cuda-toolkit-7.0.28.ebuild} | 23 +++++------------
 9 files changed, 42 insertions(+), 49 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     4d63c0dd3de6ae3c6e66bf36a05666e040377048
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 18 13:05:18 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 18 13:05:18 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4d63c0dd

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

 sci-biology/discrover/ChangeLog                    |  6 ++++++
 sci-biology/discrover/Manifest                     |  2 +-
 ...scrover-1.5.2.ebuild => discrover-1.6.0.ebuild} | 18 ++---------------
 sci-biology/discrover/discrover-9999.ebuild        | 18 ++---------------
 sci-biology/discrover/metadata.xml                 | 23 ++++++++++------------
 5 files changed, 21 insertions(+), 46 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f071dea8b894e9e56284ae7382227e0f15d06fee
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Mar 18 07:23:29 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Mar 18 07:23:29 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f071dea8

Merge remote-tracking branch 'github/master'

* github/master:
  sci-biology/discrover: version bump; drop USE flag

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     8b999163c0142206ffc896ada66052f9ea1ef7f4
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Mar 18 06:44:57 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Mar 18 06:44:57 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8b999163

Merge pull request #390 from maaskola/master

sci-biology/discrover: version bump; drop USE flag

 sci-biology/discrover/ChangeLog                    |  6 ++++++
 sci-biology/discrover/Manifest                     |  2 +-
 ...scrover-1.5.2.ebuild => discrover-1.6.0.ebuild} | 18 ++---------------
 sci-biology/discrover/discrover-9999.ebuild        | 18 ++---------------
 sci-biology/discrover/metadata.xml                 | 23 ++++++++++------------
 5 files changed, 21 insertions(+), 46 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     e3cf7d690aa3003d5ee49c7a9784155a5f784470
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 17 13:21:51 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 17 13:21:51 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e3cf7d69

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

 sci-chemistry/xplor-nih/ChangeLog             | 3 +++
 sci-chemistry/xplor-nih/xplor-nih-2.38.ebuild | 5 ++++-
 2 files changed, 7 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     8a882e8936cff1dd3f3390c13c32a37c9276d6cd
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 14 08:21:04 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Mar 14 08:21:04 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8a882e89

Merge remote-tracking branch 'github/master'

* github/master:
  new licences needed for FSL package
  sci-libs/trilinos: fix location of target config files
  sci-libs/trilinos: version bump, some preliminary metadata
  version bump
  dev-python/jupyter-nbviewer: Fix description

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     7f7a9029dd60e3a14153df8c01bbda8886dd4c69
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 14 08:12:01 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Mar 14 08:12:01 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f7a9029

Merge pull request #389 from TheChymera/licences

new licences (needed for FSL package)

 licenses/FSL    | 94 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 licenses/newmat | 30 ++++++++++++++++++
 2 files changed, 124 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     d4615f23964f114de809008b05f960662df040ca
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Mar 11 07:22:13 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Mar 11 07:22:13 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d4615f23

Merge pull request #386 from Tranquility/remove-neovim

app-editors/neovim is in the tree now

 app-editors/neovim/ChangeLog                | 22 -------------
 app-editors/neovim/metadata.xml             |  5 ---
 app-editors/neovim/neovim-9999.ebuild       | 35 ---------------------
 dev-libs/libtermkey/ChangeLog               |  9 ------
 dev-libs/libtermkey/libtermkey-9999.ebuild  | 22 -------------
 dev-libs/libtermkey/metadata.xml            |  5 ---
 dev-libs/msgpack/ChangeLog                  |  9 ------
 dev-libs/msgpack/metadata.xml               |  5 ---
 dev-libs/msgpack/msgpack-9999.ebuild        | 27 ----------------
 dev-libs/unibilium/ChangeLog                |  9 ------
 dev-libs/unibilium/Manifest                 |  1 -
 dev-libs/unibilium/metadata.xml             |  5 ---
 dev-libs/unibilium/unibilium-1.1.1.ebuild   | 20 ------------
 dev-lua/cmsgpack/ChangeLog                  | 13 --------
 dev-lua/cmsgpack/Manifest                   |  1 -
 dev-lua/cmsgpack/cmsgpack-0.3.0.ebuild      |  1 -
 dev-lua/cmsgpack/cmsgpack-9999.ebuild       | 48 -----------------------------
 dev-lua/cmsgpack/metadata.xml               |  5 ---
 dev-lua/messagepack/ChangeLog               |  9 ------
 dev-lua/messagepack/messagepack-9999.ebuild | 25 ---------------
 dev-lua/messagepack/metadata.xml            |  5 ---
 21 files changed, 281 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     ae81314422d068ab15083b6cfdf8280101a391a9
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar  9 16:44:56 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar  9 16:44:56 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ae813144

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

 sci-physics/hoomd-blue/ChangeLog              | 3 +++
 sci-physics/hoomd-blue/hoomd-blue-9999.ebuild | 1 +
 2 files changed, 4 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     fc8a70b2885e294e18ba22c5a773780fa4b3083c
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar  9 14:50:11 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar  9 14:50:11 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fc8a70b2

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

 dev-tex/pythontex/ChangeLog             |  9 ++++-
 dev-tex/pythontex/Manifest              |  2 +-
 dev-tex/pythontex/pythontex-0.12.ebuild | 70 ---------------------------------
 dev-tex/pythontex/pythontex-0.14.ebuild | 57 +++++++++++++++++++++++++++
 dev-tex/pythontex/pythontex-9999.ebuild | 50 ++++++++++-------------
 5 files changed, 86 insertions(+), 102 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5e896a2cd1336a874799f5b4e9b0bdb9b2add468
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Mar  9 14:04:12 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Mar  9 14:04:12 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5e896a2c

Merge remote-tracking branch 'github/master'

* github/master:
  Remove sci-libs/bliss which is now in the main tree

 sci-libs/bliss/ChangeLog                        |  14 -
 sci-libs/bliss/Manifest                         |   1 -
 sci-libs/bliss/bliss-0.72.ebuild                |  43 --
 sci-libs/bliss/files/bliss-0.72-autotools.patch | 159 ------
 sci-libs/bliss/files/bliss-0.72-fedora.patch    | 648 ------------------------
 sci-libs/bliss/metadata.xml                     |   9 -
 6 files changed, 874 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     d39a77634b01fe5cdbb2cd8981aad09b11420d21
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  8 18:08:55 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  8 18:08:55 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d39a7763

Merge remote-tracking branch 'github/master'

* github/master:
  dev-lang/julia: Add new dependency, fix build.
  cdfplayer: Version bump; Patch is not needed.
  sci-libs/arrayfire: Update patches
  sci-libs/armadillo: Version bump

 dev-lang/julia/ChangeLog                              |  5 ++++-
 dev-lang/julia/julia-9999.ebuild                      |  6 ++++--
 sci-libs/armadillo/ChangeLog                          |  6 ++++++
 sci-libs/armadillo/Manifest                           |  1 +
 ...adillo-4.600.4.ebuild => armadillo-4.650.2.ebuild} |  0
 sci-libs/arrayfire/ChangeLog                          |  8 ++++++++
 sci-libs/arrayfire/arrayfire-9999.ebuild              |  7 +++++--
 ...tch => arrayfire-0.9999-CMakeLists_examples.patch} |  0
 ...gtest.patch => arrayfire-0.9999-build_gtest.patch} |  0
 .../files/arrayfire-9999-CMakeLists_examples.patch    | 14 ++++++++++++++
 sci-mathematics/cdfplayer/ChangeLog                   |  9 +++++++--
 sci-mathematics/cdfplayer/Manifest                    |  2 +-
 ...cdfplayer-9.0.1.ebuild => cdfplayer-10.0.2.ebuild} | 10 +++-------
 .../cdfplayer/files/cdfplayer-9.0.1-installer.patch   | 19 -------------------
 14 files changed, 53 insertions(+), 34 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     387f0bc09564118565d681850260b101943b85f7
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  8 17:38:17 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  8 17:38:17 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=387f0bc0

Merge pull request #384 from ustcscgy/julia

dev-lang/julia: Add new dependency, fix build.

 dev-lang/julia/ChangeLog         | 5 ++++-
 dev-lang/julia/julia-9999.ebuild | 6 ++++--
 2 files changed, 8 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     2c1c888663cc27b51f123e124b5d053cdaf4e749
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  8 17:39:09 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  8 17:39:09 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2c1c8886

Merge pull request #383 from ustcscgy/cdfplayer

cdfplayer: Version bump; Patch is not needed.

 sci-mathematics/cdfplayer/ChangeLog                   |  9 +++++++--
 sci-mathematics/cdfplayer/Manifest                    |  2 +-
 ...cdfplayer-9.0.1.ebuild => cdfplayer-10.0.2.ebuild} | 10 +++-------
 .../cdfplayer/files/cdfplayer-9.0.1-installer.patch   | 19 -------------------
 4 files changed, 11 insertions(+), 29 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     b2c9731539d5bc50db97693dbef0a88de5c3cef9
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Mar  6 18:51:37 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Mar  6 18:51:37 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b2c97315

Merge branch 'master' of ssh://github.com/gentoo-science/sci

[gentoo-commits] proj/sci:master commit in: /

[git@oystercatcher mirror+tproxy]

commit:     9108d6ef60b7214bbffd62d1f335e1abe305659a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar  3 15:17:05 2015 +0000
Commit:     git@oystercatcher mirror+tproxy <git <AT> oystercatcher <DOT> gentoo <DOT> org>
CommitDate: Tue Mar  3 15:17:05 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9108d6ef

Merge remote-tracking branch 'github/master'

* github/master:
  Remove myself as maintainer
  dev-python/simplepam: Initial ebuild
  dev-python/jupyter-nbviewer: Correct license
  dev-python/jupyter-nbviewer: Initial ebuild
  dev-python/newrelic: Initial ebuild
  dev-python/jupyter-nbgrader: Update requirements
  dev-python/jupyter-nbgrader: Initial ebuild
  dev-util/amdapp: Minor fixes
  dev-util/amdapp-2.9.1: Remove trailing whitespace
  Add AMD-APPSDK license
  dev-util/amdapp-2.9.1: Version bump

 dev-python/jupyter-nbgrader/ChangeLog              |   9 +
 .../jupyter-nbgrader/jupyter-nbgrader-9999.ebuild  |  32 +++
 .../jupyter-nbgrader}/metadata.xml                 |   4 +-
 dev-python/jupyter-nbviewer/ChangeLog              |   9 +
 .../jupyter-nbviewer/jupyter-nbviewer-9999.ebuild  |  35 +++
 dev-python/jupyter-nbviewer/metadata.xml           |  10 +
 dev-python/newrelic/ChangeLog                      |   9 +
 dev-python/newrelic/Manifest                       |   1 +
 .../bbscp => dev-python/newrelic}/metadata.xml     |   5 +-
 dev-python/newrelic/newrelic-2.44.0.36.ebuild      |  35 +++
 dev-python/simplepam/ChangeLog                     |  10 +
 dev-python/simplepam/Manifest                      |   1 +
 dev-python/simplepam/metadata.xml                  |  11 +
 dev-python/simplepam/simplepam-0.1.5.ebuild        |   1 +
 .../simplepam-9999.ebuild}                         |   9 +-
 dev-util/amdapp/ChangeLog                          |   6 +
 dev-util/amdapp/Manifest                           |   2 +
 .../{amdapp-2.9.ebuild => amdapp-2.9.1.ebuild}     |  40 ++-
 licenses/AMD-APPSDK                                | 267 +++++++++++++++++++++
 profiles/license_groups                            |   2 +-
 20 files changed, 465 insertions(+), 33 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     9108d6ef60b7214bbffd62d1f335e1abe305659a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar  3 15:17:05 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar  3 15:17:05 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9108d6ef

Merge remote-tracking branch 'github/master'

* github/master:
  Remove myself as maintainer
  dev-python/simplepam: Initial ebuild
  dev-python/jupyter-nbviewer: Correct license
  dev-python/jupyter-nbviewer: Initial ebuild
  dev-python/newrelic: Initial ebuild
  dev-python/jupyter-nbgrader: Update requirements
  dev-python/jupyter-nbgrader: Initial ebuild
  dev-util/amdapp: Minor fixes
  dev-util/amdapp-2.9.1: Remove trailing whitespace
  Add AMD-APPSDK license
  dev-util/amdapp-2.9.1: Version bump

 dev-python/jupyter-nbgrader/ChangeLog              |   9 +
 .../jupyter-nbgrader/jupyter-nbgrader-9999.ebuild  |  32 +++
 .../jupyter-nbgrader}/metadata.xml                 |   4 +-
 dev-python/jupyter-nbviewer/ChangeLog              |   9 +
 .../jupyter-nbviewer/jupyter-nbviewer-9999.ebuild  |  35 +++
 dev-python/jupyter-nbviewer/metadata.xml           |  10 +
 dev-python/newrelic/ChangeLog                      |   9 +
 dev-python/newrelic/Manifest                       |   1 +
 .../bbscp => dev-python/newrelic}/metadata.xml     |   5 +-
 dev-python/newrelic/newrelic-2.44.0.36.ebuild      |  35 +++
 dev-python/simplepam/ChangeLog                     |  10 +
 dev-python/simplepam/Manifest                      |   1 +
 dev-python/simplepam/metadata.xml                  |  11 +
 dev-python/simplepam/simplepam-0.1.5.ebuild        |   1 +
 .../simplepam-9999.ebuild}                         |   9 +-
 dev-util/amdapp/ChangeLog                          |   6 +
 dev-util/amdapp/Manifest                           |   2 +
 .../{amdapp-2.9.ebuild => amdapp-2.9.1.ebuild}     |  40 ++-
 licenses/AMD-APPSDK                                | 267 +++++++++++++++++++++
 profiles/license_groups                            |   2 +-
 20 files changed, 465 insertions(+), 33 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[git@oystercatcher mirror+tproxy]

commit:     b4fb40750a0bb7037385811a4381490bb1d2704f
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar  3 09:31:06 2015 +0000
Commit:     git@oystercatcher mirror+tproxy <git <AT> oystercatcher <DOT> gentoo <DOT> org>
CommitDate: Tue Mar  3 09:31:06 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b4fb4075

Merge pull request #358 from marbre/amdapp

dev-util/amdapp-2.9.1: Version bump

 dev-util/amdapp/ChangeLog                          |   6 +
 dev-util/amdapp/Manifest                           |   2 +
 .../{amdapp-2.9.ebuild => amdapp-2.9.1.ebuild}     |  40 ++-
 licenses/AMD-APPSDK                                | 267 +++++++++++++++++++++
 profiles/license_groups                            |   2 +-
 5 files changed, 294 insertions(+), 23 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     b4fb40750a0bb7037385811a4381490bb1d2704f
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar  3 09:31:06 2015 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gentoo <DOT> org>
CommitDate: Tue Mar  3 09:31:06 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b4fb4075

Merge pull request #358 from marbre/amdapp

dev-util/amdapp-2.9.1: Version bump

 dev-util/amdapp/ChangeLog                          |   6 +
 dev-util/amdapp/Manifest                           |   2 +
 .../{amdapp-2.9.ebuild => amdapp-2.9.1.ebuild}     |  40 ++-
 licenses/AMD-APPSDK                                | 267 +++++++++++++++++++++
 profiles/license_groups                            |   2 +-
 5 files changed, 294 insertions(+), 23 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     ecec4f277c5210b0111140aa7e7b42c7f58538f8
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar  2 22:36:03 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar  2 22:36:03 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ecec4f27

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-physics/hoomd/ChangeLog         |  9 ------
 sci-physics/hoomd/hoomd-9999.ebuild | 61 -------------------------------------
 sci-physics/hoomd/metadata.xml      | 12 --------
 3 files changed, 82 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Andrew Savchenko]

commit:     074b786bd0b3751b9bb6a0498d224485dc840608
Author:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
AuthorDate: Mon Mar  2 07:15:03 2015 +0000
Commit:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
CommitDate: Mon Mar  2 07:15:03 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=074b786b

Merge remote-tracking branch 'github/master'


 sci-misc/kaldi/ChangeLog                           |   7 +
 sci-misc/kaldi/files/Makefile.patch                |  76 +++++++---
 sci-misc/kaldi/files/configure.patch               | 164 ++++++++++++---------
 sci-misc/kaldi/files/default_rules.mk.patch        |  67 ++++++---
 ...0_p20150101.ebuild => kaldi-0_p20150301.ebuild} |   5 +-
 5 files changed, 206 insertions(+), 113 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Andrew Savchenko]

commit:     dc35bdab320ee35baaac9d1f02ccf65a357e9d64
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Sun Mar  1 14:47:30 2015 +0000
Commit:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
CommitDate: Sun Mar  1 14:47:30 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=dc35bdab

Merge pull request #379 from akreal/kaldi

sci-misc/kaldi: version bump


 sci-misc/kaldi/ChangeLog                           |   7 +
 sci-misc/kaldi/files/Makefile.patch                |  76 +++++++---
 sci-misc/kaldi/files/configure.patch               | 164 ++++++++++++---------
 sci-misc/kaldi/files/default_rules.mk.patch        |  67 ++++++---
 ...0_p20150101.ebuild => kaldi-0_p20150301.ebuild} |   5 +-
 5 files changed, 206 insertions(+), 113 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     4c7b23989ecc6aa745f804657a4799543a43b162
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 28 20:53:41 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Feb 28 20:53:41 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4c7b2398

Merge pull request #377 from akreal/openfst

sci-misc/openfst: version bump


 sci-misc/openfst/ChangeLog                         |   8 +-
 sci-misc/openfst/Manifest                          |   1 +
 sci-misc/openfst/files/kaldi-openfst-1.4.1.patch   | 269 +++++++++++++++++++++
 .../{openfst-1.3.4.ebuild => openfst-1.4.1.ebuild} |  11 +-
 4 files changed, 280 insertions(+), 9 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     d7e0b7bc32f5c04146e182d999621801b3c53a07
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 28 20:53:07 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Feb 28 20:53:07 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d7e0b7bc

Merge pull request #378 from akreal/irstlm

sci-misc/irstlm: version bump


 sci-misc/irstlm/ChangeLog                             |  8 +++++++-
 sci-misc/irstlm/Manifest                              |  3 +--
 sci-misc/irstlm/irstlm-5.80.03.ebuild                 | 19 -------------------
 .../{irstlm-5.80.06.ebuild => irstlm-5.80.08.ebuild}  |  2 +-
 4 files changed, 9 insertions(+), 23 deletions(-)

[gentoo-commits] proj/sci:jlec commit in: /

[Justin Lecher]

commit:     e9d619a1095be583da8ca672892c349aa0f61bb4
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 12 13:07:49 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec 12 13:07:49 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e9d619a1

Merge pull request #300 from marbre/mendeleydesktop

sci-misc/mendeleydesktop: Version bump; Drop old


 sci-misc/mendeleydesktop/ChangeLog                                 | 6 ++++++
 sci-misc/mendeleydesktop/Manifest                                  | 7 ++-----
 ...mendeleydesktop-1.12.3.ebuild => mendeleydesktop-1.12.4.ebuild} | 0
 3 files changed, 8 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     e9d619a1095be583da8ca672892c349aa0f61bb4
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 12 13:07:49 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec 12 13:07:49 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e9d619a1

Merge pull request #300 from marbre/mendeleydesktop

sci-misc/mendeleydesktop: Version bump; Drop old


 sci-misc/mendeleydesktop/ChangeLog                                 | 6 ++++++
 sci-misc/mendeleydesktop/Manifest                                  | 7 ++-----
 ...mendeleydesktop-1.12.3.ebuild => mendeleydesktop-1.12.4.ebuild} | 0
 3 files changed, 8 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:jlec commit in: /

[Justin Lecher]

commit:     f55ccd4941f3bdda4e9e7955efbdc4d3a0bbebf8
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Nov 30 13:24:29 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Nov 30 13:24:29 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f55ccd49

Merge pull request #291 from marbre/mendeleydesktop

sci-misc/mendeleydesktop: add ebuild to overlay


 licenses/Mendeley-EULA                             | 264 +++++++++++++++++++++
 sci-misc/mendeleydesktop/ChangeLog                 |  16 ++
 sci-misc/mendeleydesktop/Manifest                  |   5 +
 .../mendeleydesktop/mendeleydesktop-1.12.3.ebuild  | 121 ++++++++++
 sci-misc/mendeleydesktop/metadata.xml              |  10 +
 5 files changed, 416 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f55ccd4941f3bdda4e9e7955efbdc4d3a0bbebf8
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Nov 30 13:24:29 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Nov 30 13:24:29 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f55ccd49

Merge pull request #291 from marbre/mendeleydesktop

sci-misc/mendeleydesktop: add ebuild to overlay


 licenses/Mendeley-EULA                             | 264 +++++++++++++++++++++
 sci-misc/mendeleydesktop/ChangeLog                 |  16 ++
 sci-misc/mendeleydesktop/Manifest                  |   5 +
 .../mendeleydesktop/mendeleydesktop-1.12.3.ebuild  | 121 ++++++++++
 sci-misc/mendeleydesktop/metadata.xml              |  10 +
 5 files changed, 416 insertions(+)

[gentoo-commits] proj/sci:jlec commit in: /

[Justin Lecher]

commit:     ba003a295a68fcd2130aeffa316626413c673078
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Dec  1 15:41:05 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec  1 15:41:05 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ba003a29

Merge pull request #298 from maaskola/add-discrover-ebuilds

Add discrover ebuilds


 sci-biology/discrover/Manifest               |  1 +
 sci-biology/discrover/discrover-1.1.2.ebuild | 74 ++++++++++++++++++++++++++++
 sci-biology/discrover/discrover-9999.ebuild  | 74 ++++++++++++++++++++++++++++
 sci-biology/discrover/metadata.xml           | 22 +++++++++
 4 files changed, 171 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ba003a295a68fcd2130aeffa316626413c673078
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Dec  1 15:41:05 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec  1 15:41:05 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ba003a29

Merge pull request #298 from maaskola/add-discrover-ebuilds

Add discrover ebuilds


 sci-biology/discrover/Manifest               |  1 +
 sci-biology/discrover/discrover-1.1.2.ebuild | 74 ++++++++++++++++++++++++++++
 sci-biology/discrover/discrover-9999.ebuild  | 74 ++++++++++++++++++++++++++++
 sci-biology/discrover/metadata.xml           | 22 +++++++++
 4 files changed, 171 insertions(+)

[gentoo-commits] proj/sci:jlec commit in: /

[Justin Lecher]

commit:     de7795666ba00a29293946aebd7d42b7eaf46986
Author:     Jauhien Piatlicki <piatlicki <AT> gmail <DOT> com>
AuthorDate: Tue Nov 18 14:55:51 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Nov 18 14:55:51 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=de779566

Merge pull request #281 from akreal/master

sci-misc/irstlm: version bump


 sci-misc/irstlm/ChangeLog                                        | 8 +++++++-
 sci-misc/irstlm/Manifest                                         | 1 +
 sci-misc/irstlm/{irstlm-5.80.03.ebuild => irstlm-5.80.06.ebuild} | 6 ++++--
 3 files changed, 12 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     de7795666ba00a29293946aebd7d42b7eaf46986
Author:     Jauhien Piatlicki <piatlicki <AT> gmail <DOT> com>
AuthorDate: Tue Nov 18 14:55:51 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Nov 18 14:55:51 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=de779566

Merge pull request #281 from akreal/master

sci-misc/irstlm: version bump


 sci-misc/irstlm/ChangeLog                                        | 8 +++++++-
 sci-misc/irstlm/Manifest                                         | 1 +
 sci-misc/irstlm/{irstlm-5.80.03.ebuild => irstlm-5.80.06.ebuild} | 6 ++++--
 3 files changed, 12 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     21edb154828b67d9691d4e0be367293e64bca9bc
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 21 20:05:58 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Feb 21 20:05:58 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=21edb154

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 sci-libs/symmetrica/Manifest                 | 2 +-
 sci-libs/symmetrica/symmetrica-2.0-r1.ebuild | 6 +++---
 sci-libs/symmetrica/symmetrica-2.0.ebuild    | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     26d988084d0691b919a48bba793ebf7e4f10d5dd
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Fri Feb 20 21:53:45 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Feb 20 21:53:45 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=26d98808

Merge pull request #371 from Tranquility/fix-neovim

Fix neovim deps


 app-editors/neovim/ChangeLog                      |  3 +++
 app-editors/neovim/neovim-9999.ebuild             | 30 +++++++++++------------
 dev-libs/libtermkey/ChangeLog                     |  9 +++++++
 dev-libs/libtermkey/libtermkey-9999.ebuild        | 22 +++++++++++++++++
 {x11-libs/tr => dev-libs/libtermkey}/metadata.xml |  0
 dev-libs/msgpack/ChangeLog                        |  9 +++++++
 {x11-libs/tr => dev-libs/msgpack}/metadata.xml    |  0
 dev-libs/msgpack/msgpack-9999.ebuild              | 27 ++++++++++++++++++++
 dev-libs/unibilium/ChangeLog                      |  9 +++++++
 dev-libs/unibilium/Manifest                       |  1 +
 {x11-libs/tr => dev-libs/unibilium}/metadata.xml  |  0
 dev-libs/unibilium/unibilium-1.1.1.ebuild         | 20 +++++++++++++++
 dev-lua/messagepack/ChangeLog                     |  9 +++++++
 dev-lua/messagepack/messagepack-9999.ebuild       | 25 +++++++++++++++++++
 {x11-libs/tr => dev-lua/messagepack}/metadata.xml |  0
 15 files changed, 148 insertions(+), 16 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     83840064f51bf3a91b94f5876d377bd1f85b18bd
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 20 16:57:32 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Feb 20 16:57:32 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=83840064

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 dev-python/astropysics/ChangeLog               | 7 +++++--
 dev-python/astropysics/astropysics-9999.ebuild | 4 ++--
 2 files changed, 7 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     af76a81827de658084ad2e85269bb605b23a1725
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 20 02:02:39 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Feb 20 02:02:39 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=af76a818

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 sci-libs/arrayfire/ChangeLog                   | 3 +++
 sci-libs/arrayfire/arrayfire-9999.ebuild       | 2 +-
 sci-libs/clfft/ChangeLog                       | 3 +++
 sci-libs/clfft/clfft-9999.ebuild               | 2 +-
 sci-mathematics/freefem++/ChangeLog            | 5 ++++-
 sci-mathematics/freefem++/Manifest             | 2 +-
 sci-mathematics/freefem++/freefem++-3.8.ebuild | 6 +++---
 7 files changed, 16 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     5411dfbeb8c13e8eb5eb0f8d4bf5e8eb0718d0b8
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Thu Feb 19 16:03:04 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Feb 19 16:03:04 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5411dfbe

Merge pull request #375 from hmmr/master

sci-biology/aghermann: make it repoman clean


 sci-biology/aghermann/ChangeLog              | 2 +-
 sci-biology/aghermann/aghermann-1.0.3.ebuild | 7 +++----
 2 files changed, 4 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     b46449a0730b60d7e4e4bdb30deeaac07a8929f5
Author:     Andrei Zavada <johnhommer <AT> gmail <DOT> com>
AuthorDate: Thu Feb 19 13:18:17 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Feb 19 13:18:17 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b46449a0

Merge branch 'master' of github.com:gentoo-science/sci

# Conflicts:
#	sci-biology/aghermann/ChangeLog
#	sci-biology/aghermann/aghermann-1.0.3.ebuild


 .travis.yml                                        |  29 ++---
 app-forensics/vine/ChangeLog                       |   5 +-
 app-forensics/vine/metadata.xml                    |   8 +-
 app-forensics/vine/vine-1.0.ebuild                 |   3 +-
 dev-cpp/eigen/ChangeLog                            |   6 +-
 dev-cpp/eigen/Manifest                             |   2 -
 dev-cpp/eigen/eigen-3.2.0-r1.ebuild                | 102 -----------------
 dev-cpp/eigen/eigen-9999.ebuild                    |   4 +-
 dev-cpp/eigen/metadata.xml                         |  18 +--
 dev-java/hdf-java/ChangeLog                        |   6 +-
 dev-java/hdf-java/hdf-java-2.9.ebuild              |   4 +-
 dev-java/hdf-java/metadata.xml                     |  12 +-
 dev-lang/conceptual/ChangeLog                      |   6 +-
 dev-lang/conceptual/conceptual-1.4.ebuild          |   8 +-
 dev-lang/conceptual/metadata.xml                   |  14 +--
 dev-lang/path64/ChangeLog                          |   6 +-
 dev-lang/path64/path64-9999.ebuild                 |   5 +-
 dev-lua/cmsgpack/ChangeLog                         |   5 +-
 dev-lua/cmsgpack/cmsgpack-0.3.0.ebuild             |  49 +--------
 dev-lua/cmsgpack/cmsgpack-9999.ebuild              |  30 ++---
 dev-ml/mlgmpidl/ChangeLog                          |   7 +-
 dev-ml/mlgmpidl/metadata.xml                       |  10 +-
 dev-ml/mlgmpidl/mlgmpidl-1.1.ebuild                |  50 ++++-----
 dev-ml/zarith/ChangeLog                            |   6 +-
 dev-ml/zarith/metadata.xml                         |  10 +-
 dev-ml/zarith/zarith-1.2.1.ebuild                  |  27 +++--
 dev-python/omniorbpy/ChangeLog                     |   6 +-
 dev-python/omniorbpy/omniorbpy-3.4.ebuild          |  12 +-
 dev-python/pythonocc/ChangeLog                     |   6 +-
 dev-python/pythonocc/pythonocc-0.5.ebuild          |   6 +-
 dev-util/amdapp/ChangeLog                          |   4 +
 dev-util/amdapp/Manifest                           |   2 -
 dev-util/amdapp/amdapp-2.8.ebuild                  |  89 ---------------
 dev-util/amdapp/amdapp-2.9.ebuild                  |  12 +-
 dev-util/amdapp/metadata.xml                       |   4 +-
 dev-util/numdiff/ChangeLog                         |   6 +-
 dev-util/numdiff/metadata.xml                      |  12 +-
 dev-util/numdiff/numdiff-5.8.1.ebuild              |  11 +-
 dev-util/nvidia-cuda-toolkit/ChangeLog             |   6 +
 ...ebuild => nvidia-cuda-toolkit-7.0.18-r1.ebuild} |   2 +
 eclass/emboss-r1.eclass                            |   2 +-
 net-ftp/bbftp-client/ChangeLog                     |   6 +-
 net-ftp/bbftp-client/bbftp-client-3.2.1.ebuild     |   6 +-
 net-ftp/bbftp-server/ChangeLog                     |   6 +-
 net-ftp/bbftp-server/bbftp-server-3.2.1.ebuild     |   6 +-
 profiles/categories                                | 121 +--------------------
 sci-astronomy/astrometry/ChangeLog                 |   6 +-
 sci-astronomy/astrometry/astrometry-0.43.ebuild    |  22 ++--
 sci-astronomy/astrometry/metadata.xml              |  10 +-
 sci-astronomy/stiff/ChangeLog                      |   5 +-
 sci-astronomy/stiff/metadata.xml                   |   4 +-
 sci-astronomy/stiff/stiff-9999.ebuild              |   4 +-
 sci-biology/Atlas2/Atlas2-1.4.3.ebuild             |   4 +-
 sci-biology/Atlas2/ChangeLog                       |   6 +-
 sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild |   9 +-
 sci-biology/Atlas_GapFill/ChangeLog                |   4 +-
 sci-biology/BBmap/BBmap-31.40.ebuild               |   6 +-
 sci-biology/BBmap/ChangeLog                        |   5 +-
 sci-biology/BG7/BG7-9999.ebuild                    |   6 +-
 sci-biology/BG7/ChangeLog                          |   6 +-
 sci-biology/BamView/BamView-1.2.11.ebuild          |   7 +-
 sci-biology/BamView/ChangeLog                      |   6 +-
 sci-biology/BamView/metadata.xml                   |   8 +-
 sci-biology/MagicViewer/ChangeLog                  |   6 +-
 sci-biology/MagicViewer/MagicViewer-1.2.1.ebuild   |  12 +-
 sci-biology/MagicViewer/metadata.xml               |  10 +-
 sci-biology/VarScan/ChangeLog                      |   6 +-
 sci-biology/VarScan/VarScan-2.3.6.ebuild           |   9 +-
 sci-biology/VarScan/metadata.xml                   |   2 +-
 sci-biology/ampliconnoise/ChangeLog                |   4 +-
 .../ampliconnoise/ampliconnoise-1.27.ebuild        |   7 +-
 sci-biology/apollo/ChangeLog                       |   5 +-
 sci-biology/apollo/apollo-9999.ebuild              |  19 ++--
 sci-biology/apollo/metadata.xml                    |  10 +-
 sci-biology/artemis/ChangeLog                      |   5 +-
 sci-biology/artemis/artemis-9999.ebuild            |  12 +-
 sci-biology/biopieces/ChangeLog                    |   5 +-
 sci-biology/biopieces/Manifest                     |   1 -
 sci-biology/biopieces/biopieces-0.51.ebuild        |  64 +----------
 sci-biology/biopieces/biopieces-9999.ebuild        |  49 +++++----
 sci-biology/cgview-bin/ChangeLog                   |   5 +-
 sci-biology/cgview-bin/cgview-bin-20131130.ebuild  |  34 +++---
 sci-biology/discrover/ChangeLog                    |   4 +
 sci-biology/discrover/discrover-1.5.2.ebuild       |  28 +++--
 sci-biology/discrover/discrover-9999.ebuild        |  29 +++--
 sci-biology/discrover/metadata.xml                 |  24 ++--
 sci-biology/igv/ChangeLog                          |   6 +-
 sci-biology/igv/igv-2.0.32.ebuild                  |  35 ------
 sci-biology/igv/igv-2.0.35.ebuild                  |  20 ++--
 sci-biology/igv/metadata.xml                       |  10 +-
 sci-biology/jtreeview/ChangeLog                    |   6 +
 sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild     |   9 +-
 sci-biology/mrbayes/ChangeLog                      |   6 +-
 sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild        |   4 +-
 sci-biology/ncbi-blast+/ChangeLog                  |   3 +
 sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild  |  16 ++-
 sci-biology/ncbi-tools++/ChangeLog                 |   5 +-
 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        |  18 +--
 sci-biology/ngsview/ChangeLog                      |   5 +-
 sci-biology/ngsview/ngsview-0.91.ebuild            |  23 ++--
 sci-biology/psychopy/ChangeLog                     |   7 +-
 sci-biology/psychopy/Manifest                      |   2 -
 sci-biology/psychopy/psychopy-1.75.01.ebuild       |  56 ----------
 sci-biology/psychopy/psychopy-1.77.02.ebuild       |  56 ----------
 sci-biology/psychopy/psychopy-1.78.00.ebuild       |   4 +-
 sci-biology/psychopy/psychopy-9999.ebuild          |   4 +-
 sci-biology/tablet/ChangeLog                       |   4 +
 sci-biology/tablet/tablet-1.13.12.17.ebuild        |  51 ---------
 sci-biology/tablet/tablet-1.14.04.10.ebuild        |  52 +--------
 sci-biology/tablet/tablet-9999.ebuild              |  28 ++---
 sci-biology/trimmomatic/ChangeLog                  |   3 +
 sci-biology/trimmomatic/trimmomatic-0.32.ebuild    |  14 +--
 sci-biology/vague-bin/ChangeLog                    |   3 +
 sci-biology/vague-bin/vague-bin-1.0.5.ebuild       |   9 +-
 sci-libs/clfft/ChangeLog                           |   5 +
 sci-libs/clfft/Manifest                            |   1 +
 .../clfft/{clfft-2.2.ebuild => clfft-2.4.ebuild}   |   0
 sci-libs/libspatialindex/ChangeLog                 |   7 +-
 .../libspatialindex/libspatialindex-1.8.5.ebuild   |  27 ++---
 sci-libs/libspatialindex/metadata.xml              |  10 +-
 sci-visualization/mantid/ChangeLog                 |   7 ++
 sci-visualization/mantid/mantid-3.3.0.ebuild       |  56 ++++++----
 sci-visualization/mantid/metadata.xml              |  28 ++---
 sci-visualization/mayavi/ChangeLog                 |   4 +
 sci-visualization/mayavi/mayavi-4.4.0.ebuild       |   6 +-
 sci-visualization/mayavi/metadata.xml              |   4 +-
 sys-apps/hwloc/ChangeLog                           |  10 ++
 sys-apps/hwloc/hwloc-1.10.1.ebuild                 |   6 +-
 sys-apps/hwloc/metadata.xml                        |  20 ++--
 sys-cluster/htcondor/ChangeLog                     |   4 +
 sys-cluster/htcondor/htcondor-8.0.0.ebuild         |  22 ++--
 sys-cluster/htcondor/htcondor-8.3.2.ebuild         |  19 ++--
 sys-cluster/lustre/ChangeLog                       |   5 +-
 sys-cluster/lustre/lustre-9999.ebuild              |   4 +-
 sys-cluster/mvapich2/ChangeLog                     |   5 +-
 sys-cluster/mvapich2/mvapich2-1.6-r1.ebuild        |   8 +-
 sys-cluster/openmpi/ChangeLog                      |   5 +
 sys-cluster/openmpi/metadata.xml                   |  24 ++--
 sys-cluster/openmpi/openmpi-1.6.5.ebuild           |  10 +-
 sys-cluster/openmpi/openmpi-1.7.3.ebuild           |   8 +-
 sys-cluster/openmpi/openmpi-1.8.1.ebuild           |   8 +-
 sys-cluster/openmpi/openmpi-1.8.3.ebuild           |   8 +-
 sys-cluster/openmpi/openmpi-1.8.4-r2.ebuild        |   6 +-
 143 files changed, 774 insertions(+), 1237 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     0562c682750524ba5abd22e21ec0820a5a1e2795
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Feb 19 13:08:05 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Feb 19 13:08:05 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0562c682

Merge pull request #373 from hmmr/master

initial ebuild for sci-biology/cnrun


 sci-biology/cnrun/ChangeLog          |  6 ++++++
 sci-biology/cnrun/Manifest           |  1 +
 sci-biology/cnrun/cnrun-2.0.2.ebuild | 23 +++++++++++++++++++++++
 sci-biology/cnrun/metadata.xml       | 29 +++++++++++++++++++++++++++++
 4 files changed, 59 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     ba04a1798863df111422eb2d4f6c8f3623aea67a
Author:     Andrei Zavada <johnhommer <AT> gmail <DOT> com>
AuthorDate: Wed Feb 18 01:22:54 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 01:22:54 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ba04a179

Merge branch 'master' of github.com:gentoo-science/sci


 dev-libs/boost/ChangeLog                           |  17 +
 dev-libs/boost/Manifest                            |   1 +
 dev-libs/boost/boost-1.56.0-r2.ebuild              | 398 +++++++++++++++++++++
 .../files/boost-1.48.0-disable_icu_rpath.patch     |  29 ++
 .../boost-1.48.0-disable_libboost_python3.patch    |  62 ++++
 .../boost-1.48.0-no_strict_aliasing_python2.patch  |  23 ++
 .../boost/files/boost-1.48.0-python_linking.patch  |  24 ++
 .../boost-1.51.0-respect_python-buildid.patch      |  69 ++++
 ...ost-1.51.0-support_dots_in_python-buildid.patch |  22 ++
 dev-libs/boost/files/boost-1.52.0-threads.patch    |  63 ++++
 .../boost/files/boost-1.55.0-context-x32.patch     |  42 +++
 .../files/boost-1.55.0-tools-c98-compat.patch      |  17 +
 .../files/boost-1.56.0-build-auto_index-tool.patch |  13 +
 dev-libs/boost/metadata.xml                        |  38 ++
 sci-biology/HTSeq/ChangeLog                        |  12 +
 sci-biology/HTSeq/HTSeq-0.6.1.ebuild               |  23 ++
 sci-biology/HTSeq/Manifest                         |   1 +
 sci-biology/{zmsort => HTSeq}/metadata.xml         |   0
 sci-biology/mip-scaffolder/ChangeLog               |  12 +
 sci-biology/mip-scaffolder/Manifest                |   1 +
 .../{zmsort => mip-scaffolder}/metadata.xml        |   0
 .../mip-scaffolder/mip-scaffolder-0.6.ebuild       |  32 ++
 sci-biology/transdecoder/ChangeLog                 |   4 +
 .../transdecoder/transdecoder-20140704.ebuild      |   2 +-
 sci-chemistry/nwchem/ChangeLog                     |   8 +
 sci-chemistry/nwchem/Manifest                      |   2 +
 .../files/nwchem-6.5-icosahedron_zcoord.patch      |  12 +
 ...26243-r5.ebuild => nwchem-6.5_p26243-r6.ebuild} |   7 +-
 sci-libs/fftw/ChangeLog                            |   5 +
 sci-libs/fftw/Manifest                             |   1 +
 .../{fftw-9999.ebuild => fftw-3.3.4-r1.ebuild}     |  54 +--
 sys-apps/hwloc/ChangeLog                           | 230 ++++++++++++
 sys-apps/hwloc/Manifest                            |   1 +
 sys-apps/hwloc/files/hwloc-1.8.1-gl.patch          |  11 +
 sys-apps/hwloc/hwloc-1.10.1.ebuild                 |  69 ++++
 sys-apps/hwloc/metadata.xml                        |  21 ++
 sys-cluster/mpich/ChangeLog                        |   8 +-
 sys-cluster/mpich/Manifest                         |   1 +
 .../{mpich-3.0.4.ebuild => mpich-3.1.3-r1.ebuild}  |  67 ++--
 sys-cluster/mpich2/ChangeLog                       |   8 +-
 .../{mpich2-1.5.ebuild => mpich2-1.5-r1.ebuild}    |  75 ++--
 sys-cluster/openmpi/ChangeLog                      |  11 +-
 sys-cluster/openmpi/Manifest                       |   1 +
 sys-cluster/openmpi/files/openmpi-ltdl.patch       |  78 ++++
 ...penmpi-1.8.3.ebuild => openmpi-1.8.4-r2.ebuild} |  96 ++---
 sys-process/numactl/ChangeLog                      |  10 +
 sys-process/numactl/Manifest                       |   1 +
 .../numactl/files/numactl-2.0.8-cpuid-pic.patch    |  17 +
 .../jrosetta => sys-process/numactl}/metadata.xml  |   2 +-
 sys-process/numactl/numactl-2.0.10-r1.ebuild       |  49 +++
 virtual/mpi/ChangeLog                              |   7 +-
 virtual/mpi/mpi-2.0-r4.ebuild                      |  25 ++
 52 files changed, 1624 insertions(+), 158 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     31bdf6865583c59d43ed095643cfb90b51a67fcd
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 09:52:00 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 09:52:00 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=31bdf686

Serial travis

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 .travis.yml | 27 +--------------------------
 1 file changed, 1 insertion(+), 26 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 1f584b0..043a371 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,23 +1,6 @@
 language: python
 python:
   - pypy
-env:
-  - JOB=0
-  - JOB=1
-  - JOB=2
-  - JOB=3
-  - JOB=4
-  - JOB=5
-  - JOB=6
-  - JOB=7
-  - JOB=8
-  - JOB=9
-  - JOB=10
-  - JOB=11
-  - JOB=12
-  - JOB=13
-  - JOB=14
-  - JOB=15
 
 before_script:
     - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr
@@ -33,15 +16,7 @@ before_script:
     - wget "http://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
     - cd travis-overlay
 script:
-    - ret=0; cx=0;
-      for x in $(cat profiles/categories); do
-      if test $(( cx++ % 16 )) -eq ${JOB}; then
-          cd ${x} && {
-            python ../../portage-master/bin/repoman full -vdx || ret=1;
-          } && cd -;
-        fi;
-      done;
-      exit "${ret}"
+    - python ../portage-master/bin/repoman full -vdx
 
 notifications:
   irc: "chat.freenode.net#gentoo-science"

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     737d5fd29d780cb48a479e5beedfa49f21216dab
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 09:28:30 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 09:28:30 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=737d5fd2

Fix path to repoman

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index bec04af..1f584b0 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -37,7 +37,7 @@ script:
       for x in $(cat profiles/categories); do
       if test $(( cx++ % 16 )) -eq ${JOB}; then
           cd ${x} && {
-            python ../portage-*/bin/repoman full -vdx || ret=1;
+            python ../../portage-master/bin/repoman full -vdx || ret=1;
           } && cd -;
         fi;
       done;

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     35c128e34b2f49f77963485308897d62b60b8b74
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 09:26:10 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 09:26:10 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=35c128e3

Do all admin tasks in the beginning

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 .travis.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 41f011c..bec04af 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -20,14 +20,14 @@ env:
   - JOB=15
 
 before_script:
+    - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr
+    - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
+    - echo "portage::250:portage,travis" >> /etc/group
     - mkdir -p travis-overlay /etc/portage/ /usr/portage/distfiles
     - mv !(travis-overlay) travis-overlay/
     - mv .git travis-overlay/
     - wget -O - "https://github.com/gentoo/portage/archive/master.tar.gz" | tar -xz
     - wget -O - "https://github.com/gentoo/gentoo-portage-rsync-mirror/archive/master.tar.gz" | tar xz -C /usr/portage --strip-components=1
-    - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr
-    - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
-    - echo "portage::250:portage,travis" >> /etc/group
     - cp portage-master/cnf/repos.conf /etc/portage/
     - ln -s /usr/portage/profiles/base/ /etc/portage/make.profile
     - wget "http://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     d1db99c46e67c06e9caff63f7e4631df9aa810fe
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 09:24:10 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 09:24:10 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d1db99c4

Create all directories in the beginning

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 .travis.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index f672eea..41f011c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -20,7 +20,7 @@ env:
   - JOB=15
 
 before_script:
-    - mkdir travis-overlay
+    - mkdir -p travis-overlay /etc/portage/ /usr/portage/distfiles
     - mv !(travis-overlay) travis-overlay/
     - mv .git travis-overlay/
     - wget -O - "https://github.com/gentoo/portage/archive/master.tar.gz" | tar -xz
@@ -28,7 +28,6 @@ before_script:
     - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr
     - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
     - echo "portage::250:portage,travis" >> /etc/group
-    - mkdir -p /etc/portage/ /usr/portage/distfiles
     - cp portage-master/cnf/repos.conf /etc/portage/
     - ln -s /usr/portage/profiles/base/ /etc/portage/make.profile
     - wget "http://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
@@ -38,7 +37,7 @@ script:
       for x in $(cat profiles/categories); do
       if test $(( cx++ % 16 )) -eq ${JOB}; then
           cd ${x} && {
-            python ../portage-*/bin/repoman full -v || ret=1;
+            python ../portage-*/bin/repoman full -vdx || ret=1;
           } && cd -;
         fi;
       done;

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b304133cb72f52cb5fb31be79d0b295415dce060
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 09:21:10 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 09:21:10 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b304133c

use stdout

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 6626863..f672eea 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -24,7 +24,7 @@ before_script:
     - mv !(travis-overlay) travis-overlay/
     - mv .git travis-overlay/
     - wget -O - "https://github.com/gentoo/portage/archive/master.tar.gz" | tar -xz
-    - wget "https://github.com/gentoo/gentoo-portage-rsync-mirror/archive/master.tar.gz" | tar xz -C /usr/portage --strip-components=1
+    - wget -O - "https://github.com/gentoo/gentoo-portage-rsync-mirror/archive/master.tar.gz" | tar xz -C /usr/portage --strip-components=1
     - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr
     - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
     - echo "portage::250:portage,travis" >> /etc/group

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     89afe3fad27dc1bbc260aeb56ba88a5bbc4addaf
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 09:17:14 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 09:17:14 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=89afe3fa

Fix traxis.yml for the overlay

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 .travis.yml | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 0fd1f46..6626863 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -20,14 +20,19 @@ env:
   - JOB=15
 
 before_script:
+    - mkdir travis-overlay
+    - mv !(travis-overlay) travis-overlay/
+    - mv .git travis-overlay/
+    - wget -O - "https://github.com/gentoo/portage/archive/master.tar.gz" | tar -xz
+    - wget "https://github.com/gentoo/gentoo-portage-rsync-mirror/archive/master.tar.gz" | tar xz -C /usr/portage --strip-components=1
     - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr
     - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
     - echo "portage::250:portage,travis" >> /etc/group
-    - ln -s "${PWD}" /usr/portage
-    - mkdir -p /etc/portage distfiles
-    - ln -s "${PWD}"/profiles/base/ /etc/portage/make.profile
-    - wget -O - "https://github.com/gentoo/portage/archive/master.tar.gz" | tar -xz
-
+    - mkdir -p /etc/portage/ /usr/portage/distfiles
+    - cp portage-master/cnf/repos.conf /etc/portage/
+    - ln -s /usr/portage/profiles/base/ /etc/portage/make.profile
+    - wget "http://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
+    - cd travis-overlay
 script:
     - ret=0; cx=0;
       for x in $(cat profiles/categories); do

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     433650a8dc4b0aba643ae8d890a5c518a4ae59da
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 09:06:20 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 09:06:20 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=433650a8

Use rsync2git version

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 .travis.yml | 59 +++++++++++++++++++++++++++++++++--------------------------
 1 file changed, 33 insertions(+), 26 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 6d0d5bd..0fd1f46 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,36 +1,43 @@
-#
-# Run repoman via travis
-# See https://github.com/mrueg/repoman-travis
-#
 language: python
 python:
-    - pypy
+  - pypy
 env:
-    - PORTAGE_VER="2.2.17"
+  - JOB=0
+  - JOB=1
+  - JOB=2
+  - JOB=3
+  - JOB=4
+  - JOB=5
+  - JOB=6
+  - JOB=7
+  - JOB=8
+  - JOB=9
+  - JOB=10
+  - JOB=11
+  - JOB=12
+  - JOB=13
+  - JOB=14
+  - JOB=15
+
 before_script:
-    - mkdir travis-overlay
-    - mv !(travis-overlay) travis-overlay/
-    - mv .git travis-overlay/
-    - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/.travis.yml" -O .travis.yml.upstream
-    - wget "https://github.com/gentoo/portage/archive/v${PORTAGE_VER}.tar.gz" -O portage-${PORTAGE_VER}.tar.gz
-    - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/spinner.sh"
-    - wget "https://github.com/gentoo/gentoo-portage-rsync-mirror/archive/master.tar.gz" -O portage-tree.tar.gz
-    - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr spinner.sh
-    - chmod a+rwx spinner.sh
+    - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr
     - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
     - echo "portage::250:portage,travis" >> /etc/group
-    - mkdir -p /etc/portage/ /usr/portage/distfiles
-    - tar xzf portage-${PORTAGE_VER}.tar.gz
-    - tar xzf portage-tree.tar.gz -C /usr/portage --strip-components=1
-    - cp portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/
-    - ln -s /usr/portage/profiles/base/ /etc/portage/make.profile
-    - wget "http://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
-    - SIZE=`stat -c %s .travis.yml.upstream`
-    - if ! cmp -n $SIZE -s .travis.yml .travis.yml.upstream; then  echo -e "\e[31m !!! .travis.yml outdated! Update available https://github.com/mrueg/repoman-travis \e[0m" > /tmp/update ; fi
-    - cd travis-overlay
+    - ln -s "${PWD}" /usr/portage
+    - mkdir -p /etc/portage distfiles
+    - ln -s "${PWD}"/profiles/base/ /etc/portage/make.profile
+    - wget -O - "https://github.com/gentoo/portage/archive/master.tar.gz" | tar -xz
+
 script:
-    - ./../spinner.sh "./../portage-${PORTAGE_VER}/bin/repoman full -d"
-# You can append own scripts after this line
+    - ret=0; cx=0;
+      for x in $(cat profiles/categories); do
+      if test $(( cx++ % 16 )) -eq ${JOB}; then
+          cd ${x} && {
+            python ../portage-*/bin/repoman full -v || ret=1;
+          } && cd -;
+        fi;
+      done;
+      exit "${ret}"
 
 notifications:
   irc: "chat.freenode.net#gentoo-science"

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c2f96bb5d6bf8f1fc68c9d50f0b14069ff13be61
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 08:31:15 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 08:31:15 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c2f96bb5

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/clfft: Version Bump


 sci-libs/clfft/ChangeLog                              | 5 +++++
 sci-libs/clfft/Manifest                               | 1 +
 sci-libs/clfft/{clfft-2.2.ebuild => clfft-2.4.ebuild} | 0
 3 files changed, 6 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     7443663af92f14af5bfc394d2dcf2c144438928f
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 08:29:02 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 08:29:02 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7443663a

use mrueg settings

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 .travis.yml | 35 ++++++++++++++++++++++-------------
 1 file changed, 22 insertions(+), 13 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index cf6287e..6d0d5bd 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,27 +1,36 @@
+#
+# Run repoman via travis
+# See https://github.com/mrueg/repoman-travis
+#
+language: python
+python:
+    - pypy
 env:
-  - PORTAGE=2.2.14
-  - PORTAGE=2.2.17
-
+    - PORTAGE_VER="2.2.17"
 before_script:
     - mkdir travis-overlay
     - mv !(travis-overlay) travis-overlay/
     - mv .git travis-overlay/
-    - wget "http://distfiles.gentoo.org/distfiles/portage-$PORTAGE.tar.bz2"
-    - wget "http://distfiles.gentoo.org/snapshots/portage-latest.tar.xz"
-    - sudo chmod 777 /etc/passwd /etc/group /etc /usr
+    - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/.travis.yml" -O .travis.yml.upstream
+    - wget "https://github.com/gentoo/portage/archive/v${PORTAGE_VER}.tar.gz" -O portage-${PORTAGE_VER}.tar.gz
+    - wget "https://raw.githubusercontent.com/mrueg/repoman-travis/master/spinner.sh"
+    - wget "https://github.com/gentoo/gentoo-portage-rsync-mirror/archive/master.tar.gz" -O portage-tree.tar.gz
+    - sudo chmod a+rwX /etc/passwd /etc/group /etc /usr spinner.sh
+    - chmod a+rwx spinner.sh
     - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
     - echo "portage::250:portage,travis" >> /etc/group
     - mkdir -p /etc/portage/ /usr/portage/distfiles
-    - tar xjf portage-$PORTAGE.tar.bz2
-    - tar xJf portage-latest.tar.xz -C /usr/
-    - cp portage-$PORTAGE/cnf/repos.conf /etc/portage/
-    - rsync --recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --checksum --quiet rsync://rsync.gentoo.org/gentoo-portage /usr/portage
+    - tar xzf portage-${PORTAGE_VER}.tar.gz
+    - tar xzf portage-tree.tar.gz -C /usr/portage --strip-components=1
+    - cp portage-${PORTAGE_VER}/cnf/repos.conf /etc/portage/
     - ln -s /usr/portage/profiles/base/ /etc/portage/make.profile
+    - wget "http://www.gentoo.org/dtd/metadata.dtd" -O /usr/portage/distfiles/metadata.dtd
+    - SIZE=`stat -c %s .travis.yml.upstream`
+    - if ! cmp -n $SIZE -s .travis.yml .travis.yml.upstream; then  echo -e "\e[31m !!! .travis.yml outdated! Update available https://github.com/mrueg/repoman-travis \e[0m" > /tmp/update ; fi
     - cd travis-overlay
-    - sed -i 's/fcmd=fcmd/fcmd=("%s -q" % fcmd)/' ./../portage-$PORTAGE/bin/repoman
-
 script:
-    - "./../portage-$PORTAGE/bin/repoman full -d -v"
+    - ./../spinner.sh "./../portage-${PORTAGE_VER}/bin/repoman full -d"
+# You can append own scripts after this line
 
 notifications:
   irc: "chat.freenode.net#gentoo-science"

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     7c7ad66a9ac7fc2ed43040e4577d1e02e7b4db67
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Tue Feb 17 21:29:05 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Feb 17 21:29:05 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7c7ad66a

Merge pull request #370 from hmmr/master

sci-biology/aghermann: initial ebuild


 sci-biology/aghermann/ChangeLog              |  6 ++++++
 sci-biology/aghermann/Manifest               |  1 +
 sci-biology/aghermann/aghermann-1.0.3.ebuild | 31 ++++++++++++++++++++++++++++
 sci-biology/aghermann/metadata.xml           | 16 ++++++++++++++
 4 files changed, 54 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     32a6811dd02ec0b1653c320beb838f177fd6197a
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 14 15:03:19 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Feb 14 15:03:19 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=32a6811d

Merge pull request #369 from LMolr/dev-util/smartgit

projects/sci: dev-util/smartgit: Version Bump (6.0.6 -> 6.5.6)


 dev-util/smartgit/ChangeLog                        | 21 +++++++++++++++++--
 dev-util/smartgit/Manifest                         |  2 +-
 ...smartgit-6.0.6.ebuild => smartgit-6.5.6.ebuild} | 24 ++++++++++++++--------
 sci-libs/libfac/Manifest                           |  1 -
 4 files changed, 36 insertions(+), 12 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     c92f4abc295fe345ce88f0c1bbd0bd7f5bbaab7a
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 16 23:53:05 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Feb 16 23:53:05 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c92f4abc

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 dev-util/smartgit/ChangeLog                        | 21 +++++++++++++++++--
 dev-util/smartgit/Manifest                         |  2 +-
 ...smartgit-6.0.6.ebuild => smartgit-6.5.6.ebuild} | 24 ++++++++++++++--------
 sci-libs/libfac/Manifest                           |  1 -
 4 files changed, 36 insertions(+), 12 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     d7ac48077334176e84cc50816ea65eb51ea23806
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Feb 14 16:15:19 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Feb 14 16:15:19 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d7ac4807

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 app-shells/mpibash/ChangeLog          | 34 ----------------------------------
 app-shells/mpibash/Manifest           |  1 -
 app-shells/mpibash/metadata.xml       |  5 -----
 app-shells/mpibash/mpibash-1.1.ebuild | 28 ----------------------------
 4 files changed, 68 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     5dc4e6ccf48b08f884961f24c2cfa6cf77bef724
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Feb 13 21:50:52 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Feb 13 21:50:52 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5dc4e6cc

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 app-shells/mpibash/ChangeLog                       |   11 +-
 app-shells/mpibash/Manifest                        |   32 +-
 .../files/bash-4.3-append-process-segfault.patch   |   18 -
 app-shells/mpibash/files/bash-4.3-compat-lvl.patch |   13 -
 .../files/bash-4.3-parse-time-keyword.patch        |   30 -
 .../mpibash/files/bash-4.3-term-cleanup.patch      |   47 -
 app-shells/mpibash/files/mpibash-4.3.patch         | 1565 --------------------
 app-shells/mpibash/metadata.xml                    |   13 +-
 app-shells/mpibash/mpibash-1.1.ebuild              |   28 +
 app-shells/mpibash/mpibash-4.3_p30-r1.ebuild       |  277 ----
 10 files changed, 40 insertions(+), 1994 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     4ed84f3cd969bf8afa2032200982aef8d639b0ec
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 13 12:12:05 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Feb 13 12:12:05 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4ed84f3c

revert back to serial repoman as parallel doesn't work with multiple portages

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 .travis.yml | 30 +-----------------------------
 1 file changed, 1 insertion(+), 29 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index f846789..cf6287e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,25 +1,6 @@
-language: python
-python:
-  - pypy
 env:
   - PORTAGE=2.2.14
   - PORTAGE=2.2.17
-  - JOB=0
-  - JOB=1
-  - JOB=2
-  - JOB=3
-  - JOB=4
-  - JOB=5
-  - JOB=6
-  - JOB=7
-  - JOB=8
-  - JOB=9
-  - JOB=10
-  - JOB=11
-  - JOB=12
-  - JOB=13
-  - JOB=14
-  - JOB=15
 
 before_script:
     - mkdir travis-overlay
@@ -40,16 +21,7 @@ before_script:
     - sed -i 's/fcmd=fcmd/fcmd=("%s -q" % fcmd)/' ./../portage-$PORTAGE/bin/repoman
 
 script:
-    - ret=0; cx=0;
-      for x in $(cat /usr/portage/profiles/categories); do
-      if test $(( cx++ % 16 )) -eq ${JOB}; then
-          cd ${x} && {
-            python ./../portage-${PORTAGE}/bin/repoman full -v -d -x || ret=1;
-          } && cd -;
-        fi;
-      done;
-      exit "${ret}"
+    - "./../portage-$PORTAGE/bin/repoman full -d -v"
 
 notifications:
   irc: "chat.freenode.net#gentoo-science"
-

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     084e15cb712950a6c580149f93c1d09c57952374
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 13 12:07:48 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Feb 13 12:07:48 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=084e15cb

Import parallel repoman checks from gentoo-rsync2git repo

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 .travis.yml | 27 ++++++++++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 9c4bdf2..f846789 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,6 +4,22 @@ python:
 env:
   - PORTAGE=2.2.14
   - PORTAGE=2.2.17
+  - JOB=0
+  - JOB=1
+  - JOB=2
+  - JOB=3
+  - JOB=4
+  - JOB=5
+  - JOB=6
+  - JOB=7
+  - JOB=8
+  - JOB=9
+  - JOB=10
+  - JOB=11
+  - JOB=12
+  - JOB=13
+  - JOB=14
+  - JOB=15
 
 before_script:
     - mkdir travis-overlay
@@ -24,7 +40,16 @@ before_script:
     - sed -i 's/fcmd=fcmd/fcmd=("%s -q" % fcmd)/' ./../portage-$PORTAGE/bin/repoman
 
 script:
-    - "python ./../portage-$PORTAGE/bin/repoman full -d -v -x"
+    - ret=0; cx=0;
+      for x in $(cat /usr/portage/profiles/categories); do
+      if test $(( cx++ % 16 )) -eq ${JOB}; then
+          cd ${x} && {
+            python ./../portage-${PORTAGE}/bin/repoman full -v -d -x || ret=1;
+          } && cd -;
+        fi;
+      done;
+      exit "${ret}"
 
 notifications:
   irc: "chat.freenode.net#gentoo-science"
+

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     be3126e586740f53e55e5bd1e7d84c17c1b32b64
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 13 11:45:11 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Feb 13 11:45:11 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=be3126e5

Use pyp as python implementation

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 .travis.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 8031e8a..9c4bdf2 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,6 +1,9 @@
+language: python
+python:
+  - pypy
 env:
   - PORTAGE=2.2.14
-  - PORTAGE=2.2.15
+  - PORTAGE=2.2.17
 
 before_script:
     - mkdir travis-overlay
@@ -21,7 +24,7 @@ before_script:
     - sed -i 's/fcmd=fcmd/fcmd=("%s -q" % fcmd)/' ./../portage-$PORTAGE/bin/repoman
 
 script:
-    - "./../portage-$PORTAGE/bin/repoman full -d -v"
+    - "python ./../portage-$PORTAGE/bin/repoman full -d -v -x"
 
 notifications:
   irc: "chat.freenode.net#gentoo-science"

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     bed6b965536d10ddf996a0b7407f26e7712a18e4
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 13 10:42:19 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Feb 13 10:42:19 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bed6b965

Report travis status on irc

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 .travis.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index db8a92b..8031e8a 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -20,5 +20,8 @@ before_script:
     - cd travis-overlay
     - sed -i 's/fcmd=fcmd/fcmd=("%s -q" % fcmd)/' ./../portage-$PORTAGE/bin/repoman
 
-script: 
+script:
     - "./../portage-$PORTAGE/bin/repoman full -d -v"
+
+notifications:
+  irc: "chat.freenode.net#gentoo-science"

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     d684e6c50462e90cb5a2a088aa185529d2047b39
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Feb 12 08:55:47 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Feb 12 08:55:47 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d684e6c5

Merge remote-tracking branch 'github/master'

* github/master:
  added support of hdf5, clean up


 sci-chemistry/votca-csg/ChangeLog             |  5 +++-
 sci-chemistry/votca-csg/votca-csg-9999.ebuild | 39 +++++++++------------------
 2 files changed, 16 insertions(+), 28 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a7c8e86aa18b2556a5bba06819e641079fcbffe6
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Feb 10 14:36:57 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Feb 10 14:36:57 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a7c8e86a

Merge remote-tracking branch 'github/master'

* github/master:
  sci-biology/vague-bin-1.0.5: Switch from git-2 to git-r3; Cleanup; Fix KEYWORDS
  sci-biology/sga-9999: Switch from git-2 to git-r3; Cleanup; Add missing die
  sci-biology/sabre-9999: Switch from git-2 to git-r3; Cleanup
  sci-biology/epga-9999: Switch from git-2 to git-r3; Cleanup


 sci-biology/epga/ChangeLog                   | 3 +++
 sci-biology/epga/epga-9999.ebuild            | 4 +---
 sci-biology/sabre/ChangeLog                  | 3 +++
 sci-biology/sabre/sabre-9999.ebuild          | 5 +----
 sci-biology/sga/ChangeLog                    | 5 ++++-
 sci-biology/sga/sga-9999.ebuild              | 8 +++-----
 sci-biology/vague-bin/ChangeLog              | 3 +++
 sci-biology/vague-bin/vague-bin-1.0.5.ebuild | 6 ++----
 8 files changed, 20 insertions(+), 17 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     a92fe7b7265416de88ea76d060a60efc68884534
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Feb  7 10:07:54 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Feb  7 10:07:54 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a92fe7b7

Merge pull request #362 from SoapZaNet/bowtie

Updated sci-biology/bowtie


 sci-biology/bowtie/ChangeLog                       |  6 ++-
 sci-biology/bowtie/Manifest                        |  3 +-
 sci-biology/bowtie/bowtie-1.1.1.ebuild             | 53 ++++++++++++++++++++++
 .../{bowtie-2.1.0.ebuild => bowtie-2.2.4.ebuild}   | 28 +++++-------
 .../bowtie/files/bowtie-2.1.0-buildsystem.patch    | 20 --------
 5 files changed, 72 insertions(+), 38 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     b6c2011d8dded3f26aec18e3c5f5eb57fbf5ae1c
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb  6 09:57:04 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Feb  6 09:57:04 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b6c2011d

Merge pull request #363 from SoapZaNet/bwa

Bump and modernize sci-biology/bwa


 sci-biology/bwa/Manifest                 |  1 +
 sci-biology/bwa/bwa-0.7.12.ebuild        | 34 ++++++++++++++++++++++++++++++++
 sci-biology/bwa/files/bwa_Makefile.patch | 27 +++++++++++++++++++++++++
 sci-biology/{trf => bwa}/metadata.xml    |  0
 4 files changed, 62 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     09aef4d1902e06ff76be71ede31e9da11b282eef
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb  6 14:23:54 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Feb  6 14:23:54 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=09aef4d1

Merge pull request #364 from j-g-/master

Fix ebuild for librecad 2.0.7


 media-gfx/librecad/librecad-2.0.7.ebuild | 6 ++++--
 media-gfx/librecad/metadata.xml          | 1 +
 2 files changed, 5 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     7a4cef5af00c759a893ac46a71e11142e88515b1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb  4 08:36:50 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb  4 08:36:50 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7a4cef5a

Merge branch 'SoapZaNet-master'

* SoapZaNet-master: (34 commits)
  sci-biology/embassy-meme: Bump eclass, Drop old
  empty package
  empty package
  sci-biology/embassy-mse: Bump eclass, drop old
  sci-biology/embassy-iprscan: Bump eclass, Drop old
  sci-biology/embassy-phylipnew: Bump eclass, drop old
  sci-biology/embassy-hmmer: Bump eclass, Drop old
  sci-biology/embassy-signature: Bump eclass, drop old
  sci-biology/embassy-esim4: Bump eclass, Drop old
  sci-biology/embassy-structure: Bump eclass, drop old
  sci-biology/embassy-emnu: Bump eclass, Drop old
  sci-biology/embassy-topo: Bump eclass, drop old
  sci-biology/embassy-domsearch: Bump eclass, Drop old
  sci-biology/embassy-vienna: Bump eclass, drop old
  sci-biology/embassy-domalign: Bump eclass, Drop old
  sci-biology/embassy-domainatrix: Bump eclass, Drop old
  sci-biology/embassy-clustalomega: Bump eclass
  sci-biology/embassy-cbstools: Bump eclass, Drop old
  sci-biology/embassy: Drop old
  sci-biology/emboss: Drop old
  ...


 eclass/{emboss.eclass => emboss-r1.eclass}         |  89 ++---
 profiles/package.mask                              |  35 +-
 sci-biology/embassy-cbstools/ChangeLog             |   7 +-
 sci-biology/embassy-cbstools/Manifest              |   2 +-
 ...r3.ebuild => embassy-cbstools-1.0.0.650.ebuild} |   6 +-
 .../files/embassy-cbstools-1.0.0-r2.patch          | 347 ------------------
 ...bassy-cbstools-1.0.0.650_fix-build-system.patch |  97 +++++
 sci-biology/embassy-cbstools/metadata.xml          |   2 +-
 .../ChangeLog                                      |   8 +-
 sci-biology/embassy-clustalomega/Manifest          |   1 +
 .../embassy-clustalomega-1.1.0.ebuild              |  13 +
 ...bassy-clustalomega-1.1.0_fix-build-system.patch |  90 +++++
 .../{trf => embassy-clustalomega}/metadata.xml     |   0
 sci-biology/embassy-domainatrix/ChangeLog          |   7 +-
 sci-biology/embassy-domainatrix/Manifest           |   2 +-
 ...6.ebuild => embassy-domainatrix-0.1.650.ebuild} |   6 +-
 .../files/embassy-domainatrix-0.1.0-r5.patch       | 346 ------------------
 ...assy-domainatrix-0.1.650_fix-build-system.patch |  91 +++++
 sci-biology/embassy-domainatrix/metadata.xml       |   2 +-
 sci-biology/embassy-domalign/ChangeLog             |   7 +-
 sci-biology/embassy-domalign/Manifest              |   2 +-
 ...0-r5.ebuild => embassy-domalign-0.1.650.ebuild} |   6 +-
 .../files/embassy-domalign-0.1.0-r5.patch          | 346 ------------------
 ...embassy-domalign-0.1.650_fix-build-system.patch |  92 +++++
 sci-biology/embassy-domalign/metadata.xml          |   2 +-
 sci-biology/embassy-domsearch/ChangeLog            |   7 +-
 sci-biology/embassy-domsearch/Manifest             |   2 +-
 ...-r5.ebuild => embassy-domsearch-0.1.650.ebuild} |   6 +-
 .../files/embassy-domsearch-0.1.0-r5.patch         | 346 ------------------
 ...mbassy-domsearch-0.1.650_fix-build-system.patch |  91 +++++
 sci-biology/embassy-domsearch/metadata.xml         |   2 +-
 sci-biology/embassy-emnu/ChangeLog                 |   7 +-
 sci-biology/embassy-emnu/Manifest                  |   2 +-
 ...1.05-r7.ebuild => embassy-emnu-1.05.650.ebuild} |   8 +-
 .../embassy-emnu/files/embassy-emnu-1.05-r7.patch  | 359 -------------------
 .../embassy-emnu-1.05.650_fix-build-system.patch   | 127 +++++++
 sci-biology/embassy-emnu/metadata.xml              |   2 +-
 sci-biology/embassy-esim4/ChangeLog                |   7 +-
 sci-biology/embassy-esim4/Manifest                 |   2 +-
 ....0-r7.ebuild => embassy-esim4-1.0.0.650.ebuild} |   6 +-
 .../files/embassy-esim4-1.0.0-r7.patch             | 345 ------------------
 .../embassy-esim4-1.0.0.650_fix-build-system.patch |  97 +++++
 sci-biology/embassy-esim4/metadata.xml             |   2 +-
 sci-biology/embassy-hmmer/ChangeLog                |   7 +-
 sci-biology/embassy-hmmer/Manifest                 |   2 +-
 ....2-r4.ebuild => embassy-hmmer-2.3.2.650.ebuild} |   8 +-
 .../files/embassy-hmmer-2.3.2-r4.patch             | 346 ------------------
 .../embassy-hmmer-2.3.2.650_fix-build-system.patch |  90 +++++
 sci-biology/embassy-hmmer/metadata.xml             |   2 +-
 sci-biology/embassy-iprscan/ChangeLog              |   7 +-
 sci-biology/embassy-iprscan/Manifest               |   2 +-
 ...-r2.ebuild => embassy-iprscan-4.3.1.650.ebuild} |   6 +-
 .../files/embassy-iprscan-4.3.1-r2.patch           | 349 ------------------
 ...mbassy-iprscan-4.3.1.650_fix-build-system.patch |  97 +++++
 sci-biology/embassy-iprscan/metadata.xml           |   2 +-
 .../{embassy-memenew => embassy-meme}/ChangeLog    |   8 +-
 sci-biology/embassy-meme/Manifest                  |   1 +
 .../embassy-meme/embassy-meme-4.7.650.ebuild       |  13 +
 .../embassy-meme-4.7.650_fix-build-system.patch    |  90 +++++
 sci-biology/{trf => embassy-meme}/metadata.xml     |   0
 .../files/embassy-memenew-4.0.0-r1.patch           | 346 ------------------
 sci-biology/embassy-memenew/metadata.xml           |   5 -
 sci-biology/embassy-mira/ChangeLog                 |  50 ---
 .../embassy-mira/files/embassy-mira-2.8.2-r2.patch | 345 ------------------
 sci-biology/embassy-mira/metadata.xml              |   5 -
 sci-biology/embassy-mse/ChangeLog                  |   6 +-
 sci-biology/embassy-mse/Manifest                   |   2 +-
 ...e-3.0.0.ebuild => embassy-mse-3.0.0.650.ebuild} |  12 +-
 .../embassy-mse-3.0.0.650_fix-build-system.patch   | 133 +++++++
 .../embassy-mse/files/embassy-mse-3.0.0.patch      | 398 ---------------------
 sci-biology/embassy-mse/metadata.xml               |   2 +-
 sci-biology/embassy-phylipnew/ChangeLog            |   7 +-
 sci-biology/embassy-phylipnew/Manifest             |   2 +-
 ...69.ebuild => embassy-phylipnew-3.69.650.ebuild} |   6 +-
 ...bassy-phylipnew-3.69.650_fix-build-system.patch |  98 +++++
 .../files/embassy-phylipnew-3.69.patch             | 346 ------------------
 sci-biology/embassy-phylipnew/metadata.xml         |   2 +-
 sci-biology/embassy-signature/ChangeLog            |   7 +-
 sci-biology/embassy-signature/Manifest             |   2 +-
 ...-r5.ebuild => embassy-signature-0.1.650.ebuild} |   6 +-
 .../files/embassy-signature-0.1.0-r5.patch         | 346 ------------------
 ...mbassy-signature-0.1.650_fix-build-system.patch |  90 +++++
 sci-biology/embassy-signature/metadata.xml         |   2 +-
 sci-biology/embassy-structure/ChangeLog            |   7 +-
 sci-biology/embassy-structure/Manifest             |   2 +-
 ...-r5.ebuild => embassy-structure-0.1.650.ebuild} |   6 +-
 .../files/embassy-structure-0.1.0-r5.patch         | 347 ------------------
 ...mbassy-structure-0.1.650_fix-build-system.patch |  90 +++++
 sci-biology/embassy-structure/metadata.xml         |   2 +-
 sci-biology/embassy-topo/ChangeLog                 |   6 +-
 sci-biology/embassy-topo/Manifest                  |   2 +-
 ...po-2.0.0.ebuild => embassy-topo-2.0.650.ebuild} |   6 +-
 .../embassy-topo/files/embassy-topo-2.0.0.patch    | 346 ------------------
 .../embassy-topo-2.0.650_fix-build-system.patch    |  97 +++++
 sci-biology/embassy-topo/metadata.xml              |   2 +-
 sci-biology/embassy-vienna/ChangeLog               |   7 +-
 sci-biology/embassy-vienna/Manifest                |   2 +-
 ...2-r2.ebuild => embassy-vienna-1.7.2.650.ebuild} |   6 +-
 .../files/embassy-vienna-1.7.2-r2.patch            | 355 ------------------
 ...embassy-vienna-1.7.2.650_fix-build-system.patch |  98 +++++
 sci-biology/embassy-vienna/metadata.xml            |   2 +-
 sci-biology/embassy/ChangeLog                      |   6 +-
 sci-biology/embassy/embassy-6.3.1.ebuild           |  43 ---
 sci-biology/embassy/embassy-6.6.0.ebuild           |  30 ++
 sci-biology/embassy/metadata.xml                   |   2 +-
 sci-biology/emboss/ChangeLog                       |   8 +-
 sci-biology/emboss/Manifest                        |   4 -
 sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild       |  94 -----
 sci-biology/emboss/emboss-6.5.7.ebuild             |  79 ----
 sci-biology/emboss/emboss-6.6.0.ebuild             |  62 +---
 .../{emboss-README.Gentoo-2 => README.gentoo}      |   4 +-
 sci-biology/emboss/files/ax_lib_mysql.m4           | 147 --------
 .../emboss/files/emboss-6.3.1_p4-r2_Makefile.patch |  47 ---
 .../emboss-6.3.1_p4-r2_compilations-paths.patch    | 315 ----------------
 .../emboss/files/emboss-6.3.1_p4-r2_libtool.patch  |  18 -
 .../emboss/files/emboss-6.3.1_p4-r2_plcol.patch    | 112 ------
 ...mboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch |  13 -
 .../files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch    |  11 +
 .../files/emboss-6.6.0_fix-build-system.patch      | 368 +++++++++++++++++++
 sci-biology/emboss/files/emboss-6.6.0_plcol.patch  | 112 ------
 .../files/emboss-6.6.0_plplot-declarations.patch   |  61 ++++
 .../emboss-6.6.0_qa-implicit-declarations.patch    |  74 ++++
 sci-biology/emboss/metadata.xml                    |   4 +-
 sci-biology/fastdnaml/fastdnaml-1.2.2_p10.ebuild   |   2 +-
 .../fastx_toolkit/fastx_toolkit-0.0.14.ebuild      |  11 +
 125 files changed, 2422 insertions(+), 6860 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Guillaume Horel]

commit:     0d9b2aae9c266a7c1538094462342af8ec964148
Author:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
AuthorDate: Sun Feb  1 03:00:09 2015 +0000
Commit:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
CommitDate: Sun Feb  1 03:00:09 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0d9b2aae

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 dev-python/nvidia-ml-py/ChangeLog                  |  8 ++
 dev-python/nvidia-ml-py/Manifest                   |  1 +
 .../nvidia-ml-py}/metadata.xml                     | 12 +--
 .../nvidia-ml-py/nvidia-ml-py-6.340.0.ebuild       | 19 +++++
 profiles/license_groups                            |  1 +
 sci-biology/discrover/ChangeLog                    |  7 ++
 sci-biology/discrover/Manifest                     |  2 +-
 ...scrover-1.4.1.ebuild => discrover-1.5.2.ebuild} | 14 +++-
 sci-biology/discrover/discrover-9999.ebuild        | 16 +++-
 sci-biology/discrover/metadata.xml                 |  5 +-
 sci-biology/scaffold_builder/ChangeLog             |  8 +-
 sci-biology/scaffold_builder/Manifest              |  2 +-
 ...403.ebuild => scaffold_builder-20131122.ebuild} | 17 ++--
 sci-biology/subread/ChangeLog                      | 13 ++++
 sci-biology/subread/Manifest                       |  1 +
 sci-biology/{zmsort => subread}/metadata.xml       |  0
 sci-biology/subread/subread-1.4.6.ebuild           | 42 ++++++++++
 sci-chemistry/gromacs/ChangeLog                    |  6 +-
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild      | 12 +--
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild      | 14 ++--
 sci-chemistry/gromacs/gromacs-9999.ebuild          | 14 ++--
 sci-chemistry/gromacs/metadata.xml                 |  6 --
 sci-libs/armadillo/ChangeLog                       |  6 ++
 sci-libs/armadillo/Manifest                        |  1 +
 ...llo-4.600.2.ebuild => armadillo-4.600.4.ebuild} |  0
 sci-libs/dealii/ChangeLog                          |  4 +
 sci-libs/dealii/dealii-8.1.0-r2.ebuild             | 12 +--
 sci-libs/dealii/dealii-8.2.1.ebuild                | 12 +--
 sci-libs/dealii/dealii-9999.ebuild                 | 12 +--
 sci-libs/dealii/metadata.xml                       |  1 -
 sci-visualization/mantid/Manifest                  |  1 +
 .../mantid/files/mantid-3.3.0-minigzip-OF.patch    | 28 +++++++
 sci-visualization/mantid/mantid-3.3.0.ebuild       | 91 ++++++++++++++++++++++
 sci-visualization/mantid/metadata.xml              | 23 ++++++
 34 files changed, 344 insertions(+), 67 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     3d7bd9110f6e0fd960e17af37721506b94197208
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Thu Jan 29 18:43:32 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Jan 29 18:43:32 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3d7bd911

Merge pull request #354 from chatcannon/Mantid

New ebuild for Mantid


 sci-visualization/mantid/Manifest                  |  1 +
 .../mantid/files/mantid-3.3.0-minigzip-OF.patch    | 28 +++++++
 sci-visualization/mantid/mantid-3.3.0.ebuild       | 91 ++++++++++++++++++++++
 sci-visualization/mantid/metadata.xml              | 23 ++++++
 4 files changed, 143 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     2de2e8d04b9ff2f7625e5127377fb9f6cf817d17
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 31 20:19:06 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Jan 31 20:19:06 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2de2e8d0

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 sci-biology/discrover/ChangeLog                    |  7 ++
 sci-biology/discrover/Manifest                     |  2 +-
 ...scrover-1.4.1.ebuild => discrover-1.5.2.ebuild} | 14 +++-
 sci-biology/discrover/discrover-9999.ebuild        | 16 +++-
 sci-biology/discrover/metadata.xml                 |  5 +-
 sci-libs/dealii/ChangeLog                          |  4 +
 sci-libs/dealii/dealii-8.1.0-r2.ebuild             | 12 +--
 sci-libs/dealii/dealii-8.2.1.ebuild                | 12 +--
 sci-libs/dealii/dealii-9999.ebuild                 | 12 +--
 sci-libs/dealii/metadata.xml                       |  1 -
 sci-visualization/mantid/Manifest                  |  1 +
 .../mantid/files/mantid-3.3.0-minigzip-OF.patch    | 28 +++++++
 sci-visualization/mantid/mantid-3.3.0.ebuild       | 91 ++++++++++++++++++++++
 sci-visualization/mantid/metadata.xml              | 23 ++++++
 14 files changed, 206 insertions(+), 22 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     330e0ddb9a4ea933b031667dfca13bdb65e063e3
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Wed Jan 28 17:14:57 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Jan 28 17:14:57 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=330e0ddb

Merge pull request #353 from maaskola/discrover

sci-biology/discrover: bump package version, add USE flag for link-time ...


 sci-biology/discrover/ChangeLog                          |  7 +++++++
 sci-biology/discrover/Manifest                           |  2 +-
 .../{discrover-1.4.1.ebuild => discrover-1.5.2.ebuild}   | 14 +++++++++++++-
 sci-biology/discrover/discrover-9999.ebuild              | 16 ++++++++++++++--
 sci-biology/discrover/metadata.xml                       |  5 ++++-
 5 files changed, 39 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     4b154286af69477d50993cae6a97dce9cdfbb4aa
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 26 07:57:36 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan 26 07:57:36 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4b154286

Merge remote-tracking branch 'github/master'

* github/master:
  Moved to tree


 licenses/Mendeley-terms | 220 ------------------------------------------------
 1 file changed, 220 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     fda5618c733e7fd752e4eed9f6fdd1f6c77ded62
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 25 16:41:36 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 25 16:41:36 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fda5618c

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/mpiblacs: Move to EAPI=5; Add missing dies
  sys-cluster/htcondor: Clean patches according to the CLEAN PATCH HOWTO
  sys-cluster/htcondor: Rename patches according to the CLEAN PATCH HOWTO
  dev-python/python-ivi: Add missing metadata.xml
  dev-python/python-{ivi,vxi11}: Remove python3_3
  dev-python/python-ivi: New package
  dev-python/python-vxi11: Add version 9999 to ChangeLog
  dev-python/python-vxi11: New package


 dev-python/python-ivi/ChangeLog                    |  9 +++++++
 dev-python/python-ivi/Manifest                     |  1 +
 dev-python/python-ivi/metadata.xml                 | 15 +++++++++++
 dev-python/python-ivi/python-ivi-0.14.9.ebuild     |  1 +
 dev-python/python-ivi/python-ivi-9999.ebuild       | 30 ++++++++++++++++++++++
 dev-python/python-vxi11/ChangeLog                  |  9 +++++++
 dev-python/python-vxi11/Manifest                   |  1 +
 dev-python/python-vxi11/metadata.xml               | 14 ++++++++++
 dev-python/python-vxi11/python-vxi11-0.7.ebuild    |  1 +
 dev-python/python-vxi11/python-vxi11-9999.ebuild   | 22 ++++++++++++++++
 sci-libs/mpiblacs/ChangeLog                        |  5 +++-
 sci-libs/mpiblacs/mpiblacs-1.1-r1.ebuild           | 10 ++++----
 ...ers-condor_config-last-rather-than-first.patch} |  8 ++++--
 ... => htcondor-8.3.2-condor_config.generic.patch} |  8 ++++--
 ... => htcondor-8.3.2-packaging_directories.patch} |  8 ++++--
 ....2.patch => htcondor-8.3.2-shadow_dlopen.patch} |  7 +++--
 sys-cluster/htcondor/htcondor-8.3.2.ebuild         |  8 +++---
 17 files changed, 139 insertions(+), 18 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     ba10fc13758ba8343c641248169fd75fdfcdea5a
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Fri Jan 23 18:18:46 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Jan 23 18:18:46 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ba10fc13

Merge pull request #352 from marbre/bokeh

dev-python/bokeh: version bump


 dev-python/{matlab_wrapper => bokeh}/ChangeLog |  8 +--
 dev-python/bokeh/Manifest                      |  1 +
 dev-python/bokeh/bokeh-0.7.1.ebuild            | 88 ++++++++++++++++++++++++++
 dev-python/bokeh/files/bokeh-0.7.1-setup.patch | 17 +++++
 dev-python/bokeh/metadata.xml                  | 12 ++++
 5 files changed, 122 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6aeca596bbcf8576c3184bc204eb54fdbb33ba24
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 23 11:51:49 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jan 23 11:51:49 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6aeca596

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/matlab_wrapper: Use ${PN} instead of package name
  dev-python/matlab_wrapper: Add to overlay

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f69b089cc12308f3e387a63576a5b334fd157ceb
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Fri Jan 23 02:55:06 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jan 23 02:55:06 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f69b089c

Merge pull request #351 from marbre/matlab_wrapper

dev-python/matlab_wrapper: Add to overlay


 dev-python/matlab_wrapper/ChangeLog                |  9 ++++++++
 dev-python/matlab_wrapper/Manifest                 |  1 +
 .../matlab_wrapper/matlab_wrapper-0.9.6.ebuild     |  1 +
 .../matlab_wrapper/matlab_wrapper-9999.ebuild      | 25 ++++++++++++++++++++++
 dev-python/matlab_wrapper/metadata.xml             | 16 ++++++++++++++
 5 files changed, 52 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     72b82ff3023586f88ad8019673a67fd757054094
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Thu Jan 22 00:14:18 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jan 22 00:14:18 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=72b82ff3

Merge pull request #345 from chatcannon/NeXus

Add ebuild for NeXus, thanks!


 sci-libs/nexus/Manifest           |  1 +
 sci-libs/nexus/metadata.xml       | 26 +++++++++++++++++++
 sci-libs/nexus/nexus-4.3.1.ebuild | 54 +++++++++++++++++++++++++++++++++++++++
 3 files changed, 81 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     c5acd3c236960cfa44ed213256e450eccb3d099d
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 22 00:10:22 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Jan 22 00:10:22 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c5acd3c2

Merge commit '9582422' (fixes #349)


 sci-visualization/mayavi/ChangeLog           |  8 ++++
 sci-visualization/mayavi/Manifest            |  1 +
 sci-visualization/mayavi/mayavi-4.4.0.ebuild | 69 ++++++++++++++++++++++++++++
 sci-visualization/mayavi/metadata.xml        | 24 ++++++++++
 4 files changed, 102 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     7b26f12a40c8a75804ebd7b337bfce5196339e3d
Author:     Jan Simons <jamasi <AT> digitac <DOT> cc>
AuthorDate: Wed Jan 21 17:19:28 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Jan 21 17:19:28 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7b26f12a

Merge branch 'master' of https://github.com/gentoo-science/sci


 app-editors/neovim/ChangeLog                       |  5 ++-
 app-editors/neovim/neovim-9999.ebuild              |  4 +-
 dev-libs/mxml/Manifest                             |  1 +
 dev-libs/mxml/metadata.xml                         | 14 +++++++
 dev-libs/mxml/mxml-2.9.ebuild                      | 19 ++++++++++
 dev-util/nvidia-cuda-gdk/ChangeLog                 |  6 ++-
 dev-util/nvidia-cuda-gdk/files/nvidia-healthmon    |  4 +-
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild  |  4 +-
 .../nvidia-cuda-sdk/nvidia-cuda-sdk-7.0.18.ebuild  |  2 +-
 .../nvidia-cuda-toolkit-7.0.18.ebuild              |  2 +-
 sci-libs/acml/ChangeLog                            |  8 +++-
 sci-libs/acml/acml-5.3.1.ebuild                    |  6 +--
 sci-libs/arrayfire/arrayfire-9999.ebuild           | 13 +++++--
 sci-libs/factory/ChangeLog                         | 13 ++++++-
 ...ory-3.1.1-r1.ebuild => factory-3.1.1-r2.ebuild} | 16 +++++---
 sci-libs/factory/factory-3.1.1.ebuild              | 44 ----------------------
 sci-misc/mendeleydesktop/ChangeLog                 |  8 +++-
 .../files/mendeleydesktop-fix-python3.patch        | 16 ++++++++
 .../mendeleydesktop/mendeleydesktop-1.13.1.ebuild  |  3 ++
 19 files changed, 116 insertions(+), 72 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     63b330dda2663fb235b238be376266778db44326
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 22 00:03:20 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Jan 22 00:03:20 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=63b330dd

Merge commit '3a74e60d0cc14df2d2c1c3d81a451e31fe8aad16'


 sci-visualization/mayavi/ChangeLog           |  8 ++++
 sci-visualization/mayavi/Manifest            |  1 +
 sci-visualization/mayavi/mayavi-4.4.0.ebuild | 69 ++++++++++++++++++++++++++++
 sci-visualization/mayavi/metadata.xml        | 24 ++++++++++
 4 files changed, 102 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     450c5f09aa0f45dc4e3eb72a9f2756a82d0ce631
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 20 11:53:27 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Jan 20 11:53:27 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=450c5f09

Merge pull request #350 from chatcannon/mxml

New ebuild for mxml (Mini-XML)


 dev-libs/mxml/Manifest        |  1 +
 dev-libs/mxml/metadata.xml    | 14 ++++++++++++++
 dev-libs/mxml/mxml-2.9.ebuild | 19 +++++++++++++++++++
 3 files changed, 34 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     2159d3c7acfbbe0ced3a4cbae87bb74479c39e03
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Tue Jan 20 22:53:02 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Jan 20 22:53:02 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2159d3c7

Merge pull request #347 from marbre/factory

sci-libs/factory: Drop old, move to EAPI=5 and add ebuild with support for static-libs use flag


 sci-libs/factory/ChangeLog                         | 13 ++++++-
 ...ory-3.1.1-r1.ebuild => factory-3.1.1-r2.ebuild} | 16 +++++---
 sci-libs/factory/factory-3.1.1.ebuild              | 44 ----------------------
 3 files changed, 22 insertions(+), 51 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b0cb459910352b9cfc41797df36cb1bbab4cbeb2
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 19 17:59:30 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan 19 17:59:30 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b0cb4599

Merge remote-tracking branch 'github/master'

* github/master:
  sci-misc/mendeleydesktop: Fix for python3
  dev-util/nvidia-cuda-gdk: Fix wrapper /opt/bin/nvidia-healthmon
  dev-util/nvidia-cuda-gdk: Update copyright year
  Drop sci-libs/libfac-3.1.0.ebuild


 dev-util/nvidia-cuda-gdk/ChangeLog                 |  6 ++++-
 dev-util/nvidia-cuda-gdk/files/nvidia-healthmon    |  4 ++--
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild  |  2 +-
 sci-libs/libfac/ChangeLog                          |  7 +++++-
 sci-libs/libfac/libfac-3.1.0.ebuild                | 27 ----------------------
 sci-misc/mendeleydesktop/ChangeLog                 |  8 +++++--
 .../files/mendeleydesktop-fix-python3.patch        | 16 +++++++++++++
 .../mendeleydesktop/mendeleydesktop-1.13.1.ebuild  |  3 +++
 8 files changed, 39 insertions(+), 34 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     1fee7aa8fbe58d1f5bc691b188fe56985c30909d
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Fri Jan 16 19:58:41 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Jan 16 19:58:41 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1fee7aa8

Merge pull request #346 from marbre/nvidia-cuda-sdk

Fix KEYWORDS in nvidia-cuda-sdk ebuild


 dev-util/nvidia-cuda-sdk/nvidia-cuda-sdk-7.0.18.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     b6a6b78ecdfec15efd305b17e7cfcc1b26002ccc
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Fri Jan 16 02:27:28 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Jan 16 02:27:28 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b6a6b78e

Merge pull request #342 from marbre/librecad

media-gfx/librecad-1.0.*: Move to EAPI=5


 media-gfx/librecad/ChangeLog             | 10 +++++++++-
 media-gfx/librecad/librecad-1.0.3.ebuild | 24 ++++++++----------------
 media-gfx/librecad/librecad-1.0.4.ebuild | 24 ++++++++----------------
 media-gfx/librecad/librecad-2.0.7.ebuild | 17 ++++++-----------
 4 files changed, 31 insertions(+), 44 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     0a893bf08ad33f380d3ee9536d261fe6a4f57550
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Fri Jan 16 02:29:42 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Jan 16 02:29:42 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0a893bf0

Merge pull request #329 from marbre/symmetrica

sci-libs/symmetrica: Move to EAPI=5 and clean the ebuild


 sci-libs/symmetrica/ChangeLog             |  4 ++++
 sci-libs/symmetrica/symmetrica-2.0.ebuild | 26 +++++++-------------------
 2 files changed, 11 insertions(+), 19 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     1d9098f34164d70997a413e5aa8601530fef2f4b
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 16 14:16:15 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Jan 16 14:16:15 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1d9098f3

Merge pull request #339 from marbre/nvidia-cuda-sdk

dev-util/nvidia-cuda-sdk: Add 7.0 release candidate


 .../ChangeLog                                      |   5 +-
 .../Manifest                                       |   0
 .../nvidia-cuda-sdk}/metadata.xml                  |   8 ++
 .../nvidia-cuda-sdk/nvidia-cuda-sdk-7.0.18.ebuild  | 151 +++++++++++++++++++++
 4 files changed, 161 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     95a07532adfe04ec4d5e258bc2ba3bac6cc9d31e
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 16 14:11:10 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Jan 16 14:11:10 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=95a07532

Merge pull request #338 from marbre/nvidia-cuda-toolkit

Add nvidia-cuda-toolkit release candidate (7.0.18)


 dev-util/nvidia-cuda-toolkit/ChangeLog             |    9 +
 dev-util/nvidia-cuda-toolkit/Manifest              |    1 +
 dev-util/nvidia-cuda-toolkit/files/cuda-config.in  |   28 +
 .../nvidia-cuda-toolkit}/metadata.xml              |    9 +
 .../nvidia-cuda-toolkit-7.0.18.ebuild              |  156 ++
 licenses/NVIDIA-CUDA                               | 2262 ++++++++++++++++++++
 6 files changed, 2465 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     1e0b6daf4f2da313a5d8b4fa9c8c786060155628
Author:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Thu Jan 15 18:23:16 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Jan 15 18:23:16 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1e0b6daf

Merge branch 'master' into librecad

Conflicts:
	media-gfx/librecad/ChangeLog


 media-gfx/librecad/ChangeLog                       |  3 ++
 media-gfx/librecad/Manifest                        |  2 +-
 ...librecad-2.0.3.ebuild => librecad-2.0.7.ebuild} |  2 +-
 sci-biology/bcftools/ChangeLog                     |  3 ++
 sci-biology/bcftools/bcftools-1.1.ebuild           |  2 +-
 sci-biology/edena/ChangeLog                        |  9 +++++
 sci-biology/edena/Manifest                         |  1 +
 sci-biology/edena/edena-3.131028.ebuild            | 35 +++++++++++++++++++
 sci-biology/{zmsort => edena}/metadata.xml         |  0
 sci-biology/mosaik/ChangeLog                       | 11 ++++--
 sci-biology/mosaik/Manifest                        |  2 +-
 .../{mosaik-2.1.33.ebuild => mosaik-2.2.3.ebuild}  | 10 ++++--
 sci-biology/ncbi-blast+/ChangeLog                  |  4 ++-
 sci-biology/ncbi-blast+/metadata.xml               | 27 +++++++++++++++
 sci-biology/quast/ChangeLog                        | 11 +++++-
 sci-biology/quast/Manifest                         |  2 +-
 .../quast/{quast-2.2.ebuild => quast-2.3.ebuild}   |  4 +--
 sci-biology/sabre/ChangeLog                        |  9 +++++
 sci-biology/{zmsort => sabre}/metadata.xml         |  0
 sci-biology/sabre/sabre-9999.ebuild                | 39 ++++++++++++++++++++++
 sci-biology/sickle/ChangeLog                       |  6 ++--
 sci-biology/sickle/sickle-9999.ebuild              |  4 +--
 sci-chemistry/nwchem/ChangeLog                     |  7 ++++
 ...26243-r4.ebuild => nwchem-6.5_p26243-r5.ebuild} |  2 +-
 24 files changed, 177 insertions(+), 18 deletions(-)

diff --cc media-gfx/librecad/ChangeLog
index 7b80bf4,dfded70..e719749
--- a/media-gfx/librecad/ChangeLog
+++ b/media-gfx/librecad/ChangeLog
@@@ -1,11 -1,10 +1,14 @@@
  # ChangeLog for media-gfx/librecad
 -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
  # $Header$
  
 +  15 Jan 2015; Marius Brehler <marbre@linux.sungazer.de>
 +  librecad-1.0.3.ebuild, librecad-1.0.4.ebuild:
 +  Move to EAPI=5
 +
+   15 Jan 2015; Dongxu Li <dongxuli2011@gmail.com> +librecad-2.0.7.ebuild, -librecad-2.0.3.ebuild:
+   Version bump: 2.0.7
+ 
    19 Sep 2014; Dongxu Li <dongxuli2011@gmail.com> : librecad-9999.ebuild:
    install appdata.xml
  

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     3b3468cf819c198a96d477f5c665940b40d3a4f4
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 15 15:56:32 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Jan 15 15:56:32 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3b3468cf

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 media-gfx/librecad/ChangeLog                                        | 4 ++++
 media-gfx/librecad/Manifest                                         | 2 +-
 media-gfx/librecad/{librecad-2.0.3.ebuild => librecad-2.0.7.ebuild} | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     e6ef02c1db4cc08ac7e97754127893aa627cd231
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan 15 11:13:34 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan 15 11:13:34 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e6ef02c1

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-chemistry/nwchem/ChangeLog                                     | 7 +++++++
 .../{nwchem-6.5_p26243-r4.ebuild => nwchem-6.5_p26243-r5.ebuild}   | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     5f86af85e0004ac47a3fed36ca1c8c92bd77160a
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan 15 09:55:55 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan 15 09:55:55 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5f86af85

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 dev-python/astropy-helpers/ChangeLog               |   5 +-
 .../astropy-helpers/astropy-helpers-0.4.1.ebuild   |  29 +--
 dev-python/astropy-helpers/metadata.xml            |   4 +-
 dev-python/astropy/ChangeLog                       |   5 +-
 licenses/Mendeley-terms                            | 220 +++++++++++++++++++++
 sci-libs/arrayfire/arrayfire-9999.ebuild           |   2 +-
 sci-libs/dealii/ChangeLog                          |   8 +-
 sci-libs/dealii/Manifest                           |   2 +
 sci-libs/dealii/dealii-8.2.0.ebuild                |   2 +-
 .../{dealii-9999.ebuild => dealii-8.2.1.ebuild}    |   2 +-
 sci-libs/dealii/dealii-9999.ebuild                 |   7 +-
 sci-libs/libspatialindex/Manifest                  |   2 +-
 .../files/libspatialindex-1.8.1-QA.patch           |  15 ++
 .../libspatialindex/libspatialindex-1.6.1.ebuild   |  19 --
 .../libspatialindex/libspatialindex-1.8.5.ebuild   |  37 ++++
 sci-libs/libspatialindex/metadata.xml              |   6 +-
 sci-misc/kaldi/ChangeLog                           |  10 +
 sci-misc/kaldi/files/Makefile.patch                |  19 ++
 sci-misc/kaldi/files/configure.patch               |  71 +++++++
 sci-misc/kaldi/files/default_rules.mk.patch        |  20 ++
 sci-misc/kaldi/kaldi-0_p20150101.ebuild            |  59 ++++++
 sci-misc/kaldi/metadata.xml                        |  12 ++
 sci-misc/mendeleydesktop/ChangeLog                 |  14 ++
 sci-misc/mendeleydesktop/Manifest                  |   2 +
 .../mendeleydesktop/mendeleydesktop-1.13.1.ebuild  | 114 +++++++++++
 sci-misc/mendeleydesktop/metadata.xml              |   9 +
 26 files changed, 633 insertions(+), 62 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     0469a57df20fa4e3f66c15f5be8ecdcda492b872
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 15 06:53:00 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jan 15 06:53:00 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0469a57d

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/dealii - version bump; update live build
  sci-libs/libspatialindex: add myself to metadata.xml
  sci-libs/libspatialindex: rm old 1.6.1
  sci-libs/libspatialindex: version bump to 1.8.5
  sci-misc/mendeleydesktop: Version bump; Drop old
  sci-misc/kaldi: Comment about special case with upstream configure script
  sci-misc/mendeleydesktop: Fix RDEPEND; 's/rm -rf/rm -r/'
  Update Mendeley-terms
  Rename Mendeley-EULA to Mendeley-terms
  sci-misc/mendeleydesktop: Add version bumped ebuild
  sci-libs/arrayfire: Fix dobin of bin2cpp
  sci-misc/kaldi: Live ebuild don't has keywords
  sci-misc/kaldi: New package

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     2700b53f02a36f786069b9ada9d346feec89ff49
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 14 09:55:18 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jan 14 09:55:18 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2700b53f

Merge pull request #337 from marbre/mendeleydesktop

sci-misc/mendeleydesktop: Version bump; Drop old


 sci-misc/mendeleydesktop/ChangeLog                                | 8 +++++++-
 sci-misc/mendeleydesktop/Manifest                                 | 4 ++--
 ...{mendeleydesktop-1.13.ebuild => mendeleydesktop-1.13.1.ebuild} | 0
 3 files changed, 9 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     aa0fc9ec83064a6f3af49e2d903fed33da350def
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Wed Jan 14 18:14:45 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jan 14 18:14:45 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=aa0fc9ec

Merge pull request #340 from hasufell/master

update sci-libs/libspatialindex to 1.8.5


 sci-libs/libspatialindex/Manifest                  |  2 +-
 .../files/libspatialindex-1.8.1-QA.patch           | 15 +++++++++
 .../libspatialindex/libspatialindex-1.6.1.ebuild   | 19 -----------
 .../libspatialindex/libspatialindex-1.8.5.ebuild   | 37 ++++++++++++++++++++++
 sci-libs/libspatialindex/metadata.xml              |  6 +++-
 5 files changed, 58 insertions(+), 21 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     020e896750029ad764032b2ad756266eaaf101b7
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Tue Jan 13 01:34:40 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Jan 13 01:34:40 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=020e8967

Merge pull request #334 from olifre/master

geant-vmc: Upstream does not provide version_info file anymore, adapt live


 sci-physics/geant-vmc/ChangeLog             | 6 +++++-
 sci-physics/geant-vmc/geant-vmc-9999.ebuild | 4 ++--
 2 files changed, 7 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     15d5a701ba649b53f5dadd8f3895d4f4f57e68af
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Mon Jan 12 23:08:18 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jan 12 23:08:18 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=15d5a701

Merge pull request #333 from marbre/arrayfire

sci-libs/arrayfire: Pull master branch; Add git url; Remove keywords


 sci-libs/arrayfire/ChangeLog               | 8 +++++++-
 sci-libs/arrayfire/arrayfire-0.9999.ebuild | 1 +
 sci-libs/arrayfire/arrayfire-9999.ebuild   | 8 ++++++--
 3 files changed, 14 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     28ff4286d12ac32377f33b52bafc5dcad27c506a
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 12 20:23:41 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jan 12 20:23:41 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=28ff4286

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 dev-libs/libconfig/ChangeLog                       |   7 ++
 dev-libs/libconfig/libconfig-9999.ebuild           |  61 ++++++++++++
 dev-libs/libconfig/metadata.xml                    |  12 +++
 licenses/{CeCILL-2.0 => CeCILL-B}                  | 108 +++++++++++----------
 sci-biology/quicktree/quicktree-1.1-r1.ebuild      |   4 +-
 sci-libs/armadillo/ChangeLog                       |   8 +-
 sci-libs/armadillo/Manifest                        |   1 +
 ...llo-4.300.9.ebuild => armadillo-4.600.2.ebuild} |   8 +-
 sci-libs/givaro/ChangeLog                          |  12 ++-
 sci-libs/givaro/Manifest                           |   5 +-
 sci-libs/givaro/givaro-3.2.13.ebuild               |  13 +--
 sci-libs/givaro/givaro-3.3.0.ebuild                |  20 +---
 sci-libs/givaro/givaro-3.8.0.ebuild                |  21 ++++
 sci-physics/qcl/ChangeLog                          |   6 +-
 sci-physics/qcl/qcl-0.6.3-r1.ebuild                |  19 ++--
 sci-physics/qcl/qcl-0.6.4.ebuild                   |  12 ++-
 16 files changed, 218 insertions(+), 99 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     9c51c07656c6facd468c128ed8742d948fa0e350
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 12 10:09:57 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jan 12 10:09:57 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9c51c076

Merge pull request #327 from marbre/libconfig

dev-libs/libconfig-9999: Add ebuild to overlay


 dev-libs/libconfig/ChangeLog             |  7 ++++
 dev-libs/libconfig/libconfig-9999.ebuild | 61 ++++++++++++++++++++++++++++++++
 dev-libs/libconfig/metadata.xml          | 12 +++++++
 3 files changed, 80 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     e544b6dc5cd601d2cd445b5e84cc9904ec953a71
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Mon Jan 12 20:23:02 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jan 12 20:23:02 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e544b6dc

Merge pull request #325 from marbre/armadillo

sci-libs/armadillo-4.600.2: Version bump, fix examples install location


 sci-libs/armadillo/ChangeLog                                      | 8 +++++++-
 sci-libs/armadillo/Manifest                                       | 1 +
 .../{armadillo-4.300.9.ebuild => armadillo-4.600.2.ebuild}        | 8 +++-----
 3 files changed, 11 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     1af990a275bf57a9c60bdbbad16ea8bcbe081f2a
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 12 10:06:41 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jan 12 10:06:41 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1af990a2

Merge pull request #324 from marbre/qcl

sci-physics/qcl: Move to EAPI=5, cleanup ebuilds


 sci-physics/qcl/ChangeLog           |  6 +++++-
 sci-physics/qcl/qcl-0.6.3-r1.ebuild | 19 +++++++++++--------
 sci-physics/qcl/qcl-0.6.4.ebuild    | 12 ++++++++----
 3 files changed, 24 insertions(+), 13 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     ed941a8691edac365a5c260451a671564d8775ad
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 12 10:05:51 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jan 12 10:05:51 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ed941a86

Merge pull request #323 from marbre/givaro

Fix and clean sci-libs/givaro ebuilds; Bump version


 licenses/{CeCILL-2.0 => CeCILL-B}    | 108 +++++++++++++++++++----------------
 sci-libs/givaro/ChangeLog            |  12 +++-
 sci-libs/givaro/Manifest             |   5 +-
 sci-libs/givaro/givaro-3.2.13.ebuild |  13 +----
 sci-libs/givaro/givaro-3.3.0.ebuild  |  20 ++-----
 sci-libs/givaro/givaro-3.8.0.ebuild  |  21 +++++++
 6 files changed, 101 insertions(+), 78 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     2cf05da5143b9f0d2b66aa6f1970f5c115e79c28
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 12 09:53:43 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jan 12 09:53:43 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2cf05da5

Merge pull request #328 from marbre/quicktree

sci-biology/quicktree: Really move to EAPI=5


 sci-biology/quicktree/quicktree-1.1-r1.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     c992ba97a44bf9870fad6abc92cb029e885fcdec
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jan 12 16:43:39 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jan 12 16:43:39 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c992ba97

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-libs/libfac/ChangeLog                          |  6 ++-
 sci-libs/libfac/libfac-3.1.0.ebuild                | 10 ++---
 sci-libs/libfac/libfac-3.1.1.ebuild                | 10 ++---
 sci-libs/matio/ChangeLog                           |  6 ++-
 sci-libs/matio/matio-1.3.4.ebuild                  | 32 +++++++---------
 ...ondor_config-last-rather-than-first-8.3.2.patch | 25 +++++++++++++
 .../files/condor_config.generic-8.3.2.patch        | 43 ++++++++++++++++++++++
 .../files/condor_shadow_dlopen-8.3.2.patch         | 11 ++++++
 ...0.0.patch => packaging_directories-8.3.2.patch} |  6 +--
 sys-cluster/htcondor/htcondor-8.3.2.ebuild         |  6 +--
 10 files changed, 115 insertions(+), 40 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     2f01524e628122a245c39c6fd913f5b2b79b9934
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 11 19:21:28 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Jan 11 19:21:28 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2f01524e

Merge pull request #330 from marbre/matio

Bring back (revised) matio ebuild


 sci-libs/matio/ChangeLog                         | 43 ++++++++++++++++++++++++
 sci-libs/matio/Manifest                          |  1 +
 sci-libs/matio/files/matio-1.3.4-autotools.patch | 29 ++++++++++++++++
 sci-libs/matio/matio-1.3.4.ebuild                | 43 ++++++++++++++++++++++++
 sci-libs/{omalloc => matio}/metadata.xml         |  7 ++--
 5 files changed, 118 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     13e31ae68a36a904b97b6e6fba81b8178a4208a6
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 11 12:10:14 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Jan 11 12:10:14 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=13e31ae6

Merge pull request #326 from marbre/matio

Remove matio from overlay, newer versions in tree


 sci-libs/matio/ChangeLog                         | 39 --------------------
 sci-libs/matio/Manifest                          |  1 -
 sci-libs/matio/files/matio-1.3.4-autotools.patch | 29 ---------------
 sci-libs/matio/matio-1.3.4.ebuild                | 47 ------------------------
 sci-libs/matio/metadata.xml                      |  9 -----
 5 files changed, 125 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     66561ba1df13f4e3580a879f5245920609e63bb0
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 11 19:07:05 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Jan 11 19:07:05 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=66561ba1

Merge pull request #331 from marbre/htcondor

Adjusted patchset for htcondor-8.3.2


 ...ondor_config-last-rather-than-first-8.3.2.patch | 25 +++++++++++++
 .../files/condor_config.generic-8.3.2.patch        | 43 ++++++++++++++++++++++
 .../files/condor_shadow_dlopen-8.3.2.patch         | 11 ++++++
 ...0.0.patch => packaging_directories-8.3.2.patch} |  6 +--
 sys-cluster/htcondor/htcondor-8.3.2.ebuild         |  6 +--
 5 files changed, 85 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     5a322c896bfeb17b1abaf00eca1096f869a7feef
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 11 10:45:09 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Jan 11 10:45:09 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5a322c89

Merge pull request #322 from marbre/libfac

sci-libs/libfac: Move to EAPI=5, clean ebuilds


 sci-libs/libfac/ChangeLog           |  6 +++++-
 sci-libs/libfac/libfac-3.1.0.ebuild | 10 +++-------
 sci-libs/libfac/libfac-3.1.1.ebuild | 10 +++-------
 3 files changed, 11 insertions(+), 15 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b57991369687010ca643fc11e2a09c7130d76add
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 11 09:12:43 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 11 09:12:43 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b5799136

Merge remote-tracking branch 'github/master'

* github/master:
  sci-libs/arrayfire: Improve and clean gtest src handling
  sci-libs/arrayfire: Fix DEPEND, unpacker is used instead of unzip
  sci-biology/rnaplex: Fixes according to jlec's advices
  sci-biology/codonw: Drop unnecessary dies
  Drop unnecessary die
  ci-biology/rnaplex: Move to EAPI=5; Update homepage and SRC_URI.
  sci-biology/codonw: Move to EAPI=5


 sci-biology/codonw/ChangeLog              |  6 +++++-
 sci-biology/codonw/codonw-1.4.4-r1.ebuild | 12 ++++++------
 sci-biology/rnaplex/ChangeLog             |  6 +++++-
 sci-biology/rnaplex/Manifest              |  2 +-
 sci-biology/rnaplex/rnaplex-0.2.ebuild    | 14 ++++----------
 sci-libs/arrayfire/arrayfire-9999.ebuild  | 13 +++++++------
 6 files changed, 28 insertions(+), 25 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     7751b06c2a4cc7cba604e7f986c7c8c49bb5a7c5
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 18:44:29 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 18:44:29 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7751b06c

Merge pull request #319 from marbre/rnaplex

ci-biology/rnaplex: Move to EAPI=5; Update homepage and SRC_URI.


 sci-biology/rnaplex/ChangeLog          |  6 +++++-
 sci-biology/rnaplex/Manifest           |  2 +-
 sci-biology/rnaplex/rnaplex-0.2.ebuild | 14 ++++----------
 3 files changed, 10 insertions(+), 12 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     968c11d9a497e51812b09b70d7e601468e962b30
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Sat Jan 10 18:22:42 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 18:22:42 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=968c11d9

Merge pull request #317 from marbre/codonw

sci-biology/codonw: Move to EAPI=5


 sci-biology/codonw/ChangeLog              |  6 +++++-
 sci-biology/codonw/codonw-1.4.4-r1.ebuild | 12 ++++++------
 2 files changed, 11 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a3fb2f2846f14b9f2dce81a74c56c2747a1f685d
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Sun Jan 11 01:10:30 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 11 01:10:30 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a3fb2f28

Merge pull request #320 from marbre/arrayfire

sci-libs/arrayfire: Fix DEPEND and replace unpacker by unpack


 sci-libs/arrayfire/arrayfire-9999.ebuild | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a8663a4f2a09f03ff25162bfb56b6d3866ee44a0
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 18:01:56 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 18:01:56 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a8663a4f

Merge pull request #312 from marbre/arrayfire

ArrayFire ebuild


 sci-libs/arrayfire/ChangeLog                       | 10 +++
 sci-libs/arrayfire/Manifest                        |  1 +
 sci-libs/arrayfire/arrayfire-9999.ebuild           | 81 ++++++++++++++++++++++
 sci-libs/arrayfire/files/CMakeLists_examples.patch | 11 +++
 sci-libs/arrayfire/files/FindCBLAS.patch           | 48 +++++++++++++
 sci-libs/arrayfire/files/build_gtest.patch         | 51 ++++++++++++++
 .../arrayfire}/metadata.xml                        | 12 ++--
 7 files changed, 208 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6f1ee4089713b543429069af689749d5943707b3
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 15:15:21 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 15:15:21 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6f1ee408

Merge pull request #316 from marbre/jeuclid-core

dev-java/jeuclid-core: Move to EAPI=5


 dev-java/jeuclid-core/ChangeLog                    | 6 +++++-
 dev-java/jeuclid-core/jeuclid-core-3.1.8.ebuild    | 4 ++--
 dev-java/jeuclid-core/jeuclid-core-3.1.9-r1.ebuild | 4 ++--
 3 files changed, 9 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     de0969dc6e88626267301e6449ba63a537830745
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 16:10:17 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 16:10:17 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=de0969dc

Merge pull request #318 from marbre/merlin

sci-biology/merlin: Move to EAPI=5


 sci-biology/merlin/ChangeLog           |  6 +++++-
 sci-biology/merlin/merlin-1.1.2.ebuild | 10 +++++-----
 2 files changed, 10 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     fe6cc50c3a170cec30479fe5796c257820e53de7
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 14:57:07 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 14:57:07 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fe6cc50c

Merge pull request #313 from marbre/InterMine

Fix InterMine QA issues


 sci-biology/InterMine/ChangeLog             | 4 ++++
 sci-biology/InterMine/InterMine-0.98.ebuild | 8 ++++----
 2 files changed, 8 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     bedef4b638d4cbead16f369c58f613487aa854d9
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 14:36:49 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 14:36:49 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bedef4b6

Merge pull request #315 from marbre/trans-abyss

sci-biology/trans-abys: Fix license and keywords


 licenses/bcca_2010                               | 453 +++++++++++++++++++++++
 sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild |   5 +-
 2 files changed, 456 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     1e18b4a7dd7146ad77b556623f8da427365e68d6
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 14:39:54 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 14:39:54 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1e18b4a7

Merge remote-tracking branch 'github/master'

* github/master:
  sci-biology/trans-abys: Fix license and keywords


 licenses/bcca_2010                               | 453 +++++++++++++++++++++++
 sci-biology/trans-abyss/trans-abyss-1.4.8.ebuild |   5 +-
 2 files changed, 456 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     205621fbbbc3cb8826bff69b48ddb61badd599fe
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 14:11:00 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 14:11:00 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=205621fb

Merge remote-tracking branch 'github/master'

* github/master:
  Fix mosstack QA warnings: Clean Manifest


 sci-astronomy/mosstack/Manifest | 1 -
 1 file changed, 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f0322e5019d42cc97f5478c89a9089e7bdd13faf
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 13:56:48 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 13:56:48 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f0322e50

Merge pull request #314 from marbre/mosstack

Fix mosstack QA warnings: Clean Manifest


 sci-astronomy/mosstack/Manifest | 1 -
 1 file changed, 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ced595b6dafab30a3203459d5aea111411ebc292
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 11:47:35 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 11:47:35 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ced595b6

Merge remote-tracking branch 'github/master'

* github/master:
  Remove Mendeley-EULA (mendeleydesktop was moved to tree)


 licenses/Mendeley-EULA | 264 -------------------------------------------------
 1 file changed, 264 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5352745ea0b8baeaf7686a3243ab4a2860193ba3
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jan  9 12:25:49 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jan  9 12:25:49 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5352745e

Merge pull request #311 from marbre/master

Remove Mendeley-EULA (mendeleydesktop was moved to tree)


 licenses/Mendeley-EULA | 264 -------------------------------------------------
 1 file changed, 264 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     4652c378f32d44e44fe3832e996d84e378bef084
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan  8 20:02:10 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan  8 20:02:10 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4652c378

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-misc/mendeleydesktop/ChangeLog                 |  22 ----
 sci-misc/mendeleydesktop/Manifest                  |   2 -
 .../mendeleydesktop/mendeleydesktop-1.12.4.ebuild  | 121 ---------------------
 sci-misc/mendeleydesktop/metadata.xml              |  10 --
 4 files changed, 155 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     4d418c5e2b4252b74b2f3ffc46d910b11904df63
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan  8 12:42:42 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan  8 12:42:42 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4d418c5e

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 virtual/blas/blas-2.1-r3.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     3163fd540c987180bf5a4029bdb4199296661bd9
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jan  8 06:57:09 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jan  8 06:57:09 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3163fd54

Merge remote-tracking branch 'github/master'

* github/master:
  Upping eigen dependency for virtual/blas


 virtual/blas/blas-2.1-r3.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     67cfe892eb32b5c8a2681d9fa3d98ce6391bd2fe
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jan  8 06:52:01 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jan  8 06:52:01 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=67cfe892

Merge pull request #310 from stharward/master

Upping eigen dependency for virtual/blas


 virtual/blas/blas-2.1-r3.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     1060b6283320864573121f3d9987d367a82668de
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Jan  6 00:18:55 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Jan  6 00:18:55 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1060b628

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 sci-biology/discrover/ChangeLog                      | 20 +++++++++++++++++++-
 sci-biology/discrover/Manifest                       |  2 +-
 ...discrover-1.3.1.ebuild => discrover-1.4.1.ebuild} | 10 ++++++----
 sci-biology/discrover/discrover-9999.ebuild          | 10 ++++++----
 sci-biology/discrover/metadata.xml                   |  5 ++++-
 5 files changed, 36 insertions(+), 11 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     d583b16070643d519149d79311aa254584cc404b
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Mon Jan  5 05:08:24 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jan  5 05:08:24 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d583b160

Merge pull request #308 from maaskola/sci-biology/discrover

sci-biology/discrover: bump minor version to 1.4.0.


 sci-biology/discrover/ChangeLog                      | 20 +++++++++++++++++++-
 sci-biology/discrover/Manifest                       |  2 +-
 ...discrover-1.3.1.ebuild => discrover-1.4.1.ebuild} | 10 ++++++----
 sci-biology/discrover/discrover-9999.ebuild          | 10 ++++++----
 sci-biology/discrover/metadata.xml                   |  5 ++++-
 5 files changed, 36 insertions(+), 11 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Andrew Savchenko]

commit:     10296e5aef4b9bd437a35dd88e2690a14de13204
Author:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
AuthorDate: Thu Jan  1 23:10:32 2015 +0000
Commit:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
CommitDate: Thu Jan  1 23:10:32 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=10296e5a

Remove stray ChangeLog from sci-libs/openblas

---
 ChangeLog | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/ChangeLog b/ChangeLog
deleted file mode 100644
index 57a6083..0000000
--- a/ChangeLog
+++ /dev/null
@@ -1,10 +0,0 @@
-# ChangeLog for layman/science
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  06 Sep 2014; Mark Wright <gienah@gentoo.org>
-  sci-libs/openblas/openblas-9999.ebuild, openblas-9999.ebuild,
-  +sci-libs/openblas/files/openblas-0.2.11-cpuid_x86.patch,
-  -sci-libs/openblas/files/openblas-9999-cpuid_x86.patch:
-  openblas-0.2.11 requires the cpuid_x86 patch
-

[gentoo-commits] proj/sci:master commit in: /

[Andrew Savchenko]

commit:     478836d33f7e9fc2f694953635aad2048468d643
Author:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
AuthorDate: Thu Jan  1 15:25:53 2015 +0000
Commit:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
CommitDate: Thu Jan  1 15:25:53 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=478836d3

Merge remote-tracking branch 'github/master'


 sci-libs/dealii/Manifest                                         | 4 ++--
 sci-libs/dealii/{dealii-8.2.0_rc2.ebuild => dealii-8.2.0.ebuild} | 0
 sci-libs/dealii/dealii-9999.ebuild                               | 5 ++++-
 3 files changed, 6 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f0041f901f4627d8702689dcc1ba6fdc69354bf3
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 26 18:09:37 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec 26 18:09:37 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f0041f90

Merge pull request #307 from mickolaine/mosstack

Update mosstack-0.6.1-r1.ebuild


 sci-astronomy/mosstack/mosstack-0.6.1-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b2b9a5a2d536ebd2bb33de136d343a7a96380f65
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 26 09:37:46 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec 26 09:37:46 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b2b9a5a2

Merge pull request #304 from yanlinlin82/master

sci-biology/bismark: Add new package.


 sci-biology/bismark/Manifest              |  1 +
 sci-biology/bismark/bismark-0.13.0.ebuild | 31 +++++++++++++++++++++++++++++++
 sci-biology/bismark/metadata.xml          | 20 ++++++++++++++++++++
 3 files changed, 52 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     afeb7087a59a7aeadd04ddcfd8c1d207673ce375
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 26 09:38:14 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec 26 09:38:14 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=afeb7087

Merge pull request #303 from mschubert/biobambam

Add sci-biology/biobambam: a tool for bam file processing


 sci-biology/biobambam/Manifest                 |  1 +
 sci-biology/biobambam/biobambam-0.0.183.ebuild | 21 +++++++++++++++++++++
 sci-biology/biobambam/metadata.xml             | 15 +++++++++++++++
 sci-libs/libmaus/Manifest                      |  1 +
 sci-libs/libmaus/libmaus-0.0.185.ebuild        | 18 ++++++++++++++++++
 sci-libs/libmaus/metadata.xml                  | 14 ++++++++++++++
 6 files changed, 70 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     57f501a36ff6270a83d6fc7e174b622435dd69b8
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 26 09:36:57 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Dec 26 09:36:57 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=57f501a3

Merge pull request #306 from mickolaine/mosstack

Mosstack - updated ebuild because of download url


 sci-astronomy/mosstack/ChangeLog                                     | 5 +++++
 sci-astronomy/mosstack/Manifest                                      | 1 +
 .../mosstack/{mosstack-0.6.1.ebuild => mosstack-0.6.1-r1.ebuild}     | 2 +-
 3 files changed, 7 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a3b30147f1697e3de4234acc90eb379453185f8f
Author:     mikko_laine <mikko.laine <AT> gmail <DOT> com>
AuthorDate: Thu Dec 25 14:52:49 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Dec 25 14:52:49 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a3b30147

Merge https://github.com/mickolaine/sci into mosstack


 dev-python/pywcsgrid2/ChangeLog                    |   3 +
 dev-python/pywcsgrid2/pywcsgrid2-9999.ebuild       |   4 +-
 licenses/atsas                                     | 211 +++++++++++++++++++++
 sci-astronomy/pyAstroStack/ChangeLog               |  21 --
 sci-astronomy/pyAstroStack/Manifest                |   1 -
 sci-astronomy/pyAstroStack/metadata.xml            |  18 --
 .../pyAstroStack/pyAstroStack-0.3.0.ebuild         |  33 ----
 sci-biology/atsas/ChangeLog                        |  25 +++
 sci-biology/atsas/Manifest                         |   1 +
 sci-biology/atsas/atsas-2.6.0.ebuild               |  76 ++++++++
 {dev-perl/BTLib => sci-biology/atsas}/metadata.xml |   0
 sci-biology/discrover/ChangeLog                    |  11 ++
 sci-biology/discrover/Manifest                     |   2 +-
 ...scrover-1.1.2.ebuild => discrover-1.3.1.ebuild} |   1 +
 sci-biology/discrover/discrover-9999.ebuild        |   1 +
 sci-chemistry/freeon/ChangeLog                     |  10 +
 sci-chemistry/freeon/Manifest                      |   1 -
 sci-chemistry/freeon/freeon-1.0.8-r1.ebuild        |  27 ---
 sci-chemistry/freeon/freeon-1.0.8.ebuild           |  25 ---
 sci-chemistry/freeon/freeon-9999.ebuild            |  11 +-
 sci-chemistry/gromacs/ChangeLog                    |   3 +
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild      |   8 +-
 sci-chemistry/nwchem/ChangeLog                     |   9 +
 ...26243-r2.ebuild => nwchem-6.5_p26243-r3.ebuild} |  56 +++---
 sci-libs/dealii/ChangeLog                          |  11 ++
 sci-libs/dealii/Manifest                           |   6 +-
 ...alii-8.1.0-r1.ebuild => dealii-8.1.0-r2.ebuild} |  61 +++---
 sci-libs/dealii/dealii-8.2.0_rc2.ebuild            |   1 +
 sci-libs/dealii/dealii-9999.ebuild                 |  69 ++++---
 sci-libs/dealii/metadata.xml                       |   1 +
 sci-libs/mlpack/ChangeLog                          |   3 +
 sci-libs/mlpack/mlpack-1.0.8.ebuild                |   2 +-
 sci-physics/atompaw/ChangeLog                      |   8 +-
 sci-physics/atompaw/Manifest                       |   1 +
 ...w-3.0.1.9-r1.ebuild => atompaw-4.0.0.10.ebuild} |  16 +-
 sci-physics/atompaw/files/4.0-longplot.patch       |  42 ++++
 sci-physics/atompaw/metadata.xml                   |  18 +-
 sys-cluster/hpx/ChangeLog                          |   7 +
 sys-cluster/hpx/Manifest                           |   2 -
 sys-cluster/hpx/hpx-0.9.7.ebuild                   |  93 ---------
 sys-cluster/hpx/hpx-0.9.8.ebuild                   |  93 ---------
 sys-cluster/hpx/hpx-9999.ebuild                    |   1 +
 42 files changed, 569 insertions(+), 424 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c1c0f6490168e4c2d43bd151e7ec697517417e50
Author:     Mikko Laine <mikko.laine <AT> gmail <DOT> com>
AuthorDate: Thu Dec 25 14:07:11 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Dec 25 14:07:11 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c1c0f649

Merge pull request #1 from gentoo-science/master

Syncing my own fork. Sorry if I'm doing this wrong...


 dev-python/pywcsgrid2/ChangeLog                    |   3 +
 dev-python/pywcsgrid2/pywcsgrid2-9999.ebuild       |   4 +-
 licenses/atsas                                     | 211 +++++++++++++++++++++
 profiles/updates/2Q-2014                           |   1 +
 sci-astronomy/mosstack/ChangeLog                   |  10 +
 sci-astronomy/mosstack/Manifest                    |   1 +
 .../{pyAstroStack => mosstack}/metadata.xml        |   6 +-
 .../mosstack-0.6.1.ebuild}                         |  10 +-
 sci-astronomy/pyAstroStack/ChangeLog               |  21 --
 sci-astronomy/pyAstroStack/Manifest                |   1 -
 sci-biology/atsas/ChangeLog                        |  25 +++
 sci-biology/atsas/Manifest                         |   1 +
 sci-biology/atsas/atsas-2.6.0.ebuild               |  76 ++++++++
 {dev-perl/BTLib => sci-biology/atsas}/metadata.xml |   0
 sci-biology/discrover/ChangeLog                    |  11 ++
 sci-biology/discrover/Manifest                     |   2 +-
 ...scrover-1.1.2.ebuild => discrover-1.3.1.ebuild} |   1 +
 sci-biology/discrover/discrover-9999.ebuild        |   1 +
 sci-chemistry/freeon/ChangeLog                     |  10 +
 sci-chemistry/freeon/Manifest                      |   1 -
 sci-chemistry/freeon/freeon-1.0.8-r1.ebuild        |  27 ---
 sci-chemistry/freeon/freeon-1.0.8.ebuild           |  25 ---
 sci-chemistry/freeon/freeon-9999.ebuild            |  11 +-
 sci-chemistry/gromacs/ChangeLog                    |   3 +
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild      |   8 +-
 sci-chemistry/nwchem/ChangeLog                     |   9 +
 ...26243-r2.ebuild => nwchem-6.5_p26243-r3.ebuild} |  56 +++---
 sci-libs/dealii/ChangeLog                          |  11 ++
 sci-libs/dealii/Manifest                           |   6 +-
 ...alii-8.1.0-r1.ebuild => dealii-8.1.0-r2.ebuild} |  61 +++---
 sci-libs/dealii/dealii-8.2.0_rc2.ebuild            |   1 +
 sci-libs/dealii/dealii-9999.ebuild                 |  69 ++++---
 sci-libs/dealii/metadata.xml                       |   1 +
 sci-libs/mlpack/ChangeLog                          |   3 +
 sci-libs/mlpack/mlpack-1.0.8.ebuild                |   2 +-
 sci-physics/atompaw/ChangeLog                      |   8 +-
 sci-physics/atompaw/Manifest                       |   1 +
 ...w-3.0.1.9-r1.ebuild => atompaw-4.0.0.10.ebuild} |  16 +-
 sci-physics/atompaw/files/4.0-longplot.patch       |  42 ++++
 sci-physics/atompaw/metadata.xml                   |  18 +-
 sys-cluster/hpx/ChangeLog                          |   7 +
 sys-cluster/hpx/Manifest                           |   2 -
 sys-cluster/hpx/hpx-0.9.7.ebuild                   |  93 ---------
 sys-cluster/hpx/hpx-0.9.8.ebuild                   |  93 ---------
 sys-cluster/hpx/hpx-9999.ebuild                    |   1 +
 45 files changed, 590 insertions(+), 380 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     739c832926b8a29cefd1eb0d90f8e2630bcbed71
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 26 01:34:52 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Dec 26 01:34:52 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=739c8329

.travis.yml: update portage version

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 1ebe1b3..db8a92b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,6 +1,6 @@
 env:
-  - PORTAGE=2.2.12
   - PORTAGE=2.2.14
+  - PORTAGE=2.2.15
 
 before_script:
     - mkdir travis-overlay

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     0d2a711e21ef7379ad027e694a2e7750e855ff37
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Dec 24 08:26:32 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Dec 24 08:26:32 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0d2a711e

Merge pull request #305 from sargas/pywcsgrid2-py3.4

dev-python/pywcsgrid2: Update pywcs/astropy dep and add python3.4


 dev-python/pywcsgrid2/ChangeLog              | 3 +++
 dev-python/pywcsgrid2/pywcsgrid2-9999.ebuild | 4 ++--
 2 files changed, 5 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     8d421b6b9859e195977cdc599756c4d92d28031d
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Wed Dec 24 18:54:41 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Dec 24 18:54:41 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8d421b6b

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 dev-python/pywcsgrid2/ChangeLog                    |  3 +
 dev-python/pywcsgrid2/pywcsgrid2-9999.ebuild       |  4 +-
 sci-libs/dealii/ChangeLog                          | 11 ++++
 sci-libs/dealii/Manifest                           |  6 +-
 ...alii-8.1.0-r1.ebuild => dealii-8.1.0-r2.ebuild} | 61 +++++++++----------
 sci-libs/dealii/dealii-8.2.0_rc2.ebuild            |  1 +
 sci-libs/dealii/dealii-9999.ebuild                 | 69 +++++++++++++---------
 sci-libs/dealii/metadata.xml                       |  1 +
 8 files changed, 92 insertions(+), 64 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     9de62a119a29eaa8b1a9a616864c452d3ae4f8c9
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Dec 15 15:23:08 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Dec 15 15:23:08 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9de62a11

Merge pull request #302 from maaskola/sci-biology/discrover

sci-biology/discrover: version bump; add to RDEPEND


 sci-biology/discrover/ChangeLog                               | 11 +++++++++++
 sci-biology/discrover/Manifest                                |  2 +-
 .../{discrover-1.1.2.ebuild => discrover-1.3.1.ebuild}        |  1 +
 sci-biology/discrover/discrover-9999.ebuild                   |  1 +
 4 files changed, 14 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     67a9c33f862597ba1d5d213b2ee8803050345b7c
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Dec 16 23:01:42 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Dec 16 23:01:42 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=67a9c33f

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 sci-biology/discrover/ChangeLog                               | 11 +++++++++++
 sci-biology/discrover/Manifest                                |  2 +-
 .../{discrover-1.1.2.ebuild => discrover-1.3.1.ebuild}        |  1 +
 sci-biology/discrover/discrover-9999.ebuild                   |  1 +
 4 files changed, 14 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5512d27df41713ff05174ba960b26e9dbdff35a3
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 14 15:41:59 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Dec 14 15:41:59 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5512d27d

Merge pull request #301 from mickolaine/mosstack

Rename pyAstroStack to Mosstack and update version


 profiles/updates/2Q-2014                            |  1 +
 sci-astronomy/mosstack/ChangeLog                    | 10 ++++++++++
 sci-astronomy/mosstack/Manifest                     |  1 +
 .../{pyAstroStack => mosstack}/metadata.xml         |  6 ++++--
 .../mosstack-0.6.1.ebuild}                          | 10 +++++-----
 sci-astronomy/pyAstroStack/ChangeLog                | 21 ---------------------
 sci-astronomy/pyAstroStack/Manifest                 |  1 -
 7 files changed, 21 insertions(+), 29 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     7e49747b5e350a6ff2936f60f2a798a8f189ce12
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Dec 15 11:57:57 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec 15 11:57:57 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7e49747b

Merge remote-tracking branch 'github/master'

* github/master:
  Delete pyAstroStack-0.3.0.ebuild
  Delete metadata.xml
  Delete Manifest
  Delete ChangeLog
  Update 2Q-2014
  sci-astronomy/mosstack: pyAstroStack renamed to Mosstack and version bumped to 0.6.1
  sci-misc/mendeleydesktop: Version bump; Drop old


 profiles/updates/2Q-2014                            |  1 +
 sci-astronomy/mosstack/ChangeLog                    | 10 ++++++++++
 sci-astronomy/mosstack/Manifest                     |  1 +
 .../{pyAstroStack => mosstack}/metadata.xml         |  6 ++++--
 .../mosstack-0.6.1.ebuild}                          | 10 +++++-----
 sci-astronomy/pyAstroStack/ChangeLog                | 21 ---------------------
 sci-astronomy/pyAstroStack/Manifest                 |  1 -
 sci-misc/mendeleydesktop/ChangeLog                  |  6 ++++++
 sci-misc/mendeleydesktop/Manifest                   |  7 ++-----
 ...-1.12.3.ebuild => mendeleydesktop-1.12.4.ebuild} |  0
 10 files changed, 29 insertions(+), 34 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     5ffbbf248348e4f0cc25a9e1be8e76e823c3599d
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Dec  9 17:58:47 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Dec  9 17:58:47 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5ffbbf24

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 sci-libs/trilinos/ChangeLog                        |  6 +++
 sci-libs/trilinos/Manifest                         |  1 +
 ...ch => trilinos-11.12.1-fix-install-paths.patch} | 57 +++++++++++-----------
 ...linos-11.4.2.ebuild => trilinos-11.12.1.ebuild} |  0
 4 files changed, 36 insertions(+), 28 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     91dd18339cb4cc27f2e19f7ab2655bb9614fbcc0
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Dec  2 08:18:15 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Dec  2 08:18:15 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=91dd1833

Merge pull request #295 from marbre/mpe2

Add mpe2 to overlay


 licenses/mpich2                                    |  39 ++++++
 sys-cluster/mpe2/ChangeLog                         |   9 ++
 sys-cluster/mpe2/Manifest                          |   1 +
 .../jrosetta => sys-cluster/mpe2}/metadata.xml     |   2 +-
 sys-cluster/mpe2/mpe2-1.3.0.ebuild                 | 142 +++++++++++++++++++++
 5 files changed, 192 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     9fe1eb6ce3cefecfaef0cda767eb23262abd792a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Dec  1 09:28:38 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec  1 09:28:38 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9fe1eb6c

Merge remote-tracking branch 'github/master'

* github/master:
  dev-util/nvidia-cuda-gdk: Remove RESTRICT, add QA_PREBUILT
  dev-util/nvidia-cuda-gdk: Fix symlink
  sci-misc/mendeleydesktop: adjust QA flags, add pkg_postrm
  sci-misc/mendeleydesktop: update Changelog and Manifest
  sci-misc/mendeleydekstop: add fdo-mime_*_database_update to pkg_postinst
  sci-misc/mendeleydesktop: make use of make_wrapper
  sci-misc/mendeleydesktop: fix missing die, EAPI and QA flags
  fixed a typo preventing AVX2 support (bug #530454)
  sci-misc/mendeleydesktop: add ebuild to overlay

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

Conflicts:
	dev-util/nvidia-cuda-gdk/ChangeLog
	dev-util/nvidia-cuda-gdk/Manifest
	dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild


 dev-util/nvidia-cuda-gdk/ChangeLog                 |   4 +
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild  |   8 +-
 licenses/Mendeley-EULA                             | 264 +++++++++++++++++++++
 sci-chemistry/gromacs/ChangeLog                    |   4 +
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild      |   2 +-
 sci-chemistry/gromacs/gromacs-9999.ebuild          |   2 +-
 sci-misc/mendeleydesktop/ChangeLog                 |  16 ++
 sci-misc/mendeleydesktop/Manifest                  |   5 +
 .../mendeleydesktop/mendeleydesktop-1.12.3.ebuild  | 121 ++++++++++
 sci-misc/mendeleydesktop/metadata.xml              |  10 +
 10 files changed, 433 insertions(+), 3 deletions(-)

diff --cc dev-util/nvidia-cuda-gdk/ChangeLog
index 2526e36,6d816c8..169f0dc
--- a/dev-util/nvidia-cuda-gdk/ChangeLog
+++ b/dev-util/nvidia-cuda-gdk/ChangeLog
@@@ -2,9 -2,10 +2,13 @@@
  # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
  # $Header: $
  
 +  01 Dec 2014; Justin Lecher <jlec@gentoo.org> nvidia-cuda-gdk-340.29.ebuild:
 +  Drop empty lines, clean variable names and quoting
 +
+   30 Nov 2014; Marius Brehler <marbre@linux.sungazer.de>
+   nvidia-cuda-gdk-340.29.ebuild:
+   Fix symlink
+ 
    19 Nov 2014; Marius Brehler <marbre@linux.sungazer.de>
    nvidia-cuda-gdk-340.29.ebuild:
    Add ~x86 keyword
diff --cc dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild
index 99a4765,27a22a0..787e371
--- a/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild
+++ b/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild
@@@ -80,9 -76,8 +83,10 @@@ src_install() 
  	fi
  
  	ebegin "Cleaning before installation..."
 -		find -type f \( -name "*.o" -o -name "*.pdf" -o -name "*.txt" -o -name "*.3" \) -delete || die
 +		find -type f \
 +			\( -name "*.o" -o -name "*.pdf" -o -name "*.txt" -o -name "*.3" \) -delete \
 +			|| die
+ 		rm -f "${S}"/nvml/lib/libnvidia-ml.so
  	eend
  
  	if use healthmon; then

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     119eee0d29ec94e1c82acae874e41d2588a48df5
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Nov 30 13:08:09 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Nov 30 13:08:09 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=119eee0d

Merge pull request #296 from marbre/nvidia-cuda-gdk

Fix symlink to library and add QA flags


 dev-util/nvidia-cuda-gdk/ChangeLog                     | 4 ++++
 dev-util/nvidia-cuda-gdk/Manifest                      | 4 ++--
 dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild | 8 +++++++-
 3 files changed, 13 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     e0a926212e3f8d791e4a7ed4103d5afb523fdc9a
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Nov 21 10:10:31 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Nov 21 10:10:31 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e0a92621

Merge pull request #292 from marbre/nvidia-cuda-gdk

nvidia-cuda-gdk: Add ~x86 keyword


 dev-util/nvidia-cuda-gdk/ChangeLog                    |  4 ++++
 dev-util/nvidia-cuda-gdk/Manifest                     |  4 ++--
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild     | 19 +++++++++++++------
 3 files changed, 19 insertions(+), 8 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     a1a467be7346e024e4f5d591f2baedb3f5eeff75
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 24 16:19:38 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Nov 24 16:19:38 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a1a467be

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 dev-util/nvidia-cuda-gdk/ChangeLog                    |  4 ++++
 dev-util/nvidia-cuda-gdk/Manifest                     |  4 ++--
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild     | 19 +++++++++++++------
 3 files changed, 19 insertions(+), 8 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5a25861869ef679d53648aa2bab1c169622952f2
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 18 19:49:40 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Nov 18 19:49:40 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5a258618

Merge pull request #288 from marbre/nvidia-cuda-gdk

New ebuild: nvidia-cuda-gdk


 dev-util/nvidia-cuda-gdk/ChangeLog                 |   9 ++
 dev-util/nvidia-cuda-gdk/Manifest                  |   6 ++
 dev-util/nvidia-cuda-gdk/files/nvidia-healthmon    |   9 ++
 dev-util/nvidia-cuda-gdk/metadata.xml              |  17 ++++
 .../nvidia-cuda-gdk/nvidia-cuda-gdk-340.29.ebuild  | 110 +++++++++++++++++++++
 licenses/NVIDIA-gdk                                |  32 ++++++
 6 files changed, 183 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     20d8482afcd98d99afdd57a44e9aec1b72af694b
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 17 07:12:53 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 17 07:12:53 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=20d8482a

Merge pull request #286 from marbre/nvidia-cuda-toolkit

dev-util/nvidia-cuda-toolkit: add version 6.5.19


 dev-util/nvidia-cuda-toolkit/ChangeLog             |   9 ++
 .../Manifest                                       |   1 +
 dev-util/nvidia-cuda-toolkit/files/cuda-config.in  |  28 ++++
 .../metadata.xml                                   |   9 +-
 .../nvidia-cuda-toolkit-6.5.19.ebuild              | 144 +++++++++++++++++++++
 5 files changed, 187 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6b012d1f1477c6124c5ba898731bdc854f6be4c3
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 17 07:12:42 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 17 07:12:42 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6b012d1f

Merge pull request #287 from marbre/nvidia-cuda-sdk

dev-util/nvidia-cuda-sdk: add version 6.5.19


 dev-util/nvidia-cuda-sdk/ChangeLog                 |   9 ++
 dev-util/nvidia-cuda-sdk/Manifest                  |   1 +
 .../nvidia-cuda-sdk}/metadata.xml                  |   8 ++
 .../nvidia-cuda-sdk/nvidia-cuda-sdk-6.5.19.ebuild  | 145 +++++++++++++++++++++
 4 files changed, 163 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     a75abfd771787cacc7a641916a5febbd9ae5f730
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sat Nov 15 00:21:33 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Nov 15 00:21:33 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a75abfd7

.travis.yml: test different portage versions

---
 .travis.yml | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 84e0f78..1ebe1b3 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,19 +1,24 @@
+env:
+  - PORTAGE=2.2.12
+  - PORTAGE=2.2.14
+
 before_script:
     - mkdir travis-overlay
     - mv !(travis-overlay) travis-overlay/
     - mv .git travis-overlay/
-    - wget "http://distfiles.gentoo.org/distfiles/portage-2.2.12.tar.bz2"
+    - wget "http://distfiles.gentoo.org/distfiles/portage-$PORTAGE.tar.bz2"
     - wget "http://distfiles.gentoo.org/snapshots/portage-latest.tar.xz"
     - sudo chmod 777 /etc/passwd /etc/group /etc /usr
     - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
     - echo "portage::250:portage,travis" >> /etc/group
     - mkdir -p /etc/portage/ /usr/portage/distfiles
-    - tar xjf portage-2.2.12.tar.bz2
+    - tar xjf portage-$PORTAGE.tar.bz2
     - tar xJf portage-latest.tar.xz -C /usr/
-    - cp portage-2.2.12/cnf/repos.conf /etc/portage/
+    - cp portage-$PORTAGE/cnf/repos.conf /etc/portage/
     - rsync --recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --checksum --quiet rsync://rsync.gentoo.org/gentoo-portage /usr/portage
     - ln -s /usr/portage/profiles/base/ /etc/portage/make.profile
     - cd travis-overlay
-    - sed -i 's/fcmd=fcmd/fcmd=("%s -q" % fcmd)/' ./../portage-2.2.12/bin/repoman
+    - sed -i 's/fcmd=fcmd/fcmd=("%s -q" % fcmd)/' ./../portage-$PORTAGE/bin/repoman
+
 script: 
-    - "./../portage-2.2.12/bin/repoman full -d -v"
+    - "./../portage-$PORTAGE/bin/repoman full -d -v"

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     6cafb4b3e28da558c814f078103c552f2e2095c4
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Nov 14 11:48:13 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Nov 14 11:48:13 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6cafb4b3

Merge pull request #285 from buzden/altgr-ergo

Alt-Ergo solver installation was fixed.


 sci-mathematics/alt-ergo/alt-ergo-0.95.2.ebuild | 1 +
 1 file changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     495c985d452e53e0f93800b7542ee82af25db869
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Nov 14 23:05:16 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Nov 14 23:05:16 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=495c985d

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 sci-mathematics/alt-ergo/alt-ergo-0.95.2.ebuild | 1 +
 1 file changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     74f1bc3d01d6297542c6a28bd87c05bbab8abb45
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Nov 14 11:41:04 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Nov 14 11:41:04 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=74f1bc3d

Merge remote-tracking branch 'github/master'

* github/master:
  sync with gx86
  deps on boost:=
  deps on boost:=


 sci-libs/votca-tools/ChangeLog                |  3 +++
 sci-libs/votca-tools/votca-tools-9999.ebuild  |  2 +-
 sci-physics/espresso++/ChangeLog              |  6 ++++++
 sci-physics/espresso++/espresso++-9999.ebuild | 10 +++-------
 4 files changed, 13 insertions(+), 8 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     0ad784c93b43903e68eb115b0445a6e2fa863601
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 13 00:15:38 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Nov 13 00:15:38 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0ad784c9

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 ...cfs-move-mdd-ofd-proc-handling-to-seq_fil.patch |  0
 .../files => patches}/bigdft-abi-1.0.4-0005.patch  |  0
 sci-geosciences/congen/ChangeLog                   |  5 +-
 sci-geosciences/congen/congen-1.6.ebuild           | 10 ++--
 sci-geosciences/congen/metadata.xml                |  2 +-
 sci-libs/driftwood/ChangeLog                       |  6 ++-
 sci-libs/driftwood/driftwood-0.87.ebuild           |  2 +
 sci-libs/driftwood/metadata.xml                    |  2 +-
 sci-libs/ni-visa/ChangeLog                         |  6 ++-
 sci-libs/ni-visa/metadata.xml                      |  6 +--
 sci-libs/ni-visa/ni-visa-0.0.1.ebuild              | 18 ++-----
 sci-mathematics/acl2/ChangeLog                     |  6 ++-
 sci-mathematics/acl2/Manifest                      |  1 -
 sci-mathematics/acl2/acl2-4.2.ebuild               | 54 --------------------
 sci-mathematics/acl2/acl2-4.3.ebuild               | 54 --------------------
 sci-mathematics/axiom/ChangeLog                    |  6 ++-
 sci-mathematics/axiom/axiom-201009.ebuild          | 31 +++++-------
 sci-mathematics/axiom/metadata.xml                 |  2 +-
 sci-mathematics/freefem++/ChangeLog                |  5 +-
 sci-mathematics/freefem++/freefem++-3.8.ebuild     | 30 ++++++------
 sci-mathematics/libsfmt/ChangeLog                  |  6 ++-
 sci-mathematics/libsfmt/libsfmt-1.3.0.ebuild       | 12 ++---
 sci-mathematics/libsfmt/metadata.xml               |  2 +-
 sci-misc/finomaton/ChangeLog                       |  6 ++-
 sci-misc/finomaton/finomaton-1.0.ebuild            |  7 ++-
 sci-misc/finomaton/metadata.xml                    |  6 +--
 sci-misc/jwnl/ChangeLog                            |  6 ++-
 sci-misc/jwnl/jwnl-1.3_rc3.ebuild                  | 11 +++--
 sci-misc/jwnl/metadata.xml                         |  8 +--
 sci-misc/kotus-sanalista/ChangeLog                 |  8 ++-
 .../kotus-sanalista/kotus-sanalista-1-r1.ebuild    |  7 +--
 sci-misc/kotus-sanalista/metadata.xml              |  8 +--
 sci-misc/omorfi/ChangeLog                          |  6 ++-
 sci-misc/omorfi/metadata.xml                       |  8 +--
 sci-misc/omorfi/omorfi-0.1_alpha.ebuild            | 15 ++----
 sci-misc/openfst/ChangeLog                         |  5 +-
 sci-misc/openfst/Manifest                          |  1 -
 sci-misc/openfst/openfst-1.2.7.ebuild              | 34 -------------
 sci-misc/opennlp-maxent/ChangeLog                  |  6 ++-
 sci-misc/opennlp-maxent/metadata.xml               |  8 +--
 .../opennlp-maxent/opennlp-maxent-2.4.0.ebuild     | 12 +++--
 sci-misc/opennlp-tools/ChangeLog                   |  6 ++-
 sci-misc/opennlp-tools/metadata.xml                | 14 +++---
 sci-misc/opennlp-tools/opennlp-tools-1.3.0.ebuild  |  7 +--
 sci-misc/stanford-parser/ChangeLog                 |  6 ++-
 sci-misc/stanford-parser/metadata.xml              |  8 +--
 .../stanford-parser/stanford-parser-1.6.ebuild     | 12 ++---
 sci-misc/stanford-tagger/ChangeLog                 |  6 ++-
 sci-misc/stanford-tagger/metadata.xml              |  8 +--
 .../stanford-tagger-20060521.ebuild                | 32 ++++++------
 sys-cluster/blcr/ChangeLog                         |  6 ++-
 sys-cluster/blcr/Manifest                          |  1 -
 sys-cluster/blcr/blcr-0.8.2.ebuild                 | 57 ----------------------
 sys-cluster/blcr/blcr-0.8.4.ebuild                 | 19 ++++----
 sys-cluster/lustre/ChangeLog                       |  4 ++
 sys-cluster/lustre/Manifest                        |  1 +
 sys-cluster/lustre/lustre-9999.ebuild              |  4 +-
 virtual/blacs/ChangeLog                            |  5 +-
 virtual/blacs/blacs-1.1.ebuild                     |  2 +-
 virtual/blacs/metadata.xml                         |  4 +-
 virtual/cblas/ChangeLog                            |  3 ++
 virtual/cblas/cblas-2.0.ebuild                     |  2 +-
 virtual/cblas/metadata.xml                         |  6 +--
 virtual/lapacke/ChangeLog                          |  6 ++-
 virtual/lapacke/lapacke-1.0.ebuild                 |  2 +-
 virtual/lapacke/lapacke-3.5.ebuild                 |  2 +-
 virtual/lapacke/metadata.xml                       |  4 +-
 virtual/scalapack/ChangeLog                        |  6 ++-
 virtual/scalapack/metadata.xml                     |  4 +-
 virtual/scalapack/scalapack-2.0.ebuild             |  2 +-
 x11-libs/tr/ChangeLog                              |  5 +-
 x11-libs/tr/Manifest                               |  2 +-
 x11-libs/tr/metadata.xml                           |  2 +-
 x11-libs/tr/tr-1.3.ebuild                          | 15 +++---
 74 files changed, 275 insertions(+), 416 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     0fa865dc049eb0a5444495d1cd8d4f3969005f9f
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 11 08:30:18 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Nov 11 08:30:18 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0fa865dc

Merge remote-tracking branch 'github/master'

* github/master:
  added multilib support (bug #528622)
  added multilib support (bug #528622)


 sci-libs/gsl/ChangeLog                             |  5 ++++
 .../gsl/{gsl-1.16-r1.ebuild => gsl-1.16-r2.ebuild} | 12 ++++----
 virtual/cblas/ChangeLog                            |  5 ++++
 virtual/cblas/cblas-2.0-r3.ebuild                  | 35 ++++++++++++++++++++++
 4 files changed, 51 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     411ea0a5adcd062481a8813703cf6445edfb52dd
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 10 15:14:17 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 10 15:14:17 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=411ea0a5

Merge remote-tracking branch 'github/master'

* github/master:
  Drop prop-flags patch for root-9999, patch fails starting from 5.34.23 and ROOT 6 master. Upstream offers configure-flags to set proper flags starting now.
  added latest dev version


 sci-physics/root/ChangeLog                                          | 6 ++++++
 sci-physics/root/root-9999.ebuild                                   | 3 ++-
 sci-visualization/gnuplot/ChangeLog                                 | 6 ++++++
 sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild                   | 2 +-
 .../gnuplot/{gnuplot-5.0.9999.ebuild => gnuplot-5.1.9999.ebuild}    | 0
 5 files changed, 15 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     85025dd8cbc3a273456f422a604f591c65e6fc42
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 10 06:59:36 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 10 06:59:36 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=85025dd8

Merge pull request #283 from olifre/master

Drop prop-flags patch for root-9999


 sci-physics/root/ChangeLog        | 6 ++++++
 sci-physics/root/root-9999.ebuild | 3 ++-
 2 files changed, 8 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     4e7d64e13e02ac4f25e493cd7cefb1dd18176370
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 27 17:18:42 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Oct 27 17:18:42 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4e7d64e1

Merge remote-tracking branch 'github/master'

* github/master:
  sci-chemistry/freeon: Drop obsolete versions
  Moved to tree
  sci-physics/root: Fix compilation with USE="mysql" wrt bug #523996; fix die_compiler message
  sync with gx86
  net-libs/xrootd: version bump and fix bug 521496
  travis.yml: use newer portage version
  fixed bash-comp (bug #526320)
  version bump


 .travis.yml                                        |  10 +-
 dev-lang/ispc/ChangeLog                            |   3 +
 dev-lang/ispc/ispc-9999.ebuild                     |   1 +
 net-libs/xrootd/ChangeLog                          | 118 +++++++++++++++++++++
 net-libs/xrootd/Manifest                           |  11 ++
 net-libs/xrootd/files/cmsd.confd                   |   9 ++
 net-libs/xrootd/files/cmsd.initd                   |  35 ++++++
 net-libs/xrootd/files/frm_purged.initd             |  35 ++++++
 net-libs/xrootd/files/frm_xfrd.initd               |  35 ++++++
 net-libs/xrootd/files/xrootd-no-werror.patch       |  11 ++
 net-libs/xrootd/files/xrootd.confd                 |  21 ++++
 net-libs/xrootd/files/xrootd.initd                 |  33 ++++++
 net-libs/xrootd/metadata.xml                       |  16 +++
 net-libs/xrootd/xrootd-4.0.4.ebuild                |  82 ++++++++++++++
 sci-biology/consed/ChangeLog                       |  41 -------
 sci-biology/consed/Manifest                        |  16 ---
 sci-biology/consed/consed-20-r1.ebuild             |  80 --------------
 sci-biology/consed/consed-21.ebuild                |  80 --------------
 sci-biology/consed/consed-22.ebuild                |  80 --------------
 sci-biology/consed/consed-23.ebuild                |  80 --------------
 sci-biology/consed/consed-24.ebuild                |  80 --------------
 sci-biology/consed/consed-25.ebuild                |  80 --------------
 sci-biology/consed/consed-26.ebuild                |  80 --------------
 sci-biology/consed/consed-27.ebuild                |  80 --------------
 sci-biology/consed/files/nLine.h.patch             |  17 ---
 .../consed/files/nextPhredPipeline.cpp.patch       |  11 --
 sci-biology/consed/metadata.xml                    |   9 --
 sci-chemistry/freeon/ChangeLog                     |   3 +
 sci-chemistry/votca-csg/ChangeLog                  |   3 +
 sci-chemistry/votca-csg/votca-csg-9999.ebuild      |   6 +-
 sci-libs/trilinos/ChangeLog                        |   6 ++
 sci-libs/trilinos/Manifest                         |   1 +
 ...linos-11.4.2.ebuild => trilinos-11.10.2.ebuild} |   4 +-
 sci-libs/trilinos/trilinos-11.4.2.ebuild           |   2 +-
 sci-physics/root/ChangeLog                         |   5 +
 sci-physics/root/root-5.34.18-r2.ebuild            |   2 +
 sci-physics/root/root-6.00.01-r1.ebuild            |   2 +
 sci-physics/root/root-6.00.02.ebuild               |  10 +-
 sci-physics/root/root-9999.ebuild                  |  10 +-
 39 files changed, 457 insertions(+), 751 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5e17effe61fea1a19ee87b9699f7d96306382874
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Oct 26 16:16:03 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Oct 26 16:16:03 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5e17effe

Merge remote-tracking branch 'github/master'

* github/master: (66 commits)
  sci-physics/root: Fix compilation with USE="mysql" wrt bug #523996; fix die_compiler message
  sync with gx86
  net-libs/xrootd: version bump and fix bug 521496
  travis.yml: use newer portage version
  fixed bash-comp (bug #526320)
  version bump
  sci-chemistry/pymol: Patch included upstream
  sci-chemistry/pymol: Fix broken plugin listing
  dev-python/ccdproc: Version bump to 0.2.1
  Thanks to kiwifb for reporting https://github.com/gentoo-science/sci/issues/280 - Fix openblas: discrepancy between installed libraries and .pc file.
  Thanks to kiwifb for reporting https://github.com/gentoo-science/sci/issues/280 - Fix openblas: discrepancy between installed libraries and .pc file.
  sci-chemistry/pymol: Fix upstream buildsystem
  The fix for Bug 524612 failed in src_install building openblas from git. The fix is to move applying the patch to src_compile after building the library, then remove config.h and config_last.h; make config.h - ignoring the spurious warning; then cp config.h to config_last.h.
  Fix Bug 524612 - [science overlay] sci-libs/openblas-0.2.11 - Assembler messages: ../kernel/x86_64/gemm_kernel_8x4_barcelona.S:451: Error: missing ')', thanks to Juergen Rose, Jean-Francis Roy and Steven Trogdon for reporting. The problem was that applying the -0.2.11-openblas_config_header_same_between_ABIs.patch patch in src_prepare() causes build failures on assembler code as the assembler does not understand sizeof(float). So delay applying the patch until src_install(). Bump openblas to 0.2.12.
  dev-python/ccdproc: Version bump to 0.2.1
  dev-cpp/eigen: version bump
  sci-chemistry/pymol: Import tree changes
  version bump
  sys-cluster/openmpi: bump
  sys-cluster/openmpi: bump
  ...


 .travis.yml                                        |  10 +-
 ChangeLog                                          |  10 +
 dev-cpp/eigen/ChangeLog                            |   5 +
 dev-cpp/eigen/Manifest                             |   2 +
 .../{eigen-3.1.4.ebuild => eigen-3.2.2.ebuild}     |   0
 dev-cpp/icnc/ChangeLog                             |   3 +
 dev-cpp/icnc/icnc-9999.ebuild                      |   5 +-
 dev-lang/ispc/ChangeLog                            |   3 +
 dev-lang/ispc/ispc-9999.ebuild                     |   1 +
 dev-lang/julia/ChangeLog                           |   5 +
 dev-lang/julia/julia-9999.ebuild                   |  59 ++--
 dev-lang/julia/metadata.xml                        |   8 +-
 dev-python/ccdproc/ChangeLog                       |   9 +-
 dev-python/ccdproc/Manifest                        |   1 +
 .../{ccdproc-0.2.ebuild => ccdproc-0.2.1.ebuild}   |   0
 eclass/fortran-int64.eclass                        | 300 +++++++++++++++++++++
 net-libs/xrootd/ChangeLog                          | 118 ++++++++
 net-libs/xrootd/Manifest                           |  11 +
 net-libs/xrootd/files/cmsd.confd                   |   9 +
 net-libs/xrootd/files/cmsd.initd                   |  35 +++
 net-libs/xrootd/files/frm_purged.initd             |  35 +++
 net-libs/xrootd/files/frm_xfrd.initd               |  35 +++
 net-libs/xrootd/files/xrootd-no-werror.patch       |  11 +
 net-libs/xrootd/files/xrootd.confd                 |  21 ++
 net-libs/xrootd/files/xrootd.initd                 |  33 +++
 net-libs/xrootd/metadata.xml                       |  16 ++
 net-libs/xrootd/xrootd-4.0.4.ebuild                |  82 ++++++
 profiles/arch/arm/use.mask                         |  10 +
 profiles/arch/m68k/use.mask                        |  10 +
 profiles/arch/sparc-fbsd/use.mask                  |  10 +
 profiles/arch/sparc/use.mask                       |  10 +
 profiles/arch/x86-fbsd/use.mask                    |  10 +
 profiles/arch/x86/use.mask                         |  10 +
 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        |   6 +-
 sci-chemistry/gromacs/ChangeLog                    |   3 +
 sci-chemistry/gromacs/gromacs-9999.ebuild          |   2 +-
 sci-chemistry/pymol/ChangeLog                      |  14 +
 sci-chemistry/pymol/files/pymol-9999-listing.patch |  17 ++
 sci-chemistry/pymol/files/pymol-9999-options.patch |  15 ++
 sci-chemistry/pymol/pymol-9999.ebuild              |   6 +-
 sci-chemistry/votca-csg/ChangeLog                  |   3 +
 sci-chemistry/votca-csg/votca-csg-9999.ebuild      |   6 +-
 sci-libs/blas-reference/ChangeLog                  |   9 +-
 ...16.ebuild => blas-reference-20131116-r1.ebuild} |   0
 .../blas-reference/blas-reference-20131116.ebuild  |  79 +++++-
 .../blas-reference/blas-reference-99999999.ebuild  |  92 +++++--
 sci-libs/blas-reference/metadata.xml               |   3 +
 sci-libs/cblas-reference/ChangeLog                 |   7 +
 .../cblas-reference-20110218-r1.ebuild             | 157 +++++++++++
 sci-libs/cblas-reference/metadata.xml              |   3 +
 sci-libs/dealii/ChangeLog                          |   7 +
 sci-libs/dealii/Manifest                           |   2 -
 sci-libs/dealii/dealii-8.0.0.ebuild                |   1 -
 ...{dealii-8.1.0.ebuild => dealii-8.1.0-r1.ebuild} |   6 +-
 .../files/dealii-8.1.0-p4est1.0-support.patch      | 271 +++++++++++++++++++
 sci-libs/lapack-reference/ChangeLog                |  50 ++++
 .../lapack-reference/lapack-reference-9999.ebuild  | 117 +++++---
 sci-libs/lapack-reference/metadata.xml             |  11 +-
 sci-libs/libsc/ChangeLog                           |   6 +
 sci-libs/libsc/Manifest                            |   2 +-
 sci-libs/libsc/libsc-0.7.3.ebuild                  |  79 ------
 sci-libs/libsc/libsc-1.0.ebuild                    |   1 -
 sci-libs/libsc/libsc-1.1.ebuild                    |   1 +
 sci-libs/libsc/metadata.xml                        |   2 +-
 sci-libs/openblas/ChangeLog                        |  64 +++++
 sci-libs/openblas/Manifest                         |   4 +-
 .../openblas/files/openblas-0.2.11-cpuid_x86.patch |  27 ++
 ...-openblas_config_header_same_between_ABIs.patch |  21 ++
 sci-libs/openblas/openblas-0.2.11.ebuild           |   1 +
 sci-libs/openblas/openblas-0.2.12.ebuild           |   1 +
 sci-libs/openblas/openblas-9999.ebuild             | 277 +++++++++++++------
 sci-libs/p4est/ChangeLog                           |   9 +
 sci-libs/p4est/Manifest                            |   2 +
 sci-libs/p4est/metadata.xml                        |   2 +-
 sci-libs/p4est/p4est-1.0.ebuild                    |   6 +-
 sci-libs/p4est/p4est-1.1.ebuild                    |   1 +
 sci-libs/pfft/ChangeLog                            |  36 +++
 sci-libs/pfft/Manifest                             |   1 +
 sci-libs/{bliss => pfft}/metadata.xml              |   0
 sci-libs/pfft/pfft-1.0.7_alpha.ebuild              |  54 ++++
 sci-libs/pfft/pfft-9999.ebuild                     |  54 ++++
 sci-libs/trilinos/ChangeLog                        |   6 +
 sci-libs/trilinos/Manifest                         |   1 +
 ...linos-11.4.2.ebuild => trilinos-11.10.2.ebuild} |   4 +-
 sci-libs/trilinos/trilinos-11.4.2.ebuild           |   2 +-
 sci-libs/xblas/ChangeLog                           |  14 +-
 sci-libs/xblas/metadata.xml                        |   3 +
 sci-libs/xblas/xblas-1.0.248-r1.ebuild             | 122 +++++++++
 sci-mathematics/scilab/Manifest                    |   1 +
 ...on.patch => scilab-5.5.1-accessviolation.patch} |   0
 ... scilab-5.5.1-fix-random-runtime-failure.patch} |   0
 ...wlinks.patch => scilab-5.5.1-followlinks.patch} |   0
 ....0-gluegen.patch => scilab-5.5.1-gluegen.patch} |   0
 ...ava-heap.patch => scilab-5.5.1-java-heap.patch} |   0
 .../scilab/files/scilab-5.5.1-missinglib.patch     |  11 +
 ...-5.5.0-nogui.patch => scilab-5.5.1-nogui.patch} |   0
 sci-mathematics/scilab/scilab-5.5.1.ebuild         | 250 +++++++++++++++++
 sci-physics/root/ChangeLog                         |   9 +
 sci-physics/root/files/root-6.00.02-tm_zone.patch  |  22 ++
 sci-physics/root/metadata.xml                      |  38 +--
 sci-physics/root/root-5.34.18-r2.ebuild            |   2 +
 sci-physics/root/root-6.00.01-r1.ebuild            |   2 +
 sci-physics/root/root-6.00.02.ebuild               |  13 +-
 sci-physics/root/root-9999.ebuild                  |  10 +-
 sys-cluster/openmpi/ChangeLog                      |   5 +
 sys-cluster/openmpi/Manifest                       |   1 +
 .../{openmpi-1.8.1.ebuild => openmpi-1.8.3.ebuild} |   0
 virtual/blas/ChangeLog                             |  11 +
 virtual/blas/blas-2.1-r2.ebuild                    |  41 +++
 virtual/blas/blas-2.1-r3.ebuild                    |  44 +++
 virtual/blas/metadata.xml                          |   4 +
 virtual/cblas/ChangeLog                            |  13 +-
 virtual/cblas/cblas-2.0-r1.ebuild                  |  28 ++
 virtual/cblas/cblas-2.0-r2.ebuild                  |  31 +++
 virtual/cblas/metadata.xml                         |   4 +
 virtual/lapack/ChangeLog                           |  10 +
 virtual/lapack/lapack-3.5-r2.ebuild                |  34 +++
 virtual/lapack/metadata.xml                        |   4 +
 118 files changed, 2850 insertions(+), 315 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     dca77c396141f47fa04a2c2362ba896d45f0728b
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Oct 24 03:40:49 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Oct 24 03:40:49 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=dca77c39

travis.yml: use newer portage version

---
 .travis.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index ec1e792..84e0f78 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -2,18 +2,18 @@ before_script:
     - mkdir travis-overlay
     - mv !(travis-overlay) travis-overlay/
     - mv .git travis-overlay/
-    - wget "http://distfiles.gentoo.org/distfiles/portage-2.2.10.tar.bz2"
+    - wget "http://distfiles.gentoo.org/distfiles/portage-2.2.12.tar.bz2"
     - wget "http://distfiles.gentoo.org/snapshots/portage-latest.tar.xz"
     - sudo chmod 777 /etc/passwd /etc/group /etc /usr
     - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
     - echo "portage::250:portage,travis" >> /etc/group
     - mkdir -p /etc/portage/ /usr/portage/distfiles
-    - tar xjf portage-2.2.10.tar.bz2
+    - tar xjf portage-2.2.12.tar.bz2
     - tar xJf portage-latest.tar.xz -C /usr/
-    - cp portage-2.2.10/cnf/repos.conf /etc/portage/
+    - cp portage-2.2.12/cnf/repos.conf /etc/portage/
     - rsync --recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --checksum --quiet rsync://rsync.gentoo.org/gentoo-portage /usr/portage
     - ln -s /usr/portage/profiles/base/ /etc/portage/make.profile
     - cd travis-overlay
-    - sed -i 's/fcmd=fcmd/fcmd=("%s -q" % fcmd)/' ./../portage-2.2.10/bin/repoman
+    - sed -i 's/fcmd=fcmd/fcmd=("%s -q" % fcmd)/' ./../portage-2.2.12/bin/repoman
 script: 
-    - "./../portage-2.2.10/bin/repoman full -d -v"
+    - "./../portage-2.2.12/bin/repoman full -d -v"

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     5b61046cc76b06a413b6a47acd22be971ef3abbe
Author:     Matthias Maier <tamiko <AT> gentoo <DOT> org>
AuthorDate: Tue Oct 21 22:34:38 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Oct 21 22:34:38 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5b61046c

Merge branch 'bump_trilinos'


 sci-libs/trilinos/ChangeLog                                         | 6 ++++++
 sci-libs/trilinos/Manifest                                          | 1 +
 .../trilinos/{trilinos-11.4.2.ebuild => trilinos-11.10.2.ebuild}    | 4 ++--
 sci-libs/trilinos/trilinos-11.4.2.ebuild                            | 2 +-
 4 files changed, 10 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     31646d46acfdfe24e2cf8425168fec93cabd31d7
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Oct 24 03:33:58 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Oct 24 03:33:58 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=31646d46

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 sci-libs/trilinos/ChangeLog                                         | 6 ++++++
 sci-libs/trilinos/Manifest                                          | 1 +
 .../trilinos/{trilinos-11.4.2.ebuild => trilinos-11.10.2.ebuild}    | 4 ++--
 sci-libs/trilinos/trilinos-11.4.2.ebuild                            | 2 +-
 4 files changed, 10 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     7b3cbc010f744fab3e6731ef3887ed72a27d14b2
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 20 18:01:13 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Oct 20 18:01:13 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7b3cbc01

Merge remote-tracking branch 'github/master'

* github/master:
  Thanks to kiwifb for reporting https://github.com/gentoo-science/sci/issues/280 - Fix openblas: discrepancy between installed libraries and .pc file.
  dev-python/ccdproc: Version bump to 0.2.1

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a6fc4907717a900bfe2fabf897d7a1cbf3b71c47
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 20 11:54:35 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Oct 20 11:54:35 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a6fc4907

Merge pull request #279 from sargas/ccdproc-0.2.1

dev-python/ccdproc: Version bump to 0.2.1


 dev-python/ccdproc/ChangeLog                                    | 9 ++++-----
 dev-python/ccdproc/Manifest                                     | 1 +
 dev-python/ccdproc/{ccdproc-0.2.ebuild => ccdproc-0.2.1.ebuild} | 0
 3 files changed, 5 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Mark Wright]

commit:     42ec32598c5929565f7c4a6793f574f318aff2b0
Author:     Mark Wright <markwright <AT> internode <DOT> on <DOT> net>
AuthorDate: Sat Oct 18 13:43:32 2014 +0000
Commit:     Mark Wright <gienah <AT> gentoo <DOT> org>
CommitDate: Sat Oct 18 13:43:32 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=42ec3259

Merge pull request #277 from gentoo-science/int64-build-eclass

Int64 build eclass


 eclass/fortran-int64.eclass                        | 300 +++++++++++++++++++++
 sci-libs/blas-reference/ChangeLog                  |   9 +-
 ...16.ebuild => blas-reference-20131116-r1.ebuild} |   0
 .../blas-reference/blas-reference-20131116.ebuild  |  79 +++++-
 .../blas-reference/blas-reference-99999999.ebuild  |  92 +++++--
 sci-libs/blas-reference/metadata.xml               |   3 +
 sci-libs/cblas-reference/ChangeLog                 |   7 +
 .../cblas-reference-20110218-r1.ebuild             | 157 +++++++++++
 sci-libs/cblas-reference/metadata.xml              |   3 +
 sci-libs/lapack-reference/ChangeLog                |  29 ++
 .../lapack-reference/lapack-reference-9999.ebuild  | 170 +++---------
 sci-libs/openblas/ChangeLog                        |   5 +
 sci-libs/openblas/openblas-9999.ebuild             | 145 ++--------
 sci-libs/xblas/ChangeLog                           |  14 +-
 sci-libs/xblas/metadata.xml                        |   3 +
 sci-libs/xblas/xblas-1.0.248-r1.ebuild             | 122 +++++++++
 virtual/blas/ChangeLog                             |   5 +
 .../{blas-2.1-r2.ebuild => blas-2.1-r3.ebuild}     |   9 +-
 virtual/cblas/ChangeLog                            |   5 +
 .../{cblas-2.0-r1.ebuild => cblas-2.0-r2.ebuild}   |  11 +-
 20 files changed, 886 insertions(+), 282 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Mark Wright]

commit:     cc60e8d1caab1b56cf059e31865e412a54097d7d
Author:     gienah <gienah <AT> gentoo <DOT> org>
AuthorDate: Sat Oct 18 10:07:28 2014 +0000
Commit:     Mark Wright <gienah <AT> gentoo <DOT> org>
CommitDate: Sat Oct 18 10:07:28 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cc60e8d1

Merge int64-eclass branch with master. lapack-reference-9999 builds and passes tests with USE=int64 xblas.


 dev-cpp/eigen/ChangeLog                            |   5 +
 dev-cpp/eigen/Manifest                             |   2 +
 .../{eigen-3.1.4.ebuild => eigen-3.2.2.ebuild}     |   0
 sci-chemistry/pymol/ChangeLog                      |   3 +
 sci-chemistry/pymol/pymol-9999.ebuild              |   6 +-
 sci-libs/dealii/ChangeLog                          |   7 +
 sci-libs/dealii/Manifest                           |   2 -
 sci-libs/dealii/dealii-8.0.0.ebuild                |   1 -
 ...{dealii-8.1.0.ebuild => dealii-8.1.0-r1.ebuild} |   6 +-
 .../files/dealii-8.1.0-p4est1.0-support.patch      | 271 +++++++++++++++++++++
 sci-libs/libsc/ChangeLog                           |   6 +
 sci-libs/libsc/Manifest                            |   2 +-
 sci-libs/libsc/libsc-0.7.3.ebuild                  |  79 ------
 sci-libs/libsc/libsc-1.0.ebuild                    |   1 -
 sci-libs/libsc/libsc-1.1.ebuild                    |   1 +
 sci-libs/libsc/metadata.xml                        |   2 +-
 sci-libs/p4est/ChangeLog                           |   9 +
 sci-libs/p4est/Manifest                            |   2 +
 sci-libs/p4est/metadata.xml                        |   2 +-
 sci-libs/p4est/p4est-1.0.ebuild                    |   6 +-
 sci-libs/p4est/p4est-1.1.ebuild                    |   1 +
 sci-libs/pfft/ChangeLog                            |  36 +++
 sci-libs/pfft/Manifest                             |   1 +
 sci-libs/{bliss => pfft}/metadata.xml              |   0
 sci-libs/pfft/pfft-1.0.7_alpha.ebuild              |  54 ++++
 sci-libs/pfft/pfft-9999.ebuild                     |  54 ++++
 sys-cluster/openmpi/ChangeLog                      |   5 +
 sys-cluster/openmpi/Manifest                       |   1 +
 .../{openmpi-1.8.1.ebuild => openmpi-1.8.3.ebuild} |   0
 29 files changed, 473 insertions(+), 92 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     c316c68b124e78d0f22423096ac66689f8e1395a
Author:     Matthias Maier <tamiko+GITHUB <AT> kyomu <DOT> 43-1 <DOT> org>
AuthorDate: Tue Oct 14 08:03:47 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Oct 14 08:03:47 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c316c68b

Merge pull request #278 from tamiko/bump_p4est

Bump sci-libs/libsc and sci-libs/p4est


 sci-libs/libsc/ChangeLog          |  6 +++
 sci-libs/libsc/Manifest           |  2 +-
 sci-libs/libsc/libsc-0.7.3.ebuild | 79 ---------------------------------------
 sci-libs/libsc/libsc-1.0.ebuild   |  1 -
 sci-libs/libsc/libsc-1.1.ebuild   |  1 +
 sci-libs/libsc/metadata.xml       |  2 +-
 sci-libs/p4est/ChangeLog          |  9 +++++
 sci-libs/p4est/Manifest           |  2 +
 sci-libs/p4est/metadata.xml       |  2 +-
 sci-libs/p4est/p4est-1.0.ebuild   |  6 +--
 sci-libs/p4est/p4est-1.1.ebuild   |  1 +
 11 files changed, 25 insertions(+), 86 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     9709669dc3f978e44a478dfe229719db96bb47f6
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Oct 16 15:49:59 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Oct 16 15:49:59 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9709669d

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 sci-libs/dealii/ChangeLog                          |   7 +
 sci-libs/dealii/Manifest                           |   2 -
 sci-libs/dealii/dealii-8.0.0.ebuild                |   1 -
 ...{dealii-8.1.0.ebuild => dealii-8.1.0-r1.ebuild} |   6 +-
 .../files/dealii-8.1.0-p4est1.0-support.patch      | 271 +++++++++++++++++++++
 sci-libs/libsc/ChangeLog                           |   6 +
 sci-libs/libsc/Manifest                            |   2 +-
 sci-libs/libsc/libsc-0.7.3.ebuild                  |  79 ------
 sci-libs/libsc/libsc-1.0.ebuild                    |   1 -
 sci-libs/libsc/libsc-1.1.ebuild                    |   1 +
 sci-libs/libsc/metadata.xml                        |   2 +-
 sci-libs/p4est/ChangeLog                           |   9 +
 sci-libs/p4est/Manifest                            |   2 +
 sci-libs/p4est/metadata.xml                        |   2 +-
 sci-libs/p4est/p4est-1.0.ebuild                    |   6 +-
 sci-libs/p4est/p4est-1.1.ebuild                    |   1 +
 16 files changed, 308 insertions(+), 90 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     1fdab26b8f60deebb1d143ed43d5aaddb31d3f3b
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Oct 10 06:26:15 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Oct 10 06:26:15 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1fdab26b

Merge pull request #276 from mschubert/ncbi-tools++

ncbi-tools++: fix prefix libdir, muparser/hdf5 use flags


 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     66ca0374f3fb5889257194e18afb1e506b68f270
Author:     Mark Wright <markwright <AT> internode <DOT> on <DOT> net>
AuthorDate: Sat Oct  4 04:24:42 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Oct  4 04:24:42 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=66ca0374

Merge pull request #194 from gentoo-science/lapack-multibuild

Lapack multibuild


 ChangeLog                                          |  10 +
 dev-lang/julia/ChangeLog                           |   5 +
 dev-lang/julia/julia-9999.ebuild                   |  59 +++-
 dev-lang/julia/metadata.xml                        |   8 +-
 profiles/arch/arm/use.mask                         |  10 +
 profiles/arch/m68k/use.mask                        |  10 +
 profiles/arch/sparc-fbsd/use.mask                  |  10 +
 profiles/arch/sparc/use.mask                       |  10 +
 profiles/arch/x86-fbsd/use.mask                    |  10 +
 profiles/arch/x86/use.mask                         |  10 +
 sci-libs/lapack-reference/ChangeLog                |  13 +
 .../lapack-reference/lapack-reference-9999.ebuild  | 188 +++++++++--
 sci-libs/lapack-reference/metadata.xml             |   1 +
 sci-libs/openblas/ChangeLog                        |  35 ++
 sci-libs/openblas/Manifest                         |   3 +-
 .../openblas/files/openblas-0.2.11-cpuid_x86.patch |  27 ++
 ...-openblas_config_header_same_between_ABIs.patch |  21 ++
 sci-libs/openblas/openblas-0.2.11.ebuild           |   1 +
 sci-libs/openblas/openblas-9999.ebuild             | 352 ++++++++++++++++-----
 virtual/blas/ChangeLog                             |   6 +
 .../{blas-2.1-r1.ebuild => blas-2.1-r2.ebuild}     |   7 +-
 virtual/blas/metadata.xml                          |   4 +
 virtual/cblas/ChangeLog                            |   8 +-
 .../{cblas-2.0.ebuild => cblas-2.0-r1.ebuild}      |  12 +-
 virtual/cblas/metadata.xml                         |   4 +
 virtual/lapack/ChangeLog                           |   6 +
 .../{lapack-3.5-r1.ebuild => lapack-3.5-r2.ebuild} |   2 +-
 virtual/lapack/metadata.xml                        |   4 +
 28 files changed, 697 insertions(+), 139 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     837c1eec6cbdfb6889198fee4b19c4f309a53a6e
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Sep 28 11:30:51 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Sep 28 11:30:51 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=837c1eec

Merge remote-tracking branch 'github/master'

* github/master:
  The dependency needs to be on xblas[fortran] otherwise libxblas won't have the required fortran symbols.
  live ebuild update
  Add xblas to the .pc file when it is in use see bug#523388
  initial commit


 dev-cpp/icnc/ChangeLog                             | 12 +++++++
 dev-cpp/icnc/icnc-9999.ebuild                      | 39 ++++++++++++++++++++++
 {app-forensics/vine => dev-cpp/icnc}/metadata.xml  |  0
 sci-libs/lapack-reference/ChangeLog                | 11 +++++-
 .../lapack-reference/lapack-reference-9999.ebuild  |  8 ++++-
 5 files changed, 68 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     3d4aafc6869e128388f00b13add95d7f815a8aff
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 24 06:45:03 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep 24 06:45:03 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3d4aafc6

Merge remote-tracking branch 'github/master'

* github/master:
  media-gfx/librecad: install appdata.xml


 media-gfx/librecad/ChangeLog            | 2 ++
 media-gfx/librecad/librecad-9999.ebuild | 2 ++
 2 files changed, 4 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a4a0ea124842f9a8f1b0bd200e7d7c4b0458cdbe
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Sep 18 20:36:55 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Sep 18 20:36:55 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a4a0ea12

Merge remote-tracking branch 'github/master'

* github/master: (71 commits)
  updated metadata.xml
  updated metadata.xml
  remove old
  libcerf patch got merged upstream
  clean up
  fixed DESCRIPTION
  fixed DESCRIPTION
  clean up
  fixed DESCRIPTION
  fixed DESCRIPTION
  fixed DESCRIPTION
  remove blank line
  fixed deps
  clean up
  clean up
  remove whitespace
  clean up
  readded die on remake
  remove last line
  remove last line
  ...


 app-admin/eselect/ChangeLog                        |    5 +
 app-admin/eselect/Manifest                         |    1 +
 ...1.4.2-r100.ebuild => eselect-1.4.3-r100.ebuild} |    2 +-
 app-vim/vim-gromacs/ChangeLog                      |    3 +
 app-vim/vim-gromacs/vim-gromacs-9999.ebuild        |    1 -
 dev-cpp/eigen/eigen-9999.ebuild                    |    8 +-
 dev-ml/zarith/ChangeLog                            |    3 +
 dev-ml/zarith/zarith-1.2.1.ebuild                  |   18 +-
 dev-python/montage-wrapper/ChangeLog               |    4 +
 .../montage-wrapper/montage-wrapper-0.9.7.ebuild   |    2 -
 dev-util/numdiff/ChangeLog                         |    6 +
 dev-util/numdiff/numdiff-5.8.1.ebuild              |   12 +-
 eclass/alternatives-2.eclass                       |    2 +-
 profiles/ChangeLog                                 |    6 +
 profiles/package.mask                              |   10 -
 sci-astronomy/pyAstroStack/ChangeLog               |    3 +
 .../pyAstroStack/pyAstroStack-0.3.0.ebuild         |    2 +-
 sci-biology/BBmap/BBmap-31.40.ebuild               |    2 +-
 sci-biology/BBmap/ChangeLog                        |    4 +-
 sci-biology/BamView/BamView-1.2.11.ebuild          |    3 +-
 sci-biology/BamView/ChangeLog                      |    5 +-
 sci-biology/{perlprimer => BamView}/metadata.xml   |    3 +
 sci-biology/CONTIGuator/CONTIGuator-2.7.ebuild     |    2 +-
 sci-biology/CONTIGuator/ChangeLog                  |    6 +
 sci-biology/IMAGE/ChangeLog                        |    4 +-
 sci-biology/IMAGE/IMAGE-2.4.1.ebuild               |    5 +-
 sci-biology/MAKER/ChangeLog                        |    4 +-
 sci-biology/MAKER/MAKER-9999.ebuild                |    5 +-
 sci-biology/MaSuRCA/ChangeLog                      |    4 +-
 sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild           |    8 +-
 sci-biology/MagicViewer/ChangeLog                  |    6 +
 sci-biology/MagicViewer/MagicViewer-1.2.1.ebuild   |    9 +-
 sci-biology/MeV/ChangeLog                          |    7 +
 sci-biology/MeV/MeV-4.8.1.ebuild                   |    2 +-
 sci-biology/{perlprimer => MeV}/metadata.xml       |    3 +
 sci-biology/RADtools/ChangeLog                     |    4 +
 sci-biology/RADtools/RADtools-1.2.4.ebuild         |    1 -
 sci-biology/RADtools/RADtools-9999.ebuild          |    1 -
 sci-biology/VarScan/ChangeLog                      |    6 +
 sci-biology/VarScan/VarScan-2.3.6.ebuild           |    2 +-
 sci-biology/bambino/ChangeLog                      |    4 +
 sci-biology/bambino/bambino-1.02.ebuild            |    4 +-
 sci-biology/bambino/bambino-1.06.ebuild            |    4 +-
 sci-biology/eval/ChangeLog                         |    4 +-
 sci-biology/eval/eval-2.2.8.ebuild                 |    4 +-
 sci-biology/fastqc/ChangeLog                       |    3 +
 sci-biology/fastqc/fastqc-0.10.1.ebuild            |    2 +-
 sci-biology/freebayes/ChangeLog                    |    4 +-
 sci-biology/freebayes/freebayes-9999.ebuild        |    2 +-
 sci-biology/geneid/ChangeLog                       |    3 +
 sci-biology/geneid/geneid-1.4.4.ebuild             |    2 +-
 sci-biology/genomeview-bin/ChangeLog               |    4 +
 .../genomeview-bin/genomeview-bin-2450.ebuild      |    2 +-
 sci-biology/manatee-jcvi/ChangeLog                 |    6 +-
 sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild |   26 +-
 sci-biology/mapview-bin/ChangeLog                  |   10 -
 sci-biology/mapview-bin/Manifest                   |    2 -
 sci-biology/mapview-bin/mapview-bin-3.4.1.ebuild   |   34 -
 sci-biology/mapview-bin/metadata.xml               |    5 -
 sci-biology/mgblast/ChangeLog                      |    4 +-
 sci-biology/mgblast/mgblast-0.1.ebuild             |   20 +-
 sci-biology/ncbi-tools++/ChangeLog                 |   15 +-
 sci-biology/ncbi-tools++/Manifest                  |    1 -
 .../files/ncbi-tools++-12.0.0-as-needed.patch      | 1867 --------------
 .../files/ncbi-tools++-9.0.0-as-needed.patch       | 1864 --------------
 .../files/ncbi-tools++-9.0.0-conf-opts.patch       |  213 --
 .../ncbi-tools++-9.0.0-disable_test_compress.patch |   15 -
 .../ncbi-tools++-9.0.0-fix-creaders-linking.patch  |   10 -
 .../ncbi-tools++-9.0.0-fix-order-of-libs.patch     |   24 -
 .../ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch  |   10 -
 ...-reference-to-GenBankReaders_Register_Id1.patch |   10 -
 ...ls++-9.0.0-remove-LZO-definition-upstream.patch |   10 -
 sci-biology/ncbi-tools++/metadata.xml              |    3 -
 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        |    3 +-
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |  329 ---
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild |  303 ---
 sci-biology/ngsview/ChangeLog                      |    4 +-
 sci-biology/ngsview/ngsview-0.91.ebuild            |    4 +-
 sci-biology/pileup/ChangeLog                       |    4 +-
 sci-biology/pileup/pileup-0.6.ebuild               |    4 +-
 sci-biology/prot4EST/ChangeLog                     |    4 +-
 sci-biology/prot4EST/prot4EST-3.1b.ebuild          |    7 +-
 sci-biology/samstat/ChangeLog                      |    3 +
 sci-biology/samstat/samstat-20130708.ebuild        |    2 +-
 sci-biology/scaffold_builder/ChangeLog             |    5 +-
 .../scaffold_builder-20130403.ebuild               |    5 +-
 sci-biology/screed/ChangeLog                       |    4 +-
 sci-biology/screed/screed-0.7.1.ebuild             |    1 -
 sci-biology/stacks/ChangeLog                       |    3 +
 sci-biology/stacks/stacks-1.16.ebuild              |    3 +-
 sci-biology/tablet-bin/ChangeLog                   |    4 +
 .../tablet-bin/tablet-bin-1.14.04.10.ebuild        |    2 +-
 sci-chemistry/chimera-bin/ChangeLog                |    4 +
 sci-chemistry/chimera-bin/Manifest                 |    6 -
 sci-chemistry/chimera-bin/chimera-bin-1.6.2.ebuild |   94 -
 sci-chemistry/chimera-bin/chimera-bin-1.8.1.ebuild |   94 -
 sci-chemistry/chimera-bin/chimera-bin-1.8.ebuild   |   94 -
 sci-chemistry/chimera-bin/chimera-bin-1.9.ebuild   |    1 -
 sci-chemistry/cs-rosetta/ChangeLog                 |    5 +-
 .../cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild |    2 +-
 sci-chemistry/freeon/ChangeLog                     |    3 +
 sci-chemistry/freeon/metadata.xml                  |    3 -
 sci-chemistry/mddnmr/ChangeLog                     |    7 +-
 sci-chemistry/module2/ChangeLog                    |    8 +-
 sci-chemistry/nmrpipe/ChangeLog                    |    8 +
 sci-chemistry/nwchem/ChangeLog                     |    3 +
 sci-chemistry/nwchem/nwchem-6.3_p2-r1.ebuild       |    4 +-
 sci-chemistry/openbabel-java/ChangeLog             |    5 +-
 .../openbabel-java/openbabel-java-9999.ebuild      |   21 +-
 sci-chemistry/openbabel-perl/ChangeLog             |    5 +-
 .../openbabel-perl/openbabel-perl-9999.ebuild      |   11 +-
 sci-chemistry/openbabel-python/ChangeLog           |    5 +-
 .../openbabel-python/openbabel-python-9999.ebuild  |   15 +-
 sci-chemistry/openbabel-ruby/ChangeLog             |    5 +-
 .../openbabel-ruby/openbabel-ruby-9999.ebuild      |   15 +-
 sci-chemistry/unio/ChangeLog                       |    9 +-
 sci-chemistry/unio/Manifest                        |    1 -
 sci-chemistry/unio/unio-2.0.2-r1.ebuild            |   67 -
 sci-chemistry/unio/unio-2.0.3.ebuild               |   67 -
 sci-libs/mkl/ChangeLog                             |    5 +
 sci-libs/mkl/Manifest                              |    1 +
 ...-11.1.0.080-r1.ebuild => mkl-11.2.0.090.ebuild} |    4 +-
 sci-libs/mlpack/ChangeLog                          |    3 +
 sci-libs/mlpack/mlpack-1.0.8.ebuild                |    2 +-
 sci-libs/p4est/ChangeLog                           |    6 +
 sci-libs/p4est/Manifest                            |    2 -
 .../p4est/files/p4est-0.3.4.2-libtool-fix.patch    |   59 -
 .../p4est-0.3.5-add_missing_autotools_files.patch  | 2535 --------------------
 sci-libs/p4est/p4est-0.3.4.2.ebuild                |   73 -
 sci-libs/p4est/p4est-0.3.5.ebuild                  |   92 -
 sci-libs/p4est/p4est-1.0.ebuild                    |    2 +-
 sci-mathematics/alt-ergo/ChangeLog                 |    4 +-
 sci-mathematics/alt-ergo/alt-ergo-0.95.2.ebuild    |   14 +-
 sci-mathematics/flocq/ChangeLog                    |    7 +-
 sci-mathematics/flocq/flocq-2.3.0.ebuild           |    3 +-
 sci-mathematics/gappa/ChangeLog                    |    3 +
 sci-mathematics/gappa/gappa-1.1.1.ebuild           |    1 -
 sci-mathematics/gappalib-coq/ChangeLog             |    4 +-
 .../gappalib-coq/gappalib-coq-1.0.0.ebuild         |    1 -
 sci-mathematics/giac/ChangeLog                     |    4 +-
 sci-mathematics/giac/giac-1.1.0.ebuild             |   23 +-
 sci-mathematics/petsc/ChangeLog                    |    4 +-
 sci-mathematics/petsc/petsc-3.4.2.ebuild           |    2 +-
 sci-mathematics/pff/ChangeLog                      |    4 +-
 sci-mathematics/pff/pff-8.4.ebuild                 |    5 +-
 sci-mathematics/why3/ChangeLog                     |    3 +
 sci-mathematics/why3/why3-0.83.ebuild              |    2 +-
 sci-misc/elmer-gui/ChangeLog                       |    9 +-
 sci-misc/elmer-gui/elmer-gui-9999.ebuild           |    6 +-
 sci-misc/elmer-gui/metadata.xml                    |    8 +
 sci-physics/abinit/ChangeLog                       |    3 +
 sci-physics/abinit/metadata.xml                    |    6 -
 sci-physics/bigdft/ChangeLog                       |    4 +-
 sci-physics/bigdft/bigdft-1.7.5.ebuild             |    1 -
 sci-visualization/gnuplot/ChangeLog                |    3 +
 sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild  |    1 +
 156 files changed, 426 insertions(+), 8114 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     1dffcb63d0f575d68e90310a41be8feacc4642ae
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 16 00:26:54 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Sep 16 00:26:54 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1dffcb63

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 dev-cpp/eigen/eigen-9999.ebuild | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     d54b6b84e7b43f2a8d3359493ec5601549fc3766
Author:     Christoph Junghans <christoph.junghans <AT> gmail <DOT> com>
AuthorDate: Mon Sep 15 21:45:51 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Sep 15 21:45:51 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d54b6b84

Merge pull request #267 from hazelnusse/eigen-9999-pr2

Looks good!


 dev-cpp/eigen/eigen-9999.ebuild | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     6532fa2dbeee197e8139b1cc985cae4e90d5fc07
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Sep 12 15:55:38 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Sep 12 15:55:38 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6532fa2d

travis.yml: make 'repoman full' verbose for output

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index ce116ca..ec1e792 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -16,4 +16,4 @@ before_script:
     - cd travis-overlay
     - sed -i 's/fcmd=fcmd/fcmd=("%s -q" % fcmd)/' ./../portage-2.2.10/bin/repoman
 script: 
-    - "./../portage-2.2.10/bin/repoman full -d"
+    - "./../portage-2.2.10/bin/repoman full -d -v"

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     df065914957ea1df742ce164e48cc33565db68cb
Author:     Jauhien Piatlicki <piatlicki <AT> gmail <DOT> com>
AuthorDate: Fri Sep 12 09:02:38 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Fri Sep 12 09:02:38 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=df065914

Merge pull request #266 from hazelnusse/eigen-9999-pr

dev-cpp/eigen: add src_unpack to ensure mercurial_src_unpack is called


 dev-cpp/eigen/eigen-9999.ebuild | 5 +++++
 1 file changed, 5 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     9cf4bc67d9685c7120c872b71acdec48deed4b2e
Author:     Jauhien Piatlicki <piatlicki <AT> gmail <DOT> com>
AuthorDate: Wed Sep 10 10:44:06 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Wed Sep 10 10:44:06 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9cf4bc67

Merge pull request #265 from sargas/casa-4.2.2

casapy-bin version bump to 4.2.2


 sci-astronomy/casapy-bin/ChangeLog                 |  7 +++
 sci-astronomy/casapy-bin/Manifest                  |  3 +-
 .../casapy-bin/casapy-bin-4.2.0_pre10_p1.ebuild    | 68 ----------------------
 .../casapy-bin-4.2.1.29047.001_p1.ebuild           |  2 +-
 ..._p1.ebuild => casapy-bin-4.2.2.30986_p1.ebuild} |  2 +-
 5 files changed, 10 insertions(+), 72 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     b15feb7b0e78bf5c17fa67e987429784e0d55931
Author:     Jauhien Piatlicki <piatlicki <AT> gmail <DOT> com>
AuthorDate: Sun Sep  7 15:40:31 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Sun Sep  7 15:40:31 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b15feb7b

Merge pull request #262 from carldong/calculix-cgx

Fixed calculix-cgx document install


 sci-libs/calculix-cgx/ChangeLog                    |  6 ++
 ...x-cgx-2.7.ebuild => calculix-cgx-2.7-r1.ebuild} |  6 +-
 .../files/02_cgx_2.7_menu_fix-freeglut_2.8.1.patch | 73 ++++++++++++++++++++++
 3 files changed, 84 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     7d27922859885b7121223a2417f955bcb6b61497
Author:     Carl Dong <carldong76 <AT> gmail <DOT> com>
AuthorDate: Sun Sep  7 00:13:57 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Sun Sep  7 00:13:57 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7d279228

Merge pull request #1 from gentoo-science/master

Sync


 dev-libs/simclist/Manifest                         |   3 -
 dev-ml/mlgmpidl/Manifest                           |   4 -
 dev-ml/ocamlgraph/Manifest                         |   4 -
 dev-ml/zarith/Manifest                             |   3 -
 dev-ml/zarith/metadata.xml                         |   4 +
 licenses/{CeCILL-2.1 => CeCILL-2.0}                | 164 ++++++-------
 licenses/HGSC-BCM                                  |   8 +
 licenses/Non-profit-OSL-3.0                        |  63 +++++
 {app-text/dgs => sci-biology/VarScan}/metadata.xml |   0
 sci-biology/eval/ChangeLog                         |   3 +
 sci-biology/eval/eval-2.2.8.ebuild                 |   3 +-
 sci-biology/sga/metadata.xml                       |   3 +
 sci-biology/sickle/sickle-9999.ebuild              |   2 +-
 sci-chemistry/gromacs/ChangeLog                    |  13 +
 sci-chemistry/gromacs/Manifest                     |   2 -
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild      |  17 +-
 sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild       | 268 ---------------------
 sci-chemistry/votca-csg/ChangeLog                  |   5 +-
 sci-chemistry/votca-csg/votca-csg-9999.ebuild      |  14 +-
 sci-chemistry/votca-csgapps/ChangeLog              |   5 +-
 .../votca-csgapps/votca-csgapps-9999.ebuild        |  10 +-
 sci-libs/calculix-ccx/ChangeLog                    |  11 +-
 sci-libs/calculix-ccx/Manifest                     |   6 +-
 ...ulix-ccx-2.2.ebuild => calculix-ccx-2.7.ebuild} |  19 +-
 .../calculix-ccx/files/01_ccx_2.2_Makefile.patch   |  23 --
 .../calculix-ccx/files/01_ccx_2.2_lapack.patch     |  21 --
 ...7_Makefile_custom_cc_flags_spooles_arpack.patch |  31 +++
 .../calculix-ccx/files/01_ccx_2.7_lapack.patch     |  11 +
 sci-libs/calculix-cgx/ChangeLog                    |  10 +-
 sci-libs/calculix-cgx/Manifest                     |   4 +-
 ...ulix-cgx-2.2.ebuild => calculix-cgx-2.7.ebuild} |  23 +-
 ... => 01_cgx_2.7_Makefile_custom_cxx_flags.patch} |  39 ++-
 sci-libs/gmsh/ChangeLog                            |  19 +-
 sci-libs/gmsh/Manifest                             |   2 +-
 sci-libs/gmsh/files/gmsh-2.5.0-libpng-1.5.patch    |  10 -
 sci-libs/gmsh/files/gmsh-2.5.0-link.patch          |  16 --
 sci-libs/gmsh/gmsh-2.5.0-r1.ebuild                 |  91 -------
 .../gmsh/{gmsh-2.5.0.ebuild => gmsh-2.8.5.ebuild}  |  10 +-
 sci-libs/gmsh/gmsh-9999.ebuild                     |  87 -------
 sci-libs/m4ri/ChangeLog                            |  24 --
 sci-libs/m4ri/Manifest                             |   2 -
 sci-libs/m4ri/m4ri-20090512.ebuild                 |  18 --
 sci-libs/m4ri/m4ri-20100221.ebuild                 |  38 ---
 sci-libs/m4ri/metadata.xml                         |   6 -
 sci-libs/med/ChangeLog                             |   6 +-
 sci-libs/med/med-2.3.6.ebuild                      |   2 +-
 sci-libs/votca-tools/ChangeLog                     |   5 +-
 sci-libs/votca-tools/votca-tools-9999.ebuild       |  12 +-
 sci-mathematics/alt-ergo/Manifest                  |   3 -
 sci-mathematics/apron/Manifest                     |   4 -
 sci-mathematics/apron/metadata.xml                 |   3 +
 sci-mathematics/flocq/Manifest                     |   3 -
 sci-mathematics/frama-c/Manifest                   |   4 -
 sci-mathematics/gappa/Manifest                     |   3 -
 sci-mathematics/gappalib-coq/Manifest              |   3 -
 sci-mathematics/giac/metadata.xml                  |   2 +-
 sci-mathematics/ltl2ba/Manifest                    |   3 -
 sci-mathematics/petsc/ChangeLog                    |   8 +
 sci-mathematics/petsc/petsc-3.4.2.ebuild           |  10 +-
 sci-mathematics/petsc/petsc-3.5.1.ebuild           |  10 +-
 sci-mathematics/pff/Manifest                       |   3 -
 sci-mathematics/why/Manifest                       |   4 -
 sci-mathematics/why/metadata.xml                   |  10 +
 sci-mathematics/why3/Manifest                      |   3 -
 sci-mathematics/why3/metadata.xml                  |   4 +
 sci-physics/bigdft/ChangeLog                       |  11 +-
 sci-physics/bigdft/Manifest                        |   2 +-
 ...bigdft-1.7_pre24.ebuild => bigdft-1.7.5.ebuild} |  77 ++++--
 .../files/bigdft-1.7-dev.24-nolib_mods.patch       |  25 --
 .../bigdft/files/bigdft-1.7.5-dynamic_memory.patch | 106 ++++++++
 .../bigdft/files/bigdft-1.7.5-pkgconfig.patch      |  10 +
 .../bigdft-abi => sci-physics/bigdft}/metadata.xml |  10 +-
 sci-physics/clip/Manifest                          |   3 -
 sci-physics/herwig++/ChangeLog                     |   8 +
 sci-physics/herwig++/Manifest                      |   1 +
 sci-physics/herwig++/herwig++-2.7.0-r1.ebuild      |   2 +-
 ...wig++-2.7.0-r1.ebuild => herwig++-2.7.1.ebuild} |   6 +-
 sci-physics/herwig++/metadata.xml                  |   2 +-
 sci-physics/looptools/ChangeLog                    |   9 +
 sci-physics/looptools/Manifest                     |   3 +
 ...akefile.patch => looptools-2.10-makefile.patch} |   8 +-
 ...{looptools-2.8.ebuild => looptools-2.10.ebuild} |   0
 ...{looptools-2.8.ebuild => looptools-2.11.ebuild} |   2 +-
 .../{looptools-2.8.ebuild => looptools-2.9.ebuild} |   2 +-
 sci-physics/rivet/ChangeLog                        |   5 +
 sci-physics/rivet/Manifest                         |   1 +
 .../{rivet-2.1.1.ebuild => rivet-2.1.2.ebuild}     |   0
 sci-physics/tauola/ChangeLog                       |  11 +-
 sci-physics/tauola/Manifest                        |   1 +
 sci-physics/tauola/files/tauola-1.1.5-doc.patch    |  11 +
 .../{tauola-1.1.4.ebuild => tauola-1.1.5.ebuild}   |   3 +-
 sci-physics/thepeg/ChangeLog                       |  15 ++
 sci-physics/thepeg/Manifest                        |   1 +
 sci-physics/thepeg/metadata.xml                    |   5 +-
 ...{thepeg-1.8.3.ebuild => thepeg-1.8.3-r1.ebuild} |   5 +
 ...epeg-1.9.0-r1.ebuild => thepeg-1.9.0-r2.ebuild} |   5 +
 ...{thepeg-1.9.1.ebuild => thepeg-1.9.1-r1.ebuild} |   5 +
 .../{thepeg-1.9.1.ebuild => thepeg-1.9.2.ebuild}   |   8 +-
 sys-cluster/mpich2/mpich2-1.5.ebuild               |   2 +-
 99 files changed, 695 insertions(+), 894 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     75ad217737584e5722cbd26fd5f8018301f3d2c9
Author:     Jauhien Piatlicki <piatlicki <AT> gmail <DOT> com>
AuthorDate: Sun Sep  7 09:47:41 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Sun Sep  7 09:47:41 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=75ad2177

Merge pull request #263 from carldong/calculix-ccx

Fixed sci-lib/calculix-ccx arpack linking problem


 sci-libs/calculix-ccx/ChangeLog                                     | 6 ++++++
 .../{calculix-ccx-2.7.ebuild => calculix-ccx-2.7-r1.ebuild}         | 1 +
 2 files changed, 7 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     42d038c8daf4b5e9b1338f955be2cb098382d8f6
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Sat Sep  6 19:45:14 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Sat Sep  6 19:45:14 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=42d038c8

Merge branch 'master' from git+ssh://git <AT> git.overlays.gentoo.org/proj/sci.git


 sci-chemistry/gromacs/ChangeLog               | 3 +++
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild | 9 ++-------
 2 files changed, 5 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     6a3a422cd40bee34b6c3eafd284e0f3b4b047653
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Fri Sep  5 15:24:24 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Fri Sep  5 15:24:24 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6a3a422c

Merge remote-tracking branch 'github/master'


 sci-libs/calculix-ccx/ChangeLog                    | 11 ++++--
 sci-libs/calculix-ccx/Manifest                     |  6 ++--
 ...ulix-ccx-2.2.ebuild => calculix-ccx-2.7.ebuild} | 19 ++++++-----
 .../calculix-ccx/files/01_ccx_2.2_Makefile.patch   | 23 -------------
 .../calculix-ccx/files/01_ccx_2.2_lapack.patch     | 21 ------------
 ...7_Makefile_custom_cc_flags_spooles_arpack.patch | 31 +++++++++++++++++
 .../calculix-ccx/files/01_ccx_2.7_lapack.patch     | 11 ++++++
 sci-libs/calculix-cgx/ChangeLog                    | 10 ++++--
 sci-libs/calculix-cgx/Manifest                     |  4 +--
 ...ulix-cgx-2.2.ebuild => calculix-cgx-2.7.ebuild} | 23 +++++++------
 ... => 01_cgx_2.7_Makefile_custom_cxx_flags.patch} | 39 +++++++++++++++++-----
 11 files changed, 116 insertions(+), 82 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     6255d4a0930c95b1dc24bc48c21568fc363fa22b
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Fri Sep  5 15:23:35 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Fri Sep  5 15:23:35 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6255d4a0

Merge remote-tracking branch 'gentoo/master'


 sci-physics/bigdft/ChangeLog                       |  11 ++-
 sci-physics/bigdft/Manifest                        |   2 +-
 ...bigdft-1.7_pre24.ebuild => bigdft-1.7.5.ebuild} |  77 +++++++++++----
 .../files/bigdft-1.7-dev.24-nolib_mods.patch       |  25 -----
 .../bigdft/files/bigdft-1.7.5-dynamic_memory.patch | 106 +++++++++++++++++++++
 .../bigdft/files/bigdft-1.7.5-pkgconfig.patch      |  10 ++
 .../bigdft-abi => sci-physics/bigdft}/metadata.xml |  10 +-
 7 files changed, 187 insertions(+), 54 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     0b4cfd3576883149e09de20e7c2015bba9a02fbc
Author:     Jauhien Piatlicki <piatlicki <AT> gmail <DOT> com>
AuthorDate: Fri Sep  5 13:30:11 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Fri Sep  5 13:30:11 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0b4cfd35

Merge pull request #261 from carldong/calculix

Updated ebuilds for calculix-ccx and calculix-cgx to 2.7


 sci-libs/calculix-ccx/ChangeLog                    | 11 ++++--
 sci-libs/calculix-ccx/Manifest                     |  6 ++--
 ...ulix-ccx-2.2.ebuild => calculix-ccx-2.7.ebuild} | 19 ++++++-----
 .../calculix-ccx/files/01_ccx_2.2_Makefile.patch   | 23 -------------
 .../calculix-ccx/files/01_ccx_2.2_lapack.patch     | 21 ------------
 ...7_Makefile_custom_cc_flags_spooles_arpack.patch | 31 +++++++++++++++++
 .../calculix-ccx/files/01_ccx_2.7_lapack.patch     | 11 ++++++
 sci-libs/calculix-cgx/ChangeLog                    | 10 ++++--
 sci-libs/calculix-cgx/Manifest                     |  4 +--
 ...ulix-cgx-2.2.ebuild => calculix-cgx-2.7.ebuild} | 23 +++++++------
 ... => 01_cgx_2.7_Makefile_custom_cxx_flags.patch} | 39 +++++++++++++++++-----
 11 files changed, 116 insertions(+), 82 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Honza Macháček]

commit:     2971f88217f015fc33a0c659047f509a5debf806
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Fri Sep  5 13:07:47 2014 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Fri Sep  5 13:07:47 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2971f882

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

Commiting the version bump of sci-physics/bigdft took me some time since
the last pull. Pulling the tree before pushing my commit.


 dev-ml/zarith/metadata.xml                      |  4 +++
 profiles/package.use.mask                       |  4 ---
 sci-biology/eval/ChangeLog                      |  3 ++
 sci-biology/eval/eval-2.2.8.ebuild              |  3 +-
 sci-chemistry/gromacs/ChangeLog                 |  3 ++
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild   |  6 +++-
 sci-libs/m4ri/ChangeLog                         | 24 ----------------
 sci-libs/m4ri/Manifest                          |  2 --
 sci-libs/m4ri/m4ri-20090512.ebuild              | 18 ------------
 sci-libs/m4ri/m4ri-20100221.ebuild              | 38 -------------------------
 sci-libs/m4ri/metadata.xml                      |  6 ----
 sci-physics/tauola/ChangeLog                    |  4 +++
 sci-physics/tauola/files/tauola-1.1.5-doc.patch | 11 +++++++
 sci-physics/tauola/tauola-1.1.5.ebuild          |  1 +
 14 files changed, 33 insertions(+), 94 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     6d416e13729a06515f1bda01bda772d2d4f19413
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Thu Sep  4 16:12:05 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Thu Sep  4 16:12:05 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6d416e13

Merge remote-tracking branch 'gentoo/master'


 sci-chemistry/gromacs/ChangeLog               | 3 +++
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild | 6 +++++-
 2 files changed, 8 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     03c02ddeca882964227eeb88160ff3c2cd201889
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Mon Sep  1 14:15:04 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Mon Sep  1 14:15:04 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=03c02dde

Merge PR #260 from Carl Dong: update sci-libs/gmsh to 2.8.5 and change EAPI to 5


 sci-libs/gmsh/ChangeLog                                      | 11 +++++++++--
 sci-libs/gmsh/Manifest                                       |  1 +
 sci-libs/gmsh/{gmsh-2.5.0-r1.ebuild => gmsh-2.5.0-r2.ebuild} |  6 +++++-
 sci-libs/gmsh/{gmsh-2.5.0.ebuild => gmsh-2.8.5.ebuild}       |  8 ++++----
 sci-libs/gmsh/gmsh-9999.ebuild                               |  2 +-
 5 files changed, 20 insertions(+), 8 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     4830f238f013cd1044dff1da9b77969ad639736e
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Aug 29 19:28:17 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Aug 29 19:28:17 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4830f238

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 dev-python/gammapy/ChangeLog                                |  6 ++++++
 dev-python/gammapy/Manifest                                 |  1 +
 .../gammapy/{gammapy-9999.ebuild => gammapy-0.1.ebuild}     | 13 +++++++------
 dev-python/gammapy/gammapy-9999.ebuild                      | 13 +++++++------
 4 files changed, 21 insertions(+), 12 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     4abd0451162b1eb90bca0209b4bd0fd84187aa8b
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 28 11:55:44 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Aug 28 11:55:44 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4abd0451

Merge pull request #259 from sargas/gammapy-0.1

dev-python/gammapy: version bump for 0.1 release


 dev-python/gammapy/ChangeLog                                |  6 ++++++
 dev-python/gammapy/Manifest                                 |  1 +
 .../gammapy/{gammapy-9999.ebuild => gammapy-0.1.ebuild}     | 13 +++++++------
 dev-python/gammapy/gammapy-9999.ebuild                      | 13 +++++++------
 4 files changed, 21 insertions(+), 12 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     42fb0758dc983df8a828fbdcc7702ee5fe12895f
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 24 12:59:23 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Aug 24 12:59:23 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=42fb0758

Merge pull request #243 from tamiko/update_dealii_live_ebuild

sci-libs/dealii-9999: Repository update, metadata.xml fixes


 sci-libs/dealii/ChangeLog          |  6 +++-
 sci-libs/dealii/dealii-9999.ebuild | 11 +++-----
 sci-libs/dealii/metadata.xml       | 58 ++++++++++++++++++++------------------
 3 files changed, 39 insertions(+), 36 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     f08a620b99f928e72e638ae887f049b8b4e832d4
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 25 22:43:11 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Aug 25 22:43:11 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f08a620b

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 sci-libs/dealii/ChangeLog          |  6 +++-
 sci-libs/dealii/dealii-9999.ebuild | 11 +++-----
 sci-libs/dealii/metadata.xml       | 58 ++++++++++++++++++++------------------
 3 files changed, 39 insertions(+), 36 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5767532529b678829a05ced26623107874f44066
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Aug 22 18:54:48 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Aug 22 18:54:48 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=57675325

Merge pull request #258 from sargas/astroquery

dev-python/astroquery: Add astroquery ebuild


 dev-python/astroquery/ChangeLog                    | 10 ++++++
 dev-python/astroquery/Manifest                     |  1 +
 .../astroquery-0.2.ebuild}                         | 38 +++++++++++++---------
 .../astroquery-9999.ebuild}                        | 38 +++++++++++++---------
 .../{astropy-helpers => astroquery}/metadata.xml   |  5 +--
 5 files changed, 60 insertions(+), 32 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f72e31d463a56363aa6a94c1c00add496c8e46e9
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 21 08:32:04 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Aug 21 08:32:04 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f72e31d4

Merge pull request #256 from marbre/nvidia-cuda-toolkit

dev-util/nvidia-cuda-toolkit: Version Bump


 dev-util/nvidia-cuda-toolkit/ChangeLog               |  6 ++++++
 dev-util/nvidia-cuda-toolkit/Manifest                |  2 ++
 ...5.11.ebuild => nvidia-cuda-toolkit-6.5.14.ebuild} | 20 ++++++--------------
 3 files changed, 14 insertions(+), 14 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b79f6fd9bf9c104e3880dccaa62d544cc0fa401a
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 21 08:32:08 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Aug 21 08:32:08 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b79f6fd9

Merge pull request #257 from marbre/nvidia-cuda-sdk

dev-util/nvidia-cuda-sdk: Version Bump


 dev-util/nvidia-cuda-sdk/ChangeLog                     |  6 ++++++
 dev-util/nvidia-cuda-sdk/Manifest                      |  1 +
 ...sdk-6.5.11.ebuild => nvidia-cuda-sdk-6.5.14.ebuild} | 18 ++++++------------
 3 files changed, 13 insertions(+), 12 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     c0cba0d05a0cee47cdfb67e6e1f0a002e7101381
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Aug 19 21:51:19 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Aug 19 21:51:19 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c0cba0d0

Merge branch 'master' of ssh://github.com/gentoo-science/sci

Conflicts:
	sci-physics/espresso/ChangeLog
	sci-physics/espresso/espresso-9999.ebuild


 dev-java/jeuclid-core/ChangeLog                    |  10 +-
 .../files/jeuclid-core-cast-issue.patch            |  18 +++
 ...e-3.1.9.ebuild => jeuclid-core-3.1.9-r1.ebuild} |  19 +--
 dev-python/astropy-helpers/ChangeLog               |  10 ++
 dev-python/astropy-helpers/Manifest                |   1 +
 .../astropy-helpers/astropy-helpers-0.4.1.ebuild   |  28 ++++
 .../astropy-helpers/astropy-helpers-9999.ebuild    |  28 ++++
 .../astropy-helpers}/metadata.xml                  |   5 +-
 dev-python/astropy/ChangeLog                       |   7 +-
 dev-python/astropy/astropy-9999.ebuild             |  50 +++++--
 dev-python/ccdproc/ChangeLog                       |  10 ++
 dev-python/ccdproc/Manifest                        |   1 +
 dev-python/ccdproc/ccdproc-0.2.ebuild              |  59 ++++++++
 dev-python/ccdproc/ccdproc-9999.ebuild             |  59 ++++++++
 dev-python/ccdproc/metadata.xml                    |  10 ++
 dev-python/gammapy/ChangeLog                       |   9 ++
 dev-python/gammapy/gammapy-9999.ebuild             |  75 +++++++++++
 dev-python/gammapy/metadata.xml                    |  10 ++
 dev-python/imageutils/ChangeLog                    |   9 ++
 dev-python/imageutils/imageutils-9999.ebuild       |  58 ++++++++
 dev-python/imageutils/metadata.xml                 |  10 ++
 dev-python/photutils/ChangeLog                     |   9 ++
 dev-python/photutils/metadata.xml                  |  10 ++
 dev-python/photutils/photutils-9999.ebuild         |  61 +++++++++
 dev-python/specutils/ChangeLog                     |   9 ++
 dev-python/specutils/metadata.xml                  |  10 ++
 dev-python/specutils/specutils-9999.ebuild         |  59 ++++++++
 sci-chemistry/curvefit/ChangeLog                   |   5 +-
 sci-chemistry/curvefit/curvefit-1.40.ebuild        |   2 +-
 sci-chemistry/mddnmr/ChangeLog                     |  10 +-
 sci-chemistry/mddnmr/Manifest                      |   3 +-
 sci-chemistry/mddnmr/mddnmr-2.1.ebuild             |  59 --------
 .../{mddnmr-2.2.ebuild => mddnmr-2.4-r1.ebuild}    |   6 +-
 sci-chemistry/mddnmr/metadata.xml                  |   2 +-
 sci-chemistry/module2/ChangeLog                    |  10 ++
 sci-chemistry/module2/Manifest                     |   1 +
 sci-chemistry/{concoord => module2}/metadata.xml   |   0
 sci-chemistry/module2/module2-0_pre20140717.ebuild |  51 +++++++
 sci-chemistry/nwchem/ChangeLog                     |  12 +-
 sci-chemistry/nwchem/Manifest                      |   1 -
 sci-chemistry/nwchem/metadata.xml                  |   3 +
 sci-chemistry/nwchem/nwchem-6.3-r1.ebuild          | 150 ---------------------
 ...wchem-6.3-r2.ebuild => nwchem-6.3_p2-r1.ebuild} |  62 ++++++++-
 sci-chemistry/pales-bin/ChangeLog                  |  13 ++
 sci-chemistry/pales-bin/Manifest                   |   1 +
 sci-chemistry/{concoord => pales-bin}/metadata.xml |   0
 .../pales-bin/pales-bin-0_pre140717.ebuild         |  26 ++++
 sci-chemistry/redcat/ChangeLog                     |  14 ++
 sci-chemistry/redcat/Manifest                      |   1 +
 sci-chemistry/redcat/files/CMakeLists.txt          |  13 ++
 sci-chemistry/{concoord => redcat}/metadata.xml    |   0
 sci-chemistry/redcat/redcat-3.ebuild               |  62 +++++++++
 sci-libs/libsc/ChangeLog                           |   6 +
 sci-libs/libsc/Manifest                            |   1 +
 sci-libs/libsc/libsc-0.7.3.ebuild                  |   8 +-
 .../libsc/{libsc-0.7.3.ebuild => libsc-1.0.ebuild} |  14 +-
 sci-libs/libsc/metadata.xml                        |  23 ++--
 sci-libs/p4est/ChangeLog                           |   6 +
 sci-libs/p4est/Manifest                            |   2 +
 sci-libs/p4est/metadata.xml                        |  29 ++--
 .../p4est/{p4est-0.3.5.ebuild => p4est-1.0.ebuild} |  33 +++--
 sci-mathematics/giac/ChangeLog                     |   3 +
 sci-mathematics/giac/Manifest                      |   3 -
 sci-mathematics/giac/giac-1.1.0.ebuild             |  20 ++-
 sci-mathematics/petsc/Manifest                     |   1 +
 ...rpath.patch => petsc-3.5.1-disable-rpath.patch} |   0
 sci-mathematics/petsc/metadata.xml                 |   4 +-
 .../{petsc-3.4.2.ebuild => petsc-3.5.1.ebuild}     |  28 ++--
 sci-physics/espresso/ChangeLog                     |   5 +-
 sci-physics/espresso/espresso-9999.ebuild          |  40 ++++--
 sci-physics/espresso/metadata.xml                  |   1 +
 sci-physics/geant-vmc/ChangeLog                    |   5 +
 sci-physics/geant-vmc/geant-vmc-9999.ebuild        |  19 +--
 73 files changed, 1041 insertions(+), 361 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     e8ac18ba130b5a9eaad7aed2a889ff3b66e0de76
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 10 08:04:32 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Aug 10 08:04:32 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e8ac18ba

Merge pull request #251 from sargas/astropy_affliates

Add some Astropy-affliated packages


 dev-python/astropy-helpers/ChangeLog               | 10 +++
 dev-python/astropy-helpers/Manifest                |  1 +
 .../astropy-helpers/astropy-helpers-0.4.1.ebuild   | 28 ++++++++
 .../astropy-helpers/astropy-helpers-9999.ebuild    | 28 ++++++++
 .../astropy-helpers}/metadata.xml                  |  5 +-
 dev-python/ccdproc/ChangeLog                       | 10 +++
 dev-python/ccdproc/Manifest                        |  1 +
 dev-python/ccdproc/ccdproc-0.2.ebuild              | 59 +++++++++++++++++
 dev-python/ccdproc/ccdproc-9999.ebuild             | 59 +++++++++++++++++
 dev-python/ccdproc/metadata.xml                    | 10 +++
 dev-python/gammapy/ChangeLog                       |  9 +++
 dev-python/gammapy/gammapy-9999.ebuild             | 75 ++++++++++++++++++++++
 dev-python/gammapy/metadata.xml                    | 10 +++
 dev-python/imageutils/ChangeLog                    |  9 +++
 dev-python/imageutils/imageutils-9999.ebuild       | 58 +++++++++++++++++
 dev-python/imageutils/metadata.xml                 | 10 +++
 dev-python/photutils/ChangeLog                     |  9 +++
 dev-python/photutils/metadata.xml                  | 10 +++
 dev-python/photutils/photutils-9999.ebuild         | 61 ++++++++++++++++++
 dev-python/specutils/ChangeLog                     |  9 +++
 dev-python/specutils/metadata.xml                  | 10 +++
 dev-python/specutils/specutils-9999.ebuild         | 59 +++++++++++++++++
 22 files changed, 538 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     b34791f7e31176f99c309d9bbd407725969941ab
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 10 08:03:42 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Aug 10 08:03:42 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b34791f7

Merge pull request #252 from Doeme/master

sci-mathematics/giac changes


 sci-mathematics/giac/ChangeLog         |  3 +++
 sci-mathematics/giac/Manifest          |  3 ---
 sci-mathematics/giac/giac-1.1.0.ebuild | 20 +++++++++++++++++++-
 3 files changed, 22 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     10192aa71af635e401f27e7a6669a4e48d52123a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 10 08:05:02 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Aug 10 08:05:02 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=10192aa7

Merge remote-tracking branch 'github/master'

* github/master:
  Remove python2.6 from astropy affliated ebuilds
  sci-mathematics/giac: Ebuild fix
  sci-mathematics/giac: EAPI bump
  sci-mathematics/giac: Ebuild improvement
  sci-mathematics/giac: Ebuild fix
  dev-python/specutils: Add specutils package
  dev-python/photutils: Add photutils package
  dev-python/imageutils: Add imageutils package
  dev-python/gammapy: Add gammapy package
  dev-python/ccdproc: Add ccdproc package
  dev-python/astropy-helpers: Add astropy-helpers package
  2.0.4 is already in main tree Revert "media-gfx/librecad: version bump 2.0.4"
  media-gfx/librecad: version bump 2.0.4
  Install the .f90 fortran includes.


 dev-python/astropy-helpers/ChangeLog               | 10 +++
 dev-python/astropy-helpers/Manifest                |  1 +
 .../astropy-helpers/astropy-helpers-0.4.1.ebuild   | 28 ++++++++
 .../astropy-helpers/astropy-helpers-9999.ebuild    | 28 ++++++++
 .../astropy-helpers}/metadata.xml                  |  5 +-
 dev-python/ccdproc/ChangeLog                       | 10 +++
 dev-python/ccdproc/Manifest                        |  1 +
 dev-python/ccdproc/ccdproc-0.2.ebuild              | 59 +++++++++++++++++
 dev-python/ccdproc/ccdproc-9999.ebuild             | 59 +++++++++++++++++
 dev-python/ccdproc/metadata.xml                    | 10 +++
 dev-python/gammapy/ChangeLog                       |  9 +++
 dev-python/gammapy/gammapy-9999.ebuild             | 75 ++++++++++++++++++++++
 dev-python/gammapy/metadata.xml                    | 10 +++
 dev-python/imageutils/ChangeLog                    |  9 +++
 dev-python/imageutils/imageutils-9999.ebuild       | 58 +++++++++++++++++
 dev-python/imageutils/metadata.xml                 | 10 +++
 dev-python/photutils/ChangeLog                     |  9 +++
 dev-python/photutils/metadata.xml                  | 10 +++
 dev-python/photutils/photutils-9999.ebuild         | 61 ++++++++++++++++++
 dev-python/specutils/ChangeLog                     |  9 +++
 dev-python/specutils/metadata.xml                  | 10 +++
 dev-python/specutils/specutils-9999.ebuild         | 59 +++++++++++++++++
 sci-mathematics/giac/ChangeLog                     |  3 +
 sci-mathematics/giac/Manifest                      |  3 -
 sci-mathematics/giac/giac-1.1.0.ebuild             | 20 +++++-
 sci-mathematics/petsc/petsc-3.5.1.ebuild           |  5 +-
 26 files changed, 563 insertions(+), 8 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     d6150c37ccf1e22f75b381a3068d71e6bcbab811
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 11 17:21:21 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Aug 11 17:21:21 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d6150c37

Merge pull request #254 from sargas/modernize-astropy-ebuild

dev-python/astropy: Update astropy live ebuild deps and python support


 dev-python/astropy/ChangeLog           |  7 ++++-
 dev-python/astropy/astropy-9999.ebuild | 50 ++++++++++++++++++++++++----------
 2 files changed, 42 insertions(+), 15 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     d6150c37ccf1e22f75b381a3068d71e6bcbab811
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 11 17:21:21 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Aug 11 17:21:21 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d6150c37

Merge pull request #254 from sargas/modernize-astropy-ebuild

dev-python/astropy: Update astropy live ebuild deps and python support


 dev-python/astropy/ChangeLog           |  7 ++++-
 dev-python/astropy/astropy-9999.ebuild | 50 ++++++++++++++++++++++++----------
 2 files changed, 42 insertions(+), 15 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     175aa81811a1e9d827d3ed98a5778c2a8a1aa86b
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 11 21:38:46 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Aug 11 21:38:46 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=175aa818

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 dev-python/astropy/ChangeLog           |  7 ++++-
 dev-python/astropy/astropy-9999.ebuild | 50 ++++++++++++++++++++++++----------
 2 files changed, 42 insertions(+), 15 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     175aa81811a1e9d827d3ed98a5778c2a8a1aa86b
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 11 21:38:46 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Aug 11 21:38:46 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=175aa818

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 dev-python/astropy/ChangeLog           |  7 ++++-
 dev-python/astropy/astropy-9999.ebuild | 50 ++++++++++++++++++++++++----------
 2 files changed, 42 insertions(+), 15 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     10192aa71af635e401f27e7a6669a4e48d52123a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 10 08:05:02 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Aug 10 08:05:02 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=10192aa7

Merge remote-tracking branch 'github/master'

* github/master:
  Remove python2.6 from astropy affliated ebuilds
  sci-mathematics/giac: Ebuild fix
  sci-mathematics/giac: EAPI bump
  sci-mathematics/giac: Ebuild improvement
  sci-mathematics/giac: Ebuild fix
  dev-python/specutils: Add specutils package
  dev-python/photutils: Add photutils package
  dev-python/imageutils: Add imageutils package
  dev-python/gammapy: Add gammapy package
  dev-python/ccdproc: Add ccdproc package
  dev-python/astropy-helpers: Add astropy-helpers package
  2.0.4 is already in main tree Revert "media-gfx/librecad: version bump 2.0.4"
  media-gfx/librecad: version bump 2.0.4
  Install the .f90 fortran includes.


 dev-python/astropy-helpers/ChangeLog               | 10 +++
 dev-python/astropy-helpers/Manifest                |  1 +
 .../astropy-helpers/astropy-helpers-0.4.1.ebuild   | 28 ++++++++
 .../astropy-helpers/astropy-helpers-9999.ebuild    | 28 ++++++++
 .../astropy-helpers}/metadata.xml                  |  5 +-
 dev-python/ccdproc/ChangeLog                       | 10 +++
 dev-python/ccdproc/Manifest                        |  1 +
 dev-python/ccdproc/ccdproc-0.2.ebuild              | 59 +++++++++++++++++
 dev-python/ccdproc/ccdproc-9999.ebuild             | 59 +++++++++++++++++
 dev-python/ccdproc/metadata.xml                    | 10 +++
 dev-python/gammapy/ChangeLog                       |  9 +++
 dev-python/gammapy/gammapy-9999.ebuild             | 75 ++++++++++++++++++++++
 dev-python/gammapy/metadata.xml                    | 10 +++
 dev-python/imageutils/ChangeLog                    |  9 +++
 dev-python/imageutils/imageutils-9999.ebuild       | 58 +++++++++++++++++
 dev-python/imageutils/metadata.xml                 | 10 +++
 dev-python/photutils/ChangeLog                     |  9 +++
 dev-python/photutils/metadata.xml                  | 10 +++
 dev-python/photutils/photutils-9999.ebuild         | 61 ++++++++++++++++++
 dev-python/specutils/ChangeLog                     |  9 +++
 dev-python/specutils/metadata.xml                  | 10 +++
 dev-python/specutils/specutils-9999.ebuild         | 59 +++++++++++++++++
 sci-mathematics/giac/ChangeLog                     |  3 +
 sci-mathematics/giac/Manifest                      |  3 -
 sci-mathematics/giac/giac-1.1.0.ebuild             | 20 +++++-
 sci-mathematics/petsc/petsc-3.5.1.ebuild           |  5 +-
 26 files changed, 563 insertions(+), 8 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     e8ac18ba130b5a9eaad7aed2a889ff3b66e0de76
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 10 08:04:32 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Aug 10 08:04:32 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e8ac18ba

Merge pull request #251 from sargas/astropy_affliates

Add some Astropy-affliated packages


 dev-python/astropy-helpers/ChangeLog               | 10 +++
 dev-python/astropy-helpers/Manifest                |  1 +
 .../astropy-helpers/astropy-helpers-0.4.1.ebuild   | 28 ++++++++
 .../astropy-helpers/astropy-helpers-9999.ebuild    | 28 ++++++++
 .../astropy-helpers}/metadata.xml                  |  5 +-
 dev-python/ccdproc/ChangeLog                       | 10 +++
 dev-python/ccdproc/Manifest                        |  1 +
 dev-python/ccdproc/ccdproc-0.2.ebuild              | 59 +++++++++++++++++
 dev-python/ccdproc/ccdproc-9999.ebuild             | 59 +++++++++++++++++
 dev-python/ccdproc/metadata.xml                    | 10 +++
 dev-python/gammapy/ChangeLog                       |  9 +++
 dev-python/gammapy/gammapy-9999.ebuild             | 75 ++++++++++++++++++++++
 dev-python/gammapy/metadata.xml                    | 10 +++
 dev-python/imageutils/ChangeLog                    |  9 +++
 dev-python/imageutils/imageutils-9999.ebuild       | 58 +++++++++++++++++
 dev-python/imageutils/metadata.xml                 | 10 +++
 dev-python/photutils/ChangeLog                     |  9 +++
 dev-python/photutils/metadata.xml                  | 10 +++
 dev-python/photutils/photutils-9999.ebuild         | 61 ++++++++++++++++++
 dev-python/specutils/ChangeLog                     |  9 +++
 dev-python/specutils/metadata.xml                  | 10 +++
 dev-python/specutils/specutils-9999.ebuild         | 59 +++++++++++++++++
 22 files changed, 538 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b34791f7e31176f99c309d9bbd407725969941ab
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 10 08:03:42 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Aug 10 08:03:42 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b34791f7

Merge pull request #252 from Doeme/master

sci-mathematics/giac changes


 sci-mathematics/giac/ChangeLog         |  3 +++
 sci-mathematics/giac/Manifest          |  3 ---
 sci-mathematics/giac/giac-1.1.0.ebuild | 20 +++++++++++++++++++-
 3 files changed, 22 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     3b9949d13d0724d43415d7f46dc54406c7b70bc1
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Sun Aug  3 16:52:22 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Aug  3 16:52:22 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3b9949d1

Merge pull request #248 from mrestelli/petsc

Install the .f90 fortran includes and the missing .so


 sci-mathematics/petsc/petsc-3.5.1.ebuild | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Guillaume Horel]

commit:     e642edf2bb5462db41297168d2b8381466df1b33
Author:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
AuthorDate: Sun Jul 27 13:08:42 2014 +0000
Commit:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
CommitDate: Sun Jul 27 13:08:42 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e642edf2

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 dev-ml/mlgmpidl/Manifest                           |  2 +-
 dev-ml/mlgmpidl/mlgmpidl-1.1.ebuild                |  4 +-
 dev-ml/ocamlgraph/Manifest                         |  2 +-
 dev-ml/ocamlgraph/ocamlgraph-1.8.5.ebuild          |  4 +-
 dev-ml/zarith/Manifest                             |  2 +-
 dev-ml/zarith/zarith-1.2.1.ebuild                  |  4 +-
 dev-python/ffc/ChangeLog                           |  9 ++++
 dev-python/ffc/Manifest                            |  1 +
 dev-python/ffc/ffc-1.3.0.ebuild                    | 10 +++-
 .../ffc/{ffc-1.3.0.ebuild => ffc-1.4.0.ebuild}     | 10 +++-
 dev-python/fiat/ChangeLog                          | 14 ++++-
 dev-python/fiat/Manifest                           |  2 +
 .../fiat/{fiat-1.1.ebuild => fiat-1.3.0.ebuild}    | 13 +++--
 .../fiat/{fiat-1.1.ebuild => fiat-1.4.0.ebuild}    | 13 +++--
 dev-python/instant/ChangeLog                       | 10 +++-
 dev-python/instant/Manifest                        |  2 +
 .../{instant-1.2.0.ebuild => instant-1.3.0.ebuild} |  9 ++--
 .../{instant-1.2.0.ebuild => instant-1.4.0.ebuild} |  9 ++--
 dev-python/ufl/ChangeLog                           | 10 +++-
 dev-python/ufl/Manifest                            |  4 +-
 dev-python/ufl/metadata.xml                        |  3 ++
 .../ufl/{ufl-0.5.4.ebuild => ufl-1.3.0.ebuild}     | 11 ++--
 .../ufl/{ufl-0.5.4.ebuild => ufl-1.4.0.ebuild}     | 11 ++--
 sci-chemistry/module2/ChangeLog                    | 10 ++++
 sci-chemistry/module2/Manifest                     |  1 +
 sci-chemistry/{concoord => module2}/metadata.xml   |  0
 sci-chemistry/module2/module2-0_pre20140717.ebuild | 51 ++++++++++++++++++
 sci-chemistry/pales-bin/ChangeLog                  | 13 +++++
 sci-chemistry/pales-bin/Manifest                   |  1 +
 sci-chemistry/{concoord => pales-bin}/metadata.xml |  0
 .../pales-bin/pales-bin-0_pre140717.ebuild         | 26 +++++++++
 sci-chemistry/redcat/ChangeLog                     | 14 +++++
 sci-chemistry/redcat/Manifest                      |  1 +
 sci-chemistry/redcat/files/CMakeLists.txt          | 13 +++++
 sci-chemistry/{concoord => redcat}/metadata.xml    |  0
 sci-chemistry/redcat/redcat-3.ebuild               | 62 ++++++++++++++++++++++
 sci-libs/libsc/ChangeLog                           |  6 +++
 sci-libs/libsc/Manifest                            |  1 +
 sci-libs/libsc/libsc-0.7.3.ebuild                  |  8 +--
 .../libsc/{libsc-0.7.3.ebuild => libsc-1.0.ebuild} | 14 ++---
 sci-libs/libsc/metadata.xml                        | 23 ++++----
 sci-libs/p4est/ChangeLog                           |  6 +++
 sci-libs/p4est/Manifest                            |  2 +
 sci-libs/p4est/metadata.xml                        | 29 +++++-----
 .../p4est/{p4est-0.3.5.ebuild => p4est-1.0.ebuild} | 33 +++++++-----
 sci-mathematics/alt-ergo/Manifest                  |  2 +-
 sci-mathematics/alt-ergo/alt-ergo-0.95.2.ebuild    |  8 +--
 sci-mathematics/apron/ChangeLog                    |  4 ++
 sci-mathematics/apron/Manifest                     |  4 +-
 sci-mathematics/apron/apron-0.9.10-r1.ebuild       | 20 ++-----
 sci-mathematics/apron/apron-0.9.10.ebuild          |  6 +--
 sci-mathematics/flocq/Manifest                     |  2 +-
 sci-mathematics/flocq/flocq-2.3.0.ebuild           |  4 +-
 sci-mathematics/frama-c/Manifest                   |  2 +-
 sci-mathematics/frama-c/frama-c-20140301.ebuild    |  4 +-
 sci-mathematics/giac/Manifest                      |  2 +-
 sci-mathematics/giac/giac-1.1.0.ebuild             |  2 +-
 sci-mathematics/ltl2ba/Manifest                    |  2 +-
 sci-mathematics/petsc/Manifest                     |  1 +
 ...rpath.patch => petsc-3.5.1-disable-rpath.patch} |  0
 sci-mathematics/petsc/metadata.xml                 |  4 +-
 .../{petsc-3.4.2.ebuild => petsc-3.5.1.ebuild}     | 25 ++++-----
 sci-mathematics/ufc/ChangeLog                      | 10 +++-
 sci-mathematics/ufc/Manifest                       |  3 +-
 .../ufc/{ufc-1.4.2.ebuild => ufc-2.3.0.ebuild}     |  7 ++-
 sci-mathematics/why/Manifest                       |  2 +-
 sci-mathematics/why/why-2.34.ebuild                |  9 ++--
 sci-mathematics/why3/Manifest                      |  2 +-
 sci-mathematics/why3/why3-0.83.ebuild              |  7 +--
 sci-physics/geant-vmc/ChangeLog                    |  5 ++
 sci-physics/geant-vmc/geant-vmc-9999.ebuild        | 19 ++-----
 sci-visualization/gnuplot/ChangeLog                |  9 ++++
 ...lot-4.7.9999.ebuild => gnuplot-5.0.9999.ebuild} |  1 +
 sys-cluster/hpx/hpx-0.9.8.ebuild                   | 13 ++---
 sys-cluster/hpx/hpx-9999.ebuild                    | 13 ++---
 75 files changed, 476 insertions(+), 189 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     2edd62fde212ab32ff071ec86cc486abc0267119
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jul 27 08:58:25 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jul 27 08:58:25 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2edd62fd

Merge pull request #246 from olifre/master

geant-vmc-9999: Make "test" really work, some doc-related fixes. 


 sci-physics/geant-vmc/ChangeLog             |  5 +++++
 sci-physics/geant-vmc/geant-vmc-9999.ebuild | 19 +++++--------------
 2 files changed, 10 insertions(+), 14 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jens-Malte Gottfried]

commit:     a3bd195b7158ecac600824a83e45c37bb756ab9a
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jul 23 11:47:33 2014 +0000
Commit:     Jens-Malte Gottfried <jmg <AT> godefridus <DOT> de>
CommitDate: Wed Jul 23 11:47:33 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a3bd195b

Merge pull request #245 from tamiko/bump_libsc_and_p4est

Bump sci-libs/libsc and sci-libs/p4est


 sci-libs/libsc/ChangeLog                           |  6 ++++
 sci-libs/libsc/Manifest                            |  1 +
 sci-libs/libsc/libsc-0.7.3.ebuild                  |  8 +++---
 .../libsc/{libsc-0.7.3.ebuild => libsc-1.0.ebuild} | 14 +++------
 sci-libs/libsc/metadata.xml                        | 23 +++++++--------
 sci-libs/p4est/ChangeLog                           |  6 ++++
 sci-libs/p4est/Manifest                            |  2 ++
 sci-libs/p4est/metadata.xml                        | 29 ++++++++++---------
 .../p4est/{p4est-0.3.5.ebuild => p4est-1.0.ebuild} | 33 +++++++++++++---------
 9 files changed, 70 insertions(+), 52 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jens-Malte Gottfried]

commit:     7f5a4407073d33b13897c7d375ccb421d56a7e55
Author:     Jens Malte Gottfried <jmgottfried <AT> web <DOT> de>
AuthorDate: Thu Jul 24 21:50:35 2014 +0000
Commit:     Jens-Malte Gottfried <jmg <AT> godefridus <DOT> de>
CommitDate: Thu Jul 24 21:50:35 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7f5a4407

Merge github.com:gentoo-science/sci


 sci-libs/libsc/ChangeLog                           |  6 ++++
 sci-libs/libsc/Manifest                            |  1 +
 sci-libs/libsc/libsc-0.7.3.ebuild                  |  8 +++---
 .../libsc/{libsc-0.7.3.ebuild => libsc-1.0.ebuild} | 14 +++------
 sci-libs/libsc/metadata.xml                        | 23 +++++++--------
 sci-libs/p4est/ChangeLog                           |  6 ++++
 sci-libs/p4est/Manifest                            |  2 ++
 sci-libs/p4est/metadata.xml                        | 29 ++++++++++---------
 .../p4est/{p4est-0.3.5.ebuild => p4est-1.0.ebuild} | 33 +++++++++++++---------
 9 files changed, 70 insertions(+), 52 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f37972d5928712dfd733e77fae22401e3824aa2e
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jul 22 06:24:17 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jul 22 06:24:17 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f37972d5

Merge remote-tracking branch 'github/master'

* github/master:
  moved to gx86
  more corrections
  incorporated fixes from hpx-0.9.8 ebuild
  dropped no superfluous setting
  HPX live ebuild now reflects changes in trunk
  alt-ergo/alt-ergo-0.95.2: fix gui building
  dev-ml/zarith-1.2.1: fix doc building
  Fix manifests regression
  Several DESTDIR fixes
  sci-mathematics/apron: force j1 for make
  fixed dependency issue
  added keyword
  version bump
  version bump
  Added keyword
  version bump
  version bump
  version bump


 dev-ml/mlgmpidl/Manifest                           |  2 +-
 dev-ml/mlgmpidl/mlgmpidl-1.1.ebuild                |  4 +-
 dev-ml/ocamlgraph/Manifest                         |  2 +-
 dev-ml/ocamlgraph/ocamlgraph-1.8.5.ebuild          |  4 +-
 dev-ml/zarith/Manifest                             |  2 +-
 dev-ml/zarith/zarith-1.2.1.ebuild                  |  4 +-
 dev-python/ffc/ChangeLog                           |  9 ++++
 dev-python/ffc/Manifest                            |  1 +
 dev-python/ffc/ffc-1.3.0.ebuild                    | 10 ++++-
 .../ffc/{ffc-1.3.0.ebuild => ffc-1.4.0.ebuild}     | 10 ++++-
 dev-python/fiat/ChangeLog                          | 14 ++++++-
 dev-python/fiat/Manifest                           |  2 +
 .../fiat/{fiat-1.1.ebuild => fiat-1.3.0.ebuild}    | 13 +++---
 .../fiat/{fiat-1.1.ebuild => fiat-1.4.0.ebuild}    | 13 +++---
 dev-python/instant/ChangeLog                       | 10 ++++-
 dev-python/instant/Manifest                        |  2 +
 .../{instant-1.2.0.ebuild => instant-1.3.0.ebuild} |  9 ++--
 .../{instant-1.2.0.ebuild => instant-1.4.0.ebuild} |  9 ++--
 dev-python/ufl/ChangeLog                           | 10 ++++-
 dev-python/ufl/Manifest                            |  4 +-
 dev-python/ufl/metadata.xml                        |  3 ++
 .../ufl/{ufl-0.5.4.ebuild => ufl-1.3.0.ebuild}     | 11 +++--
 .../ufl/{ufl-0.5.4.ebuild => ufl-1.4.0.ebuild}     | 11 +++--
 sci-libs/libcerf/ChangeLog                         | 13 ------
 sci-libs/libcerf/Manifest                          |  1 -
 sci-libs/libcerf/files/libcerf-1.3-autotools.patch | 48 ----------------------
 sci-libs/libcerf/libcerf-1.3.ebuild                | 22 ----------
 sci-libs/libcerf/metadata.xml                      |  5 ---
 sci-mathematics/alt-ergo/Manifest                  |  2 +-
 sci-mathematics/alt-ergo/alt-ergo-0.95.2.ebuild    |  8 ++--
 sci-mathematics/apron/ChangeLog                    |  4 ++
 sci-mathematics/apron/Manifest                     |  4 +-
 sci-mathematics/apron/apron-0.9.10-r1.ebuild       | 20 ++-------
 sci-mathematics/apron/apron-0.9.10.ebuild          |  6 +--
 sci-mathematics/flocq/Manifest                     |  2 +-
 sci-mathematics/flocq/flocq-2.3.0.ebuild           |  4 +-
 sci-mathematics/frama-c/Manifest                   |  2 +-
 sci-mathematics/frama-c/frama-c-20140301.ebuild    |  4 +-
 sci-mathematics/giac/Manifest                      |  2 +-
 sci-mathematics/giac/giac-1.1.0.ebuild             |  2 +-
 sci-mathematics/ltl2ba/Manifest                    |  2 +-
 sci-mathematics/ufc/ChangeLog                      | 10 ++++-
 sci-mathematics/ufc/Manifest                       |  3 +-
 .../ufc/{ufc-1.4.2.ebuild => ufc-2.3.0.ebuild}     |  7 ++--
 sci-mathematics/why/Manifest                       |  2 +-
 sci-mathematics/why/why-2.34.ebuild                |  9 ++--
 sci-mathematics/why3/Manifest                      |  2 +-
 sci-mathematics/why3/why3-0.83.ebuild              |  7 ++--
 sys-cluster/hpx/hpx-0.9.8.ebuild                   | 13 +++---
 sys-cluster/hpx/hpx-9999.ebuild                    | 13 ++----
 50 files changed, 182 insertions(+), 194 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     0480b95104407451ce055cff97178a1009651553
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Jul 21 22:47:13 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jul 21 22:47:13 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0480b951

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 dev-python/ffc/ChangeLog                                   |  9 +++++++++
 dev-python/ffc/Manifest                                    |  1 +
 dev-python/ffc/ffc-1.3.0.ebuild                            | 10 +++++++++-
 dev-python/ffc/{ffc-1.3.0.ebuild => ffc-1.4.0.ebuild}      | 10 +++++++++-
 dev-python/fiat/ChangeLog                                  | 14 ++++++++++++--
 dev-python/fiat/Manifest                                   |  2 ++
 dev-python/fiat/{fiat-1.1.ebuild => fiat-1.3.0.ebuild}     | 13 ++++++++-----
 dev-python/fiat/{fiat-1.1.ebuild => fiat-1.4.0.ebuild}     | 13 ++++++++-----
 dev-python/instant/ChangeLog                               | 10 ++++++++--
 dev-python/instant/Manifest                                |  2 ++
 .../instant/{instant-1.2.0.ebuild => instant-1.3.0.ebuild} |  9 ++++++---
 .../instant/{instant-1.2.0.ebuild => instant-1.4.0.ebuild} |  9 ++++++---
 dev-python/ufl/ChangeLog                                   | 10 ++++++++--
 dev-python/ufl/Manifest                                    |  4 +++-
 dev-python/ufl/metadata.xml                                |  3 +++
 dev-python/ufl/{ufl-0.5.4.ebuild => ufl-1.3.0.ebuild}      | 11 ++++++++---
 dev-python/ufl/{ufl-0.5.4.ebuild => ufl-1.4.0.ebuild}      | 11 ++++++++---
 sci-mathematics/ufc/ChangeLog                              | 10 +++++++++-
 sci-mathematics/ufc/Manifest                               |  3 ++-
 sci-mathematics/ufc/{ufc-1.4.2.ebuild => ufc-2.3.0.ebuild} |  7 +++----
 sys-cluster/hpx/hpx-0.9.8.ebuild                           | 13 +++++--------
 sys-cluster/hpx/hpx-9999.ebuild                            | 13 ++++---------
 22 files changed, 133 insertions(+), 54 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     12589e905208f336c0b4459c8813d779d703a9a1
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Mon Jul 21 15:34:55 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jul 21 15:34:55 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=12589e90

Merge /usr/local/portage/andis_overlay


 sys-cluster/hpx/hpx-9999.ebuild | 1 -
 1 file changed, 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     a10f8fd148a2a2bec41379df4c64fcdf3a388165
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Mon Jul 21 20:19:20 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jul 21 20:19:20 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a10f8fd1

merge


 app-doc/root-docs/ChangeLog                        |  25 ++
 app-doc/root-docs/Manifest                         |   2 +
 ...html.patch => root-docs-5.34.01-makehtml.patch} |  30 +-
 .../files/root-docs-6.00.01-cernbuild.patch        |  16 -
 .../files/root-docs-6.00.01-fillpatterns.patch     |  30 ++
 .../files/root-docs-6.00.01-makehtml.patch         |   4 +-
 ...-6.00.01.ebuild => root-docs-5.34.18-r2.ebuild} |   7 +-
 ...-6.00.01.ebuild => root-docs-6.00.01-r1.ebuild} |   2 +-
 app-doc/root-docs/root-docs-6.00.02.ebuild         |   1 +
 app-doc/root-docs/root-docs-9999.ebuild            |   2 +-
 dev-lang/julia/ChangeLog                           |   2 +-
 dev-lang/julia/julia-9999.ebuild                   |  18 +-
 dev-python/ffc/ChangeLog                           |  17 +-
 dev-python/ffc/Manifest                            |   2 +
 dev-python/ffc/ffc-1.3.0.ebuild                    |  26 ++
 dev-python/ffc/ffc-1.4.0.ebuild                    |  26 ++
 dev-python/fiat/ChangeLog                          |  14 +-
 dev-python/fiat/Manifest                           |   2 +
 dev-python/fiat/fiat-1.3.0.ebuild                  |  24 ++
 dev-python/fiat/fiat-1.4.0.ebuild                  |  24 ++
 dev-python/instant/ChangeLog                       |  10 +-
 dev-python/instant/Manifest                        |   2 +
 dev-python/instant/instant-1.3.0.ebuild            |  21 +
 dev-python/instant/instant-1.4.0.ebuild            |  21 +
 dev-python/ufl/ChangeLog                           |  10 +-
 dev-python/ufl/Manifest                            |   4 +-
 dev-python/ufl/metadata.xml                        |   3 +
 dev-python/ufl/ufl-1.3.0.ebuild                    |  23 ++
 dev-python/ufl/ufl-1.4.0.ebuild                    |  23 ++
 dev-util/nvidia-cuda-sdk/ChangeLog                 |   9 +
 dev-util/nvidia-cuda-sdk/Manifest                  |   1 +
 dev-util/nvidia-cuda-sdk/metadata.xml              |  13 +
 .../nvidia-cuda-sdk/nvidia-cuda-sdk-6.5.11.ebuild  | 151 +++++++
 dev-util/nvidia-cuda-toolkit/ChangeLog             |   9 +
 dev-util/nvidia-cuda-toolkit/Manifest              |   2 +
 dev-util/nvidia-cuda-toolkit/files/cuda-config.in  |  28 ++
 dev-util/nvidia-cuda-toolkit/metadata.xml          |  14 +
 .../nvidia-cuda-toolkit-6.5.11.ebuild              | 152 +++++++
 sci-biology/Atlas-Link/Atlas-Link-0.01.ebuild      |  26 ++
 sci-biology/Atlas-Link/ChangeLog                   |  10 +
 sci-biology/Atlas-Link/Manifest                    |   1 +
 .../Atlas-Link}/metadata.xml                       |   0
 sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild           |   3 +-
 sci-biology/caftools/ChangeLog                     |   7 +-
 sci-biology/caftools/caftools-2.0.2.ebuild         |   2 +-
 sci-biology/clview/ChangeLog                       |   6 +
 sci-biology/clview/Manifest                        |   4 +-
 sci-biology/clview/clview-0.1.ebuild               |   2 +-
 sci-biology/emboss/ChangeLog                       |   6 +
 sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild       |   1 +
 ...mboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch |  13 +
 sci-biology/gap2caf/ChangeLog                      |   7 +-
 sci-biology/gap2caf/gap2caf-2.1.0.ebuild           |   1 +
 sci-biology/jellyfish/ChangeLog                    |   9 +
 sci-biology/jellyfish/Manifest                     |   2 +
 sci-biology/jellyfish/jellyfish-2.1.3.ebuild       |  18 +
 .../jellyfish}/metadata.xml                        |   0
 sci-biology/tablet-bin/ChangeLog                   |   6 +
 sci-biology/tablet-bin/Manifest                    |   1 +
 .../tablet-bin-1.14.04.10.ebuild}                  |  11 +-
 sci-biology/tablet/ChangeLog                       |   8 +
 sci-biology/tablet/Manifest                        |   2 -
 sci-biology/tablet/tablet-1.13.12.17.ebuild        |  85 ++--
 sci-biology/tablet/tablet-1.14.04.10.ebuild        |  51 +++
 sci-biology/tablet/tablet-9999.ebuild              |  77 +---
 sci-chemistry/cpmgfit/ChangeLog                    |  10 +
 sci-chemistry/cpmgfit/Manifest                     |   1 +
 sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild          |  49 +++
 sci-chemistry/{burrow-owl => cpmgfit}/metadata.xml |   0
 sci-chemistry/direx/ChangeLog                      |  16 -
 sci-chemistry/direx/Manifest                       |   1 -
 sci-chemistry/direx/direx-0.2.ebuild               |  42 --
 sci-chemistry/direx/metadata.xml                   |   5 -
 sci-chemistry/gromacs/ChangeLog                    |   4 +
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild      |  25 +-
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild      |   7 +-
 sci-chemistry/hydronmr/ChangeLog                   |   3 +
 sci-chemistry/hydronmr/hydronmr-7c.ebuild          |   3 -
 sci-chemistry/nmrpipe/ChangeLog                    |  10 +-
 .../nmrpipe/nmrpipe-8.1.2013.218.23.09-r1.ebuild   |  11 +-
 sci-chemistry/unio/ChangeLog                       |   3 +
 sci-chemistry/unio/unio-2.0.3-r1.ebuild            |   6 +-
 sci-libs/cblas-reference/ChangeLog                 |   4 +
 .../cblas-reference-20110218.ebuild                |   2 +-
 sci-libs/fftw/ChangeLog                            |   3 +
 sci-libs/fftw/fftw-9999.ebuild                     |   5 +-
 sci-libs/gsl/ChangeLog                             |   6 +-
 sci-libs/gsl/gsl-1.16-r1.ebuild                    |   2 +-
 sci-libs/libcerf/ChangeLog                         |  13 +
 sci-libs/libcerf/Manifest                          |   1 +
 sci-libs/libcerf/files/libcerf-1.3-autotools.patch |  48 +++
 sci-libs/libcerf/libcerf-1.3.ebuild                |  22 ++
 .../neovim => sci-libs/libcerf}/metadata.xml       |   0
 .../files/scilab-5.5.0-accessviolation.patch       |  32 +-
 sci-mathematics/scilab/scilab-5.5.0.ebuild         |   4 +
 sci-mathematics/ufc/ChangeLog                      |  10 +-
 sci-mathematics/ufc/Manifest                       |   3 +-
 sci-mathematics/ufc/ufc-2.3.0.ebuild               |  19 +
 sci-physics/abinit/ChangeLog                       |   5 +
 .../abinit/files/7.6.3-libabinit_options.patch     |  80 ++++
 sci-physics/espresso++/ChangeLog                   |   3 +
 sci-physics/espresso++/espresso++-9999.ebuild      |   1 +
 sci-physics/geant-vmc/ChangeLog                    |   8 +
 sci-physics/geant-vmc/geant-vmc-9999.ebuild        |  79 ++++
 sci-physics/geant-vmc/metadata.xml                 |   3 +
 sci-physics/root/ChangeLog                         |  38 ++
 sci-physics/root/Manifest                          |   2 +
 sci-physics/root/files/root-5.32.00-dotfont.patch  |  58 +++
 .../root/files/root-5.32.00-prop-flags.patch       |  15 +
 .../root/files/root-5.34.05-nobyte-compile.patch   | 137 +++++++
 .../root/files/root-5.34.18-tutorials-path.patch   |  94 +++++
 sci-physics/root/files/root-6.00.01-cling.patch    |  19 +
 .../root/files/root-6.00.01-tutorials-path.patch   |  39 ++
 sci-physics/root/metadata.xml                      |   2 +
 ...{root-6.00.01.ebuild => root-5.34.18-r2.ebuild} | 173 +++-----
 ...{root-6.00.01.ebuild => root-6.00.01-r1.ebuild} |  18 +-
 .../{root-6.00.01.ebuild => root-6.00.02.ebuild}   |  17 +-
 sci-physics/root/root-9999.ebuild                  | 439 ++++++++++++++++++++-
 sci-physics/vgm/ChangeLog                          |  10 +
 sci-physics/vgm/vgm-3.06.ebuild                    |   2 +-
 .../vgm/{vgm-3.06.ebuild => vgm-9999.ebuild}       |  33 +-
 sci-visualization/gnuplot/ChangeLog                |   9 +
 ...lot-4.7.9999.ebuild => gnuplot-5.0.9999.ebuild} |   1 +
 123 files changed, 2319 insertions(+), 465 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     d2c686f21482d72aa0a210ae3d45b4d8d08e4f3c
Author:     Christoph Junghans <christoph.junghans <AT> googlemail <DOT> com>
AuthorDate: Mon Jul 21 21:19:23 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jul 21 21:19:23 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d2c686f2

Merge pull request #244 from gentryx/master

fixed HPX live ebuild


 sys-cluster/hpx/hpx-0.9.8.ebuild | 13 +++++--------
 sys-cluster/hpx/hpx-9999.ebuild  | 13 ++++---------
 2 files changed, 9 insertions(+), 17 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     a2a4f4884319c4ce9b539716ed17951c4abcd3d4
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Mon Jul 21 15:06:10 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jul 21 15:06:10 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a2a4f488

Merge https://github.com/gentoo-science/sci


 app-doc/root-docs/ChangeLog                        |  25 ++
 app-doc/root-docs/Manifest                         |   2 +
 ...html.patch => root-docs-5.34.01-makehtml.patch} |  30 +-
 .../files/root-docs-6.00.01-cernbuild.patch        |  16 -
 .../files/root-docs-6.00.01-fillpatterns.patch     |  30 ++
 .../files/root-docs-6.00.01-makehtml.patch         |   4 +-
 ...-6.00.01.ebuild => root-docs-5.34.18-r2.ebuild} |   7 +-
 ...-6.00.01.ebuild => root-docs-6.00.01-r1.ebuild} |   2 +-
 app-doc/root-docs/root-docs-6.00.02.ebuild         |   1 +
 app-doc/root-docs/root-docs-9999.ebuild            |   2 +-
 dev-lang/julia/ChangeLog                           |   2 +-
 dev-lang/julia/julia-9999.ebuild                   |  18 +-
 dev-python/ffc/ChangeLog                           |  17 +-
 dev-python/ffc/Manifest                            |   2 +
 dev-python/ffc/ffc-1.3.0.ebuild                    |  26 ++
 dev-python/ffc/ffc-1.4.0.ebuild                    |  26 ++
 dev-python/fiat/ChangeLog                          |  14 +-
 dev-python/fiat/Manifest                           |   2 +
 dev-python/fiat/fiat-1.3.0.ebuild                  |  24 ++
 dev-python/fiat/fiat-1.4.0.ebuild                  |  24 ++
 dev-python/instant/ChangeLog                       |  10 +-
 dev-python/instant/Manifest                        |   2 +
 dev-python/instant/instant-1.3.0.ebuild            |  21 +
 dev-python/instant/instant-1.4.0.ebuild            |  21 +
 dev-python/ufl/ChangeLog                           |  10 +-
 dev-python/ufl/Manifest                            |   4 +-
 dev-python/ufl/metadata.xml                        |   3 +
 dev-python/ufl/ufl-1.3.0.ebuild                    |  23 ++
 dev-python/ufl/ufl-1.4.0.ebuild                    |  23 ++
 dev-util/nvidia-cuda-sdk/ChangeLog                 |   9 +
 dev-util/nvidia-cuda-sdk/Manifest                  |   1 +
 dev-util/nvidia-cuda-sdk/metadata.xml              |  13 +
 .../nvidia-cuda-sdk/nvidia-cuda-sdk-6.5.11.ebuild  | 151 +++++++
 dev-util/nvidia-cuda-toolkit/ChangeLog             |   9 +
 dev-util/nvidia-cuda-toolkit/Manifest              |   2 +
 dev-util/nvidia-cuda-toolkit/files/cuda-config.in  |  28 ++
 dev-util/nvidia-cuda-toolkit/metadata.xml          |  14 +
 .../nvidia-cuda-toolkit-6.5.11.ebuild              | 152 +++++++
 sci-biology/Atlas-Link/Atlas-Link-0.01.ebuild      |  26 ++
 sci-biology/Atlas-Link/ChangeLog                   |  10 +
 sci-biology/Atlas-Link/Manifest                    |   1 +
 .../Atlas-Link}/metadata.xml                       |   0
 sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild           |   3 +-
 sci-biology/caftools/ChangeLog                     |   7 +-
 sci-biology/caftools/caftools-2.0.2.ebuild         |   2 +-
 sci-biology/clview/ChangeLog                       |   6 +
 sci-biology/clview/Manifest                        |   4 +-
 sci-biology/clview/clview-0.1.ebuild               |   2 +-
 sci-biology/emboss/ChangeLog                       |   6 +
 sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild       |   1 +
 ...mboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch |  13 +
 sci-biology/gap2caf/ChangeLog                      |   7 +-
 sci-biology/gap2caf/gap2caf-2.1.0.ebuild           |   1 +
 sci-biology/jellyfish/ChangeLog                    |   9 +
 sci-biology/jellyfish/Manifest                     |   2 +
 sci-biology/jellyfish/jellyfish-2.1.3.ebuild       |  18 +
 .../jellyfish}/metadata.xml                        |   0
 sci-biology/tablet-bin/ChangeLog                   |   6 +
 sci-biology/tablet-bin/Manifest                    |   1 +
 .../tablet-bin-1.14.04.10.ebuild}                  |  11 +-
 sci-biology/tablet/ChangeLog                       |   8 +
 sci-biology/tablet/Manifest                        |   2 -
 sci-biology/tablet/tablet-1.13.12.17.ebuild        |  85 ++--
 sci-biology/tablet/tablet-1.14.04.10.ebuild        |  51 +++
 sci-biology/tablet/tablet-9999.ebuild              |  77 +---
 sci-chemistry/cpmgfit/ChangeLog                    |  10 +
 sci-chemistry/cpmgfit/Manifest                     |   1 +
 sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild          |  49 +++
 sci-chemistry/{burrow-owl => cpmgfit}/metadata.xml |   0
 sci-chemistry/direx/ChangeLog                      |  16 -
 sci-chemistry/direx/Manifest                       |   1 -
 sci-chemistry/direx/direx-0.2.ebuild               |  42 --
 sci-chemistry/direx/metadata.xml                   |   5 -
 sci-chemistry/gromacs/ChangeLog                    |   4 +
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild      |  25 +-
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild      |   7 +-
 sci-chemistry/hydronmr/ChangeLog                   |   3 +
 sci-chemistry/hydronmr/hydronmr-7c.ebuild          |   3 -
 sci-chemistry/nmrpipe/ChangeLog                    |  10 +-
 .../nmrpipe/nmrpipe-8.1.2013.218.23.09-r1.ebuild   |  11 +-
 sci-chemistry/unio/ChangeLog                       |   3 +
 sci-chemistry/unio/unio-2.0.3-r1.ebuild            |   6 +-
 sci-libs/cblas-reference/ChangeLog                 |   4 +
 .../cblas-reference-20110218.ebuild                |   2 +-
 sci-libs/fftw/ChangeLog                            |   3 +
 sci-libs/fftw/fftw-9999.ebuild                     |   5 +-
 sci-libs/gsl/ChangeLog                             |   6 +-
 sci-libs/gsl/gsl-1.16-r1.ebuild                    |   2 +-
 sci-libs/libcerf/ChangeLog                         |  13 +
 sci-libs/libcerf/Manifest                          |   1 +
 sci-libs/libcerf/files/libcerf-1.3-autotools.patch |  48 +++
 sci-libs/libcerf/libcerf-1.3.ebuild                |  22 ++
 .../neovim => sci-libs/libcerf}/metadata.xml       |   0
 .../files/scilab-5.5.0-accessviolation.patch       |  32 +-
 sci-mathematics/scilab/scilab-5.5.0.ebuild         |   4 +
 sci-mathematics/ufc/ChangeLog                      |  10 +-
 sci-mathematics/ufc/Manifest                       |   3 +-
 sci-mathematics/ufc/ufc-2.3.0.ebuild               |  19 +
 sci-physics/abinit/ChangeLog                       |   5 +
 .../abinit/files/7.6.3-libabinit_options.patch     |  80 ++++
 sci-physics/espresso++/ChangeLog                   |   3 +
 sci-physics/espresso++/espresso++-9999.ebuild      |   1 +
 sci-physics/geant-vmc/ChangeLog                    |   8 +
 sci-physics/geant-vmc/geant-vmc-9999.ebuild        |  79 ++++
 sci-physics/geant-vmc/metadata.xml                 |   3 +
 sci-physics/root/ChangeLog                         |  38 ++
 sci-physics/root/Manifest                          |   2 +
 sci-physics/root/files/root-5.32.00-dotfont.patch  |  58 +++
 .../root/files/root-5.32.00-prop-flags.patch       |  15 +
 .../root/files/root-5.34.05-nobyte-compile.patch   | 137 +++++++
 .../root/files/root-5.34.18-tutorials-path.patch   |  94 +++++
 sci-physics/root/files/root-6.00.01-cling.patch    |  19 +
 .../root/files/root-6.00.01-tutorials-path.patch   |  39 ++
 sci-physics/root/metadata.xml                      |   2 +
 ...{root-6.00.01.ebuild => root-5.34.18-r2.ebuild} | 173 +++-----
 ...{root-6.00.01.ebuild => root-6.00.01-r1.ebuild} |  18 +-
 .../{root-6.00.01.ebuild => root-6.00.02.ebuild}   |  17 +-
 sci-physics/root/root-9999.ebuild                  | 439 ++++++++++++++++++++-
 sci-physics/vgm/ChangeLog                          |  10 +
 sci-physics/vgm/vgm-3.06.ebuild                    |   2 +-
 .../vgm/{vgm-3.06.ebuild => vgm-9999.ebuild}       |  33 +-
 sci-visualization/gnuplot/ChangeLog                |   9 +
 ...lot-4.7.9999.ebuild => gnuplot-5.0.9999.ebuild} |   1 +
 123 files changed, 2319 insertions(+), 465 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Guillaume Horel]

commit:     876e4967993df2006e894bf39b90a576161f6c85
Author:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
AuthorDate: Sat Jul 12 19:54:20 2014 +0000
Commit:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
CommitDate: Sat Jul 12 19:54:20 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=876e4967

Merge branch 'master' of github.com:gentoo-science/sci


 dev-python/ffc/ChangeLog                              | 8 ++++++--
 dev-python/ffc/Manifest                               | 1 +
 dev-python/ffc/{ffc-1.2.0.ebuild => ffc-1.3.0.ebuild} | 6 +++---
 3 files changed, 10 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f4fb99c2eb4d279057f4a3eb02cdb6e28bd0c811
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 10 06:58:56 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jul 10 06:58:56 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f4fb99c2

Merge pull request #240 from marbre/nvidia-cuda-sdk

dev-util/nvidia-cuda-sdk: add version 6.5.11


 dev-util/nvidia-cuda-sdk/ChangeLog                 |   9 ++
 .../Manifest                                       |   1 -
 .../nvidia-cuda-sdk}/metadata.xml                  |   7 +-
 .../nvidia-cuda-sdk/nvidia-cuda-sdk-6.5.11.ebuild  | 151 +++++++++++++++++++++
 4 files changed, 166 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c3a57542d1576356a1f114ce0436eda76475d2d3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 10 08:53:38 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jul 10 08:53:38 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c3a57542

Merge remote-tracking branch 'github/master'

* github/master:
  dev-util/nvidia-cuda-sdk: add version 6.5.11
  dev-util/nvidia-cuda-toolkit: dev-util/nvidia-cuda-toolkit: add version 6.5.11

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     3f966a37b79e4bdf4d804528b9f56fd89167a4d7
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 10 06:35:05 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jul 10 06:35:05 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3f966a37

Merge pull request #239 from marbre/nvidia-cuda-toolkit

dev-util/nvidia-cuda-toolkit: add version 6.5.11


 dev-util/nvidia-cuda-toolkit/ChangeLog             |   9 ++
 dev-util/nvidia-cuda-toolkit/Manifest              |   2 +
 dev-util/nvidia-cuda-toolkit/files/cuda-config.in  |  28 ++++
 dev-util/nvidia-cuda-toolkit/metadata.xml          |  14 ++
 .../nvidia-cuda-toolkit-6.5.11.ebuild              | 152 +++++++++++++++++++++
 5 files changed, 205 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     8b089a49addab2d4249ef31e8a4dd6f2d4bfa129
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jul  7 06:36:37 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jul  7 06:36:37 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8b089a49

Merge remote-tracking branch 'github/master'

* github/master:
  dev-python/bokeh: dev-python/bokeh: New version with python3 support for bug #516052
  dev-python/bokeh: dev-python/bokeh: Copy latest ebuild from portage
  Add subslot dependency on clhep, we need to rebuild for each clhep subslot change.
  New live ebuild for VGM, adapting to fixes for cmake install paths in upstream (no need to manually install in ebuild anymore). Released VGM-4.00 does not have these fixes yet, I am discussing with upstream whether they can also provide some tarballs of released versions (as sourceforge svn-snapshotting is unusable for us) and delay packaging of VGM-4.00 until then.
  New live ebuild, using cmake-buildsystem (upstream switches to cmake for next release), add flags for g4root and mtroot. Adapt to upstream's fixes concerning install paths, we don't need to do manually installation anymore. I will skip geant-vmc-3.00b01 from packaging, it does not include those fixes yet.


 dev-python/bokeh/ChangeLog                         | 11 +++
 dev-python/bokeh/Manifest                          |  1 +
 dev-python/bokeh/bokeh-0.4.4.ebuild                | 98 ++++++++++++++++++++++
 .../bokeh/files/bokeh-0.4.4-fix_test_object.patch  | 32 +++++++
 dev-python/bokeh/metadata.xml                      | 15 ++++
 sci-physics/geant-vmc/ChangeLog                    |  8 ++
 sci-physics/geant-vmc/geant-vmc-9999.ebuild        | 79 +++++++++++++++++
 sci-physics/geant-vmc/metadata.xml                 |  3 +
 sci-physics/vgm/ChangeLog                          | 10 +++
 sci-physics/vgm/vgm-3.06.ebuild                    |  2 +-
 .../vgm/{vgm-3.06.ebuild => vgm-9999.ebuild}       | 33 ++++----
 11 files changed, 273 insertions(+), 19 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     e0a781d012ab42cb83834449ec575d213982ac55
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jul  7 06:36:08 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jul  7 06:36:08 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e0a781d0

Merge pull request #236 from olifre/master

New live ebuild for VGM and Geant-VMC


 sci-physics/geant-vmc/ChangeLog                    |  8 +++
 sci-physics/geant-vmc/geant-vmc-9999.ebuild        | 79 ++++++++++++++++++++++
 sci-physics/geant-vmc/metadata.xml                 |  3 +
 sci-physics/vgm/ChangeLog                          | 10 +++
 sci-physics/vgm/vgm-3.06.ebuild                    |  2 +-
 .../vgm/{vgm-3.06.ebuild => vgm-9999.ebuild}       | 33 ++++-----
 6 files changed, 116 insertions(+), 19 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     0db28ec6a3046b2a46e1a7fa9ced8933050ee34e
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jul  7 06:35:43 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jul  7 06:35:43 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0db28ec6

Merge pull request #237 from aufau/bokeh

dev-python/bokeh (in the main tree): Fix bug #516052


 dev-python/bokeh/ChangeLog                         | 11 +++
 dev-python/bokeh/Manifest                          |  1 +
 dev-python/bokeh/bokeh-0.4.4.ebuild                | 98 ++++++++++++++++++++++
 .../bokeh/files/bokeh-0.4.4-fix_test_object.patch  | 32 +++++++
 dev-python/bokeh/metadata.xml                      | 15 ++++
 5 files changed, 157 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     5fd9da33ef1ab875640131b3529f66126d3e4beb
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Thu Jul  3 15:35:44 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Thu Jul  3 15:35:44 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5fd9da33

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 sci-biology/jellyfish/ChangeLog                    |  9 +++
 sci-biology/jellyfish/Manifest                     |  2 +
 sci-biology/jellyfish/jellyfish-2.1.3.ebuild       | 18 +++++
 .../jellyfish}/metadata.xml                        |  0
 sci-biology/tablet-bin/ChangeLog                   |  6 ++
 sci-biology/tablet-bin/Manifest                    |  1 +
 ...3.12.17.ebuild => tablet-bin-1.14.04.10.ebuild} |  9 ++-
 sci-biology/tablet/ChangeLog                       |  8 ++
 sci-biology/tablet/Manifest                        |  2 -
 sci-biology/tablet/tablet-1.13.12.17.ebuild        | 85 ++++++----------------
 sci-biology/tablet/tablet-1.14.04.10.ebuild        | 51 +++++++++++++
 sci-biology/tablet/tablet-9999.ebuild              | 77 ++++----------------
 sci-chemistry/cpmgfit/ChangeLog                    | 10 +++
 sci-chemistry/cpmgfit/Manifest                     |  1 +
 .../cpmgfit-1.43.ebuild}                           | 15 ++--
 sci-chemistry/{burrow-owl => cpmgfit}/metadata.xml |  0
 sci-libs/cblas-reference/ChangeLog                 |  4 +
 .../cblas-reference-20110218.ebuild                |  2 +-
 sci-physics/espresso++/ChangeLog                   |  3 +
 sci-physics/espresso++/espresso++-9999.ebuild      |  1 +
 sci-physics/root/ChangeLog                         |  8 ++
 .../root/files/root-6.00.01-tutorials-path.patch   | 12 +++
 sci-physics/root/root-6.00.01-r1.ebuild            |  4 +-
 sci-physics/root/root-9999.ebuild                  |  5 ++
 24 files changed, 192 insertions(+), 141 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     e0c67d74a37873343bce304224680fe667b8e6a5
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Jul  2 22:04:50 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Jul  2 22:04:50 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e0c67d74

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-visualization/visit/visit-2.7.3.ebuild | 1 +
 1 file changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     d5a89aa4a76938fbe69a3b65044a47d764f28a83
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jul  2 23:14:10 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jul  2 23:14:10 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d5a89aa4

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-physics/espresso++/ChangeLog              | 3 +++
 sci-physics/espresso++/espresso++-9999.ebuild | 1 +
 2 files changed, 4 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     3f9a22710564f34ee1ce48811ad5185e9d5867eb
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jul  2 22:41:48 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jul  2 22:41:48 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3f9a2271

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 app-doc/root-docs/ChangeLog                        |  12 +
 .../files/root-docs-6.00.01-cernbuild.patch        |  16 -
 .../files/root-docs-6.00.01-makehtml.patch         |   4 +-
 ...-6.00.01.ebuild => root-docs-6.00.01-r1.ebuild} |   3 +-
 app-doc/root-docs/root-docs-9999.ebuild            |   2 +-
 dev-python/pynomo/ChangeLog                        |   9 +
 dev-python/pynomo/Manifest                         |   1 +
 .../cdfplayer => dev-python/pynomo}/metadata.xml   |   8 +-
 dev-python/pynomo/pynomo-0.2.2.ebuild              |  35 ++
 sci-libs/cblas-reference/ChangeLog                 |   4 +
 .../cblas-reference-20110218.ebuild                |   2 +-
 sci-libs/gsl/ChangeLog                             |   6 +-
 sci-libs/gsl/gsl-1.16-r1.ebuild                    |   2 +-
 sci-physics/root/ChangeLog                         |  18 +
 sci-physics/root/files/root-6.00.01-cling.patch    |  19 +
 .../root/files/root-6.00.01-tutorials-path.patch   |  39 ++
 ...{root-6.00.01.ebuild => root-6.00.01-r1.ebuild} |  16 +-
 sci-physics/root/root-9999.ebuild                  | 440 ++++++++++++++++++++-
 sci-visualization/visit/visit-2.7.3.ebuild         |   1 +
 19 files changed, 599 insertions(+), 38 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Francois Bissey]

commit:     6e46701e689734b1e8ee8357d60f6988568db76a
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Wed Jul  2 16:29:54 2014 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Wed Jul  2 16:29:54 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6e46701e

Merge pull request #235 from gentryx/master

added lib path for VisIt's libsim and friends


 sci-visualization/visit/visit-2.7.3.ebuild | 1 +
 1 file changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Francois Bissey]

commit:     82c44a73de1b7eb9452360c199ee07175e1d2bab
Author:     François Bissey <francois.bissey <AT> canterbury <DOT> ac <DOT> nz>
AuthorDate: Wed Jul  2 22:12:00 2014 +0000
Commit:     Francois Bissey <f.r.bissey <AT> massey <DOT> ac <DOT> nz>
CommitDate: Wed Jul  2 22:12:00 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=82c44a73

Merge remote-tracking branch 'github/master'


 sci-visualization/visit/visit-2.7.3.ebuild | 1 +
 1 file changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     8f0faf663a2f8d573a894bc9caf749b08dadb5db
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Wed Jul  2 11:13:53 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Wed Jul  2 11:13:53 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8f0faf66

Merge remote-tracking branch 'gentoo/master' into upstream-master


 sci-libs/gsl/ChangeLog          | 6 +++++-
 sci-libs/gsl/gsl-1.16-r1.ebuild | 2 +-
 2 files changed, 6 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     1657a8c2ac1a10fb4c78f0714284f771594ae560
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jul  1 18:17:06 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Tue Jul  1 18:17:06 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1657a8c2

Merge pull request #234 from aufau/pynomo

dev-python/pynomo: New package for bug #515682


 dev-python/pynomo/ChangeLog                        |  9 ++++++
 dev-python/pynomo/Manifest                         |  1 +
 .../cdfplayer => dev-python/pynomo}/metadata.xml   |  8 ++---
 dev-python/pynomo/pynomo-0.2.2.ebuild              | 35 ++++++++++++++++++++++
 4 files changed, 49 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6ec285dbfdde397189c30cf467ee238c9004ec01
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jul  1 06:52:28 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jul  1 06:52:28 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6ec285db

Merge branch 'jonasstein-master'

* jonasstein-master:
  add Clip4, the Cologne Laue Indexiation Program


 sci-physics/clip/Manifest                |  4 ++++
 sci-physics/clip/clip-4.0.0_beta2.ebuild | 39 ++++++++++++++++++++++++++++++++
 sci-physics/clip/metadata.xml            |  9 ++++++++
 3 files changed, 52 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     e1256845f910ad1a6314ecbc48c1f66fe9cd5473
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 28 21:22:59 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Sat Jun 28 21:22:59 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e1256845

Merge remote-tracking branch 'gentoo/master' into upstream-master


 sci-biology/BamView/BamView-1.2.11.ebuild          |    5 +-
 .../VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild   |    2 +-
 sci-biology/barrnap/ChangeLog                      |   15 +
 sci-biology/barrnap/barrnap-0.3.ebuild             |   18 +
 .../ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch |   44 +
 .../files/ncbi-tools++-12.0.0-fix-install.patch    |   11 +
 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        |   27 +-
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |   17 +-
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild |   20 +-
 sci-biology/prot4EST/prot4EST-3.1b.ebuild          |    1 +
 sci-chemistry/chimera-bin/ChangeLog                |    6 +-
 sci-chemistry/chimera-bin/Manifest                 |    2 +
 ...era-bin-1.6.2.ebuild => chimera-bin-1.9.ebuild} |    0
 sci-libs/bigdft-abi/ChangeLog                      |   12 +-
 ...-1.0.4-r2.ebuild => bigdft-abi-1.0.4-r3.ebuild} |   70 +-
 .../bigdft-abi/files/bigdft-abi-1.0.4-0002.patch   |   37 +
 .../bigdft-abi/files/bigdft-abi-1.0.4-0003.patch   |   49 +
 .../bigdft-abi/files/bigdft-abi-1.0.4-0004.patch   |   20 +
 .../bigdft-abi/files/bigdft-abi-1.0.4-0005.patch   | 5317 ++++++++++++++++++++
 .../bigdft-abi/files/bigdft-abi-1.0.4-0006.patch   |   43 +
 .../bigdft-abi/files/bigdft-abi-1.0.4-0007.patch   |  344 ++
 .../files/bigdft-abi-1.0.4-tests.tar.bz2           |  Bin 402968 -> 0 bytes
 sci-libs/bigdft-abi/metadata.xml                   |   14 +-
 sci-libs/libxc/ChangeLog                           |    4 +
 sci-libs/libxc/libxc-2.0.3.ebuild                  |    6 +-
 sci-physics/abinit/ChangeLog                       |    9 +-
 sci-physics/abinit/Manifest                        |    1 +
 .../{abinit-7.4.2.ebuild => abinit-7.6.4.ebuild}   |  116 +-
 sci-physics/abinit/metadata.xml                    |   23 +-
 29 files changed, 6111 insertions(+), 122 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     a9e6832d9c8c00bb95a22bb0ae50ef7eb8c91001
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 26 13:30:00 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 26 13:30:00 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a9e6832d

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-chemistry/gromacs/ChangeLog                 | 3 +++
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild   | 8 +-------
 sci-mathematics/Macaulay2/ChangeLog             | 3 +++
 sci-mathematics/Macaulay2/Macaulay2-9999.ebuild | 1 +
 4 files changed, 8 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     9acd42a26e63e8c3bca06a7a89231045005c4f79
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 14 19:03:14 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Sat Jun 14 19:03:14 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9acd42a2

Merge pull request #232 from JelteF/neovim

Use CFLAGS needed to get a working executable for neovim


 app-editors/neovim/ChangeLog          | 4 ++++
 app-editors/neovim/neovim-9999.ebuild | 7 ++++++-
 2 files changed, 10 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     bd2baf69972227f40db299daeba7c7347367f11c
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 14 18:59:53 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Sat Jun 14 18:59:53 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bd2baf69

Merge pull request #231 from TheChymera/nipype

Added vital dep for sci-libs/nipype


 sci-libs/nipype/nipype-9999.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Thomas Kahle]

commit:     bb5fb7fae21613a5410ece404f76aa44401f9b89
Author:     Thomas Kahle <thomas.kahle <AT> ovgu <DOT> de>
AuthorDate: Tue Jun 10 21:08:14 2014 +0000
Commit:     Thomas Kahle <tom111 <AT> gmx <DOT> de>
CommitDate: Tue Jun 10 21:08:14 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bb5fb7fa

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

[gentoo-commits] proj/sci:master commit in: /

[Thomas Kahle]

commit:     a2b22c4d88ff0718cf8ec8d3aa8e205bf69ca0ce
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 10 16:39:05 2014 +0000
Commit:     Thomas Kahle <tom111 <AT> gmx <DOT> de>
CommitDate: Tue Jun 10 16:39:05 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a2b22c4d

Merge github.com:gentoo-science/sci


 sci-visualization/visit/Manifest                                         | 1 +
 ..._symlink_visit_dir.patch => visit-2.7.3-dont_symlink_visit_dir.patch} | 0
 .../files/{visit-2.7.1-findpython.patch => visit-2.7.3-findpython.patch} | 0
 .../files/{visit-2.7.1-findsilo.patch => visit-2.7.3-findsilo.patch}     | 0
 .../visit/files/{visit-2.7.1-findvtk.patch => visit-2.7.3-findvtk.patch} | 0
 .../visit/files/{visit-2.7.1-vtklibs.patch => visit-2.7.3-vtklibs.patch} | 0
 sci-visualization/visit/{visit-2.7.2.ebuild => visit-2.7.3.ebuild}       | 0
 7 files changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Thomas Kahle]

commit:     4285dcb6b92c75f4e367e40f5ce6d5bd8a7fa5d6
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Mon Jun  9 22:27:07 2014 +0000
Commit:     Thomas Kahle <tom111 <AT> gmx <DOT> de>
CommitDate: Mon Jun  9 22:27:07 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4285dcb6

Merge pull request #230 from gentryx/master

added ebuild for VisIt 2.7.3


 sci-visualization/visit/Manifest                                         | 1 +
 ..._symlink_visit_dir.patch => visit-2.7.3-dont_symlink_visit_dir.patch} | 0
 .../files/{visit-2.7.1-findpython.patch => visit-2.7.3-findpython.patch} | 0
 .../files/{visit-2.7.1-findsilo.patch => visit-2.7.3-findsilo.patch}     | 0
 .../visit/files/{visit-2.7.1-findvtk.patch => visit-2.7.3-findvtk.patch} | 0
 .../visit/files/{visit-2.7.1-vtklibs.patch => visit-2.7.3-vtklibs.patch} | 0
 sci-visualization/visit/{visit-2.7.2.ebuild => visit-2.7.3.ebuild}       | 0
 7 files changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Thomas Kahle]

commit:     c34045502b327f53d01e060c91dfc22346c29538
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 10 16:38:40 2014 +0000
Commit:     Thomas Kahle <tom111 <AT> gmx <DOT> de>
CommitDate: Tue Jun 10 16:38:40 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c3404550

updated for travis ci

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index 4a2dc95..2ff12d5 100644
--- a/README.md
+++ b/README.md
@@ -11,3 +11,5 @@ Ask for help on irc in #gentoo-science @ freenode.
 
 Report bugs on the [github issues site](https://github.com/gentoo-science/sci/issues)
 
+
+[![Build Status](https://travis-ci.org/gentoo-science/sci.svg?branch=master)](https://travis-ci.org/gentoo-science/sci)

[gentoo-commits] proj/sci:master commit in: /

[Thomas Kahle]

commit:     63efaf1c45ed3a9086474d35bb838915030e6ae3
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 10 16:32:42 2014 +0000
Commit:     Thomas Kahle <tom111 <AT> gmx <DOT> de>
CommitDate: Tue Jun 10 16:32:42 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=63efaf1c

added a travis repoman check

---
 .travis.yml | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..ce116ca
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,19 @@
+before_script:
+    - mkdir travis-overlay
+    - mv !(travis-overlay) travis-overlay/
+    - mv .git travis-overlay/
+    - wget "http://distfiles.gentoo.org/distfiles/portage-2.2.10.tar.bz2"
+    - wget "http://distfiles.gentoo.org/snapshots/portage-latest.tar.xz"
+    - sudo chmod 777 /etc/passwd /etc/group /etc /usr
+    - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
+    - echo "portage::250:portage,travis" >> /etc/group
+    - mkdir -p /etc/portage/ /usr/portage/distfiles
+    - tar xjf portage-2.2.10.tar.bz2
+    - tar xJf portage-latest.tar.xz -C /usr/
+    - cp portage-2.2.10/cnf/repos.conf /etc/portage/
+    - rsync --recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --checksum --quiet rsync://rsync.gentoo.org/gentoo-portage /usr/portage
+    - ln -s /usr/portage/profiles/base/ /etc/portage/make.profile
+    - cd travis-overlay
+    - sed -i 's/fcmd=fcmd/fcmd=("%s -q" % fcmd)/' ./../portage-2.2.10/bin/repoman
+script: 
+    - "./../portage-2.2.10/bin/repoman full -d"

[gentoo-commits] proj/sci:master commit in: /

[Thomas Kahle]

commit:     1bb2b9573d6eae4bd47fe6acebe14d3d2aa2b9c5
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 10 16:32:42 2014 +0000
Commit:     Thomas Kahle <tom111 <AT> gmx <DOT> de>
CommitDate: Tue Jun 10 21:06:45 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1bb2b957

added a travis repoman check

---
 .travis.yml | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..ce116ca
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,19 @@
+before_script:
+    - mkdir travis-overlay
+    - mv !(travis-overlay) travis-overlay/
+    - mv .git travis-overlay/
+    - wget "http://distfiles.gentoo.org/distfiles/portage-2.2.10.tar.bz2"
+    - wget "http://distfiles.gentoo.org/snapshots/portage-latest.tar.xz"
+    - sudo chmod 777 /etc/passwd /etc/group /etc /usr
+    - echo "portage:x:250:250:portage:/var/tmp/portage:/bin/false" >> /etc/passwd
+    - echo "portage::250:portage,travis" >> /etc/group
+    - mkdir -p /etc/portage/ /usr/portage/distfiles
+    - tar xjf portage-2.2.10.tar.bz2
+    - tar xJf portage-latest.tar.xz -C /usr/
+    - cp portage-2.2.10/cnf/repos.conf /etc/portage/
+    - rsync --recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --checksum --quiet rsync://rsync.gentoo.org/gentoo-portage /usr/portage
+    - ln -s /usr/portage/profiles/base/ /etc/portage/make.profile
+    - cd travis-overlay
+    - sed -i 's/fcmd=fcmd/fcmd=("%s -q" % fcmd)/' ./../portage-2.2.10/bin/repoman
+script: 
+    - "./../portage-2.2.10/bin/repoman full -d"

[gentoo-commits] proj/sci:master commit in: /

[Thomas Kahle]

commit:     4899aa52e88bdc7f8e90777497b204ed1b178418
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 10 16:38:40 2014 +0000
Commit:     Thomas Kahle <tom111 <AT> gmx <DOT> de>
CommitDate: Tue Jun 10 21:06:45 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4899aa52

updated for travis ci

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index 4a2dc95..2ff12d5 100644
--- a/README.md
+++ b/README.md
@@ -11,3 +11,5 @@ Ask for help on irc in #gentoo-science @ freenode.
 
 Report bugs on the [github issues site](https://github.com/gentoo-science/sci/issues)
 
+
+[![Build Status](https://travis-ci.org/gentoo-science/sci.svg?branch=master)](https://travis-ci.org/gentoo-science/sci)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     a2723b601e04fbaefe1a6e8e125644a98d0f9ccd
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Jun  9 16:12:37 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Jun  9 16:12:37 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a2723b60

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-chemistry/coot/ChangeLog        | 5 ++++-
 sci-chemistry/coot/Manifest         | 2 +-
 sci-chemistry/coot/coot-9999.ebuild | 7 ++-----
 3 files changed, 7 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     c8dfc022d933e817aa7b0a18be5ffdce5a00d481
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Jun  3 16:31:14 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Jun  3 16:31:14 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c8dfc022

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 dev-lang/vtune/ChangeLog                                 |  5 +++++
 dev-lang/vtune/Manifest                                  |  1 +
 ...13.1.12.305106.ebuild => vtune-13.1.17.353306.ebuild} |  4 ++--
 sci-libs/ghmm/ChangeLog                                  |  6 +++++-
 sci-libs/ghmm/files/ghmm-9999-clapack.patch              | 11 +++++++++++
 sci-libs/ghmm/files/ghmm-9999-respect.patch              |  8 +++-----
 sci-libs/ghmm/ghmm-9999.ebuild                           |  1 +
 sci-libs/mkl/ChangeLog                                   |  5 +++++
 sci-libs/mkl/Manifest                                    |  1 +
 .../mkl/{mkl-11.1.2.144.ebuild => mkl-11.1.3.174.ebuild} |  4 ++--
 sci-physics/qcl/ChangeLog                                |  8 +++++++-
 sci-physics/qcl/Manifest                                 |  9 +++++----
 ...qcl-0.6.3-makefile.patch => qcl-0.6.4-makefile.patch} | 10 +++++-----
 .../qcl/{qcl-0.6.3-r1.ebuild => qcl-0.6.4.ebuild}        | 13 ++++++-------
 sys-cluster/openmpi/ChangeLog                            |  7 ++++++-
 sys-cluster/openmpi/Manifest                             |  1 +
 .../{openmpi-1.7.3.ebuild => openmpi-1.8.1.ebuild}       | 16 ++++++++++++----
 17 files changed, 78 insertions(+), 32 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     8435a4772300545ddda9a8b92c6c70334b3043a1
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Jun  2 16:59:18 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Jun  2 16:59:18 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8435a477

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 dev-lang/berkeley_upc/ChangeLog                    |   8 +-
 dev-lang/berkeley_upc/Manifest                     |   1 +
 ...pc-2.16.2.ebuild => berkeley_upc-2.18.2.ebuild} |   0
 dev-lang/berkeley_upc/metadata.xml                 |   3 +-
 dev-lang/berkeley_upc_translator/ChangeLog         |   9 +-
 dev-lang/berkeley_upc_translator/Manifest          |   1 +
 .../berkeley_upc_translator-2.16.2.ebuild          |   2 +-
 .../berkeley_upc_translator-2.18.0.ebuild          |   2 +-
 ...build => berkeley_upc_translator-2.18.2.ebuild} |   2 +-
 dev-lang/berkeley_upc_translator/metadata.xml      |   3 +-
 sci-biology/bedtools/ChangeLog                     |   6 ++
 sci-biology/bedtools/Manifest                      |   2 +-
 ...dtools-2.19.1.ebuild => bedtools-2.20.1.ebuild} |   0
 sci-biology/cd-hit-auxtools/ChangeLog              |  14 +++
 sci-biology/cd-hit-auxtools/Manifest               |   2 +
 .../cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild     |  44 ++++++++
 sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch |  47 ++++++++
 .../cd-hit-auxtools}/metadata.xml                  |   0
 sci-biology/cd-hit/ChangeLog                       |  12 +++
 sci-biology/cd-hit/Manifest                        |   1 +
 sci-biology/cd-hit/cd-hit-4.6.1.ebuild             |  44 ++++++++
 sci-biology/cd-hit/files/4.6.1-gentoo.patch        | 118 +++++++++++++++++++++
 sci-biology/cd-hit/metadata.xml                    |  23 ++++
 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        |   3 +
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |   4 +
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild |   5 +
 sci-biology/ugene/ChangeLog                        |   9 ++
 sci-biology/ugene/Manifest                         |   1 +
 .../nMOLDYN => sci-biology/ugene}/metadata.xml     |   2 +-
 sci-biology/ugene/ugene-1.13.3.ebuild              |  35 ++++++
 sci-physics/openmx/ChangeLog                       |   8 +-
 sci-physics/openmx/Manifest                        |   2 +-
 .../{openmx-3.7.6.ebuild => openmx-3.7.8.ebuild}   |   2 +-
 sys-cluster/lustre/ChangeLog                       |   7 ++
 ...cfs-update-zfs-proc-handling-to-seq_files.patch |   2 +-
 ...cfs-move-mdd-ofd-proc-handling-to-seq_fil.patch |   2 +-
 ...m-Backport-shrinker-changes-from-upstream.patch |   2 +-
 sys-cluster/lustre/lustre-9999.ebuild              |   2 +
 38 files changed, 415 insertions(+), 15 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     1877cb5623f96f8c3ce50b1f73a23a94c2a4ec85
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jun  3 00:24:48 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jun  3 00:24:48 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1877cb56

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 dev-lang/berkeley_upc/ChangeLog                             |  8 +++++++-
 dev-lang/berkeley_upc/Manifest                              |  1 +
 ...erkeley_upc-2.16.2.ebuild => berkeley_upc-2.18.2.ebuild} |  0
 dev-lang/berkeley_upc/metadata.xml                          |  3 ++-
 dev-lang/berkeley_upc_translator/ChangeLog                  |  9 ++++++++-
 dev-lang/berkeley_upc_translator/Manifest                   |  1 +
 .../berkeley_upc_translator-2.16.2.ebuild                   |  2 +-
 .../berkeley_upc_translator-2.18.0.ebuild                   |  2 +-
 ...-2.16.2.ebuild => berkeley_upc_translator-2.18.2.ebuild} |  2 +-
 dev-lang/berkeley_upc_translator/metadata.xml               |  3 ++-
 sci-astronomy/casapy-bin/ChangeLog                          |  6 ++++++
 sci-astronomy/casapy-bin/Manifest                           |  1 +
 ...2.021_p1.ebuild => casapy-bin-4.2.1.29047.001_p1.ebuild} |  0
 sci-libs/ghmm/ChangeLog                                     |  6 +++++-
 sci-libs/ghmm/files/ghmm-9999-clapack.patch                 | 11 +++++++++++
 sci-libs/ghmm/files/ghmm-9999-respect.patch                 |  8 +++-----
 sci-libs/ghmm/ghmm-9999.ebuild                              |  1 +
 sci-physics/openmx/ChangeLog                                |  8 +++++++-
 sci-physics/openmx/Manifest                                 |  2 +-
 .../openmx/{openmx-3.7.6.ebuild => openmx-3.7.8.ebuild}     |  2 +-
 sci-physics/qcl/ChangeLog                                   |  8 +++++++-
 sci-physics/qcl/Manifest                                    |  9 +++++----
 .../{qcl-0.6.3-makefile.patch => qcl-0.6.4-makefile.patch}  | 10 +++++-----
 sci-physics/qcl/{qcl-0.6.3-r1.ebuild => qcl-0.6.4.ebuild}   | 13 ++++++-------
 24 files changed, 83 insertions(+), 33 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     17cc47ca38ccf147936547d1d57ba20385ae176a
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Mon Jun  2 20:30:37 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Mon Jun  2 20:30:37 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=17cc47ca

Merge branch 'upstream-master' into gentoo-master


 sci-physics/qcl/ChangeLog                                   |  8 +++++++-
 sci-physics/qcl/Manifest                                    |  9 +++++----
 .../{qcl-0.6.3-makefile.patch => qcl-0.6.4-makefile.patch}  | 10 +++++-----
 sci-physics/qcl/{qcl-0.6.3-r1.ebuild => qcl-0.6.4.ebuild}   | 13 ++++++-------
 4 files changed, 23 insertions(+), 17 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     ac43a14d3a8e7d6469cf6fd137728665e7021be7
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Mon Jun  2 12:10:19 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Mon Jun  2 12:10:19 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ac43a14d

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci into gentoo-master


 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild   | 3 +++
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 4 ++++
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild    | 5 +++++
 3 files changed, 12 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     d5fd5017e7bca7ab9e13671d7d60b8dcf5791ead
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Mon Jun  2 12:07:44 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Mon Jun  2 12:07:44 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d5fd5017

Merge remote-tracking branch 'gentoo/master' into upstream-master


 sci-biology/cd-hit-auxtools/ChangeLog              |  14 +++
 sci-biology/cd-hit-auxtools/Manifest               |   2 +
 .../cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild     |  44 ++++++++
 sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch |  47 ++++++++
 .../cd-hit-auxtools}/metadata.xml                  |   0
 sci-biology/cd-hit/ChangeLog                       |  12 +++
 sci-biology/cd-hit/Manifest                        |   1 +
 sci-biology/cd-hit/cd-hit-4.6.1.ebuild             |  44 ++++++++
 sci-biology/cd-hit/files/4.6.1-gentoo.patch        | 118 +++++++++++++++++++++
 sci-biology/cd-hit/metadata.xml                    |  23 ++++
 sci-biology/ugene/ChangeLog                        |   9 ++
 sci-biology/ugene/Manifest                         |   1 +
 .../nMOLDYN => sci-biology/ugene}/metadata.xml     |   2 +-
 sci-biology/ugene/ugene-1.13.3.ebuild              |  35 ++++++
 14 files changed, 351 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     d2eee77e01938d323acecef76cd4e6a148bd7628
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Sun Jun  1 16:29:29 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Sun Jun  1 16:29:29 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d2eee77e

Merge remote-tracking branch 'gentoo/master' into upstream-master


 sci-biology/bedtools/ChangeLog                                     | 6 ++++++
 sci-biology/bedtools/Manifest                                      | 2 +-
 .../bedtools/{bedtools-2.19.1.ebuild => bedtools-2.20.1.ebuild}    | 0
 sys-cluster/lustre/ChangeLog                                       | 7 +++++++
 ...0001-LU-3319-procfs-update-zfs-proc-handling-to-seq_files.patch | 2 +-
 ...0002-LU-3319-procfs-move-mdd-ofd-proc-handling-to-seq_fil.patch | 2 +-
 .../0003-LU-4416-mm-Backport-shrinker-changes-from-upstream.patch  | 2 +-
 sys-cluster/lustre/lustre-9999.ebuild                              | 2 ++
 8 files changed, 19 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     7078e8bfcae1c3da2b8d32e73d7091227209488a
Author:     Jauhien Piatlicki <piatlicki <AT> gmail <DOT> com>
AuthorDate: Sun Jun  1 16:24:32 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Sun Jun  1 16:24:32 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7078e8bf

Merge pull request #229 from jauhien/master

dev-lang/berkeley_upc, dev-lang/berkeley_upc_translator: version bump to 2.18.2


 dev-lang/berkeley_upc/ChangeLog                                  | 8 +++++++-
 dev-lang/berkeley_upc/Manifest                                   | 1 +
 .../{berkeley_upc-2.16.2.ebuild => berkeley_upc-2.18.2.ebuild}   | 0
 dev-lang/berkeley_upc/metadata.xml                               | 3 ++-
 dev-lang/berkeley_upc_translator/ChangeLog                       | 9 ++++++++-
 dev-lang/berkeley_upc_translator/Manifest                        | 1 +
 .../berkeley_upc_translator-2.16.2.ebuild                        | 2 +-
 .../berkeley_upc_translator-2.18.0.ebuild                        | 2 +-
 ...lator-2.16.2.ebuild => berkeley_upc_translator-2.18.2.ebuild} | 2 +-
 dev-lang/berkeley_upc_translator/metadata.xml                    | 3 ++-
 10 files changed, 24 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Jauhien Piatlicki]

commit:     3751a04d3152832cf00dcf5a75523fa8e6bb166b
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Mon May 26 23:34:47 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Mon May 26 23:34:47 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3751a04d

Merge pull request #227 from sargas/casapy-bin

sci-astronomy/casapy-bin: casapy-bin version bump to 4.2.1


 sci-astronomy/casapy-bin/ChangeLog                                  | 6 ++++++
 sci-astronomy/casapy-bin/Manifest                                   | 1 +
 ...2.0.28322.021_p1.ebuild => casapy-bin-4.2.1.29047.001_p1.ebuild} | 0
 3 files changed, 7 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     cd8763680dc286107f13f042f28b866f057def04
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon May 12 02:18:11 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon May 12 02:18:11 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cd876368

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 app-editors/neovim/ChangeLog                       |  3 ++
 app-editors/neovim/neovim-9999.ebuild              |  4 +-
 dev-db/cppdb/ChangeLog                             | 26 -----------
 dev-db/cppdb/Manifest                              |  1 -
 dev-db/cppdb/cppdb-0.3.1-r1.ebuild                 | 50 ----------------------
 dev-db/cppdb/metadata.xml                          | 14 ------
 dev-lua/cmsgpack/ChangeLog                         | 10 +++++
 dev-lua/cmsgpack/Manifest                          |  1 +
 dev-lua/cmsgpack/cmsgpack-0.3.0.ebuild             | 48 +++++++++++++++++++++
 dev-lua/cmsgpack/cmsgpack-9999.ebuild              | 48 +++++++++++++++++++++
 .../neovim => dev-lua/cmsgpack}/metadata.xml       |  0
 11 files changed, 113 insertions(+), 92 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     462fb38d58011521d9201de3a373ce4ec4475639
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat May 10 16:55:17 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat May 10 16:55:17 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=462fb38d

Merge pull request #224 from JelteF/neovim

Update dependencies of neovim and add dev-lua/cmsgpack, which is one of them.


 app-editors/neovim/ChangeLog                       |  3 ++
 app-editors/neovim/neovim-9999.ebuild              |  4 +-
 dev-lua/cmsgpack/ChangeLog                         | 10 +++++
 dev-lua/cmsgpack/Manifest                          |  1 +
 dev-lua/cmsgpack/cmsgpack-0.3.0.ebuild             | 48 ++++++++++++++++++++++
 dev-lua/cmsgpack/cmsgpack-9999.ebuild              | 48 ++++++++++++++++++++++
 .../neovim => dev-lua/cmsgpack}/metadata.xml       |  0
 7 files changed, 113 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     64af80673e08e58cea2175a692eaf96ef4863a55
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat May 10 09:51:06 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat May 10 09:51:06 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=64af8067

Merge pull request #226 from jauhien/master

dev-db/cppdb: imported to the main tree


 dev-db/cppdb/ChangeLog             | 26 --------------------
 dev-db/cppdb/Manifest              |  1 -
 dev-db/cppdb/cppdb-0.3.1-r1.ebuild | 50 --------------------------------------
 dev-db/cppdb/metadata.xml          | 14 -----------
 4 files changed, 91 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     d036cb4404d2824b5ba169c628e8e9615ca40408
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed May  7 23:19:29 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed May  7 23:19:29 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d036cb44

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-biology/biopython/ChangeLog                    | 40 ----------------
 sci-biology/biopython/Manifest                     |  2 -
 sci-biology/biopython/biopython-1.62-r3.ebuild     | 53 ----------------------
 sci-biology/biopython/biopython-1.62-r4.ebuild     | 53 ----------------------
 sci-biology/biopython/biopython-1.63-r1.ebuild     | 53 ----------------------
 .../biopython/files/SffIO_broken_padding.patch     | 27 -----------
 .../biopython/files/SffIO_error_in_check_eof.patch | 14 ------
 .../biopython/files/biopython-1.51-flex.patch      | 21 ---------
 .../biopython/files/biopython-1.62-SffIO.patch     | 36 ---------------
 sci-biology/biopython/metadata.xml                 |  5 --
 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        | 16 +++----
 sci-chemistry/phenix-bin/ChangeLog                 |  5 ++
 sci-chemistry/phenix-bin/Manifest                  |  1 +
 ....8.4.1496.ebuild => phenix-bin-1.9.1690.ebuild} |  7 ++-
 14 files changed, 17 insertions(+), 316 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     75d4c8b583274a530238bdeaab757d344b1fd027
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Apr 22 11:56:21 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Apr 22 11:56:21 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=75d4c8b5

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sys-cluster/lustre/ChangeLog                       |   26 +
 ...fs-Move-NRS-TBF-proc-handling-to-seq_fil.patch} |    6 +-
 .../0001-LU-3319-procfs-fix-symlink-handling.patch | 1132 --------------------
 ...fs-update-zfs-proc-handling-to-seq_files.patch} |   14 +-
 ...ocfs-move-osp-proc-handling-to-seq_files.patch} |    4 +-
 ...ocfs-move-lod-proc-handling-to-seq_files.patch} |    8 +-
 ...rocfs-move-mgs-proc-handling-to-seq_files.patch |  356 ------
 ...fs-move-mdt-mds-proc-handling-to-seq_fil.patch} |   22 +-
 ...fs-move-mdd-ofd-proc-handling-to-seq_fil.patch} |  103 +-
 ...-Backport-shrinker-changes-from-upstream.patch} |   16 +-
 ...cfs-update-ldiskfs-proc-handling-to-seq_f.patch |  826 --------------
 sys-cluster/lustre/lustre-9999.ebuild              |   26 +-
 12 files changed, 114 insertions(+), 2425 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     baeda3304a774b18b67c61d40403ebce0b87af61
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 18 18:12:39 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 18 18:12:39 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=baeda330

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 dev-python/montage-wrapper/ChangeLog               |  9 ++
 dev-python/montage-wrapper/Manifest                |  1 +
 dev-python/montage-wrapper/metadata.xml            | 11 +++
 .../montage-wrapper/montage-wrapper-0.9.7.ebuild   | 41 +++++++++
 licenses/Montage                                   | 90 ++++++++++++++++++++
 media-gfx/brlcad/Manifest                          |  1 -
 media-gfx/librecad/Manifest                        |  1 -
 sci-astronomy/montage/ChangeLog                    | 14 ++++
 sci-astronomy/montage/Manifest                     |  2 +
 .../montage/files/montage-3.3-gcc48.patch          | 97 ++++++++++++++++++++++
 sci-astronomy/{swarp => montage}/metadata.xml      |  4 +-
 sci-astronomy/montage/montage-3.3.ebuild           | 55 ++++++++++++
 sci-astronomy/pyAstroStack/ChangeLog               | 18 ++++
 sci-astronomy/pyAstroStack/Manifest                |  1 +
 sci-astronomy/pyAstroStack/metadata.xml            | 18 ++++
 .../pyAstroStack/pyAstroStack-0.3.0.ebuild         | 33 ++++++++
 x11-misc/envytools/ChangeLog                       |  3 +
 x11-misc/envytools/envytools-9999.ebuild           |  4 +-
 18 files changed, 397 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     577b6a4015db9bccc6cdc149362b79c29104d7c6
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Wed Apr 16 22:48:31 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Apr 16 22:48:31 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=577b6a40

Merge pull request #221 from erasmuswill/x11-misc/envytools

x11-misc/envytools: Updated github url, Resolves gentoo-science/sci#103


 x11-misc/envytools/ChangeLog             | 3 +++
 x11-misc/envytools/envytools-9999.ebuild | 4 ++--
 2 files changed, 5 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     0b8172fd76954a9566db00a291d5257a1e9fc49b
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Apr 16 13:56:22 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Apr 16 13:56:22 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0b8172fd

Merge pull request #218 from mickolaine/pyastrostack

sci-overlay/sci: Added an ebuild for pyAstroStack


 media-gfx/brlcad/Manifest                          |  1 -
 media-gfx/librecad/Manifest                        |  1 -
 sci-astronomy/pyAstroStack/ChangeLog               | 18 ++++++++++++
 sci-astronomy/pyAstroStack/Manifest                |  1 +
 sci-astronomy/pyAstroStack/metadata.xml            | 18 ++++++++++++
 .../pyAstroStack/pyAstroStack-0.3.0.ebuild         | 33 ++++++++++++++++++++++
 6 files changed, 70 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     9ba460a10da414e1132f9367deec2baf3673eaf5
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Apr 16 22:32:02 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Apr 16 22:32:02 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9ba460a1

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 media-gfx/brlcad/Manifest                          |  1 -
 media-gfx/librecad/Manifest                        |  1 -
 sci-astronomy/pyAstroStack/ChangeLog               | 18 ++++++++++++
 sci-astronomy/pyAstroStack/Manifest                |  1 +
 sci-astronomy/pyAstroStack/metadata.xml            | 18 ++++++++++++
 .../pyAstroStack/pyAstroStack-0.3.0.ebuild         | 33 ++++++++++++++++++++++
 6 files changed, 70 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     a3f21b1be8d0728b8c0db329fcead567ec3dd84d
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Apr 16 15:51:59 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Apr 16 15:51:59 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a3f21b1b

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 sci-biology/VelvetOptimiser/ChangeLog              | 13 +++++++++
 sci-biology/VelvetOptimiser/Manifest               |  1 +
 .../VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild   | 29 +++++++++++++++++++
 .../VelvetOptimiser}/metadata.xml                  |  0
 sci-biology/barrnap/ChangeLog                      |  9 ++++++
 sci-biology/barrnap/Manifest                       |  1 +
 sci-biology/barrnap/barrnap-0.3.ebuild             | 22 +++++++++++++++
 .../barrnap}/metadata.xml                          |  0
 sci-biology/bedtools/ChangeLog                     |  9 ++++++
 sci-biology/bedtools/Manifest                      |  1 +
 sci-biology/bedtools/bedtools-2.19.1.ebuild        | 33 ++++++++++++++++++++++
 sci-biology/bedtools/metadata.xml                  | 16 +++++++++++
 sci-biology/nesoni/ChangeLog                       | 10 +++++++
 sci-biology/nesoni/Manifest                        |  1 +
 .../nesoni}/metadata.xml                           |  0
 sci-biology/nesoni/nesoni-0.117.ebuild             | 33 ++++++++++++++++++++++
 sci-biology/velvetk/ChangeLog                      |  9 ++++++
 sci-biology/velvetk/Manifest                       |  1 +
 .../velvetk}/metadata.xml                          |  0
 sci-biology/velvetk/velvetk-20120606.ebuild        | 29 +++++++++++++++++++
 sci-chemistry/gromacs/ChangeLog                    |  4 +++
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild      | 12 ++++++--
 sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild       | 12 ++++++--
 sci-chemistry/gromacs/gromacs-9999.ebuild          | 12 ++++++--
 sci-chemistry/gromacs/metadata.xml                 |  1 +
 sci-libs/etsf_io/ChangeLog                         | 13 ++++++++-
 sci-libs/etsf_io/Manifest                          |  1 +
 ...tsf_io-1.0.3-r2.ebuild => etsf_io-1.0.4.ebuild} |  3 +-
 sci-libs/libxc/ChangeLog                           | 12 +++++++-
 sci-libs/libxc/Manifest                            |  3 ++
 .../{libxc-2.0.1.ebuild => libxc-2.0.3.ebuild}     |  0
 .../{libxc-2.0.1.ebuild => libxc-2.1.0.ebuild}     |  0
 .../{libxc-2.0.1.ebuild => libxc-2.2.0.ebuild}     |  0
 33 files changed, 280 insertions(+), 10 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     d041503e76e53efb5b6f7b6cce7aaf1542d03de4
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 14 15:55:14 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Apr 14 15:55:14 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d041503e

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 app-editors/neovim/neovim-9999.ebuild | 1 +
 1 file changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Honza Macháček]

commit:     5266b33235bf8ed1645ff353dd6d371d18e34bb4
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Tue Apr 15 14:29:58 2014 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Tue Apr 15 14:29:58 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5266b332

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

sci-libs/etsf_io bumped to version 1.0.4


 app-editors/neovim/neovim-9999.ebuild              |    1 +
 dev-python/ffnet/ChangeLog                         |    6 +-
 dev-python/ffnet/Manifest                          |    2 +-
 .../{ffnet-0.6.2.ebuild => ffnet-0.7.1.ebuild}     |   23 +-
 dev-python/ffnet/metadata.xml                      |   10 +-
 sci-biology/VelvetOptimiser/ChangeLog              |   13 +
 sci-biology/VelvetOptimiser/Manifest               |    1 +
 .../VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild   |   29 +
 .../VelvetOptimiser}/metadata.xml                  |    0
 sci-biology/barrnap/ChangeLog                      |    9 +
 sci-biology/barrnap/Manifest                       |    1 +
 sci-biology/barrnap/barrnap-0.3.ebuild             |   22 +
 .../barrnap}/metadata.xml                          |    0
 sci-biology/consed/ChangeLog                       |   11 +
 sci-biology/consed/consed-20-r1.ebuild             |    7 +-
 sci-biology/consed/consed-21.ebuild                |    7 +-
 sci-biology/consed/consed-22.ebuild                |    7 +-
 sci-biology/consed/consed-23.ebuild                |    7 +-
 sci-biology/consed/consed-24.ebuild                |    7 +-
 sci-biology/consed/consed-25.ebuild                |    7 +-
 sci-biology/consed/consed-26.ebuild                |    7 +-
 sci-biology/consed/consed-27.ebuild                |    7 +-
 sci-biology/mira/ChangeLog                         |    5 +
 sci-biology/mira/Manifest                          |    1 +
 .../{mira-4.0_rc4.ebuild => mira-4.0.1.ebuild}     |    0
 sci-biology/nesoni/ChangeLog                       |   10 +
 sci-biology/nesoni/Manifest                        |    1 +
 .../nesoni}/metadata.xml                           |    0
 sci-biology/nesoni/nesoni-0.117.ebuild             |   33 +
 sci-biology/velvetk/ChangeLog                      |    9 +
 sci-biology/velvetk/Manifest                       |    1 +
 .../velvetk}/metadata.xml                          |    0
 sci-biology/velvetk/velvetk-20120606.ebuild        |   29 +
 sci-chemistry/gromacs/ChangeLog                    |   12 +
 sci-chemistry/gromacs/Manifest                     |    4 +-
 ...cs-5.0_beta1.ebuild => gromacs-5.0.9999.ebuild} |   56 +-
 ...{gromacs-9999.ebuild => gromacs-5.0_rc1.ebuild} |   51 +-
 sci-chemistry/gromacs/gromacs-9999.ebuild          |   47 +-
 sci-chemistry/gromacs/metadata.xml                 |   12 +-
 sci-libs/dcmtk/ChangeLog                           |   14 +-
 sci-libs/dcmtk/Manifest                            |    4 +-
 sci-libs/dcmtk/dcmtk-3.5.4-r3.ebuild               |   71 -
 sci-libs/dcmtk/dcmtk-3.5.5_pre20101008.ebuild      |   79 -
 sci-libs/dcmtk/dcmtk-3.6.0.ebuild                  |   72 +
 sci-libs/dcmtk/files/02_dcmtk_3.6.0-1.patch        |   89 +
 sci-libs/dcmtk/files/07_doxygen.patch              | 1804 ++++++++++++++++++++
 sci-libs/dcmtk/files/bug674361.patch               | 1015 +++++++++++
 sci-libs/dcmtk/files/dcmtk-asneeded.patch          |   16 +
 sci-libs/dcmtk/files/dcmtk_version_number.patch    |  131 ++
 sci-libs/dcmtk/files/doubledes.patch               |   31 +
 sci-libs/dcmtk/files/fixnull.patch                 |   36 +
 sci-libs/dcmtk/files/noleak.patch                  |   36 +
 sci-libs/dcmtk/files/nothrow.patch                 |   76 +
 sci-libs/dcmtk/files/prefs.patch                   |   26 +
 .../files/regression_stacksequenceisodd.patch      |   98 ++
 .../dcmtk/files/use_correct_number_of_TS.patch     |   19 +
 sci-libs/dcmtk/metadata.xml                        |   30 +-
 sci-libs/itk/ChangeLog                             |   11 +
 sci-libs/itk/Manifest                              |    2 +
 ...p-TransformFileReader-TransformFileWriter.patch |   50 +
 ...itkQuasiNewtonOptimizerv4-wrapping-warnin.patch |   28 +
 ...itkGradientDescentOptimizerv4-wrapping-wa.patch |   73 +
 ...OptimizerParameterScalesEstimatorTemplate.patch |   30 +
 .../0005-make-gdcm-helper-library-static.patch     |   11 +
 sci-libs/itk/files/nrrdio-linking.patch            |   15 +
 .../itk/{itk-4.4.2-r1.ebuild => itk-4.5.1.ebuild}  |   76 +-
 sci-mathematics/pulp/ChangeLog                     |    6 +-
 sci-mathematics/pulp/Manifest                      |    2 +-
 .../pulp/{pulp-1.5.3.ebuild => pulp-1.5.6.ebuild}  |   16 +-
 sci-visualization/visit/visit-2.7.2.ebuild         |    6 +
 70 files changed, 4124 insertions(+), 304 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     51745b131d5c80ef70624b1e835ea763050c12d8
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Apr 15 08:52:08 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Apr 15 08:52:08 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=51745b13

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 app-editors/neovim/neovim-9999.ebuild         |  1 +
 sci-chemistry/gromacs/ChangeLog               |  4 ++++
 sci-chemistry/gromacs/gromacs-5.0.9999.ebuild | 12 ++++++++++--
 sci-chemistry/gromacs/gromacs-5.0_rc1.ebuild  | 12 ++++++++++--
 sci-chemistry/gromacs/gromacs-9999.ebuild     | 12 ++++++++++--
 sci-chemistry/gromacs/metadata.xml            |  1 +
 6 files changed, 36 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     312820dda699d6ed17a1b430cb0cbfb3116dfee2
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 15 00:00:21 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Apr 15 00:00:21 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=312820dd

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 app-editors/neovim/neovim-9999.ebuild | 1 +
 1 file changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     bb6034788c0813df0c74104bffbf5da3855119df
Author:     Christoph Junghans <christoph.junghans <AT> googlemail <DOT> com>
AuthorDate: Fri Apr 11 13:42:31 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Apr 11 13:42:31 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bb603478

Merge pull request #217 from glubo/master

app-editors/neovim: Added luajit dependency.


 app-editors/neovim/neovim-9999.ebuild | 1 +
 1 file changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     5cdf64649280508520fc9b96b6926e0ce2c0d283
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 12 12:29:38 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 12 12:29:38 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5cdf6464

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 dev-python/ffnet/ChangeLog                         |    6 +-
 dev-python/ffnet/Manifest                          |    2 +-
 .../{ffnet-0.6.2.ebuild => ffnet-0.7.1.ebuild}     |   23 +-
 dev-python/ffnet/metadata.xml                      |   10 +-
 sci-chemistry/gromacs/ChangeLog                    |    8 +
 sci-chemistry/gromacs/Manifest                     |    4 +-
 ...cs-5.0_beta1.ebuild => gromacs-5.0.9999.ebuild} |   50 +-
 ...{gromacs-9999.ebuild => gromacs-5.0_rc1.ebuild} |   43 +-
 sci-chemistry/gromacs/gromacs-9999.ebuild          |   39 +-
 sci-chemistry/gromacs/metadata.xml                 |   11 +-
 sci-libs/dcmtk/ChangeLog                           |   14 +-
 sci-libs/dcmtk/Manifest                            |    4 +-
 sci-libs/dcmtk/dcmtk-3.5.4-r3.ebuild               |   71 -
 sci-libs/dcmtk/dcmtk-3.5.5_pre20101008.ebuild      |   79 -
 sci-libs/dcmtk/dcmtk-3.6.0.ebuild                  |   72 +
 sci-libs/dcmtk/files/02_dcmtk_3.6.0-1.patch        |   89 +
 sci-libs/dcmtk/files/07_doxygen.patch              | 1804 ++++++++++++++++++++
 sci-libs/dcmtk/files/bug674361.patch               | 1015 +++++++++++
 sci-libs/dcmtk/files/dcmtk-asneeded.patch          |   16 +
 sci-libs/dcmtk/files/dcmtk_version_number.patch    |  131 ++
 sci-libs/dcmtk/files/doubledes.patch               |   31 +
 sci-libs/dcmtk/files/fixnull.patch                 |   36 +
 sci-libs/dcmtk/files/noleak.patch                  |   36 +
 sci-libs/dcmtk/files/nothrow.patch                 |   76 +
 sci-libs/dcmtk/files/prefs.patch                   |   26 +
 .../files/regression_stacksequenceisodd.patch      |   98 ++
 .../dcmtk/files/use_correct_number_of_TS.patch     |   19 +
 sci-libs/dcmtk/metadata.xml                        |   30 +-
 sci-libs/itk/ChangeLog                             |   11 +
 sci-libs/itk/Manifest                              |    2 +
 ...p-TransformFileReader-TransformFileWriter.patch |   50 +
 ...itkQuasiNewtonOptimizerv4-wrapping-warnin.patch |   28 +
 ...itkGradientDescentOptimizerv4-wrapping-wa.patch |   73 +
 ...OptimizerParameterScalesEstimatorTemplate.patch |   30 +
 .../0005-make-gdcm-helper-library-static.patch     |   11 +
 sci-libs/itk/files/nrrdio-linking.patch            |   15 +
 .../itk/{itk-4.4.2-r1.ebuild => itk-4.5.1.ebuild}  |   76 +-
 sci-mathematics/pulp/ChangeLog                     |    6 +-
 sci-mathematics/pulp/Manifest                      |    2 +-
 .../pulp/{pulp-1.5.3.ebuild => pulp-1.5.6.ebuild}  |   16 +-
 sci-visualization/visit/visit-2.7.2.ebuild         |    6 +
 41 files changed, 3872 insertions(+), 297 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     a5f3da451a5cc8216e6ca352847ee87d718483bb
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Apr  9 15:58:05 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Apr  9 15:58:05 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a5f3da45

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 dev-python/ffnet/ChangeLog                         |  6 ++-
 dev-python/ffnet/Manifest                          |  2 +-
 .../{ffnet-0.6.2.ebuild => ffnet-0.7.1.ebuild}     | 23 +++++-----
 dev-python/ffnet/metadata.xml                      | 10 ++---
 sci-chemistry/gromacs/ChangeLog                    |  8 ++++
 sci-chemistry/gromacs/Manifest                     |  4 +-
 ...cs-5.0_beta1.ebuild => gromacs-5.0.9999.ebuild} | 50 +++++++++++-----------
 ...{gromacs-9999.ebuild => gromacs-5.0_rc1.ebuild} | 43 ++++++++++---------
 sci-chemistry/gromacs/gromacs-9999.ebuild          | 39 +++++++++--------
 sci-chemistry/gromacs/metadata.xml                 | 11 +++--
 sci-mathematics/pulp/ChangeLog                     |  6 ++-
 sci-mathematics/pulp/Manifest                      |  2 +-
 .../pulp/{pulp-1.5.3.ebuild => pulp-1.5.6.ebuild}  | 16 +++----
 13 files changed, 120 insertions(+), 100 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     d73e26855af17da657e6f494636f437c82e48bfb
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Apr  7 16:56:14 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Apr  7 16:56:14 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d73e2685

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-visualization/visit/visit-2.7.2.ebuild | 6 ++++++
 1 file changed, 6 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     55175ad9d048a86aa1cd0e74f7ba79d6c1988a34
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Sun Apr  6 19:55:40 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Apr  6 19:55:40 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=55175ad9

Merge /usr/local/portage/andis_overlay


 sci-visualization/visit/visit-2.7.2.ebuild | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c08e747edfee2002c03680118284fb9398cea1bd
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Apr  9 11:07:37 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Apr  9 11:07:37 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c08e747e

Merge remote-tracking branch 'github/master'

* github/master:
  dropped backticks
  now symlinking Python packages instead of modifying the environment
  add Python packages to path


 sci-visualization/visit/visit-2.7.2.ebuild | 6 ++++++
 1 file changed, 6 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     adca6662ff0fed292452c814cbbc78340cc1537f
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Mon Apr  7 02:16:00 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Apr  7 02:16:00 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=adca6662

Merge pull request #211 from gentryx/master

add VisIt's Python packages to PYTHONPATH


 sci-visualization/visit/visit-2.7.2.ebuild | 6 ++++++
 1 file changed, 6 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     02de10bd67500f24e0ee4b5a697ce64d67796664
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Thu Apr  3 12:09:11 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Apr  3 12:09:11 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=02de10bd

Merge /usr/local/portage/andis_overlay


 sci-visualization/visit/visit-2.7.2.ebuild | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     2e4622ac92274f7c92ffb0e6bb813f208943d5cb
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Thu Apr  3 12:07:51 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Apr  3 12:07:51 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2e4622ac

Merge https://github.com/gentoo-science/sci


 dev-lang/julia/ChangeLog                           |    4 +
 dev-lang/julia/files/julia-nopatchelf.patch        |   14 -
 dev-lang/julia/julia-9999.ebuild                   |  119 +-
 dev-lang/julia/metadata.xml                        |    4 +-
 dev-libs/double-conversion/ChangeLog               |   18 -
 dev-libs/double-conversion/Manifest                |    1 -
 .../double-conversion-1.1.1.ebuild                 |   46 -
 .../files/double-conversion-1.1.1-scons.patch      |   26 -
 dev-libs/double-conversion/metadata.xml            |   11 -
 dev-libs/utf8proc/ChangeLog                        |    4 +
 dev-libs/utf8proc/metadata.xml                     |   11 +-
 dev-libs/utf8proc/utf8proc-1.1.6.ebuild            |    5 +-
 sci-biology/RADtools/ChangeLog                     |   10 +
 sci-biology/RADtools/Manifest                      |    2 +
 sci-biology/RADtools/RADtools-1.2.4.ebuild         |   37 +
 sci-biology/RADtools/RADtools-9999.ebuild          |   37 +
 .../RADtools}/metadata.xml                         |    0
 sci-biology/YASRA/ChangeLog                        |   10 +-
 sci-biology/YASRA/Manifest                         |    2 +-
 .../YASRA/{YASRA-2.32.ebuild => YASRA-2.33.ebuild} |    0
 sci-biology/biopieces/ChangeLog                    |   11 +
 sci-biology/biopieces/Manifest                     |    1 +
 sci-biology/biopieces/biopieces-0.51.ebuild        |   63 ++
 sci-biology/biopieces/biopieces-9999.ebuild        |   63 ++
 .../biopieces}/metadata.xml                        |    0
 sci-biology/consed/ChangeLog                       |    7 +-
 sci-biology/consed/consed-20-r1.ebuild             |    1 +
 sci-biology/consed/consed-21.ebuild                |    1 +
 sci-biology/consed/consed-22.ebuild                |    1 +
 sci-biology/consed/consed-23.ebuild                |    1 +
 sci-biology/consed/consed-24.ebuild                |    1 +
 sci-biology/consed/consed-25.ebuild                |    1 +
 sci-biology/consed/consed-26.ebuild                |    1 +
 sci-biology/consed/consed-27.ebuild                |    1 +
 sci-biology/khmer/ChangeLog                        |    4 +
 sci-biology/khmer/khmer-9999.ebuild                |   36 +-
 sci-biology/scan_for_matches/ChangeLog             |   10 +
 sci-biology/scan_for_matches/Manifest              |    1 +
 .../scan_for_matches}/metadata.xml                 |    0
 .../scan_for_matches-20121220.ebuild               |   26 +
 sci-biology/stacks/ChangeLog                       |   10 +
 sci-biology/stacks/Manifest                        |    1 +
 .../stacks}/metadata.xml                           |    0
 sci-biology/stacks/stacks-1.16.ebuild              |   49 +
 sci-biology/tablet/ChangeLog                       |   12 +
 sci-biology/tablet/Manifest                        |    2 +
 .../{tablet-bin => tablet}/files/response.varfile  |    0
 .../tablet}/metadata.xml                           |    0
 .../tablet-1.13.12.17.ebuild}                      |    2 +-
 .../tablet-9999.ebuild}                            |   24 +-
 sci-chemistry/erkale/ChangeLog                     |   10 +
 sci-chemistry/erkale/erkale-9999.ebuild            |   70 ++
 sci-chemistry/erkale/metadata.xml                  |   18 +
 sci-physics/geant-vmc/ChangeLog                    |   10 +
 sci-physics/geant-vmc/Manifest                     |    1 +
 sci-physics/geant-vmc/geant-vmc-3.1.15a.ebuild     |    2 +-
 ...-vmc-4.2.15.ebuild => geant-vmc-4.2.15a.ebuild} |    0
 sci-physics/genfit/ChangeLog                       |    6 +-
 sci-physics/genfit/Manifest                        |    2 +-
 sci-physics/genfit/genfit-02.00.00.ebuild          |    5 +-
 sci-physics/vgm/ChangeLog                          |    5 +-
 sci-physics/vgm/Manifest                           |    2 +-
 sci-physics/vgm/vgm-3.06.ebuild                    |    5 +-
 sys-cluster/lustre/ChangeLog                       |   37 +
 ...ld-make-AC-check-for-linux-arch-sandbox-f.patch |   95 --
 .../0001-LU-3319-procfs-fix-symlink-handling.patch | 1132 ++++++++++++++++++++
 ...cfs-Move-NRS-TBF-proc-handling-to-seq_fil.patch |  123 +++
 ...fs-update-zfs-proc-handling-to-seq_files.patch} |   67 +-
 .../0004-LU-3319-procfs-fix-symlink-handling.patch |  371 -------
 ...ocfs-move-mgs-proc-handling-to-seq_files.patch} |   22 +-
 ...rocfs-move-osp-proc-handling-to-seq_files.patch |  192 ++--
 ...rocfs-move-lod-proc-handling-to-seq_files.patch |  200 ++--
 ...fs-move-mdt-mds-proc-handling-to-seq_fil.patch} |  215 ++--
 ...fs-move-mdd-ofd-proc-handling-to-seq_fil.patch} |  455 +++++---
 ...cfs-update-ldiskfs-proc-handling-to-seq_f.patch |  203 ++--
 ...0010-LU-3319-lprocfs-client-side-cleanups.patch |  463 --------
 ...m-Backport-shrinker-changes-from-upstream.patch |  757 +++++++++++++
 ...-LU-3974-llite-use-new-struct-dir_context.patch |  254 -----
 ...-LU-3974-llite-invalidatepage-api-changed.patch |  134 ---
 .../lustre/files/lustre-readline6.3_fix.patch      |   13 +
 sys-cluster/lustre/lustre-9999.ebuild              |   17 +-
 81 files changed, 3439 insertions(+), 2138 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     bf90dacfc751aad48b8a73b9af89714a53be6243
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Apr  3 10:10:43 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Thu Apr  3 10:10:43 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bf90dacf

Merge pull request #215 from olifre/fix-sf-zip-snapshots

Fix sf zip snapshots, see #214


 sci-physics/genfit/ChangeLog              | 6 +++++-
 sci-physics/genfit/Manifest               | 2 +-
 sci-physics/genfit/genfit-02.00.00.ebuild | 5 ++++-
 sci-physics/vgm/ChangeLog                 | 5 ++++-
 sci-physics/vgm/Manifest                  | 2 +-
 sci-physics/vgm/vgm-3.06.ebuild           | 5 ++++-
 6 files changed, 19 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     08d6120de0152a671785c1e041b8e782c1999c10
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Thu Apr  3 02:46:33 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Thu Apr  3 02:46:33 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=08d6120d

Merge pull request #213 from olifre/geant-vmc-syntaxfix

Fix syntax bug in dependency atom (sci-physics/geant-vmc-3.1.15a)


 sci-physics/geant-vmc/ChangeLog                | 4 ++++
 sci-physics/geant-vmc/geant-vmc-3.1.15a.ebuild | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     48f1f0bb4c0c3ede558e26119c0927600a61ae5b
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Apr  2 23:05:08 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Apr  2 23:05:08 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=48f1f0bb

Merge github.com:gentoo-science/sci


 sci-chemistry/erkale/ChangeLog          | 10 +++++
 sci-chemistry/erkale/erkale-9999.ebuild | 70 +++++++++++++++++++++++++++++++++
 sci-chemistry/erkale/metadata.xml       | 18 +++++++++
 3 files changed, 98 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     c9dbdb89a16a41a6d89fc8e0e6d91277664360d8
Author:     Reinis <rei4dan <AT> gmail <DOT> com>
AuthorDate: Wed Apr  2 16:51:07 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Apr  2 16:51:07 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c9dbdb89

Merge pull request #193 from Reinis/erkale

Add sci-chemistry/erkale


 sci-chemistry/erkale/ChangeLog          | 10 +++++
 sci-chemistry/erkale/erkale-9999.ebuild | 70 +++++++++++++++++++++++++++++++++
 sci-chemistry/erkale/metadata.xml       | 18 +++++++++
 3 files changed, 98 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     429c64f9bb22d0835d2827c1be3b6399da906971
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Apr  2 15:42:26 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Apr  2 15:42:26 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=429c64f9

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-biology/consed/ChangeLog                       |    7 +-
 sci-biology/consed/consed-20-r1.ebuild             |    1 +
 sci-biology/consed/consed-21.ebuild                |    1 +
 sci-biology/consed/consed-22.ebuild                |    1 +
 sci-biology/consed/consed-23.ebuild                |    1 +
 sci-biology/consed/consed-24.ebuild                |    1 +
 sci-biology/consed/consed-25.ebuild                |    1 +
 sci-biology/consed/consed-26.ebuild                |    1 +
 sci-biology/consed/consed-27.ebuild                |    1 +
 sys-cluster/lustre/ChangeLog                       |   37 +
 ...ld-make-AC-check-for-linux-arch-sandbox-f.patch |   95 --
 .../0001-LU-3319-procfs-fix-symlink-handling.patch | 1132 ++++++++++++++++++++
 ...cfs-Move-NRS-TBF-proc-handling-to-seq_fil.patch |  123 +++
 ...fs-update-zfs-proc-handling-to-seq_files.patch} |   67 +-
 .../0004-LU-3319-procfs-fix-symlink-handling.patch |  371 -------
 ...ocfs-move-mgs-proc-handling-to-seq_files.patch} |   22 +-
 ...rocfs-move-osp-proc-handling-to-seq_files.patch |  192 ++--
 ...rocfs-move-lod-proc-handling-to-seq_files.patch |  200 ++--
 ...fs-move-mdt-mds-proc-handling-to-seq_fil.patch} |  215 ++--
 ...fs-move-mdd-ofd-proc-handling-to-seq_fil.patch} |  455 +++++---
 ...cfs-update-ldiskfs-proc-handling-to-seq_f.patch |  203 ++--
 ...0010-LU-3319-lprocfs-client-side-cleanups.patch |  463 --------
 ...m-Backport-shrinker-changes-from-upstream.patch |  757 +++++++++++++
 ...-LU-3974-llite-use-new-struct-dir_context.patch |  254 -----
 ...-LU-3974-llite-invalidatepage-api-changed.patch |  134 ---
 .../lustre/files/lustre-readline6.3_fix.patch      |   13 +
 sys-cluster/lustre/lustre-9999.ebuild              |   17 +-
 27 files changed, 2829 insertions(+), 1936 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     5e5963586602ef69944f9db25782bf31e4ee97be
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Mon Mar 31 23:18:30 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Mar 31 23:18:30 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5e596358

Merge pull request #212 from olifre/geant-vmc-update

Version bump of sci-physics/geant-vmc


 sci-physics/geant-vmc/ChangeLog                                     | 6 ++++++
 sci-physics/geant-vmc/Manifest                                      | 1 +
 .../geant-vmc/{geant-vmc-4.2.15.ebuild => geant-vmc-4.2.15a.ebuild} | 0
 3 files changed, 7 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     fc77fc17602843baf8c48bd7364bfd5223cd13e1
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Mon Mar 31 15:28:15 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Mon Mar 31 15:28:15 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fc77fc17

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     e72e2383278d1f91d8a962b41f7827cccea0c25c
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 28 07:53:04 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Fri Mar 28 07:53:04 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e72e2383

Merge pull request #210 from ustcscgy/patch-1

sys-cluster/hpx-0.9.7: fix a typo


 sys-cluster/hpx/hpx-0.9.7.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     f15e5fa4a05a114db4bbcb79bfb99a2cbed64cad
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Fri Mar 28 00:46:29 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Fri Mar 28 00:46:29 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f15e5fa4

Merge pull request #207 from olifre/genfit-live

Add live-ebuild, add subslot-dependencies 


 sci-physics/genfit/ChangeLog                       | 12 ++++++++++++
 sci-physics/genfit/genfit-02.00.00.ebuild          | 22 ++++++++++++----------
 .../{genfit-02.00.00.ebuild => genfit-9999.ebuild} | 22 ++++++++++++----------
 3 files changed, 36 insertions(+), 20 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     8ba110ef03788e23441ab08aae99ae69f97eb739
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 28 13:56:22 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 28 13:56:22 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8ba110ef

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-chemistry/ball/ChangeLog                       |  3 ++
 sci-chemistry/ball/ball-9999.ebuild                | 35 +++++++++++++++-------
 sci-chemistry/chemBuild/ChangeLog                  |  5 ++++
 sci-chemistry/chemBuild/Manifest                   |  1 +
 ...emBuild-1.0.3.ebuild => chemBuild-1.0.4.ebuild} |  0
 sci-chemistry/specView/ChangeLog                   |  5 ++++
 sci-chemistry/specView/Manifest                    |  1 +
 ...cView-1.0.3.ebuild => specView-1.0.3_p2.ebuild} |  2 +-
 sci-misc/fitscut/ChangeLog                         |  7 +++--
 sci-misc/fitscut/Manifest                          |  2 +-
 sci-misc/fitscut/fitscut-1.4.4.ebuild              | 23 +++++++-------
 sci-misc/fitscut/metadata.xml                      |  2 +-
 sci-physics/geant-vmc/ChangeLog                    |  5 ++++
 sci-physics/geant-vmc/geant-vmc-3.1.15a.ebuild     |  2 +-
 sci-physics/geant-vmc/geant-vmc-4.2.14b.ebuild     |  2 +-
 sci-physics/geant-vmc/geant-vmc-4.2.15.ebuild      |  2 +-
 sci-physics/vgm/ChangeLog                          |  4 +++
 sci-physics/vgm/vgm-3.06.ebuild                    |  2 +-
 18 files changed, 72 insertions(+), 31 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     fcddf2f89394114878d074e151ea097ff8d674b0
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 27 08:29:47 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Thu Mar 27 08:29:47 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fcddf2f8

Merge pull request #208 from olifre/vgm-subslot

Add subslot-dependency on sci-physics/root, rebuilding is needed on each...


 sci-physics/vgm/ChangeLog       | 4 ++++
 sci-physics/vgm/vgm-3.06.ebuild | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     5c8403357131f2fc81f80bbf0f6984cb1dd8a03a
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 27 08:29:37 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Thu Mar 27 08:29:37 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5c840335

Merge pull request #209 from olifre/geant-vmc

Add subslot-dependency on sci-physics/root, rebuilding is needed on each...


 sci-physics/geant-vmc/ChangeLog                | 5 +++++
 sci-physics/geant-vmc/geant-vmc-3.1.15a.ebuild | 2 +-
 sci-physics/geant-vmc/geant-vmc-4.2.14b.ebuild | 2 +-
 sci-physics/geant-vmc/geant-vmc-4.2.15.ebuild  | 2 +-
 4 files changed, 8 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     87320a08fb1de005c38354df180351bf417bf341
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 25 10:46:38 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 25 10:46:38 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=87320a08

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-libs/mkl/ChangeLog                                           | 5 +++++
 sci-libs/mkl/Manifest                                            | 1 +
 sci-libs/mkl/{mkl-11.1.0.080-r1.ebuild => mkl-11.1.2.144.ebuild} | 4 ++--
 3 files changed, 8 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     598ffcc8b0cc7934c060f41fa700f91b5d27f846
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Mar 24 15:28:33 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Mar 24 15:28:33 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=598ffcc8

Merge remote-tracking branch 'github/master'

* github/master:
  media-gfx/librecad: version bump 2.0.3

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     0e63bdb46c078b43aaa7c4e628713f5308dec756
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 15:48:13 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 15:48:13 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0e63bdb4

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 dev-libs/libflatarray/ChangeLog                    |  7 +++
 dev-libs/libflatarray/Manifest                     |  1 +
 dev-libs/libflatarray/libflatarray-0.1.1.ebuild    | 52 ++++++++++++++++++
 dev-libs/libflatarray/libflatarray-9999.ebuild     | 52 ++++++++++++++++++
 dev-libs/libflatarray/metadata.xml                 | 19 +++++++
 sci-astronomy/missfits/ChangeLog                   |  6 ++
 sci-astronomy/missfits/Manifest                    |  1 +
 sci-astronomy/missfits/missfits-2.8.0.ebuild       |  1 +
 sci-astronomy/missfits/missfits-9999.ebuild        |  6 +-
 sci-astronomy/psfex/ChangeLog                      |  6 ++
 sci-astronomy/psfex/Manifest                       |  1 +
 .../{psfex-3.9.1.ebuild => psfex-3.17.0.ebuild}    |  0
 sci-astronomy/psfex/psfex-9999.ebuild              |  4 +-
 sci-astronomy/sextractor/ChangeLog                 |  6 ++
 sci-astronomy/sextractor/Manifest                  |  1 +
 sci-astronomy/sextractor/sextractor-2.19.5.ebuild  |  1 +
 sci-astronomy/sextractor/sextractor-9999.ebuild    |  6 +-
 sci-astronomy/skymaker/ChangeLog                   |  6 ++
 sci-astronomy/skymaker/Manifest                    |  1 +
 sci-astronomy/skymaker/skymaker-3.10.5.ebuild      |  1 +
 sci-astronomy/skymaker/skymaker-9999.ebuild        |  6 +-
 sci-astronomy/stiff/ChangeLog                      |  6 ++
 sci-astronomy/stiff/Manifest                       |  1 +
 sci-astronomy/stiff/stiff-2.4.0.ebuild             |  1 +
 sci-astronomy/stiff/stiff-9999.ebuild              | 10 ++--
 sci-astronomy/stuff/ChangeLog                      |  6 ++
 sci-astronomy/stuff/Manifest                       |  1 +
 sci-astronomy/stuff/stuff-1.26.0.ebuild            |  1 +
 sci-astronomy/stuff/stuff-9999.ebuild              |  6 +-
 sci-astronomy/swarp/ChangeLog                      |  6 ++
 sci-astronomy/swarp/Manifest                       |  1 +
 sci-astronomy/swarp/swarp-2.38.0.ebuild            |  1 +
 sci-astronomy/swarp/swarp-9999.ebuild              |  4 +-
 sci-astronomy/weightwatcher/ChangeLog              |  7 +++
 sci-astronomy/weightwatcher/Manifest               |  1 +
 .../files/weightwatcher-1.8.10-configure.patch     | 41 --------------
 .../weightwatcher/weightwatcher-1.12.ebuild        |  1 +
 .../weightwatcher/weightwatcher-9999.ebuild        |  6 +-
 sci-chemistry/unio/ChangeLog                       |  5 ++
 .../{unio-2.0.3.ebuild => unio-2.0.3-r1.ebuild}    |  5 ++
 sci-libs/libgeodecomp/ChangeLog                    |  8 +++
 sci-libs/libgeodecomp/libgeodecomp-9999.ebuild     |  5 ++
 sci-libs/libgeodecomp/metadata.xml                 |  2 +-
 sci-physics/genfit/ChangeLog                       | 19 +++++++
 sci-physics/genfit/Manifest                        |  1 +
 sci-physics/genfit/genfit-02.00.00.ebuild          | 54 ++++++++++++++++++
 sci-physics/genfit/metadata.xml                    | 31 +++++++++++
 sci-physics/vgm/ChangeLog                          |  6 +-
 sci-physics/vgm/Manifest                           |  1 +
 sci-physics/vgm/vgm-3.06.ebuild                    | 16 ++++--
 sci-visualization/gnuplot/ChangeLog                | 11 +++-
 sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild  | 64 +++-------------------
 sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild  | 50 +++--------------
 sci-visualization/visit/Manifest                   |  1 +
 ...ch => visit-2.7.2-dont_symlink_visit_dir.patch} |  0
 ...ndpython.patch => visit-2.7.2-findpython.patch} |  0
 ...1-findsilo.patch => visit-2.7.2-findsilo.patch} |  0
 ...7.1-findvtk.patch => visit-2.7.2-findvtk.patch} |  0
 ...7.1-vtklibs.patch => visit-2.7.2-vtklibs.patch} |  0
 .../{visit-2.7.1.ebuild => visit-2.7.2.ebuild}     |  0
 60 files changed, 389 insertions(+), 174 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     d295207cfcf820c62b83d56ad9d0f9fa744e6ebe
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 23 07:30:27 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Mar 23 07:30:27 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d295207c

Merge pull request #205 from olifre/master

Initial version of genfit-ebuild.


 sci-physics/genfit/ChangeLog              | 19 +++++++++++
 sci-physics/genfit/Manifest               |  1 +
 sci-physics/genfit/genfit-02.00.00.ebuild | 54 +++++++++++++++++++++++++++++++
 sci-physics/genfit/metadata.xml           | 31 ++++++++++++++++++
 4 files changed, 105 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     58712900bf2b055e71b052a2b09d3758b3eea608
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 23 13:58:04 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Mar 23 13:58:04 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=58712900

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 sci-physics/genfit/ChangeLog                       | 19 ++++++++
 sci-physics/genfit/Manifest                        |  1 +
 sci-physics/genfit/genfit-02.00.00.ebuild          | 54 ++++++++++++++++++++++
 sci-physics/genfit/metadata.xml                    | 31 +++++++++++++
 sci-physics/vgm/ChangeLog                          |  6 ++-
 sci-physics/vgm/Manifest                           |  1 +
 sci-physics/vgm/vgm-3.06.ebuild                    | 16 ++++---
 sci-visualization/visit/Manifest                   |  1 +
 ...ch => visit-2.7.2-dont_symlink_visit_dir.patch} |  0
 ...ndpython.patch => visit-2.7.2-findpython.patch} |  0
 ...1-findsilo.patch => visit-2.7.2-findsilo.patch} |  0
 ...7.1-findvtk.patch => visit-2.7.2-findvtk.patch} |  0
 ...7.1-vtklibs.patch => visit-2.7.2-vtklibs.patch} |  0
 .../{visit-2.7.1.ebuild => visit-2.7.2.ebuild}     |  0
 14 files changed, 122 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     f13508bd92de122884445d2871918ec5a58d5ef5
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 23 07:28:52 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Mar 23 07:28:52 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f13508bd

Merge pull request #206 from olifre/vgm

Address ebuild-issues: Use zip-snapshot instead of repo-tag, 


 sci-physics/vgm/ChangeLog       |  6 +++++-
 sci-physics/vgm/Manifest        |  1 +
 sci-physics/vgm/vgm-3.06.ebuild | 16 ++++++++++------
 3 files changed, 16 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     581b4892935fb3041f19785357f2b6df3b7c5ba7
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Sat Mar 22 09:50:12 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Mar 22 09:50:12 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=581b4892

merge


 dev-libs/libflatarray/ChangeLog                    |  7 ++++
 dev-libs/libflatarray/Manifest                     |  1 +
 dev-libs/libflatarray/metadata.xml                 |  2 +-
 sci-astronomy/missfits/ChangeLog                   |  6 ++++
 sci-astronomy/missfits/Manifest                    |  1 +
 sci-astronomy/missfits/missfits-2.8.0.ebuild       |  1 +
 sci-astronomy/missfits/missfits-9999.ebuild        |  6 ++--
 sci-astronomy/psfex/ChangeLog                      |  6 ++++
 sci-astronomy/psfex/Manifest                       |  1 +
 .../{psfex-3.9.1.ebuild => psfex-3.17.0.ebuild}    |  0
 sci-astronomy/psfex/psfex-9999.ebuild              |  4 +--
 sci-astronomy/sextractor/ChangeLog                 |  6 ++++
 sci-astronomy/sextractor/Manifest                  |  1 +
 sci-astronomy/sextractor/sextractor-2.19.5.ebuild  |  1 +
 sci-astronomy/sextractor/sextractor-9999.ebuild    |  6 ++--
 sci-astronomy/skymaker/ChangeLog                   |  6 ++++
 sci-astronomy/skymaker/Manifest                    |  1 +
 sci-astronomy/skymaker/skymaker-3.10.5.ebuild      |  1 +
 sci-astronomy/skymaker/skymaker-9999.ebuild        |  6 ++--
 sci-astronomy/stiff/ChangeLog                      |  6 ++++
 sci-astronomy/stiff/Manifest                       |  1 +
 sci-astronomy/stiff/stiff-2.4.0.ebuild             |  1 +
 sci-astronomy/stiff/stiff-9999.ebuild              | 10 +++---
 sci-astronomy/stuff/ChangeLog                      |  6 ++++
 sci-astronomy/stuff/Manifest                       |  1 +
 sci-astronomy/stuff/stuff-1.26.0.ebuild            |  1 +
 sci-astronomy/stuff/stuff-9999.ebuild              |  6 ++--
 sci-astronomy/swarp/ChangeLog                      |  6 ++++
 sci-astronomy/swarp/Manifest                       |  1 +
 sci-astronomy/swarp/swarp-2.38.0.ebuild            |  1 +
 sci-astronomy/swarp/swarp-9999.ebuild              |  4 +--
 sci-astronomy/weightwatcher/ChangeLog              |  7 ++++
 sci-astronomy/weightwatcher/Manifest               |  1 +
 .../files/weightwatcher-1.8.10-configure.patch     | 41 ----------------------
 .../weightwatcher/weightwatcher-1.12.ebuild        |  1 +
 .../weightwatcher/weightwatcher-9999.ebuild        |  6 ++--
 sci-biology/FLASH/ChangeLog                        |  9 +++++
 sci-biology/FLASH/FLASH-1.2.9.ebuild               | 22 ++++++++++++
 sci-biology/FLASH/Manifest                         |  1 +
 .../Bio-BigFile => sci-biology/FLASH}/metadata.xml |  0
 sci-biology/conifer/ChangeLog                      |  9 +++++
 sci-biology/conifer/Manifest                       |  1 +
 sci-biology/conifer/conifer-0.2.2.ebuild           | 25 +++++++++++++
 .../conifer}/metadata.xml                          |  0
 sci-biology/khmer/ChangeLog                        | 22 ++++++++++++
 sci-biology/khmer/Manifest                         |  1 +
 sci-biology/khmer/khmer-0.8.ebuild                 | 39 ++++++++++++++++++++
 sci-biology/khmer/khmer-9999.ebuild                | 40 +++++++++++++++++++++
 .../Bio-BigFile => sci-biology/khmer}/metadata.xml |  0
 sci-biology/samstat/ChangeLog                      |  9 +++++
 sci-biology/samstat/Manifest                       |  1 +
 .../samstat}/metadata.xml                          |  0
 sci-biology/samstat/samstat-20130708.ebuild        | 29 +++++++++++++++
 sci-biology/screed/ChangeLog                       | 10 ++++++
 sci-biology/screed/Manifest                        |  1 +
 .../screed}/metadata.xml                           |  0
 sci-biology/screed/screed-0.7.1.ebuild             | 19 ++++++++++
 sci-chemistry/shiftx2/ChangeLog                    |  5 ++-
 .../shiftx2/shiftx2-1.07_p20120106.ebuild          |  2 +-
 sci-chemistry/unio/ChangeLog                       |  5 +++
 .../{unio-2.0.3.ebuild => unio-2.0.3-r1.ebuild}    |  5 +++
 sci-libs/armadillo/ChangeLog                       |  6 ++++
 sci-libs/armadillo/Manifest                        |  2 +-
 ...llo-4.000.3.ebuild => armadillo-4.100.2.ebuild} |  0
 sci-libs/libgeodecomp/ChangeLog                    |  8 +++++
 sci-libs/libgeodecomp/libgeodecomp-9999.ebuild     |  3 +-
 sci-libs/libgeodecomp/metadata.xml                 |  2 +-
 67 files changed, 367 insertions(+), 72 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     e14f436ac3b4f078960a97435292ba338c306b12
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Sat Mar 22 09:50:27 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Mar 22 09:50:27 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e14f436a

Merge /usr/local/portage/andis_overlay


 sci-visualization/visit/Manifest                                         | 1 +
 ..._symlink_visit_dir.patch => visit-2.7.2-dont_symlink_visit_dir.patch} | 0
 .../files/{visit-2.7.1-findpython.patch => visit-2.7.2-findpython.patch} | 0
 .../files/{visit-2.7.1-findsilo.patch => visit-2.7.2-findsilo.patch}     | 0
 .../visit/files/{visit-2.7.1-findvtk.patch => visit-2.7.2-findvtk.patch} | 0
 .../visit/files/{visit-2.7.1-vtklibs.patch => visit-2.7.2-vtklibs.patch} | 0
 sci-visualization/visit/{visit-2.7.1.ebuild => visit-2.7.2.ebuild}       | 1 +
 7 files changed, 2 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     5b8cf7c40658b3147cac7bf1e7309dcf4b172ed5
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 22 10:03:19 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Mar 22 10:03:19 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5b8cf7c4

Merge pull request #204 from gentryx/master

Updated ebuild for VisIt to 2.7.2


 sci-visualization/visit/Manifest                                         | 1 +
 ..._symlink_visit_dir.patch => visit-2.7.2-dont_symlink_visit_dir.patch} | 0
 .../files/{visit-2.7.1-findpython.patch => visit-2.7.2-findpython.patch} | 0
 .../files/{visit-2.7.1-findsilo.patch => visit-2.7.2-findsilo.patch}     | 0
 .../visit/files/{visit-2.7.1-findvtk.patch => visit-2.7.2-findvtk.patch} | 0
 .../visit/files/{visit-2.7.1-vtklibs.patch => visit-2.7.2-vtklibs.patch} | 0
 sci-visualization/visit/{visit-2.7.1.ebuild => visit-2.7.2.ebuild}       | 0
 7 files changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     7a05af9b65c8a39edd17e84d73d66c3f754a1d44
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Sat Mar 22 09:44:53 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Mar 22 09:44:53 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7a05af9b

Merge /usr/local/portage/andis_overlay


 sci-libs/libgeodecomp/libgeodecomp-9999.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5c934f9a41f943341fd4eb00403068f91d0fb355
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 22 09:45:03 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Mar 22 09:45:03 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5c934f9a

Merge remote-tracking branch 'github/master'

* github/master:
  sci-astronomy/weightwatcher: Add new version linked to live one
  sci-astronomy/swarp: Add new version linked to live one
  sci-astronomy/stuff: Add new version linked to live one
  sci-astronomy/stiff: Add new version linked to live one
  sci-astronomy/skymaker: Add new version linked to live one
  sci-astronomy/sextractor: Add new version linked to live one
  sci-astronomy/psfex: Add new version linked to live one
  sci-astronomy/missfits: Add new version linked to live one
  sci-chemistry/unio: Add symlinks for all apps
  sci-biology/khmer: Drop nose requirement during build
  sci-chemistry/shiftx2: Drop python2.6 support
  sci-libs/armadillo: Version bump
  sci-biology/screed: New addition written by me
  sci-biology/khmer: Unbundle zlib and bzpi2; bump to disturils-r1; respect CFLAGS
  sci-biology/samstat: new package
  sci-biology/khmer: revert to distutils to obey sandbox violation
  sci-biology/khmer: new package
  sci/biology/FLASH: new package
  sci-biology/conifer: new package

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c8fcc489c48ef3dbed8f4ff532e717b22769e7b4
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Mon Mar 17 07:00:05 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Mar 17 07:00:05 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c8fcc489

Merge /usr/local/portage/andis_overlay


 dev-libs/libflatarray/metadata.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     3a51163e4ade6bf734ef975ab35fd0b1ac4e808a
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Mon Mar 17 06:57:53 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Mar 17 06:57:53 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3a51163e

Merge https://github.com/gentoo-science/sci


 app-editors/neovim/ChangeLog                       |    9 +
 .../omniorbpy => app-editors/neovim}/metadata.xml  |    0
 app-editors/neovim/neovim-9999.ebuild              |   29 +
 app-text/jabref/ChangeLog                          |    5 +
 app-text/jabref/Manifest                           |    1 +
 ...ref-2.10_beta2-r1.ebuild => jabref-2.10.ebuild} |    2 +-
 dev-java/glazedlists/ChangeLog                     |   12 +
 dev-java/glazedlists/Manifest                      |    1 +
 .../files/glazedlists-1.8.0-build.xml.patch        |   57 +
 dev-java/glazedlists/glazedlists-1.8.0.ebuild      |   50 +
 .../utf8proc => dev-java/glazedlists}/metadata.xml |    2 +-
 dev-lang/vtune/ChangeLog                           |    7 +-
 dev-lang/vtune/Manifest                            |    1 +
 ...2.305106.ebuild => vtune-13.1.13.313935.ebuild} |    4 +-
 dev-python/healpy/ChangeLog                        |    6 +
 dev-python/healpy/Manifest                         |    2 +-
 .../{healpy-1.7.3.ebuild => healpy-1.7.4.ebuild}   |    0
 dev-python/theano/ChangeLog                        |   12 -
 dev-python/theano/Manifest                         |    1 -
 dev-python/theano/metadata.xml                     |   13 -
 dev-python/theano/theano-0.6.0_rc3.ebuild          |   33 -
 dev-util/intel-ocl-sdk/ChangeLog                   |    7 +-
 dev-util/intel-ocl-sdk/Manifest                    |    1 +
 ...385.ebuild => intel-ocl-sdk-3.2.1.16712.ebuild} |    6 +-
 profiles/package.mask                              |   43 -
 profiles/updates/1Q-2014                           |    1 +
 sci-astronomy/astrometry/ChangeLog                 |    5 +-
 sci-astronomy/astrometry/astrometry-0.43.ebuild    |   18 +-
 sci-astronomy/eye/ChangeLog                        |    8 +-
 sci-astronomy/eye/Manifest                         |    1 -
 sci-astronomy/eye/eye-1.4.1.ebuild                 |   32 -
 sci-astronomy/eye/eye-9999.ebuild                  |   16 +-
 sci-astronomy/eye/files/eye-1.4.1-configure.patch  |   58 -
 sci-astronomy/eye/metadata.xml                     |    4 +-
 sci-astronomy/missfits/ChangeLog                   |    8 +-
 sci-astronomy/missfits/Manifest                    |    1 -
 .../missfits/files/missfits-2.4.0-configure.patch  |  108 -
 sci-astronomy/missfits/missfits-2.4.0.ebuild       |   29 -
 sci-astronomy/missfits/missfits-9999.ebuild        |   11 +-
 sci-astronomy/psfex/ChangeLog                      |    8 +-
 sci-astronomy/psfex/metadata.xml                   |   10 +-
 sci-astronomy/psfex/psfex-3.9.1-r1.ebuild          |   54 -
 sci-astronomy/psfex/psfex-3.9.1.ebuild             |    1 +
 sci-astronomy/psfex/psfex-9999.ebuild              |   28 +-
 sci-astronomy/scamp/ChangeLog                      |    7 +-
 sci-astronomy/scamp/metadata.xml                   |   10 +-
 sci-astronomy/scamp/scamp-1.7.0-r2.ebuild          |   24 +-
 sci-astronomy/scamp/scamp-9999.ebuild              |   26 +-
 sci-astronomy/sextractor/ChangeLog                 |    7 +-
 .../sextractor/sextractor-2.8.6-r1.ebuild          |    5 +-
 sci-astronomy/sextractor/sextractor-9999.ebuild    |   24 +-
 sci-astronomy/skymaker/ChangeLog                   |    7 +-
 sci-astronomy/skymaker/Manifest                    |    1 -
 .../skymaker/files/skymaker-configure.patch        |   40 -
 sci-astronomy/skymaker/skymaker-3.3.3.ebuild       |   27 -
 sci-astronomy/skymaker/skymaker-9999.ebuild        |   15 +-
 sci-astronomy/stiff/ChangeLog                      |    7 +-
 sci-astronomy/stiff/metadata.xml                   |    4 +-
 sci-astronomy/stiff/stiff-9999.ebuild              |    3 +-
 sci-astronomy/stuff/ChangeLog                      |    7 +-
 sci-astronomy/stuff/Manifest                       |    1 -
 sci-astronomy/stuff/files/stuff-configure.patch    |   65 -
 sci-astronomy/stuff/stuff-1.19.ebuild              |   27 -
 sci-astronomy/stuff/stuff-9999.ebuild              |   15 +-
 sci-astronomy/swarp/ChangeLog                      |    5 +-
 sci-astronomy/swarp/swarp-9999.ebuild              |   19 +-
 sci-astronomy/weightwatcher/ChangeLog              |    7 +-
 sci-astronomy/weightwatcher/Manifest               |    1 -
 .../weightwatcher/weightwatcher-1.8.10.ebuild      |   29 -
 .../weightwatcher/weightwatcher-9999.ebuild        |   13 +-
 sci-chemistry/coot/coot-9999.ebuild                |    2 +-
 sci-chemistry/freeon/ChangeLog                     |    7 +
 sci-chemistry/freeon/Manifest                      |    4 -
 sci-chemistry/freeon/freeon-1.0.4.ebuild           |   33 -
 sci-chemistry/freeon/freeon-1.0.5.ebuild           |   33 -
 sci-chemistry/freeon/freeon-1.0.6.ebuild           |   33 -
 sci-chemistry/freeon/freeon-1.0.7.ebuild           |   25 -
 sci-chemistry/freeon/freeon-9999.ebuild            |    4 +-
 sci-chemistry/gromacs/ChangeLog                    |    6 +
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild      |    2 +-
 sci-chemistry/gromacs/gromacs-9999.ebuild          |    6 +-
 sci-chemistry/phenix-bin/ChangeLog                 |    5 +-
 .../phenix-bin/phenix-bin-1.8.4.1496.ebuild        |    7 +-
 sci-chemistry/pymol/pymol-9999.ebuild              |    2 +-
 sci-chemistry/ucsf-tools/ChangeLog                 |   11 -
 sci-chemistry/ucsf-tools/Manifest                  |    2 -
 sci-chemistry/ucsf-tools/metadata.xml              |    5 -
 sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild    |   43 -
 sci-chemistry/usf-tools/usf-tools-9999.ebuild      |    2 +-
 sci-chemistry/votca-csg/votca-csg-9999.ebuild      |    2 +-
 .../votca-csgapps/votca-csgapps-9999.ebuild        |    2 +-
 sci-libs/blastdb/blastdb-9999.ebuild               |    2 +-
 sci-libs/dealii/ChangeLog                          |    9 +
 sci-libs/dealii/dealii-8.0.0.ebuild                |    2 +-
 sci-libs/dealii/dealii-8.1.0.ebuild                |  118 +-
 sci-libs/dealii/dealii-9999.ebuild                 |   46 +-
 sci-libs/dealii/metadata.xml                       |    2 +-
 sci-libs/libsc/ChangeLog                           |    9 +
 sci-libs/libsc/Manifest                            |    1 +
 .../libsc-0.7.3.ebuild}                            |   38 +-
 sci-libs/{factory => libsc}/metadata.xml           |    8 +-
 sci-libs/mkl/ChangeLog                             |    7 +-
 sci-libs/mkl/Manifest                              |    1 +
 ...-11.1.0.080-r1.ebuild => mkl-11.1.1.106.ebuild} |    4 +-
 sci-libs/o2scl/ChangeLog                           |    8 +-
 sci-libs/o2scl/Manifest                            |    2 +-
 .../{o2scl-0.913.ebuild => o2scl-0.914.ebuild}     |    0
 sci-libs/openlibm/openlibm-9999.ebuild             |    3 +-
 sci-libs/p4est/ChangeLog                           |   11 +
 sci-libs/p4est/Manifest                            |    1 +
 ...l-fix.patch => p4est-0.3.4.2-libtool-fix.patch} |    0
 .../p4est-0.3.5-add_missing_autotools_files.patch  | 2535 ++++++++++++++++++++
 sci-libs/p4est/p4est-0.3.4.2.ebuild                |    4 +-
 .../{p4est-0.3.4.2.ebuild => p4est-0.3.5.ebuild}   |   29 +-
 sci-libs/pagmo/pagmo-9999.ebuild                   |    2 +-
 sci-libs/pmx/ChangeLog                             |    3 +
 sci-libs/pmx/pmx-9999.ebuild                       |   12 +-
 sci-libs/spglib/ChangeLog                          |   14 +
 sci-libs/spglib/Manifest                           |    1 +
 sci-libs/spglib/files/spglib-openmp.patch          |   22 +
 .../scirenderer => sci-libs/spglib}/metadata.xml   |    6 +-
 sci-libs/spglib/spglib-1.6.0.ebuild                |   34 +
 sci-libs/votca-tools/votca-tools-9999.ebuild       |    2 +-
 sci-mathematics/frama-c/ChangeLog                  |    8 +-
 sci-mathematics/frama-c/Manifest                   |    1 +
 sci-mathematics/frama-c/files/frama-c-make.patch   |   12 +
 .../frama-c/files/frama-c-ocaml-4.01.patch         |  145 ++
 ...a-c-20120901.ebuild => frama-c-20130601.ebuild} |   14 +-
 sci-mathematics/mdp/mdp-9999.ebuild                |    2 +-
 sci-mathematics/z3/ChangeLog                       |    8 +-
 sci-mathematics/z3/z3-9999.ebuild                  |    3 +-
 .../elmer-meshgen2d/elmer-meshgen2d-9999.ebuild    |    2 +-
 sci-visualization/visit/visit-2.7.1.ebuild         |    1 -
 sys-cluster/charm/ChangeLog                        |    8 +
 sys-cluster/charm/Manifest                         |    1 +
 ...-6.6.0_rc1-r1.ebuild => charm-6.6.0_rc2.ebuild} |    4 +-
 sys-cluster/lustre/ChangeLog                       |   15 +
 ...ld-make-AC-check-for-linux-arch-sandbox-f.patch |    2 +-
 ...cfs-update-zfs-proc-handling-to-seq_files.patch |   10 +-
 ...rocfs-move-mgs-proc-handling-to-seq_files.patch |    2 +-
 .../0004-LU-3319-procfs-fix-symlink-handling.patch |   26 +-
 ...rocfs-move-osp-proc-handling-to-seq_files.patch |   26 +-
 ...rocfs-move-lod-proc-handling-to-seq_files.patch |   14 +-
 ...cfs-move-mdd-ofd-proc-handling-to-seq_fil.patch |  133 +-
 ...cfs-move-mdt-mds-proc-handling-to-seq_fil.patch |   20 +-
 ...cfs-update-ldiskfs-proc-handling-to-seq_f.patch |   38 +-
 ...0010-LU-3319-lprocfs-client-side-cleanups.patch |    8 +-
 ...-LU-3974-llite-use-new-struct-dir_context.patch |   20 +-
 ...-LU-3974-llite-invalidatepage-api-changed.patch |    2 +-
 149 files changed, 3657 insertions(+), 1141 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     643319497854c35ed2791950f93835d4621326f1
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 18 20:17:52 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Mar 18 20:17:52 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=64331949

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-biology/khmer/ChangeLog                        |  6 ++++
 sci-biology/khmer/Manifest                         |  1 +
 sci-biology/khmer/khmer-0.8.ebuild                 | 38 ++++++++++++++++++++++
 sci-biology/khmer/khmer-9999.ebuild                | 21 ++++++++++--
 sci-biology/screed/ChangeLog                       | 10 ++++++
 sci-biology/screed/Manifest                        |  1 +
 .../screed}/metadata.xml                           |  0
 sci-biology/screed/screed-0.7.1.ebuild             | 19 +++++++++++
 8 files changed, 94 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     c4669fc3e62b672c899f2de52bb48b12563a8a3a
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Mar 17 16:32:32 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Mar 17 16:32:32 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c4669fc3

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-astronomy/astrometry/ChangeLog              |  5 ++++-
 sci-astronomy/astrometry/astrometry-0.43.ebuild | 18 +++++++++++++-----
 2 files changed, 17 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     3b82c56618ddd200e2e48c21a669e9f5bf4250df
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 18 19:26:31 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 18 19:26:31 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3b82c566

Merge remote-tracking branch 'github/master'

* github/master:
  Use python-single-r1 and fix typo for USE=extra


 sci-astronomy/astrometry/ChangeLog              |  5 ++++-
 sci-astronomy/astrometry/astrometry-0.43.ebuild | 18 +++++++++++++-----
 2 files changed, 17 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     55f47fef68aab56d7401983a1c1f2d8d9a712125
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Mon Mar 17 00:46:37 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Mar 17 00:46:37 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=55f47fef

Merge pull request #202 from sargas/astrometry

Use python-single-r1 and fix typo for USE=extra


 sci-astronomy/astrometry/ChangeLog              |  5 ++++-
 sci-astronomy/astrometry/astrometry-0.43.ebuild | 18 +++++++++++++-----
 2 files changed, 17 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     f5cc74af500062cf4840e213a006ed86222d2014
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Mon Mar  3 18:52:59 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Mar  3 18:52:59 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f5cc74af

Merge pull request #201 from xhochy/intel-ocl-sdk-3.2.1.16712

[intel-ocl-sdk] Bump to 3.2.1.16712


 dev-util/intel-ocl-sdk/ChangeLog                                   | 7 ++++++-
 dev-util/intel-ocl-sdk/Manifest                                    | 1 +
 ...ocl-sdk-3.1.1.11385.ebuild => intel-ocl-sdk-3.2.1.16712.ebuild} | 6 +++---
 3 files changed, 10 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     a7d3da5e7b85995850f39e481c3e46f82293a861
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Sun Mar  2 22:19:32 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Sun Mar  2 22:19:32 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a7d3da5e

Merge pull request #200 from tamiko/minor_fixups_for_dealii

Minor fixups for dealii


 sci-libs/dealii/ChangeLog           |   9 +++
 sci-libs/dealii/dealii-8.0.0.ebuild |   2 +-
 sci-libs/dealii/dealii-8.1.0.ebuild | 118 +++++++++++++++++++++++++++++++++++-
 sci-libs/dealii/dealii-9999.ebuild  |  46 ++++----------
 sci-libs/dealii/metadata.xml        |   2 +-
 5 files changed, 140 insertions(+), 37 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     870c1f0e8d736e3741e5d2289bc29f7e9df13d15
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Sun Mar  2 18:59:14 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Sun Mar  2 18:59:14 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=870c1f0e

Merge pull request #199 from tamiko/bump_p4est

Bump p4est; new ebuild for libsc


 sci-libs/libsc/ChangeLog                           |    9 +
 sci-libs/libsc/Manifest                            |    1 +
 .../libsc-0.7.3.ebuild}                            |   38 +-
 sci-libs/{factory => libsc}/metadata.xml           |    8 +-
 sci-libs/p4est/ChangeLog                           |   11 +
 sci-libs/p4est/Manifest                            |    1 +
 ...l-fix.patch => p4est-0.3.4.2-libtool-fix.patch} |    0
 .../p4est-0.3.5-add_missing_autotools_files.patch  | 2535 ++++++++++++++++++++
 sci-libs/p4est/p4est-0.3.4.2.ebuild                |    4 +-
 .../{p4est-0.3.4.2.ebuild => p4est-0.3.5.ebuild}   |   29 +-
 10 files changed, 2609 insertions(+), 27 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a783a7b7b0afed4b03c9377d0b960d592aa085dc
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 21 16:19:06 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Feb 21 16:19:06 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a783a7b7

Merge remote-tracking branch 'github/master'

* github/master:
  simplified path setting for access daemon
  merged sed commands into one
  switched to saner prefix for access daemon
  now using correct prefix for install prefix
  fixed download link
  dropped superfluous patch and related use flag from likwid 3.1.1
  renamed patch to include version number
  renamed patch to include version number
  added ebuild/patches for likwid-3.1.1


 sys-apps/likwid/Manifest                           |  1 +
 .../files/{likwid.patch => likwid-3.0-paths.patch} |  0
 sys-apps/likwid/files/likwid-3.1.1-paths.patch     | 22 ++++++++++++++++++++++
 .../likwid/files/likwid-3.1.1-shared_lib.patch     | 12 ++++++++++++
 sys-apps/likwid/likwid-3.0.ebuild                  |  2 +-
 .../{likwid-3.0.ebuild => likwid-3.1.1.ebuild}     | 15 +++++++--------
 6 files changed, 43 insertions(+), 9 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ecc578c7b67f79304a0eba5cd669bcfe8d8ff4c0
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Thu Feb 20 20:50:19 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Feb 20 20:50:19 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ecc578c7

Merge pull request #195 from gentryx/master

Updated ebuilds for Likwid


 sys-apps/likwid/Manifest                           |  1 +
 .../files/{likwid.patch => likwid-3.0-paths.patch} |  0
 sys-apps/likwid/files/likwid-3.1.1-paths.patch     | 22 ++++++++++++++++++++++
 .../likwid/files/likwid-3.1.1-shared_lib.patch     | 12 ++++++++++++
 sys-apps/likwid/likwid-3.0.ebuild                  |  2 +-
 .../{likwid-3.0.ebuild => likwid-3.1.1.ebuild}     | 15 +++++++--------
 6 files changed, 43 insertions(+), 9 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     e07504d34caf5bdb816f3db4db98bfad109fed95
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed Feb 19 01:22:43 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 19 01:22:43 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e07504d3

Merge /usr/local/portage/andis_overlay


 sys-apps/likwid/files/likwid-3.1.1-paths.patch | 7 +------
 sys-apps/likwid/likwid-3.1.1.ebuild            | 4 ++--
 2 files changed, 3 insertions(+), 8 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     7afad7a8f21779b7fc12c5832e3dae121ce1cd7f
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed Feb 19 01:14:38 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 19 01:14:38 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7afad7a8

Merge /usr/local/portage/andis_overlay


 sys-apps/likwid/likwid-3.1.1.ebuild | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     af5fb18841469d76274166e75223f13c4d92acbd
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed Feb 19 00:47:46 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 19 00:47:46 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=af5fb188

Merge /usr/local/portage/andis_overlay


 sys-apps/likwid/files/likwid-3.1.1-paths.patch | 2 +-
 sys-apps/likwid/likwid-3.1.1.ebuild            | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     1c2ef69b02228f0689cb1216b8b502d8426111d0
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed Feb 19 00:01:55 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 19 00:01:55 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1c2ef69b

Merge /usr/local/portage/andis_overlay


 sys-apps/likwid/Manifest                           |  1 +
 .../files/{likwid.patch => likwid-3.0-paths.patch} |  0
 sys-apps/likwid/files/likwid-3.1.1-paths.patch     | 27 ++++++++++++++++++++++
 .../likwid/files/likwid-3.1.1-shared_lib.patch     | 12 ++++++++++
 sys-apps/likwid/likwid-3.0.ebuild                  |  2 +-
 .../{likwid-3.0.ebuild => likwid-3.1.1.ebuild}     | 11 ++++-----
 6 files changed, 46 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     0482bace62aa8960784f7650bae968969480d479
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Thu Feb 20 18:33:21 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Thu Feb 20 18:33:21 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0482bace

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-chemistry/gromacs/ChangeLog           | 3 +++
 sci-chemistry/gromacs/gromacs-9999.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     f03cc52282f9c8143ce3be1e9fbd258c7a65e410
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 19 07:59:24 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Wed Feb 19 07:59:24 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f03cc522

Merge pull request #196 from ustcscgy/visit

sci-visualization/visit: remove redundant dependency


 sci-visualization/visit/visit-2.7.1.ebuild | 1 -
 1 file changed, 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     2f68e5ea68f9a9d3c8fc7c301b21d0cd712b67e9
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 17 04:49:06 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Feb 17 04:49:06 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2f68e5ea

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-chemistry/gromacs/ChangeLog                           |  3 +++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild             | 10 +++++-----
 sci-libs/armadillo/ChangeLog                              |  7 ++++---
 sci-libs/armadillo/Manifest                               |  1 +
 sci-libs/armadillo/armadillo-4.000.3.ebuild               |  1 -
 ...{armadillo-4.000.3.ebuild => armadillo-4.000.4.ebuild} |  1 -
 sci-libs/armadillo/files/armadillo-opt_wrapper.patch      | 15 ---------------
 sci-physics/espresso++/ChangeLog                          |  3 +++
 sci-physics/espresso++/espresso++-9999.ebuild             |  7 ++++++-
 9 files changed, 22 insertions(+), 26 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Reinis Danne]

commit:     499c23ae09f46f7906960825ac09a42594ee91fd
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Sat Feb 15 23:49:49 2014 +0000
Commit:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Sat Feb 15 23:49:49 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=499c23ae

Merge pull request #192 from Reinis/fix_mlpack_test_build

sci-libs/mlpack: Fix build with FEATURES=test


 sci-libs/mlpack/ChangeLog                         |  4 ++++
 sci-libs/mlpack/files/mlpack-1.0.8-uint32_t.patch | 16 ++++++++++++++++
 sci-libs/mlpack/mlpack-1.0.8.ebuild               |  4 +++-
 3 files changed, 23 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Reinis Danne]

commit:     5ed90a02f0196b790d969b2f26dfc7a3462f453b
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Sat Feb 15 23:48:58 2014 +0000
Commit:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Sat Feb 15 23:48:58 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5ed90a02

Merge pull request #191 from Reinis/arma_no_wrapper

sci-libs/armadillo: Add patch with option to disable wrapper


 sci-libs/armadillo/ChangeLog                         |  4 ++++
 sci-libs/armadillo/armadillo-4.000.3.ebuild          |  1 +
 sci-libs/armadillo/files/armadillo-opt_wrapper.patch | 15 +++++++++++++++
 3 files changed, 20 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Reinis Danne]

commit:     4c920ad2a4e9ae8ce39fd19bf9e10ae5200e3cb9
Author:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
AuthorDate: Fri Feb 14 18:18:46 2014 +0000
Commit:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Fri Feb 14 18:18:46 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4c920ad2

Merge github.com:gentoo-science/sci


 sci-astronomy/casapy-bin/ChangeLog                                  | 6 ++++++
 sci-astronomy/casapy-bin/Manifest                                   | 1 +
 ...n-4.2.0_pre10_p1.ebuild => casapy-bin-4.2.0.28322.021_p1.ebuild} | 5 +++--
 3 files changed, 10 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Reinis Danne]

commit:     fdaf4148720d38a69ae5644fed000c8d5d14d84d
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Thu Feb 13 18:16:46 2014 +0000
Commit:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Thu Feb 13 18:16:46 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fdaf4148

Merge pull request #190 from sargas/casapy-4.2-bump

sci-astronomy/casapy-bin: Version Bump


 sci-astronomy/casapy-bin/ChangeLog                                  | 6 ++++++
 sci-astronomy/casapy-bin/Manifest                                   | 1 +
 ...n-4.2.0_pre10_p1.ebuild => casapy-bin-4.2.0.28322.021_p1.ebuild} | 5 +++--
 3 files changed, 10 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     09ce860f19b899ef5cbc25705320195fa0ffe1f9
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Sun Feb  9 01:47:08 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Sun Feb  9 01:47:08 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=09ce860f

Merge pull request #187 from xhochy/julia-prefix

[dev-lang/julia] PREFIX is now prefix


 dev-lang/julia/ChangeLog         | 3 +++
 dev-lang/julia/julia-9999.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     9de8955dc583b938473febeeb20ef3864d4bace2
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Thu Feb  6 19:47:52 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Thu Feb  6 19:47:52 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9de8955d

Merge branch 'master' of github.com:gentoo-science/sci


 dev-python/pywcsgrid2/ChangeLog                    | 12 ++++
 dev-python/pywcsgrid2/metadata.xml                 | 11 ++++
 dev-python/pywcsgrid2/pywcsgrid2-9999.ebuild       | 25 ++++++++
 profiles/package.mask                              |  1 +
 sci-astronomy/casapy-bin/ChangeLog                 |  9 +++
 sci-astronomy/casapy-bin/Manifest                  |  1 +
 .../casapy-bin/casapy-bin-4.2.0_pre10_p1.ebuild    | 68 ++++++++++++++++++++++
 sci-astronomy/casapy-bin/metadata.xml              | 10 ++++
 8 files changed, 137 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     856f7fd45376dcdc0ff150511e255f83264262ca
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Wed Feb  5 20:10:02 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Wed Feb  5 20:10:02 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=856f7fd4

Merge pull request #184 from sargas/casapy

sci-astronomy/casapy-bin: Add ebuild for casapy


 sci-astronomy/casapy-bin/ChangeLog                 |  9 +++
 sci-astronomy/casapy-bin/Manifest                  |  1 +
 .../casapy-bin/casapy-bin-4.2.0_pre10_p1.ebuild    | 68 ++++++++++++++++++++++
 sci-astronomy/casapy-bin/metadata.xml              | 10 ++++
 4 files changed, 88 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     998c4c7ff8c4300e630f0bb600820df5d01febf8
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Wed Feb  5 20:06:20 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Wed Feb  5 20:06:20 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=998c4c7f

Merge pull request #186 from sargas/pywcsgrid2

dev-python/pywcsgrid2: Add ebuild for git version of pywcsgrid2


 dev-python/pywcsgrid2/ChangeLog              | 12 ++++++++++++
 dev-python/pywcsgrid2/metadata.xml           | 11 +++++++++++
 dev-python/pywcsgrid2/pywcsgrid2-9999.ebuild | 25 +++++++++++++++++++++++++
 profiles/package.mask                        |  1 +
 4 files changed, 49 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     d4296028031b43115b922b13a6154164ce0a3a26
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Wed Feb  5 04:38:13 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Wed Feb  5 04:38:13 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d4296028

Merge branch 'master' of github.com:gentoo-science/sci

Conflicts:
	sci-physics/lammps/ChangeLog
	sci-physics/lammps/lammps-20140201.ebuild


 sci-physics/lammps/ChangeLog               | 4 ++--
 sci-visualization/visit/visit-2.7.1.ebuild | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     c11973e9a47feb7d6a5399b257d92661bdf1d6e2
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Tue Feb  4 22:28:53 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Tue Feb  4 22:28:53 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c11973e9

Merge /usr/local/portage/andis_overlay


 sci-visualization/visit/visit-2.7.1.ebuild | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     d2fbe4e17b78187fa5efca81d4e493983dd184b7
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Tue Feb  4 22:32:16 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Tue Feb  4 22:32:16 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d2fbe4e1

Merge pull request #185 from gentryx/master

added debug and threads use flags to VisIt


 sci-visualization/visit/visit-2.7.1.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     4699286b40f5015a4041568ffc38fd983d905ecd
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Tue Feb  4 22:04:51 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Tue Feb  4 22:04:51 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4699286b

Merge https://github.com/gentoo-science/sci


 dev-python/healpy/ChangeLog                              |  8 +++++++-
 dev-python/healpy/Manifest                               |  2 +-
 .../healpy/{healpy-1.6.2.ebuild => healpy-1.7.3.ebuild}  |  2 +-
 dev-python/healpy/metadata.xml                           |  3 +++
 sci-astronomy/chealpix/ChangeLog                         |  8 +++++++-
 sci-astronomy/chealpix/Manifest                          |  2 +-
 .../{chealpix-3.11.ebuild => chealpix-3.11.2.ebuild}     | 10 ++--------
 sci-astronomy/healpix_cxx/ChangeLog                      |  8 +++++++-
 sci-astronomy/healpix_cxx/Manifest                       |  2 +-
 ...healpix_cxx-3.11.ebuild => healpix_cxx-3.11.2.ebuild} | 16 +++++-----------
 sci-libs/atlas/ChangeLog                                 |  6 +++++-
 sci-libs/atlas/atlas-3.10.1-r1.ebuild                    |  2 +-
 sci-libs/atlas/atlas-3.10.1-r2.ebuild                    |  2 +-
 sci-physics/geant-vmc/ChangeLog                          |  5 +++++
 sci-physics/geant-vmc/geant-vmc-4.2.14b.ebuild           |  2 +-
 sci-physics/geant-vmc/geant-vmc-4.2.15.ebuild            |  2 +-
 sci-physics/lammps/Manifest                              |  2 +-
 17 files changed, 50 insertions(+), 32 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     b406a6e8a7d82ce30b809fbc537a8c10dfd72d47
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Sun Feb  2 23:25:43 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Sun Feb  2 23:25:43 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b406a6e8

Merge pull request #183 from olifre/master

Make header installation work again


 sci-physics/geant-vmc/ChangeLog                | 5 +++++
 sci-physics/geant-vmc/geant-vmc-4.2.14b.ebuild | 2 +-
 sci-physics/geant-vmc/geant-vmc-4.2.15.ebuild  | 2 +-
 3 files changed, 7 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Reinis Danne]

commit:     37f148f61177cc1a5d25e4f093281e2bdd4c9829
Author:     Justin <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Feb  2 08:50:52 2014 +0000
Commit:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Sun Feb  2 08:50:52 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=37f148f6

Merge pull request #182 from gentryx/master

added use-flags for silo and netcdf to VisIt


 .../visit/files/visit-2.7.1-findsilo.patch            | 12 ++++++++++++
 sci-visualization/visit/metadata.xml                  |  3 +++
 sci-visualization/visit/visit-2.7.1.ebuild            | 19 ++++++++++++++-----
 3 files changed, 29 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Reinis Danne]

commit:     3ca6bd749548f22479211bd96621ac415126778c
Author:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
AuthorDate: Sun Feb  2 16:59:33 2014 +0000
Commit:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Sun Feb  2 16:59:33 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3ca6bd74

Merge github.com:gentoo-science/sci


 .../visit/files/visit-2.7.1-findsilo.patch            | 12 ++++++++++++
 sci-visualization/visit/metadata.xml                  |  3 +++
 sci-visualization/visit/visit-2.7.1.ebuild            | 19 ++++++++++++++-----
 3 files changed, 29 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Reinis Danne]

commit:     79571933bc8708ed73dd48aed08066d5c331326b
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Sun Feb  2 07:49:21 2014 +0000
Commit:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Sun Feb  2 07:49:21 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=79571933

Merge /usr/local/portage/andis_overlay


 .../visit/files/visit-2.7.1-findsilo.patch            | 12 ++++++++++++
 sci-visualization/visit/metadata.xml                  |  3 +++
 sci-visualization/visit/visit-2.7.1.ebuild            | 19 ++++++++++++++-----
 3 files changed, 29 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     670fbb56a906bfdd68fffbeb458354ebcb996054
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Sat Feb  1 23:06:10 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Sat Feb  1 23:06:10 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=670fbb56

Merge branch 'master' of github.com:gentoo-science/sci


 sci-libs/silo/silo-4.9.1.ebuild | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     54c3d36e9e8a6d98694feb49df8b220e7d62d558
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Sat Feb  1 22:38:15 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Sat Feb  1 22:38:15 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=54c3d36e

Merge pull request #181 from gentryx/master

Resolved two minor issues in the Silo ebuild


 sci-libs/silo/silo-4.9.1.ebuild | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     c7b4a91a8a297ef5cf28b48ef15f7ee051d4035c
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Sat Feb  1 21:27:04 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Sat Feb  1 21:27:04 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c7b4a91a

Merge /usr/local/portage/andis_overlay


 sci-libs/silo/silo-4.9.1.ebuild | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5614ffab3d353ff5506040b3005a5458b36c48be
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 29 11:39:25 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jan 29 11:39:25 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5614ffab

Be more precise on the branching

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 CONTRIBUTING.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 8f02ccc..99561d0 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -64,9 +64,9 @@ In order to send pull request and ask for inclusion of your changes you need to
     hub fork
 
 ###Branch out for contribution
-It is always convenient for development as well as for the review and merging process, if the development is done in branches.
+It is always convenient for development as well as for the review and merging process, if the development is done in branches. Let's branch the overlay into a local branch named PACKAGE_NAME.
 
-    git checkout -b my-feature master
+    git checkout -b PACKAGE_NAME master
 
 For the fastest process during merging it is best to have a single branch per package.
 
@@ -83,9 +83,9 @@ Once *all* reported problems are resolved, you can commit it
     repo-commit "Here we write a comprehensible commit message"
 
 ###Push to Github and make a pull request
-Next we push back the changes to our fork and send a pull-request to the overlay maintainers.
+Next we push back the changes in the PACKAGE_NAME branch to our fork and send a pull-request to the overlay maintainers.
 
-    hub push YOUR_GITHUB_USER
+    hub push YOUR_GITHUB_USER PACKAGE_NAME
     hub pull-request
 
 Lastly you need to wait for review comments and the merge of your work. If you feel that they are slacking, don't bother to ping them again. In case you need to include some improvements, just commit your work again using *repo-commit* and push it again to your fork. No need to send another pull-request as your new changes will be added to the original one.

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     409af0e21620744afad8881fee12eb03381d90ce
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed Jan 29 07:57:50 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jan 29 07:57:50 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=409af0e2

Merge /usr/local/portage/andis_overlay


 sci-visualization/visit/visit-2.7.1.ebuild | 1 +
 1 file changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     06981272b078338e233d43bc7a9718b1e479d33b
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed Jan 29 09:12:49 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jan 29 09:12:49 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=06981272

Merge /usr/local/portage/andis_overlay


 sci-visualization/visit/visit-2.7.1.ebuild | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     09df0fea2d50a612a4a17f9dcac3835d7d3a9935
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed Jan 29 07:56:14 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jan 29 07:56:14 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=09df0fea

Merge https://github.com/gentoo-science/sci


 CONTRIBUTING.md                                    | 147 ++++++++++++++++++++-
 README.md                                          |  13 +-
 app-text/jabref/ChangeLog                          |   5 +
 app-text/jabref/jabref-2.9.2-r1.ebuild             |   5 +-
 sci-libs/atlas/Manifest                            |   1 +
 ...las-3.10.1-r1.ebuild => atlas-3.10.1-r2.ebuild} |   2 +-
 sci-libs/lapack-reference/ChangeLog                |   6 +
 sci-libs/lapack-reference/Manifest                 |   1 +
 ...-3.4.2.ebuild => lapack-reference-3.5.0.ebuild} |   0
 sci-libs/lapacke-reference/ChangeLog               |   6 +
 sci-libs/lapacke-reference/Manifest                |   1 +
 ...3.4.2.ebuild => lapacke-reference-3.5.0.ebuild} |   0
 .../lapacke-reference-9999.ebuild                  |   4 +-
 sci-libs/plasma/ChangeLog                          |  10 +-
 sci-libs/plasma/Manifest                           |   4 +-
 .../{plasma-2.5.1.ebuild => plasma-2.5.2.ebuild}   |  25 ++--
 .../{plasma-2.4.6.ebuild => plasma-2.6.0.ebuild}   |  37 ++++--
 sci-libs/tmglib/ChangeLog                          |   5 +
 sci-libs/tmglib/Manifest                           |   1 +
 .../{tmglib-3.4.2.ebuild => tmglib-3.5.0.ebuild}   |   4 +-
 scripts/merge-dualHEAD                             |  64 +++++++++
 virtual/blas/blas-2.1-r1.ebuild                    |   6 +-
 .../{lapack-3.4-r1.ebuild => lapack-3.5.ebuild}    |  16 +--
 virtual/lapacke/ChangeLog                          |   8 +-
 .../geant-3.ebuild => lapacke/lapacke-3.5.ebuild}  |  12 +-
 25 files changed, 324 insertions(+), 59 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     38d2d59503b2a1861e728dcdb287523b2b376d5e
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Tue Jan 28 15:32:14 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jan 28 15:32:14 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=38d2d595

Merge /usr/local/portage/andis_overlay


 sci-libs/libgeodecomp/libgeodecomp-9999.ebuild |  8 ++++----
 sci-libs/libgeodecomp/metadata.xml             |  2 +-
 sci-visualization/visit/metadata.xml           | 18 ++++++++++++++++++
 sci-visualization/visit/visit-2.7.1.ebuild     |  9 +++++----
 sys-cluster/hpx/hpx-0.9.7.ebuild               |  2 +-
 5 files changed, 29 insertions(+), 10 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     df425688dbfd97abd4f739b6256b92c12b15b3c6
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Tue Jan 28 15:36:32 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jan 28 15:36:32 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=df425688

Merge /usr/local/portage/andis_overlay


 sys-cluster/hpx/hpx-0.9.7.ebuild | 1 -
 1 file changed, 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     20ea2b1d7d23d513210be8f215ab02e32f465dd1
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Tue Jan 28 08:43:19 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jan 28 08:43:19 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=20ea2b1d

Merge /usr/local/portage/andis_overlay


 sci-libs/libgeodecomp/libgeodecomp-0.3.1.ebuild    |   4 +-
 sci-libs/libgeodecomp/libgeodecomp-9999.ebuild     |  40 +++++-
 sci-libs/libgeodecomp/metadata.xml                 |  24 ++++
 sci-visualization/visit/Manifest                   |   1 +
 .../files/visit-2.7.1-dont_symlink_visit_dir.patch |  18 +++
 .../visit/files/visit-2.7.1-findpython.patch       |  19 +++
 .../visit/files/visit-2.7.1-findvtk.patch          |  24 ++++
 .../visit/files/visit-2.7.1-vtklibs.patch          | 142 +++++++++++++++++++++
 sci-visualization/visit/visit-2.7.1.ebuild         |  67 ++++++++++
 sys-cluster/hpx/Manifest                           |   1 +
 .../hpx/{hpx-0.9.5.ebuild => hpx-0.9.7.ebuild}     |  19 ++-
 .../hpx/{hpx-0.9.5.ebuild => hpx-9999.ebuild}      |  19 ++-
 12 files changed, 359 insertions(+), 19 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6ace09df5c61584d5d1e6c0056d13f90ef9d1730
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 29 07:46:53 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jan 29 07:46:53 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6ace09df

Ask for a branch per package

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 CONTRIBUTING.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 529a502..8f02ccc 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -68,6 +68,8 @@ It is always convenient for development as well as for the review and merging pr
 
     git checkout -b my-feature master
 
+For the fastest process during merging it is best to have a single branch per package.
+
 ###Work on the package
 Now you are ready to work on your package of interest. Once you are finished you should _always_ use **[repoman](http://dev.gentoo.org/~zmedico/portage/doc/man/repoman.1.html)** to do a static analysis of your work.
 

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     57722cb21e5e4e4ec7414994c0a2db7bd6c2ac39
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Tue Jan 28 19:37:39 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Jan 28 19:37:39 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=57722cb2

Merge pull request #178 from gentoo-science/docs

More elloborate contribution description


 CONTRIBUTING.md        | 145 ++++++++++++++++++++++++++++++++++++++++++++++++-
 README.md              |  11 ++--
 scripts/merge-dualHEAD |  64 ++++++++++++++++++++++
 3 files changed, 211 insertions(+), 9 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     acf33c055c69ea49417449c7bd0d6a56bbfd61d8
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 28 19:43:57 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Jan 28 19:43:57 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=acf33c05

spelling

---
 CONTRIBUTING.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 7da80ca..529a502 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,10 +1,10 @@
 #Contributions to the Gentoo Science Overlay
 
-This guide summerizes the contribution and merging procedures for the Gentoo Science overlay on Github. For more information please visit the [Science Project page](https://wiki.gentoo.org/wiki/Project:Science/Contributing) in the [Gentoo wiki](https://wiki.gentoo.org/).
+This guide summarizes the contribution and merging procedures for the Gentoo Science overlay on Github. For more information please visit the [Science Project page](https://wiki.gentoo.org/wiki/Project:Science/Contributing) in the [Gentoo wiki](https://wiki.gentoo.org/).
 
 ----
 ##Prerequisite
-For the most convinient way to work with the overlay you should fulfill all prerequisites.
+For the most convenient way to work with the overlay you should fulfill all prerequisites.
 
 ###Required
 
@@ -44,7 +44,7 @@ Now git will sign your commits to the overlay by using the gpg key.
 
 * **Install [repo-commit](https://bitbucket.org/gentoo/repo-commit/)**, *A repository commit helper*
 
-*repo-commit* sanitizes your commit in a convinient way.
+*repo-commit* sanitizes your commit in a convenient way.
 
     emerge app-portage/repo-commit
 
@@ -69,7 +69,7 @@ It is always convenient for development as well as for the review and merging pr
     git checkout -b my-feature master
 
 ###Work on the package
-Now you are ready to work on your package of interest. Once you are finished you should _always_ use **[repoman](http://dev.gentoo.org/~zmedico/portage/doc/man/repoman.1.html)** to do a statical analysis of your work.
+Now you are ready to work on your package of interest. Once you are finished you should _always_ use **[repoman](http://dev.gentoo.org/~zmedico/portage/doc/man/repoman.1.html)** to do a static analysis of your work.
 
 This can be done with
 

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     52ba39a6693b0f0e0c7e4e1ceda5a63141bdf8ee
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 28 19:45:49 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Jan 28 19:45:49 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=52ba39a6

add overlay homepage

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index 446e73a..4a2dc95 100644
--- a/README.md
+++ b/README.md
@@ -2,8 +2,12 @@
 
 An overlay for Gentoo, geared towards scientific packages.
 
+Homepage: [Science Project page](https://wiki.gentoo.org/wiki/Project:Science/Overlay)
+
+
 Please fork! We will merge! See [this](https://github.com/gentoo-science/sci/blob/master/CONTRIBUTING.md) document for more instructions.
 
 Ask for help on irc in #gentoo-science @ freenode.
 
 Report bugs on the [github issues site](https://github.com/gentoo-science/sci/issues)
+

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     2244b4474757c2c17d0d363764c400f6379f80c2
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 22 11:00:55 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Jan 22 11:00:55 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2244b447

Finalizing the Contribution instructions

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 CONTRIBUTING.md | 29 +++++++++++++++++------------
 1 file changed, 17 insertions(+), 12 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index b156ca0..3d02fa6 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -5,7 +5,9 @@
 
 ###Requiered
 
-* Everybody who wants to contribute should own an account at [github](https://github.com/join). Please register yourself there.
+* **Account at [github](https://github.com/join)**
+
+Everybody who wants to contribute needs to own an account. Please register yourself there.
 
 ###Recommended
 * **Define echangelog user**
@@ -38,7 +40,7 @@ First clone the overlay
     hub clone gentoo-science/sci
 
 
-In order to send pull request and ask for inclusion of your changes you need to have your own fork of the overlay on github. You can do this by
+In order to send pull request and ask for inclusion of your changes you need to have your own fork of the overlay on github. You can do this by issuing
 
     cd sci
     hub fork
@@ -65,14 +67,14 @@ Next we push back the changes to our fork and send a pull-request to the overlay
     hub push YOUR_GITHUB_USER
     hub pull-request
 
-Lastly you need to wait for review comments and the merge of your work. In case you need to include some improvements, just commit your work again using repoman and push it again to your fork.
+Lastly you need to wait for review comments and the merge of your work. In case you need to include some improvements, just commit your work again using repoman and push it again to your fork. No need to send another pull-request as you new changes will be added the original one.
 
 ----
 ##For Maintainers
 
-**The merging of pull request should only be done by gentoo developers.**
+**The merging of pull request should only be done by gentoo developers!**
 
-If you feel that they are slacking, don't bother to ping them again.
+If you feel that they are slacking, don't bother to ping them again. If you like to become a dev yourself, prove some contribution and ping us via sci@gentoo.org or on irc in #gentoo-science @ freenode.
 
 ###Prerequisite
 
@@ -82,17 +84,18 @@ Make sure you have both repos (github & gentoo.org) as remotes defined.
 
 should give
 
-> github	git@github.com:gentoo-science/sci.git (fetch)
+>github	git@github.com:gentoo-science/sci.git (fetch)
 >
-> github	git@github.com:gentoo-science/sci.git (push)
+>github	git@github.com:gentoo-science/sci.git (push)
 >
-> origin	git+ssh://git@git.overlays.gentoo.org/proj/sci.git (fetch)
+>origin	git+ssh://git@git.overlays.gentoo.org/proj/sci.git (fetch)
 >
-> origin	git+ssh://git@git.overlays.gentoo.org/proj/sci.git (push)
+>origin	git+ssh://git@git.overlays.gentoo.org/proj/sci.git (push)
+
 
-In the beginning you should review the pull request on github directly and recommend as much improvements as possible. Once everything is fine or you like to fix the rest yourself, you can use the follow command to get the pull-request in a new branch in you repo.
+In the beginning you should review the pull request on github directly and recommend as much improvements as possible. Once everything is fine or you like to fix the rest yourself, simply can use the follow command to get the pull-request in a new branch in you repo.
 
-    hub checkout https://github.com/gentoo-science/sci/pull/176
+    hub checkout https://github.com/gentoo-science/sci/pull/PULLREQUEST-NUMBER
 
 Now check the package by building and installing it, and run *repoman* in the package dir. If this is also fine, merge the branch into the master
 
@@ -103,7 +106,9 @@ Finally use the script **merge-dualHEAD** from the *scripts* directory to merge
 
 
 ---
-####.
+####Contribution to the document
+Justin Lecher <jlec@gentoo.org>
+
 This document is available under [Creative Commons Attribution ShareAlike 4.0](http://creativecommons.org/licenses/by-sa/4.0)
 
 ![ccsa-4 icon](http://i.creativecommons.org/l/by-sa/4.0/88x31.png)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     c2d0b387ea31a0f0f9103b38fb015954812de514
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 25 13:45:30 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Sat Jan 25 13:45:30 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c2d0b387

Fix some typos
Add Sebastien to the list of contributors

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 CONTRIBUTING.md | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 3d02fa6..6f47e97 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -3,7 +3,7 @@
 ----
 ##Prerequisite
 
-###Requiered
+###Required
 
 * **Account at [github](https://github.com/join)**
 
@@ -67,14 +67,14 @@ Next we push back the changes to our fork and send a pull-request to the overlay
     hub push YOUR_GITHUB_USER
     hub pull-request
 
-Lastly you need to wait for review comments and the merge of your work. In case you need to include some improvements, just commit your work again using repoman and push it again to your fork. No need to send another pull-request as you new changes will be added the original one.
+Lastly you need to wait for review comments and the merge of your work. In case you need to include some improvements, just commit your work again using repoman and push it again to your fork. No need to send another pull-request as your new changes will be added to the original one.
 
 ----
 ##For Maintainers
 
 **The merging of pull request should only be done by gentoo developers!**
 
-If you feel that they are slacking, don't bother to ping them again. If you like to become a dev yourself, prove some contribution and ping us via sci@gentoo.org or on irc in #gentoo-science @ freenode.
+If you feel that they are slacking, don't bother to ping them again. If you would like to become a dev yourself, prove some contribution and ping us via sci@gentoo.org or on irc in #gentoo-science @ freenode.
 
 ###Prerequisite
 
@@ -107,6 +107,7 @@ Finally use the script **merge-dualHEAD** from the *scripts* directory to merge
 
 ---
 ####Contribution to the document
+Sebastien Fabbro <bicatali@gentoo.org>
 Justin Lecher <jlec@gentoo.org>
 
 This document is available under [Creative Commons Attribution ShareAlike 4.0](http://creativecommons.org/licenses/by-sa/4.0)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     5dcfbeaf5f310bc47e909acef735b2b877c597a3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 26 09:17:44 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Sun Jan 26 09:17:44 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5dcfbeaf

Vastely update and rewrite the text
Include commends from bicatali

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 CONTRIBUTING.md | 73 +++++++++++++++++++++++++++++++++++++++++----------------
 1 file changed, 53 insertions(+), 20 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 6f47e97..7da80ca 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,16 +1,27 @@
 #Contributions to the Gentoo Science Overlay
 
+This guide summerizes the contribution and merging procedures for the Gentoo Science overlay on Github. For more information please visit the [Science Project page](https://wiki.gentoo.org/wiki/Project:Science/Contributing) in the [Gentoo wiki](https://wiki.gentoo.org/).
+
 ----
 ##Prerequisite
+For the most convinient way to work with the overlay you should fulfill all prerequisites.
 
 ###Required
 
+* **Install git**
+
+The Science overlay is controlled by [git](http://git-scm.com/). You can install it with
+
+    emerge dev-vcs/git
+
+Familiarize yourself with git and visit [http://git-scm.com/documentation](http://git-scm.com/documentation) for documentation.
+
 * **Account at [github](https://github.com/join)**
 
-Everybody who wants to contribute needs to own an account. Please register yourself there.
+Everybody who wants to contribute needs to own an account @ [Github](http://github.com/). Please register yourself [there](https://github.com/join).
 
 ###Recommended
-* **Define echangelog user**
+* **Define the echangelog user**
 
 Make sure the ECHANGELOG_USER variable is present in your environment.
 
@@ -23,58 +34,69 @@ Create a [gpg key](http://www.gossamer-threads.com/lists/gentoo/dev/268496?do=po
 
     git config --global user.signingkey <gpg-key-id>
 
+Now git will sign your commits to the overlay by using the gpg key.
 
-* **Install [hub](http://hub.github.com/)**, the "command-line wrapper for git that makes you better at GitHub".
+* **Install [hub](http://hub.github.com/)**, the *command-line wrapper for git that makes you better at GitHub*.
 
-This file will use *hub* because of it's convenience when working with github.
+*hub* can be used equivalent to to *git* and upstream even recommends *"alias git='hub'*.
 
     emerge dev-vcs/hub
 
+* **Install [repo-commit](https://bitbucket.org/gentoo/repo-commit/)**, *A repository commit helper*
 
-----
-##For Contributors
+*repo-commit* sanitizes your commit in a convinient way.
 
+    emerge app-portage/repo-commit
 
-First clone the overlay
+---
+##Contributing ebuilds
 
-    hub clone gentoo-science/sci
+###Clone the overlay
 
+Create a local checkout of the overlay
 
+    hub clone gentoo-science/sci
+
+###Fork the overlay
 In order to send pull request and ask for inclusion of your changes you need to have your own fork of the overlay on github. You can do this by issuing
 
     cd sci
     hub fork
 
-Now you are ready to start your work.
-
+###Branch out for contribution
 It is always convenient for development as well as for the review and merging process, if the development is done in branches.
 
     git checkout -b my-feature master
 
-Now you can work on you package of interest. Once you are finished you should _always_ use **[repoman](http://dev.gentoo.org/~zmedico/portage/doc/man/repoman.1.html)** to check, verify and commit your changes.
+###Work on the package
+Now you are ready to work on your package of interest. Once you are finished you should _always_ use **[repoman](http://dev.gentoo.org/~zmedico/portage/doc/man/repoman.1.html)** to do a statical analysis of your work.
 
-Static analysis can be done with
+This can be done with
 
     repoman full
 
+###Commit your work
 Once *all* reported problems are resolved, you can commit it
 
-    echangelog "Here we write a comprehensible ChangeLog message"
-    repoman -m "Here we write a comprehensible commit message" commit
+    repo-commit "Here we write a comprehensible commit message"
 
+###Push to Github and make a pull request
 Next we push back the changes to our fork and send a pull-request to the overlay maintainers.
 
     hub push YOUR_GITHUB_USER
     hub pull-request
 
-Lastly you need to wait for review comments and the merge of your work. In case you need to include some improvements, just commit your work again using repoman and push it again to your fork. No need to send another pull-request as your new changes will be added to the original one.
+Lastly you need to wait for review comments and the merge of your work. If you feel that they are slacking, don't bother to ping them again. In case you need to include some improvements, just commit your work again using *repo-commit* and push it again to your fork. No need to send another pull-request as your new changes will be added to the original one.
+
+###What's next?
+If you would like to get direct access to the overlay, prove some contribution and ping us via sci@gentoo.org or on irc in #gentoo-science @ freenode. If you would like to become a dev yourself, prove some more contributions and again, contact us. We are always looking for new candidates.
 
 ----
-##For Maintainers
+##Merging contributions
+
+**It is important, that if you merge a pull request, you should feel as responsible as if you have written the commits yourself!**
 
-**The merging of pull request should only be done by gentoo developers!**
 
-If you feel that they are slacking, don't bother to ping them again. If you would like to become a dev yourself, prove some contribution and ping us via sci@gentoo.org or on irc in #gentoo-science @ freenode.
 
 ###Prerequisite
 
@@ -93,21 +115,32 @@ should give
 >origin	git+ssh://git@git.overlays.gentoo.org/proj/sci.git (push)
 
 
-In the beginning you should review the pull request on github directly and recommend as much improvements as possible. Once everything is fine or you like to fix the rest yourself, simply can use the follow command to get the pull-request in a new branch in you repo.
+###Review process
+
+In the beginning you should review the pull request on github directly and recommend as much improvements as possible. By this you train the new contributor towards becoming a new dev, which should be our final goal.
+
+####Checking out the pull-request as local branch
+Once everything is fine or you like to fix the rest yourself, simply use the following command to get the pull-request in a new branch in your repo.
 
     hub checkout https://github.com/gentoo-science/sci/pull/PULLREQUEST-NUMBER
 
-Now check the package by building and installing it, and run *repoman* in the package dir. If this is also fine, merge the branch into the master
+####Testing and repoman check
+Now check the package by building and installing it, and run *repoman* in the package dir. Remember, when merging a pull request you take the responsibility for the quality of the commit.
+
+####Merge the pull-request branch into master
+If this is also fine, merge the branch into the master
 
     git checkout master
     git merge USER-BRANCH
 
+####Merging the two remote HEADs
 Finally use the script **merge-dualHEAD** from the *scripts* directory to merge the github and gentoo.org remote repo.
 
 
 ---
 ####Contribution to the document
 Sebastien Fabbro <bicatali@gentoo.org>
+
 Justin Lecher <jlec@gentoo.org>
 
 This document is available under [Creative Commons Attribution ShareAlike 4.0](http://creativecommons.org/licenses/by-sa/4.0)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     ff2f54a1757b1ba362116a39747bba5714bd5947
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 22 11:38:47 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Jan 22 11:38:47 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ff2f54a1

Adopt README

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 README.md | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index d4dc43f..446e73a 100644
--- a/README.md
+++ b/README.md
@@ -1,12 +1,9 @@
-Gentoo Science Overlay
-======================
+#Gentoo Science Overlay
 
 An overlay for Gentoo, geared towards scientific packages.
 
-Please fork! We will merge!
+Please fork! We will merge! See [this](https://github.com/gentoo-science/sci/blob/master/CONTRIBUTING.md) document for more instructions.
 
-Ask for help in #gentoo-science in irc freenode.
+Ask for help on irc in #gentoo-science @ freenode.
 
-Report issues on the github site:
-
-https://github.com/gentoo-science/sci/issues
+Report bugs on the [github issues site](https://github.com/gentoo-science/sci/issues)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     a3f4fd29d5d2b87b5bd04cb9d5ab57db266cc27d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 22 09:50:08 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Jan 22 09:50:08 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a3f4fd29

For Contributors ready

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 CONTRIBUTING.md | 65 +++++++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 63 insertions(+), 2 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 7579f6d..f4e7e95 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,7 +1,68 @@
 #Contributions to the Gentoo Science Overlay
 
+----
 ##Prerequisite
 
-###For Contributors
+###Requiered
 
-###For Maintainers
+* Everybody who wants to contribute should own an account at [github](https://github.com/join). Please register yourself there.
+
+###Recommended
+* **Define echangelog user**
+
+Make sure the ECHANGELOG_USER variable is present in your environment.
+
+    echo 'export ECHANGELOG_USER="John Smith <john@smith.com>"' >> ~/.bashrc
+
+###Optional
+* **Setup commit signing**
+
+Create a [gpg key](http://www.gossamer-threads.com/lists/gentoo/dev/268496?do=post_view_threaded) if you don't have one already and make git use it.
+
+    git config --global user.signingkey <gpg-key-id>
+
+
+* **Install [hub](http://hub.github.com/)**, the "command-line wrapper for git that makes you better at GitHub".
+
+This file will use *hub* because of it's convenience when working with github.
+
+    emerge dev-vcs/hub
+
+
+----
+##For Contributors
+
+
+First clone the overlay
+
+    hub clone gentoo-science/sci
+
+
+    cd sci
+
+
+It is always convenient for development as well as for the review and merging process, if the development is done in branches.
+
+    git checkout -b my-feature master
+
+Now you can work on you package of interest. Once you are finished you should _always_ use **[repoman](http://dev.gentoo.org/~zmedico/portage/doc/man/repoman.1.html)** to check, verify and commit your changes.
+
+Static analysis can be done with
+
+    repoman full
+
+Once *all* reported problems are resolved, you can commit it
+
+    echangelog "Here we write a comprehensible ChangeLog message"
+    repoman -m "Here we write a comprehensible commit message" commit
+
+
+
+----
+##For Maintainers
+
+
+---
+This document is available under [Creative Commons Attribution ShareAlike 4.0](http://creativecommons.org/licenses/by-sa/4.0)
+
+![ccsa-4 icon](http://i.creativecommons.org/l/by-sa/4.0/88x31.png)
\ No newline at end of file

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     6a671b25edf542c6c9efdcdc4a9b318feaa4a99e
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Wed Jan 22 10:38:39 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Jan 22 10:38:39 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6a671b25

Add Maintainer section

---
 CONTRIBUTING.md | 43 ++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 42 insertions(+), 1 deletion(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index f4e7e95..b156ca0 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -38,8 +38,12 @@ First clone the overlay
     hub clone gentoo-science/sci
 
 
+In order to send pull request and ask for inclusion of your changes you need to have your own fork of the overlay on github. You can do this by
+
     cd sci
+    hub fork
 
+Now you are ready to start your work.
 
 It is always convenient for development as well as for the review and merging process, if the development is done in branches.
 
@@ -56,13 +60,50 @@ Once *all* reported problems are resolved, you can commit it
     echangelog "Here we write a comprehensible ChangeLog message"
     repoman -m "Here we write a comprehensible commit message" commit
 
+Next we push back the changes to our fork and send a pull-request to the overlay maintainers.
+
+    hub push YOUR_GITHUB_USER
+    hub pull-request
 
+Lastly you need to wait for review comments and the merge of your work. In case you need to include some improvements, just commit your work again using repoman and push it again to your fork.
 
 ----
 ##For Maintainers
 
+**The merging of pull request should only be done by gentoo developers.**
+
+If you feel that they are slacking, don't bother to ping them again.
+
+###Prerequisite
+
+Make sure you have both repos (github & gentoo.org) as remotes defined.
+
+    git remote -v
+
+should give
+
+> github	git@github.com:gentoo-science/sci.git (fetch)
+>
+> github	git@github.com:gentoo-science/sci.git (push)
+>
+> origin	git+ssh://git@git.overlays.gentoo.org/proj/sci.git (fetch)
+>
+> origin	git+ssh://git@git.overlays.gentoo.org/proj/sci.git (push)
+
+In the beginning you should review the pull request on github directly and recommend as much improvements as possible. Once everything is fine or you like to fix the rest yourself, you can use the follow command to get the pull-request in a new branch in you repo.
+
+    hub checkout https://github.com/gentoo-science/sci/pull/176
+
+Now check the package by building and installing it, and run *repoman* in the package dir. If this is also fine, merge the branch into the master
+
+    git checkout master
+    git merge USER-BRANCH
+
+Finally use the script **merge-dualHEAD** from the *scripts* directory to merge the github and gentoo.org remote repo.
+
 
 ---
+####.
 This document is available under [Creative Commons Attribution ShareAlike 4.0](http://creativecommons.org/licenses/by-sa/4.0)
 
-![ccsa-4 icon](http://i.creativecommons.org/l/by-sa/4.0/88x31.png)
\ No newline at end of file
+![ccsa-4 icon](http://i.creativecommons.org/l/by-sa/4.0/88x31.png)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     ce38f6d073ea33663fd44e5a2cdf1749b7e7c80c
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 27 17:01:38 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Jan 27 17:01:38 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ce38f6d0

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 dev-lang/julia/ChangeLog                           |   3 +
 dev-lang/julia/julia-9999.ebuild                   |   1 +
 dev-libs/utf8proc/ChangeLog                        |   9 +
 dev-libs/utf8proc/Manifest                         |   1 +
 .../utf8proc/files/utf8proc-1.1.6-buildflags.patch |  11 +
 .../utf8proc/files/utf8proc-1.1.6-soname.patch     |  11 +
 .../jrosetta => dev-libs/utf8proc}/metadata.xml    |   0
 dev-libs/utf8proc/utf8proc-1.1.6.ebuild            |  36 ++
 .../files/ncbi-tools++-12.0.0-as-needed.patch      | 555 +++++++++++----------
 .../files/ncbi-tools++-12.0.0-conf-opts.patch      | 183 +------
 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        |  14 +-
 sys-cluster/modules/ChangeLog                      |   8 +-
 .../files/{modules.sh.in => modules.new.sh.in}     |   3 +-
 sys-cluster/modules/modules-3.2.9c-r1.ebuild       |   4 +-
 sys-cluster/modules/modules-3.2.9c.ebuild          |   4 +-
 15 files changed, 388 insertions(+), 455 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     bcbb6cc0e241c75e3d7db3cf386f58c945846aed
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 28 17:46:34 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Jan 28 17:46:34 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bcbb6cc0

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 app-text/jabref/ChangeLog                      | 10 ++++
 app-text/jabref/Manifest                       |  1 -
 app-text/jabref/jabref-2.10_beta-r1.ebuild     | 65 --------------------------
 app-text/jabref/jabref-2.10_beta.ebuild        | 35 --------------
 app-text/jabref/jabref-2.10_beta2-r1.ebuild    |  1 +
 app-text/jabref/jabref-2.10_beta2.ebuild       | 35 --------------
 app-text/jabref/jabref-2.9.2-r1.ebuild         |  5 +-
 sci-chemistry/gromacs/ChangeLog                |  4 ++
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild  |  4 +-
 sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild |  1 +
 sci-chemistry/gromacs/gromacs-9999.ebuild      |  1 +
 11 files changed, 21 insertions(+), 141 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     c7ea1bbbe10b86be160b847f6403b3a1d53928e6
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 21 22:05:16 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Jan 21 22:05:16 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c7ea1bbb

Merge github.com:gentoo-science/sci


 CONTRIBUTING.md              |   7 +++
 eclass/alternatives-2.eclass | 138 +++++++++++++++++++++++++++++++------------
 2 files changed, 107 insertions(+), 38 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     5c8dd0a5aa610fed5bfe89dab8d7ccddce47e0ea
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 21 17:23:23 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Jan 21 17:23:23 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5c8dd0a5

Merge github.com:gentoo-science/sci


 app-admin/eselect/ChangeLog                        |   7 +-
 ...elect-1.3.8-r100.ebuild => eselect-9999.ebuild} |  26 ++-
 eclass/alternatives-2.eclass                       |  19 +-
 licenses/HSL                                       | 222 ---------------------
 profiles/package.mask                              |   1 +
 5 files changed, 31 insertions(+), 244 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     61ae4aa548103c7933d8fedd8021ab936c195cd8
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 20 23:24:26 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Jan 20 23:24:26 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=61ae4aa5

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 sci-biology/tablet-bin/ChangeLog                                 | 9 +++++++--
 sci-biology/tablet-bin/Manifest                                  | 2 +-
 ...tablet-bin-1.13.05.17.ebuild => tablet-bin-1.13.12.17.ebuild} | 5 +++--
 3 files changed, 11 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     bce2af6aa439a5a40c95eb2e0b52df628ef8f7ef
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 20 19:03:41 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Jan 20 19:03:41 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bce2af6a

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 sci-biology/fastx_toolkit/ChangeLog                                 | 6 ++++++
 sci-biology/fastx_toolkit/Manifest                                  | 2 +-
 .../{fastx_toolkit-0.0.13.2.ebuild => fastx_toolkit-0.0.14.ebuild}  | 2 +-
 3 files changed, 8 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     d693cd3ce055457c84dea17d954531ca6b5b1a73
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 17 17:27:57 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Fri Jan 17 17:27:57 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d693cd3c

Merge github.com:gentoo-science/sci


 sci-libs/coinhsl/ChangeLog                         |  18 ---
 sci-libs/coinhsl/Manifest                          |   2 -
 sci-libs/coinhsl/coinhsl-2012.12.21.ebuild         |  36 ------
 sci-libs/coinhsl/coinhsl-2013.06.18.ebuild         |  32 ------
 sci-libs/coinhsl/metadata.xml                      |  12 --
 sci-libs/coinor-alps/ChangeLog                     |  30 -----
 sci-libs/coinor-alps/Manifest                      |   1 -
 sci-libs/coinor-alps/coinor-alps-1.4.7.ebuild      |  67 -----------
 sci-libs/coinor-alps/metadata.xml                  |  13 ---
 sci-libs/coinor-bcp/ChangeLog                      |  21 ----
 sci-libs/coinor-bcp/Manifest                       |   1 -
 sci-libs/coinor-bcp/coinor-bcp-1.3.7.ebuild        |  56 ---------
 sci-libs/coinor-bcp/metadata.xml                   |  13 ---
 sci-libs/coinor-bcps/ChangeLog                     |  21 ----
 sci-libs/coinor-bcps/Manifest                      |   1 -
 sci-libs/coinor-bcps/coinor-bcps-0.93.8.ebuild     |  67 -----------
 sci-libs/coinor-bcps/metadata.xml                  |  13 ---
 sci-libs/coinor-blis/ChangeLog                     |  30 -----
 sci-libs/coinor-blis/Manifest                      |   1 -
 sci-libs/coinor-blis/coinor-blis-0.93.8.ebuild     |  65 -----------
 sci-libs/coinor-blis/metadata.xml                  |  12 --
 sci-libs/coinor-bonmin/ChangeLog                   |  24 ----
 sci-libs/coinor-bonmin/Manifest                    |   1 -
 sci-libs/coinor-bonmin/coinor-bonmin-1.7.3.ebuild  |  72 ------------
 sci-libs/coinor-bonmin/metadata.xml                |  13 ---
 sci-libs/coinor-buildtools/ChangeLog               |  15 ---
 .../coinor-buildtools-0.7.9.ebuild                 |  38 -------
 sci-libs/coinor-buildtools/metadata.xml            |   9 --
 sci-libs/coinor-cbc/ChangeLog                      |  39 -------
 sci-libs/coinor-cbc/Manifest                       |   1 -
 sci-libs/coinor-cbc/coinor-cbc-2.8.7.ebuild        |  83 --------------
 sci-libs/coinor-cbc/metadata.xml                   |  11 --
 sci-libs/coinor-cgl/ChangeLog                      |  36 ------
 sci-libs/coinor-cgl/Manifest                       |   1 -
 sci-libs/coinor-cgl/coinor-cgl-0.58.4.ebuild       |  73 ------------
 sci-libs/coinor-cgl/metadata.xml                   |  12 --
 sci-libs/coinor-clp/ChangeLog                      |  43 -------
 sci-libs/coinor-clp/Manifest                       |   1 -
 sci-libs/coinor-clp/coinor-clp-1.15.5.ebuild       | 112 ------------------
 .../files/coinor-clp-1.15.1-mpi-header.patch       |  12 --
 sci-libs/coinor-clp/metadata.xml                   |  20 ----
 sci-libs/coinor-couenne/ChangeLog                  |  21 ----
 sci-libs/coinor-couenne/Manifest                   |   1 -
 .../coinor-couenne/coinor-couenne-0.4.6.ebuild     |  59 ----------
 sci-libs/coinor-couenne/metadata.xml               |  12 --
 sci-libs/coinor-cppad/ChangeLog                    |  37 ------
 sci-libs/coinor-cppad/Manifest                     |   1 -
 sci-libs/coinor-cppad/coinor-cppad-20131207.ebuild |  54 ---------
 sci-libs/coinor-cppad/metadata.xml                 |  14 ---
 sci-libs/coinor-csdp/ChangeLog                     |  12 --
 sci-libs/coinor-csdp/Manifest                      |   1 -
 sci-libs/coinor-csdp/coinor-csdp-6.1.1.ebuild      | 100 ----------------
 sci-libs/coinor-csdp/metadata.xml                  |  16 ---
 sci-libs/coinor-dip/ChangeLog                      |   9 --
 sci-libs/coinor-dip/Manifest                       |   1 -
 sci-libs/coinor-dip/coinor-dip-0.83.2.ebuild       |  62 ----------
 sci-libs/coinor-dip/metadata.xml                   |  14 ---
 sci-libs/coinor-dylp/ChangeLog                     |  21 ----
 sci-libs/coinor-dylp/Manifest                      |   1 -
 sci-libs/coinor-dylp/coinor-dylp-1.9.3.ebuild      |  66 -----------
 sci-libs/coinor-dylp/metadata.xml                  |  12 --
 sci-libs/coinor-flopcpp/ChangeLog                  |  21 ----
 sci-libs/coinor-flopcpp/Manifest                   |   1 -
 .../coinor-flopcpp/coinor-flopcpp-1.1.6.ebuild     |  67 -----------
 sci-libs/coinor-flopcpp/metadata.xml               |  14 ---
 sci-libs/coinor-mp/ChangeLog                       |  24 ----
 sci-libs/coinor-mp/Manifest                        |   1 -
 sci-libs/coinor-mp/coinor-mp-1.7.5.ebuild          |  56 ---------
 sci-libs/coinor-mp/metadata.xml                    |  11 --
 sci-libs/coinor-netlib/ChangeLog                   |  25 ----
 sci-libs/coinor-netlib/Manifest                    |   1 -
 sci-libs/coinor-netlib/coinor-netlib-1.2.6.ebuild  |  23 ----
 sci-libs/coinor-netlib/metadata.xml                |   9 --
 sci-libs/coinor-os/ChangeLog                       |  15 ---
 sci-libs/coinor-os/Manifest                        |   1 -
 sci-libs/coinor-os/coinor-os-2.8.2.ebuild          |  67 -----------
 sci-libs/coinor-os/metadata.xml                    |  11 --
 sci-libs/coinor-osi/ChangeLog                      |  33 ------
 sci-libs/coinor-osi/Manifest                       |   1 -
 sci-libs/coinor-osi/coinor-osi-0.106.4.ebuild      |  76 -------------
 sci-libs/coinor-osi/metadata.xml                   |  15 ---
 sci-libs/coinor-sample/ChangeLog                   |  43 -------
 sci-libs/coinor-sample/Manifest                    |   1 -
 sci-libs/coinor-sample/coinor-sample-1.2.9.ebuild  |  23 ----
 sci-libs/coinor-sample/metadata.xml                |   9 --
 sci-libs/coinor-smi/ChangeLog                      |   9 --
 sci-libs/coinor-smi/Manifest                       |   1 -
 sci-libs/coinor-smi/coinor-smi-0.93.3.ebuild       |  69 -----------
 sci-libs/coinor-smi/metadata.xml                   |  18 ---
 sci-libs/coinor-symphony/ChangeLog                 |  33 ------
 sci-libs/coinor-symphony/Manifest                  |   1 -
 .../coinor-symphony/coinor-symphony-5.5.6.ebuild   |  89 ---------------
 sci-libs/coinor-symphony/metadata.xml              |  18 ---
 sci-libs/coinor-utils/ChangeLog                    |  39 -------
 sci-libs/coinor-utils/Manifest                     |   1 -
 sci-libs/coinor-utils/coinor-utils-2.9.10.ebuild   |  85 --------------
 sci-libs/coinor-utils/metadata.xml                 |  15 ---
 sci-libs/coinor-vol/ChangeLog                      |  24 ----
 sci-libs/coinor-vol/Manifest                       |   1 -
 sci-libs/coinor-vol/coinor-vol-1.4.3.ebuild        |  71 ------------
 sci-libs/coinor-vol/metadata.xml                   |  10 --
 sci-libs/ipopt/ChangeLog                           |  40 -------
 sci-libs/ipopt/Manifest                            |   1 -
 sci-libs/ipopt/files/ipopt-3.11.2-mpi-header.patch |  14 ---
 sci-libs/ipopt/ipopt-3.11.6.ebuild                 | 100 ----------------
 sci-libs/ipopt/metadata.xml                        |  18 ---
 sci-libs/lemon/ChangeLog                           |  38 -------
 sci-libs/lemon/Manifest                            |   1 -
 sci-libs/lemon/files/lemon-1.3-multilib.patch      |  18 ---
 sci-libs/lemon/files/lemon-1.3-underlinking.patch  |  47 --------
 sci-libs/lemon/lemon-1.3-r1.ebuild                 |  83 --------------
 sci-libs/lemon/metadata.xml                        |  23 ----
 sci-libs/magma/ChangeLog                           |  52 ---------
 sci-libs/magma/Manifest                            |   1 -
 .../magma/files/magma-1.2.1-no-cuda-driver.patch   |  38 -------
 sci-libs/magma/magma-1.4.0.ebuild                  | 126 ---------------------
 sci-libs/magma/metadata.xml                        |  15 ---
 sci-libs/scalapack/ChangeLog                       |   8 +-
 ...pack-2.0.2.ebuild => scalapack-2.0.2-r1.ebuild} |   4 +-
 119 files changed, 9 insertions(+), 3292 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     8e0fd242591a6596aedb323d7655a69090334b8f
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 20 17:53:04 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Jan 20 17:53:04 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8e0fd242

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci

Conflicts:
	virtual/lapack/ChangeLog


 app-admin/eselect/ChangeLog                        |  4 +-
 dev-lang/julia/julia-9999.ebuild                   | 18 +++++-
 dev-lang/vtune/ChangeLog                           |  2 +-
 dev-libs/asmjit/ChangeLog                          |  2 +-
 dev-perl/Bio-BigFile/ChangeLog                     |  2 +-
 dev-python/opal-client/ChangeLog                   |  2 +-
 dev-python/pythonocc/ChangeLog                     |  8 +--
 profiles/package.use.mask                          |  3 +
 sci-biology/YASRA/ChangeLog                        |  2 +-
 sci-biology/clover/ChangeLog                       |  2 +-
 sci-biology/cutadapt/ChangeLog                     |  2 +-
 sci-biology/fastx_toolkit/ChangeLog                |  5 +-
 .../fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild    |  5 +-
 sci-biology/lastz/ChangeLog                        |  4 +-
 sci-biology/mrfast/ChangeLog                       |  2 +-
 sci-biology/mrsfast/ChangeLog                      |  2 +-
 sci-biology/sequin/ChangeLog                       |  2 +-
 sci-biology/tablet-bin/ChangeLog                   |  4 +-
 sci-chemistry/avogadro2/ChangeLog                  |  3 +
 sci-chemistry/avogadro2/avogadro2-0.7.2.ebuild     |  7 ++-
 sci-chemistry/chimera-bin/ChangeLog                |  4 +-
 sci-chemistry/drawxtl/ChangeLog                    |  2 +-
 sci-chemistry/mddnmr/ChangeLog                     |  2 +-
 sci-chemistry/modeller/ChangeLog                   |  2 +-
 sci-chemistry/nmrpipe/ChangeLog                    | 10 ++--
 sci-chemistry/phenix-bin/ChangeLog                 |  2 +-
 sci-chemistry/polygon/ChangeLog                    |  2 +-
 sci-chemistry/simpson/ChangeLog                    |  2 +-
 sci-chemistry/specView/ChangeLog                   |  2 +-
 sci-chemistry/unio/ChangeLog                       |  2 +-
 sci-geosciences/pydap/ChangeLog                    |  2 +-
 sci-geosciences/pydap_handlers_hdf5/ChangeLog      |  2 +-
 sci-geosciences/pydap_handlers_netcdf/ChangeLog    |  2 +-
 sci-geosciences/pydap_handlers_sql/ChangeLog       |  2 +-
 sci-geosciences/pydap_responses_kml/ChangeLog      |  2 +-
 sci-geosciences/pydap_responses_matlab/ChangeLog   |  2 +-
 sci-geosciences/pydap_responses_netcdf/ChangeLog   |  2 +-
 sci-geosciences/pydap_responses_wms/ChangeLog      |  2 +-
 sci-libs/libgeodecomp/Manifest                     |  1 +
 ...comp-0.2.0.ebuild => libgeodecomp-0.3.1.ebuild} |  0
 sci-libs/libxc/ChangeLog                           |  2 +-
 sci-libs/mkl/ChangeLog                             |  2 +-
 sci-libs/msms/ChangeLog                            |  4 +-
 sci-libs/silo/Manifest                             |  1 +
 sci-libs/silo/files/silo-4.9.1-qtlibs.patch        | 66 ++++++++++++++++++++++
 sci-libs/silo/metadata.xml                         | 18 ++++++
 sci-libs/silo/silo-4.9.1.ebuild                    | 35 ++++++++++++
 .../gappalib-coq/gappalib-coq-0.18.0.ebuild        |  2 +-
 sci-mathematics/mdp/ChangeLog                      |  2 +-
 sci-misc/nltk/ChangeLog                            |  2 +-
 skel.ChangeLog                                     |  2 +-
 skel.ebuild                                        |  2 +-
 skel.metadata.xml                                  |  1 -
 sys-cluster/pyslice/ChangeLog                      |  2 +-
 virtual/blas/ChangeLog                             |  6 +-
 .../blas/{blas-2.1.ebuild => blas-2.1-r1.ebuild}   | 21 +++++--
 virtual/lapack/ChangeLog                           |  9 ++-
 .../{lapack-3.4.ebuild => lapack-3.4-r1.ebuild}    | 18 +++++-
 virtual/lapack/lapack-3.5.ebuild                   | 12 +++-
 virtual/lapack/metadata.xml                        |  4 +-
 60 files changed, 263 insertions(+), 76 deletions(-)

diff --cc virtual/blas/blas-2.1-r1.ebuild
index ae69926,e9762fe..6eb12ed
--- a/virtual/blas/blas-2.1-r1.ebuild
+++ b/virtual/blas/blas-2.1-r1.ebuild
@@@ -10,9 -12,11 +12,11 @@@ SRC_URI="
  
  LICENSE=""
  SLOT="0"
--KEYWORDS="~amd64 ~x86 ~amd64-linux"
++KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
  IUSE="doc"
- RDEPEND="|| (
+ 
+ RDEPEND="
+ 	|| (
  		>=sci-libs/blas-reference-20110417
  		>=dev-cpp/eigen-3.1.2
  		sci-libs/atlas[fortran]
@@@ -23,3 -27,12 +27,12 @@@
  	)
  	doc? ( >=app-doc/blas-docs-3.2 )"
  DEPEND=""
+ 
+ pkg_pretend() {
 -	if [[ -e "${EPREFIX}"/usr/$(get_libdir)/lib${PN}.so ]]; then
++	if [[ -e "${EROOT%/}"/usr/$(get_libdir)/lib${PN}.so ]]; then
+ 		ewarn "You have still the old ${PN} library symlink present"
+ 		ewarn "Please delete"
 -		ewarn "${EPREFIX}/usr/$(get_libdir)/lib${PN}.so"
++		ewarn "${EROOT%/}/usr/$(get_libdir)/lib${PN}.so"
+ 		ewarn "to avoid problems with new ${PN} structure"
+ 	fi
+ }
diff --cc virtual/lapack/lapack-3.5.ebuild
index 226cf97,b662bb4..ea254e5
--- a/virtual/lapack/lapack-3.5.ebuild
+++ b/virtual/lapack/lapack-3.5.ebuild
@@@ -2,8 -2,10 +2,8 @@@
  # Distributed under the terms of the GNU General Public License v2
  # $Header: $
  
- EAPI=2
+ EAPI=5
  
 -inherit multilib
 -
  DESCRIPTION="Virtual for Linear Algebra Package FORTRAN 77 implementation"
  HOMEPAGE=""
  SRC_URI=""
@@@ -19,3 -22,14 +19,13 @@@ RDEPEND="|| 
  	)
  	doc? ( >=app-doc/lapack-docs-3.3 )"
  DEPEND=""
+ 
++
+ pkg_pretend() {
 -	if [[ -e "${EPREFIX}"/usr/$(get_libdir)/lib${PN}.so ]]; then
++	if [[ -e "${EROOT%/}"/usr/$(get_libdir)/lib${PN}.so ]]; then
+ 		ewarn "You have still the old ${PN} library symlink present"
+ 		ewarn "Please delete"
 -		ewarn "${EPREFIX}/usr/$(get_libdir)/lib${PN}.so"
++		ewarn "${EROOT%/}/usr/$(get_libdir)/lib${PN}.so"
+ 		ewarn "to avoid problems with new ${PN} structure"
+ 	fi
+ }

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     87a2c5d53fdd78f94a8f9de19c6439084e7169cf
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 16 22:43:43 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Thu Jan 16 22:43:43 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=87a2c5d5

Merge github.com:gentoo-science/sci


 dev-cpp/eigen/ChangeLog                            |  8 +++-
 dev-cpp/eigen/Manifest                             |  1 +
 .../{eigen-9999.ebuild => eigen-3.2.0-r1.ebuild}   | 11 ++++-
 dev-cpp/eigen/metadata.xml                         | 14 +++---
 profiles/package.use.mask                          |  6 ++-
 sci-chemistry/avogadro2/ChangeLog                  | 10 ++++
 sci-chemistry/avogadro2/Manifest                   |  1 +
 sci-chemistry/avogadro2/avogadro2-0.7.2.ebuild     | 43 +++++++++++++++++
 sci-chemistry/{coot => avogadro2}/metadata.xml     |  4 +-
 sci-chemistry/chimera-bin/ChangeLog                |  7 ++-
 sci-chemistry/chimera-bin/Manifest                 |  2 +
 ...era-bin-1.8.ebuild => chimera-bin-1.8.1.ebuild} |  2 +-
 sci-chemistry/pymol/ChangeLog                      |  8 +++-
 sci-chemistry/pymol/Manifest                       |  2 +-
 sci-chemistry/pymol/pymol-9999.ebuild              | 13 ++---
 sci-chemistry/unio/ChangeLog                       |  7 ++-
 sci-chemistry/unio/Manifest                        |  1 +
 .../{unio-2.0.2-r1.ebuild => unio-2.0.3.ebuild}    |  4 +-
 sci-libs/avogadro-libs/ChangeLog                   | 18 -------
 sci-libs/avogadro-libs/Manifest                    |  1 -
 sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild  | 46 ------------------
 .../files/avogadro-libs-0.6.0-underlinking.patch   | 14 ------
 sci-libs/avogadro-libs/metadata.xml                | 14 ------
 sci-libs/chemkit/ChangeLog                         | 10 ----
 sci-libs/chemkit/Manifest                          |  1 -
 sci-libs/chemkit/chemkit-0.1.ebuild                | 55 ----------------------
 sci-libs/chemkit/metadata.xml                      | 11 -----
 sci-libs/lemon/ChangeLog                           |  4 ++
 sci-libs/lemon/files/lemon-1.3-underlinking.patch  | 47 ++++++++++++++++++
 .../{lemon-1.3.ebuild => lemon-1.3-r1.ebuild}      |  7 ++-
 sci-libs/openlibm/ChangeLog                        |  4 ++
 .../openlibm/files/openlibm-extras-soname.patch    | 11 -----
 sci-libs/openlibm/files/openlibm-soname.patch      | 11 -----
 sci-libs/openlibm/openlibm-9999.ebuild             | 10 ++--
 sys-cluster/openmpi/Manifest                       |  1 +
 sys-cluster/openmpi/metadata.xml                   |  2 +
 .../{openmpi-1.6.5.ebuild => openmpi-1.7.3.ebuild} | 27 +++++------
 37 files changed, 198 insertions(+), 240 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     1851cf074d03e9179ee1d629062697527af4188f
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 11 22:34:53 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Sat Jan 11 22:34:53 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1851cf07

Merge github.com:gentoo-science/sci


 dev-java/gluegen/Manifest                          |   2 +-
 ...y-jars.patch => 2.1.4_rc1-dont-copy-jars.patch} |   0
 ...dont-strip.patch => 2.1.4_rc1-dont-strip.patch} |   0
 ...ive.patch => 2.1.4_rc1-dont-test-archive.patch} |   0
 ...en-2.1.4_p1.ebuild => gluegen-2.1.4_rc1.ebuild} |   2 +-
 dev-java/jogl/ChangeLog                            |   6 +-
 dev-java/jogl/Manifest                             |   1 +
 dev-java/jogl/jogl-2.1.4_rc1.ebuild                |  74 +++
 media-gfx/librecad/ChangeLog                       |   3 +
 media-gfx/librecad/Manifest                        |   1 +
 sci-chemistry/chemBuild/ChangeLog                  |   5 +-
 sci-chemistry/chemBuild/chemBuild-1.0.3.ebuild     |   4 +-
 sci-chemistry/pesto/ChangeLog                      |   9 +
 sci-chemistry/{burrow-owl => pesto}/metadata.xml   |   0
 sci-chemistry/pesto/pesto-9999.ebuild              |  29 ++
 sci-chemistry/specView/ChangeLog                   |   5 +-
 sci-chemistry/specView/specView-1.0.3.ebuild       |   4 +-
 sci-libs/pmx/ChangeLog                             |  10 +
 sci-libs/pmx/metadata.xml                          |  13 +
 sci-libs/pmx/pmx-9999.ebuild                       |  26 ++
 sci-libs/vtk/ChangeLog                             | 495 +++++++++++++++++++++
 sci-libs/vtk/Manifest                              |   2 +
 sci-libs/vtk/files/vtk-6.0.0-install.patch         |  19 +
 sci-libs/vtk/files/vtk-6.0.0-netcdf.patch          |  75 ++++
 sci-libs/vtk/files/vtk-6.0.0-system.patch          |  27 ++
 sci-libs/vtk/files/vtk-6.0.0-vtkpython.patch       |  12 +
 sci-libs/vtk/metadata.xml                          |  19 +
 sci-libs/vtk/vtk-6.0.0.ebuild                      | 321 +++++++++++++
 .../scilab/files/scilab-5.5.0_beta1-nogui.patch    |  13 +
 sci-mathematics/scilab/scilab-5.5.0_beta1.ebuild   |  64 ++-
 30 files changed, 1199 insertions(+), 42 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     d6072a88ee04e6064163eb6e28341bdb530541c9
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 13 17:21:59 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Jan 13 17:21:59 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d6072a88

Merge github.com:gentoo-science/sci


 sci-chemistry/pesto/ChangeLog                      |   3 +
 sci-chemistry/pesto/pesto-9999.ebuild              |  13 +-
 sci-libs/cblas-reference/ChangeLog                 |   6 +-
 .../cblas-reference-20110218.ebuild                |   5 +-
 sci-libs/lemon/ChangeLog                           |   6 +-
 sci-libs/lemon/files/lemon-1.3-multilib.patch      |  18 +
 sci-libs/lemon/lemon-1.3.ebuild                    |   5 +-
 sci-libs/lemon/metadata.xml                        |  22 +-
 sci-libs/vtk/ChangeLog                             | 495 ---------------------
 sci-libs/vtk/Manifest                              |   2 -
 sci-libs/vtk/files/vtk-6.0.0-install.patch         |  19 -
 sci-libs/vtk/files/vtk-6.0.0-netcdf.patch          |  75 ----
 sci-libs/vtk/files/vtk-6.0.0-system.patch          |  27 --
 sci-libs/vtk/files/vtk-6.0.0-vtkpython.patch       |  12 -
 sci-libs/vtk/metadata.xml                          |  19 -
 sci-libs/vtk/vtk-6.0.0.ebuild                      | 321 -------------
 16 files changed, 60 insertions(+), 988 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     7e0fbaae91e26cc25f91eba2c5a3dc370c567115
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 11 22:33:33 2014 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Sat Jan 11 22:33:33 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7e0fbaae

Merge remote-tracking branch 'origin/master'


 app-benchmarks/numbench/ChangeLog                  |    5 +-
 app-benchmarks/numbench/numbench-9999.ebuild       |    4 +-
 app-doc/root-docs/ChangeLog                        |  108 -
 app-doc/root-docs/Manifest                         |    2 -
 .../files/root-docs-5.34.01-makehtml.patch         |   51 -
 app-doc/root-docs/metadata.xml                     |   14 -
 app-doc/root-docs/root-docs-5.34.10.ebuild         |   77 -
 app-doc/root-docs/root-docs-5.34.13.ebuild         |   77 -
 app-doc/root-docs/root-docs-9999.ebuild            |   97 -
 app-portage/g-octave/ChangeLog                     |    5 +-
 app-portage/g-octave/g-octave-9999.ebuild          |    5 +-
 app-text/jabref/ChangeLog                          |   55 +-
 app-text/jabref/Manifest                           |    1 +
 app-text/jabref/jabref-2.10_beta-r1.ebuild         |   65 +
 app-text/jabref/jabref-2.10_beta2-r1.ebuild        |   69 +
 ...ef-2.9.2-r1.ebuild => jabref-2.10_beta2.ebuild} |   20 +-
 app-text/jabref/jabref-2.9.2-r1.ebuild             |   12 +-
 app-text/jabref/jabref-2.9.2.ebuild                |   28 -
 app-text/jabref/metadata.xml                       |    8 +-
 app-vim/vim-gromacs/ChangeLog                      |    6 +-
 app-vim/vim-gromacs/metadata.xml                   |    4 +-
 app-vim/vim-gromacs/vim-gromacs-9999.ebuild        |   10 +-
 dev-java/fits/ChangeLog                            |   10 +
 dev-java/fits/fits-1.11.0-r1.ebuild                |   69 +
 dev-java/fits/fits-1.11.0.ebuild                   |   54 -
 dev-java/fits/metadata.xml                         |    4 +-
 dev-java/gluegen/ChangeLog                         |   16 +-
 dev-java/gluegen/Manifest                          |    1 +
 .../gluegen/files/2.1.4_p1-dont-copy-jars.patch    |   17 +
 dev-java/gluegen/files/2.1.4_p1-dont-strip.patch   |   22 +
 .../gluegen/files/2.1.4_p1-dont-test-archive.patch |   16 +
 dev-java/gluegen/gluegen-2.1.4_p1.ebuild           |   74 +
 dev-java/joda-convert/ChangeLog                    |   10 -
 dev-java/joda-convert/Manifest                     |    1 -
 dev-java/joda-convert/files/1.2-build.xml          |   99 -
 dev-java/joda-convert/joda-convert-1.2.ebuild      |   45 -
 dev-java/joda-time/ChangeLog                       |   10 -
 dev-java/joda-time/Manifest                        |    1 -
 dev-java/joda-time/joda-time-2.1.ebuild            |   47 -
 dev-java/joda-time/metadata.xml                    |    5 -
 dev-java/jogl/ChangeLog                            |    6 +-
 dev-java/jogl/Manifest                             |    2 +-
 .../jogl/{jogl-1.1.1.ebuild => jogl-1.1.1a.ebuild} |   18 +-
 dev-lang/ispc/ChangeLog                            |    8 +-
 dev-lang/ispc/ispc-9999.ebuild                     |   16 +-
 dev-lang/julia/ChangeLog                           |    5 +-
 dev-lang/julia/julia-9999.ebuild                   |    9 +-
 dev-lang/julia/metadata.xml                        |    4 +-
 dev-lang/path64/ChangeLog                          |    5 +-
 dev-lang/path64/path64-9999.ebuild                 |   18 +-
 dev-libs/libcuda/ChangeLog                         |    8 +-
 dev-libs/libcuda/libcuda-9999.ebuild               |   25 +-
 dev-libs/libcuda/metadata.xml                      |    8 +-
 dev-libs/libgdev/ChangeLog                         |    8 +-
 dev-libs/libgdev/libgdev-9999.ebuild               |   28 +-
 dev-libs/libgdev/metadata.xml                      |    8 +-
 dev-python/RecSQL/ChangeLog                        |    5 +-
 dev-python/RecSQL/RecSQL-9999.ebuild               |    4 +-
 dev-python/astropy/ChangeLog                       |    5 +-
 dev-python/astropy/astropy-9999.ebuild             |    6 +-
 dev-python/astropysics/ChangeLog                   |    5 +-
 dev-python/astropysics/astropysics-9999.ebuild     |    4 +-
 dev-python/dimensionful/ChangeLog                  |    5 +-
 dev-python/dimensionful/dimensionful-9999.ebuild   |    4 +-
 dev-tex/pythontex/ChangeLog                        |    8 +
 .../pythontex}/metadata.xml                        |    5 +-
 dev-tex/pythontex/pythontex-0.12.ebuild            |   24 +-
 dev-tex/pythontex/pythontex-9999.ebuild            |   33 +-
 eclass/alternatives-2.eclass                       |    2 +-
 media-gfx/librecad/ChangeLog                       |    9 +-
 media-gfx/librecad/Manifest                        |    1 -
 media-gfx/librecad/librecad-2.0.0_rc2.ebuild       |   45 -
 media-gfx/librecad/librecad-9999.ebuild            |    4 +-
 media-gfx/librecad/metadata.xml                    |   20 +-
 profiles/package.mask                              |   15 -
 profiles/package.use.mask                          |    7 +
 profiles/updates/4Q-2013                           |    1 +
 sci-biology/BG7/BG7-9999.ebuild                    |   22 +-
 sci-biology/BG7/ChangeLog                          |    5 +-
 .../omniorbpy => sci-biology/BG7}/metadata.xml     |    0
 sci-biology/amos/ChangeLog                         |    6 +
 sci-biology/amos/Manifest                          |    1 -
 sci-biology/amos/amos-3.1.0-r1.ebuild              |   30 -
 sci-biology/amos/amos-9999.ebuild                  |    8 +-
 sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch    |   15 -
 ...mos-3.1.0-goBambus2.py-indent-and-cleanup.patch |   25 -
 sci-biology/amos/files/amos.m4.patch               |   49 -
 sci-biology/artemis/ChangeLog                      |    6 +-
 sci-biology/artemis/artemis-9999.ebuild            |   34 +-
 sci-biology/artemis/metadata.xml                   |   10 +-
 sci-biology/bamtools/ChangeLog                     |    6 +-
 sci-biology/bamtools/bamtools-9999.ebuild          |   10 +-
 sci-biology/bamtools/metadata.xml                  |   12 +-
 sci-biology/biopython/ChangeLog                    |  346 --
 sci-biology/biopython/Manifest                     |    1 -
 sci-biology/biopython/biopython-1.62-r1.ebuild     |   51 -
 .../biopython/files/biopython-1.62-SffIO.patch     |   36 -
 sci-biology/biopython/metadata.xml                 |    5 -
 sci-biology/blasr/ChangeLog                        |    5 +-
 sci-biology/blasr/blasr-9999.ebuild                |    6 +-
 sci-biology/est2uni/ChangeLog                      |    6 +-
 sci-biology/est2uni/est2uni-9999.ebuild            |   23 +-
 sci-biology/est2uni/metadata.xml                   |   10 +-
 sci-biology/fastx_toolkit/ChangeLog                |    6 +-
 .../fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild    |    9 +-
 .../fastx_toolkit}/metadata.xml                    |    0
 sci-biology/genepop/ChangeLog                      |    6 +-
 sci-biology/genepop/Manifest                       |    2 +-
 ...{genepop-4.0.10.ebuild => genepop-4.2.1.ebuild} |   31 +-
 sci-biology/genepop/metadata.xml                   |   10 +-
 sci-biology/mira/ChangeLog                         |    7 +-
 sci-biology/mira/Manifest                          |    6 -
 sci-biology/mira/mira-3.4.0.1.ebuild               |   62 -
 sci-biology/mira/mira-3.4.1.1.ebuild               |   61 -
 sci-biology/mira/mira-3.9.15.ebuild                |   64 -
 sci-biology/mira/mira-3.9.9.ebuild                 |   61 -
 sci-biology/mira/mira-4.0_rc2.ebuild               |   80 -
 sci-biology/mira/mira-4.0_rc4.ebuild               |    6 +-
 sci-biology/miranda/ChangeLog                      |    6 +-
 sci-biology/miranda/metadata.xml                   |   10 +-
 sci-biology/miranda/miranda-3.3a.ebuild            |    4 +-
 sci-biology/mne-python/ChangeLog                   |    8 +
 .../mne-python}/metadata.xml                       |    0
 sci-biology/mne-python/mne-python-0.7.ebuild       |   56 +-
 sci-biology/mne-python/mne-python-9999.ebuild      |   56 +-
 sci-biology/mosaik/ChangeLog                       |    6 +-
 sci-biology/mosaik/Manifest                        |    1 -
 sci-biology/mosaik/metadata.xml                    |   10 +-
 sci-biology/mosaik/mosaik-1.1.0021.ebuild          |   40 -
 sci-biology/mosaik/mosaik-2.1.33.ebuild            |   38 +-
 sci-biology/mosaik/mosaik-9999.ebuild              |   36 +-
 sci-biology/mrfast/ChangeLog                       |    9 +
 sci-biology/mrfast/Manifest                        |    2 +-
 .../mrfast-2.1.0.3-disc_buffer_overflow.patch      |   52 -
 sci-biology/mrfast/metadata.xml                    |   10 +-
 ...mrfast-2.1.0.3.ebuild => mrfast-2.6.0.1.ebuild} |   23 +-
 sci-biology/mrsfast/ChangeLog                      |    8 +
 sci-biology/mrsfast/Manifest                       |    2 +-
 sci-biology/mrsfast/metadata.xml                   |   10 +-
 sci-biology/mrsfast/mrsfast-2.3.0.2.ebuild         |   30 -
 .../mrsfast-2.6.0.4.ebuild}                        |   25 +-
 sci-biology/psychopy/ChangeLog                     |    5 +-
 sci-biology/psychopy/psychopy-9999.ebuild          |   10 +-
 sci-biology/pybrain/ChangeLog                      |    5 +-
 sci-biology/pybrain/pybrain-9999.ebuild            |    7 +-
 sci-biology/pysurfer/ChangeLog                     |    8 +
 .../pysurfer}/metadata.xml                         |    0
 sci-biology/pysurfer/pysurfer-0.4.ebuild           |   14 +-
 sci-biology/pysurfer/pysurfer-9999.ebuild          |   16 +-
 sci-biology/staden/ChangeLog                       |    6 +-
 sci-biology/staden/metadata.xml                    |   10 +-
 sci-biology/staden/staden-2.0.0_beta9.ebuild       |    4 +-
 sci-biology/staden/staden-9999.ebuild              |   70 +-
 sci-biology/symap/ChangeLog                        |    5 +-
 .../omniorbpy => sci-biology/symap}/metadata.xml   |    0
 sci-biology/symap/symap-4.0.ebuild                 |   19 +-
 sci-chemistry/GromacsWrapper/ChangeLog             |    5 +-
 .../GromacsWrapper/GromacsWrapper-9999.ebuild      |   10 +-
 sci-chemistry/ball/ChangeLog                       |    5 +-
 sci-chemistry/ball/ball-9999.ebuild                |    4 +-
 sci-chemistry/bist/ChangeLog                       |    6 +-
 sci-chemistry/bist/bist-0.5.1-r1.ebuild            |    6 +-
 sci-chemistry/bist/metadata.xml                    |    8 +-
 sci-chemistry/burrow-owl/ChangeLog                 |    4 +
 sci-chemistry/burrow-owl/burrow-owl-9999.ebuild    |    9 +-
 sci-chemistry/burrow-owl/metadata.xml              |    2 +-
 sci-chemistry/dl_poly/ChangeLog                    |    4 +
 sci-chemistry/dl_poly/dl_poly-1.9.ebuild           |    2 +-
 sci-chemistry/dl_poly/dl_poly-4.05.ebuild          |    2 +-
 sci-chemistry/drawxtl/ChangeLog                    |    9 +-
 sci-chemistry/drawxtl/Manifest                     |    4 +-
 .../{drawxtl-44.ebuild => drawxtl-45.ebuild}       |   40 +-
 .../{drawxtl-54.ebuild => drawxtl-55.ebuild}       |   30 +-
 sci-chemistry/drawxtl/files/54-gcc44.patch         |   11 -
 sci-chemistry/drawxtl/files/54-ldflags.patch       |   11 -
 .../{44-gentoo.patch => drawxtl-45-gentoo.patch}   |   40 +-
 .../{54-gentoo.patch => drawxtl-55-gentoo.patch}   |   35 +-
 sci-chemistry/drawxtl/metadata.xml                 |    4 +-
 sci-chemistry/freeon/ChangeLog                     |   10 +-
 sci-chemistry/freeon/Manifest                      |    4 -
 sci-chemistry/freeon/freeon-1.0.1.ebuild           |   26 -
 sci-chemistry/freeon/freeon-1.0.2.ebuild           |   26 -
 sci-chemistry/freeon/freeon-1.0.3.ebuild           |   33 -
 sci-chemistry/freeon/freeon-1.0.ebuild             |   27 -
 sci-chemistry/freeon/freeon-9999.ebuild            |   13 +-
 sci-chemistry/freeon/metadata.xml                  |    2 +-
 sci-chemistry/gromacs/ChangeLog                    |   10 +-
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild      |   10 +-
 sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild     |    8 +-
 sci-chemistry/gromacs/gromacs-9999.ebuild          |    8 +-
 sci-chemistry/hydronmr/ChangeLog                   |    5 +-
 sci-chemistry/hydronmr/hydronmr-7c.ebuild          |    4 +-
 sci-chemistry/mtz2hkl/ChangeLog                    |    6 +-
 sci-chemistry/mtz2hkl/metadata.xml                 |    2 +-
 sci-chemistry/mtz2hkl/mtz2hkl-0.3.ebuild           |   17 +-
 sci-chemistry/mtz2sca/ChangeLog                    |    6 +-
 sci-chemistry/mtz2sca/metadata.xml                 |    2 +-
 sci-chemistry/mtz2sca/mtz2sca-0.3.ebuild           |   17 +-
 sci-chemistry/openbabel-java/ChangeLog             |    5 +-
 .../openbabel-java/openbabel-java-9999.ebuild      |   15 +-
 sci-chemistry/openbabel-perl/ChangeLog             |    5 +-
 .../openbabel-perl/openbabel-perl-9999.ebuild      |    6 +-
 sci-chemistry/openbabel-python/ChangeLog           |    5 +-
 .../openbabel-python/openbabel-python-9999.ebuild  |    5 +-
 sci-chemistry/openbabel-ruby/ChangeLog             |    5 +-
 .../openbabel-ruby/openbabel-ruby-9999.ebuild      |    7 +-
 sci-chemistry/openbabel/ChangeLog                  |    6 +-
 sci-chemistry/openbabel/metadata.xml               |   18 +-
 sci-chemistry/openbabel/openbabel-9999.ebuild      |    9 +-
 sci-chemistry/shiftx/ChangeLog                     |    5 +-
 sci-chemistry/shiftx/shiftx-1.1.ebuild             |   16 +-
 sci-chemistry/wxmacmolplt/ChangeLog                |   19 -
 sci-chemistry/wxmacmolplt/Manifest                 |    2 -
 .../wxmacmolplt/files/wxmacmolplt-7.4.3-glew.patch |   12 -
 sci-chemistry/wxmacmolplt/metadata.xml             |   11 -
 sci-chemistry/wxmacmolplt/wxmacmolplt-7.4.3.ebuild |   44 -
 sci-chemistry/wxmacmolplt/wxmacmolplt-7.5.ebuild   |   44 -
 sci-electronics/tnt/ChangeLog                      |    6 +-
 sci-electronics/tnt/Manifest                       |    2 +-
 .../tnt/files/tnt-1.2.2-autotools.patch            |  277 +
 sci-electronics/tnt/metadata.xml                   |    2 +-
 sci-electronics/tnt/tnt-1.2.2.ebuild               |   40 +-
 sci-geosciences/fullprof-bin/Manifest              |    1 -
 sci-libs/cblas-reference/ChangeLog                 |    4 +
 .../cblas-reference-20110218.ebuild                |   14 +-
 sci-libs/cblas-reference/metadata.xml              |    4 +-
 sci-libs/cgnslib/ChangeLog                         |    8 +-
 sci-libs/cgnslib/Manifest                          |    3 +-
 sci-libs/cgnslib/cgnslib-3.2.1.ebuild              |   49 +
 sci-libs/cgnslib/files/cgnslib-3.2.1-cmake.patch   |  149 +
 sci-libs/cgnslib/metadata.xml                      |    5 +-
 sci-libs/dealii/ChangeLog                          |    9 +
 sci-libs/dealii/Manifest                           |    2 +
 .../{dealii-8.0.0.ebuild => dealii-8.1.0.ebuild}   |    0
 sci-libs/dealii/dealii-9999.ebuild                 |   46 +-
 sci-libs/dealii/metadata.xml                       |   42 +-
 sci-libs/fftw/ChangeLog                            |    5 +-
 sci-libs/fftw/fftw-9999.ebuild                     |    4 +-
 sci-libs/fgsl/ChangeLog                            |    6 +-
 sci-libs/fgsl/fgsl-0.9.3.ebuild                    |   30 +-
 sci-libs/fgsl/fgsl-0.9.4.ebuild                    |   29 +-
 sci-libs/fgsl/metadata.xml                         |   12 +-
 sci-libs/ghmm/ChangeLog                            |    8 +-
 sci-libs/ghmm/files/ghmm-9999-link.patch           |   24 +
 sci-libs/ghmm/files/ghmm-9999-obsolete.patch       |   13 +
 sci-libs/ghmm/files/ghmm-9999-out-of-source.patch  |   40 +
 sci-libs/ghmm/files/ghmm-9999-respect.patch        |   12 +
 sci-libs/ghmm/ghmm-9999.ebuild                     |   55 +-
 sci-libs/itk/ChangeLog                             |    5 +-
 sci-libs/itk/metadata.xml                          |   20 +-
 sci-libs/magma/ChangeLog                           |   10 +
 sci-libs/magma/Manifest                            |    1 -
 sci-libs/magma/magma-1.3.0.ebuild                  |  142 -
 sci-libs/magma/magma-1.4.0.ebuild                  |   62 +-
 sci-libs/nibabel/ChangeLog                         |    8 +
 sci-libs/nibabel/metadata.xml                      |   18 +-
 sci-libs/nibabel/nibabel-1.3.0.ebuild              |    4 +-
 sci-libs/nibabel/nibabel-9999.ebuild               |    8 +-
 sci-libs/nipy/ChangeLog                            |    8 +
 sci-libs/nipy/metadata.xml                         |   12 +-
 sci-libs/nipy/nipy-0.3.0.ebuild                    |   10 +-
 sci-libs/nipy/nipy-9999.ebuild                     |   12 +-
 sci-libs/nipype/ChangeLog                          |    8 +
 sci-libs/nipype/metadata.xml                       |   12 +-
 sci-libs/nipype/nipype-9999.ebuild                 |    9 +-
 sci-libs/openblas/ChangeLog                        |    6 +-
 sci-libs/openblas/metadata.xml                     |   12 +-
 sci-libs/openblas/openblas-9999.ebuild             |   19 +-
 sci-libs/openlibm/ChangeLog                        |    6 +-
 sci-libs/openlibm/metadata.xml                     |    4 +-
 sci-libs/openlibm/openlibm-9999.ebuild             |   16 +-
 sci-libs/pagmo/ChangeLog                           |    8 +-
 sci-libs/pagmo/metadata.xml                        |   10 +-
 sci-libs/pagmo/pagmo-9999.ebuild                   |   20 +-
 sci-libs/pydicom/ChangeLog                         |    8 +
 .../omniorbpy => sci-libs/pydicom}/metadata.xml    |    0
 sci-libs/pydicom/pydicom-0.9.8.ebuild              |    6 +-
 sci-libs/starparse/ChangeLog                       |   14 +
 sci-libs/starparse/Manifest                        |    1 -
 .../starparse/files/starparse-9999-guile1.8.patch  |   60 +
 sci-libs/starparse/metadata.xml                    |    2 +-
 sci-libs/starparse/starparse-1.0.ebuild            |   28 -
 sci-libs/starparse/starparse-9999.ebuild           |   18 +-
 sci-libs/starparse/starparse-9999_pre10.ebuild     |   27 -
 sci-libs/trilinos/ChangeLog                        |    9 +-
 sci-libs/trilinos/metadata.xml                     |   64 +-
 sci-libs/trilinos/trilinos-11.0.3.ebuild           |   11 +-
 sci-libs/trilinos/trilinos-11.4.2.ebuild           |    4 +-
 sci-mathematics/cipi/ChangeLog                     |    5 +-
 sci-mathematics/cipi/Manifest                      |    1 +
 sci-mathematics/cipi/cipi-1.0.ebuild               |    9 +-
 sci-mathematics/cipi/metadata.xml                  |   12 +-
 sci-mathematics/open-axiom/ChangeLog               |    6 +-
 sci-mathematics/open-axiom/Manifest                |    1 +
 sci-mathematics/open-axiom/metadata.xml            |    4 +-
 sci-mathematics/open-axiom/open-axiom-1.4.2.ebuild |   37 +
 sci-mathematics/petsc/ChangeLog                    |    6 +-
 sci-mathematics/petsc/Manifest                     |    1 -
 sci-mathematics/petsc/metadata.xml                 |    2 +
 sci-mathematics/petsc/petsc-3.3_p5.ebuild          |  223 -
 sci-mathematics/petsc/petsc-3.4.2.ebuild           |   22 +-
 sci-mathematics/polymake/ChangeLog                 |    8 -
 sci-mathematics/polymake/Manifest                  |    1 -
 sci-mathematics/polymake/files/2.10-soname.patch   |   11 -
 .../files/polymake-2.11-drop-jreality.patch        |   25 -
 sci-mathematics/polymake/metadata.xml              |   17 -
 sci-mathematics/polymake/polymake-2.11-r1.ebuild   |   82 -
 sci-misc/elmer-meta/ChangeLog                      |    6 +-
 sci-misc/elmer-meta/elmer-meta-6.0_p4651.ebuild    |    5 +-
 sci-misc/elmer-meta/elmer-meta-9999.ebuild         |    5 +-
 sci-misc/simx/ChangeLog                            |    6 +-
 sci-misc/simx/metadata.xml                         |    2 +-
 sci-misc/simx/simx-0.1.ebuild                      |   16 +-
 sci-misc/simx/simx-9999.ebuild                     |   18 +-
 .../fullprof-bin/ChangeLog                         |    6 +-
 sci-physics/fullprof-bin/Manifest                  |    1 +
 .../fullprof-bin/fullprof-bin-20313.04.ebuild      |    2 +-
 .../fullprof-bin/metadata.xml                      |    0
 sci-physics/geant-vmc/ChangeLog                    |   13 +-
 sci-physics/geant-vmc/Manifest                     |    1 +
 sci-physics/geant-vmc/geant-vmc-4.2.14b.ebuild     |   14 +-
 ...-vmc-4.2.14b.ebuild => geant-vmc-4.2.15.ebuild} |   13 +-
 sci-physics/geant-vmc/metadata.xml                 |   10 +-
 sci-physics/lammps/ChangeLog                       |   71 -
 sci-physics/lammps/Manifest                        |    8 -
 sci-physics/lammps/lammps-20130816.ebuild          |  115 -
 sci-physics/lammps/lammps-20130830.ebuild          |  115 -
 sci-physics/lammps/lammps-20130917.ebuild          |  115 -
 sci-physics/lammps/lammps-20130923.ebuild          |  115 -
 sci-physics/lammps/lammps-20130930.ebuild          |  115 -
 sci-physics/lammps/lammps-20131111.ebuild          |  115 -
 sci-physics/lammps/lammps-20131123.ebuild          |  115 -
 sci-physics/lammps/lammps-20131201.ebuild          |  115 -
 sci-physics/lammps/metadata.xml                    |   31 -
 sci-physics/root/ChangeLog                         |   19 +-
 sci-physics/root/Manifest                          |    7 -
 .../root/files/root-5.28.00b-asneeded.patch        |   20 +
 .../root/files/root-5.28.00b-prop-ldflags.patch    |   13 +
 sci-physics/root/files/root-5.28.00b-unuran.patch  |   39 +
 .../files/root-5.32.00-explicit-functions.patch    |   18 +
 .../root/files/root-5.32.00-nobyte-compile.patch   |  137 +
 .../root/files/root-5.32.00-rmkdepend.patch        |   21 +
 sci-physics/root/files/root-5.32.00-rusage.patch   |   12 +
 sci-physics/root/metadata.xml                      |    1 +
 sci-physics/root/root-5.34.13.ebuild               |  425 --
 sci-physics/root/root-9999.ebuild                  |   21 +-
 sci-visualization/labplot/ChangeLog                |    8 +
 sci-visualization/labplot/labplot-9999.ebuild      |    5 +-
 sci-visualization/labplot/metadata.xml             |    2 +-
 sys-cluster/charm/ChangeLog                        |   20 +-
 sys-cluster/charm/Manifest                         |    2 +-
 sys-cluster/charm/charm-6.5.1-r2.ebuild            |  209 -
 ...m-6.5.1-r3.ebuild => charm-6.6.0_rc1-r1.ebuild} |   48 +-
 sys-cluster/lustre/ChangeLog                       |   91 +-
 ...ld-make-AC-check-for-linux-arch-sandbox-f.patch |   10 +-
 ...6-kernel-Kernel-update-for-3.7.2-201.fc18.patch |  169 -
 ...3-ldiskfs-ldiskfs-patches-for-3.11.1-fc19.patch | 5997 ++++++++++++++++++++
 ...rnel-3.9-hlist_for_each_entry-uses-3-args.patch |  117 -
 ...74-llite-dentry-d_compare-changes-in-3.11.patch |  132 +
 ...79-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch |   82 -
 ...-LU-3974-llite-use-new-struct-dir_context.patch |  276 +
 ...-LU-3974-llite-invalidatepage-api-changed.patch |  134 +
 ...cfs-move-llite-proc-handling-over-to-seq_.patch | 1334 +++++
 ...cfs-move-lmv-proc-handling-over-to-seq_fi.patch |  409 ++
 ...cfs-move-ldlm-proc-handling-over-to-seq_f.patch |  789 +++
 ...cfs-move-ost-proc-handling-over-to-seq_fi.patch |  174 +
 ...cfs-update-shared-server-side-core-proc-h.patch | 1260 ++++
 ...cfs-update-zfs-proc-handling-to-seq_files.patch |  171 +
 ...rocfs-move-mgs-proc-handling-to-seq_files.patch |  351 ++
 ...rocfs-move-ofd-proc-handling-to-seq_files.patch |  759 +++
 ...rocfs-move-lod-proc-handling-to-seq_files.patch |  589 ++
 ...rocfs-move-osp-proc-handling-to-seq_files.patch |  779 +++
 ...cfs-move-mdt-mds-proc-handling-to-seq_fil.patch | 1483 +++++
 ...rocfs-move-mdd-proc-handling-to-seq_files.patch |  788 +++
 ...cfs-update-ldiskfs-proc-handling-to-seq_f.patch |  748 +++
 sys-cluster/lustre/lustre-9999.ebuild              |   42 +-
 sys-cluster/nullmpi/ChangeLog                      |    5 +-
 sys-cluster/nullmpi/nullmpi-9999.ebuild            |    8 +-
 x11-misc/envytools/ChangeLog                       |    5 +-
 x11-misc/envytools/envytools-9999.ebuild           |    4 +-
 380 files changed, 19211 insertions(+), 5844 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     b42aab43eec7b89f6525be7cc8697c59f80cd60d
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 15 02:33:20 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Sun Dec 15 02:33:20 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b42aab43

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 app-text/jabref/ChangeLog                          |  3 +++
 app-text/jabref/metadata.xml                       |  2 +-
 sci-chemistry/freeon/ChangeLog                     |  3 +++
 sci-chemistry/freeon/metadata.xml                  |  2 +-
 sci-chemistry/mdsctk/ChangeLog                     |  9 +++++++++
 sci-chemistry/mdsctk/Manifest                      |  2 +-
 .../{mdsctk-1.1.0.ebuild => mdsctk-1.2.0.ebuild}   | 18 ++++++++----------
 sci-physics/espresso/ChangeLog                     |  3 +++
 sci-physics/espresso/espresso-9999.ebuild          |  6 +++---
 sci-physics/lammps/ChangeLog                       |  3 +++
 sci-physics/lammps/metadata.xml                    |  2 +-
 sci-physics/tauola/ChangeLog                       | 10 ++++++++++
 sci-physics/tauola/Manifest                        |  1 +
 ...-makefile.patch => tauola-1.1.4-makefile.patch} |  2 +-
 sci-physics/tauola/metadata.xml                    | 20 +++++++++-----------
 sci-physics/tauola/tauola-1.1.3.ebuild             | 20 +++++++++++---------
 .../{tauola-1.1.3.ebuild => tauola-1.1.4.ebuild}   | 22 ++++++++++++----------
 sci-physics/tauola/tauola-9999.ebuild              | 19 ++++++++++---------
 sys-cluster/charm/ChangeLog                        |  3 +++
 sys-cluster/charm/metadata.xml                     |  2 +-
 sys-cluster/modules/ChangeLog                      |  3 +++
 sys-cluster/modules/metadata.xml                   |  2 +-
 22 files changed, 98 insertions(+), 59 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     3e7363bf0d1a095b6598ec17934dcf14738dc706
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Dec  9 18:51:15 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Dec  9 18:51:15 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3e7363bf

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 app-admin/eselect/ChangeLog                        |   5 +
 app-admin/eselect/Manifest                         |   1 +
 ...t-1.3.7-r100.ebuild => eselect-1.4-r100.ebuild} |   4 +-
 dev-python/numpydoc/ChangeLog                      |  31 -----
 dev-python/numpydoc/Manifest                       |   1 -
 dev-python/numpydoc/metadata.xml                   |  11 --
 dev-python/numpydoc/numpydoc-0.4.ebuild            |  25 ----
 sci-biology/brat/ChangeLog                         |   8 +-
 sci-biology/brat/Manifest                          |   2 +-
 sci-biology/brat/brat-1.1.13.ebuild                |  22 ----
 sci-biology/brat/brat-1.2.4.ebuild                 |  43 +++++++
 sci-biology/brat/metadata.xml                      |  10 +-
 sci-chemistry/ball/ball-9999.ebuild                |   9 +-
 sci-chemistry/ball/files/ball-9999-libsvm.patch    |  24 ----
 sci-libs/mkl/ChangeLog                             |   5 +
 sci-libs/mkl/Manifest                              |   6 -
 sci-libs/mkl/mkl-11.0.3.163.ebuild                 | 131 ---------------------
 sci-libs/mkl/mkl-11.0.5.192.ebuild                 | 131 ---------------------
 ...-11.1.0.080.ebuild => mkl-11.1.0.080-r1.ebuild} |   3 +-
 sci-libs/xraylib/ChangeLog                         |   7 ++
 sci-libs/xraylib/Manifest                          |   1 +
 sci-libs/xraylib/metadata.xml                      |  38 ++++++
 sci-libs/xraylib/xraylib-2.16.0.ebuild             |  84 +++++++++++++
 sci-mathematics/acl2/ChangeLog                     |   5 +-
 sci-mathematics/acl2/Manifest                      |   3 +
 sci-mathematics/acl2/acl2-6.3.ebuild               |  69 +++++++++++
 sci-mathematics/acl2/metadata.xml                  |  32 +++--
 27 files changed, 306 insertions(+), 405 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     78a4d3c1f4bb4a78fb44bb127a31a7dad2e58b11
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Dec 10 16:50:48 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Dec 10 16:50:48 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=78a4d3c1

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-mathematics/acl2/acl2-6.3.ebuild              |   4 +-
 sci-physics/root/ChangeLog                        |   5 +
 sci-physics/root/Manifest                         |   7 +-
 sci-physics/root/files/root-5.28.00b-unuran.patch |  39 ---
 sci-physics/root/root-5.34.10-r2.ebuild           | 408 ----------------------
 sci-physics/root/root-5.34.13.ebuild              |  22 +-
 6 files changed, 29 insertions(+), 456 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Guillaume Horel]

commit:     ef53d574a5c73a13b09c0f83f6a9894f506aa960
Author:     Thrasibule <guillaume.horel <AT> gmail <DOT> com>
AuthorDate: Mon Jan 27 02:46:21 2014 +0000
Commit:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
CommitDate: Mon Jan 27 02:46:21 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ef53d574

Merge pull request #179 from xhochy/julia-utf8proc

Add missing dependency utf8proc for Julia


 dev-lang/julia/ChangeLog                           |  3 ++
 dev-lang/julia/julia-9999.ebuild                   |  1 +
 dev-libs/utf8proc/ChangeLog                        |  9 ++++++
 dev-libs/utf8proc/Manifest                         |  1 +
 .../utf8proc/files/utf8proc-1.1.6-buildflags.patch | 11 +++++++
 .../utf8proc/files/utf8proc-1.1.6-soname.patch     | 11 +++++++
 .../jrosetta => dev-libs/utf8proc}/metadata.xml    |  0
 dev-libs/utf8proc/utf8proc-1.1.6.ebuild            | 36 ++++++++++++++++++++++
 8 files changed, 72 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     efdfeb5e791069bf25575029a48cd572cb3bd792
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Sat Jan 25 22:37:07 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Sat Jan 25 22:37:07 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=efdfeb5e

Merge branch 'master' of github.com:gentoo-science/sci


 CONTRIBUTING.md                                    |   7 +
 app-admin/eselect/ChangeLog                        |  11 +-
 ...elect-1.3.8-r100.ebuild => eselect-9999.ebuild} |  26 +-
 dev-cpp/eigen/ChangeLog                            |   8 +-
 dev-cpp/eigen/Manifest                             |   1 +
 .../{eigen-9999.ebuild => eigen-3.2.0-r1.ebuild}   |  11 +-
 dev-cpp/eigen/metadata.xml                         |  14 +-
 dev-lang/julia/julia-9999.ebuild                   |  18 +-
 dev-lang/vtune/ChangeLog                           |   2 +-
 dev-libs/asmjit/ChangeLog                          |   2 +-
 dev-perl/Bio-BigFile/ChangeLog                     |   2 +-
 dev-python/opal-client/ChangeLog                   |   2 +-
 dev-python/pythonocc/ChangeLog                     |   8 +-
 eclass/alternatives-2.eclass                       | 147 ++++--
 licenses/HSL                                       | 222 ---------
 media-gfx/librecad/ChangeLog                       |   3 +
 media-gfx/librecad/Manifest                        |   1 +
 profiles/package.mask                              |   1 +
 profiles/package.use.mask                          |   9 +-
 sci-biology/YASRA/ChangeLog                        |   2 +-
 sci-biology/clover/ChangeLog                       |   2 +-
 sci-biology/cutadapt/ChangeLog                     |   2 +-
 sci-biology/fastx_toolkit/ChangeLog                |  11 +-
 sci-biology/fastx_toolkit/Manifest                 |   2 +-
 ...0.0.13.2.ebuild => fastx_toolkit-0.0.14.ebuild} |   7 +-
 sci-biology/lastz/ChangeLog                        |   4 +-
 sci-biology/mrfast/ChangeLog                       |   2 +-
 sci-biology/mrsfast/ChangeLog                      |   2 +-
 .../files/ncbi-tools++-12.0.0-as-needed.patch      | 555 +++++++++++----------
 .../files/ncbi-tools++-12.0.0-conf-opts.patch      | 183 +------
 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        |  14 +-
 sci-biology/sequin/ChangeLog                       |   2 +-
 sci-biology/tablet-bin/ChangeLog                   |  13 +-
 sci-biology/tablet-bin/Manifest                    |   2 +-
 ...3.05.17.ebuild => tablet-bin-1.13.12.17.ebuild} |   5 +-
 sci-chemistry/avogadro2/ChangeLog                  |  13 +
 sci-chemistry/avogadro2/Manifest                   |   1 +
 sci-chemistry/avogadro2/avogadro2-0.7.2.ebuild     |  48 ++
 sci-chemistry/{coot => avogadro2}/metadata.xml     |   4 +-
 sci-chemistry/chimera-bin/ChangeLog                |   9 +-
 sci-chemistry/chimera-bin/Manifest                 |   2 +
 ...era-bin-1.8.ebuild => chimera-bin-1.8.1.ebuild} |   2 +-
 sci-chemistry/drawxtl/ChangeLog                    |   2 +-
 sci-chemistry/mddnmr/ChangeLog                     |   2 +-
 sci-chemistry/modeller/ChangeLog                   |   2 +-
 sci-chemistry/nmrpipe/ChangeLog                    |  10 +-
 sci-chemistry/pesto/ChangeLog                      |  12 +
 sci-chemistry/{burrow-owl => pesto}/metadata.xml   |   0
 sci-chemistry/pesto/pesto-9999.ebuild              |  38 ++
 sci-chemistry/phenix-bin/ChangeLog                 |   2 +-
 sci-chemistry/polygon/ChangeLog                    |   2 +-
 sci-chemistry/pymol/ChangeLog                      |   8 +-
 sci-chemistry/pymol/Manifest                       |   2 +-
 sci-chemistry/pymol/pymol-9999.ebuild              |  13 +-
 sci-chemistry/simpson/ChangeLog                    |   2 +-
 sci-chemistry/specView/ChangeLog                   |   2 +-
 sci-chemistry/unio/ChangeLog                       |   7 +-
 sci-chemistry/unio/Manifest                        |   1 +
 .../{unio-2.0.2-r1.ebuild => unio-2.0.3.ebuild}    |   4 +-
 sci-geosciences/pydap/ChangeLog                    |   2 +-
 sci-geosciences/pydap_handlers_hdf5/ChangeLog      |   2 +-
 sci-geosciences/pydap_handlers_netcdf/ChangeLog    |   2 +-
 sci-geosciences/pydap_handlers_sql/ChangeLog       |   2 +-
 sci-geosciences/pydap_responses_kml/ChangeLog      |   2 +-
 sci-geosciences/pydap_responses_matlab/ChangeLog   |   2 +-
 sci-geosciences/pydap_responses_netcdf/ChangeLog   |   2 +-
 sci-geosciences/pydap_responses_wms/ChangeLog      |   2 +-
 sci-libs/avogadro-libs/ChangeLog                   |  18 -
 sci-libs/avogadro-libs/Manifest                    |   1 -
 sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild  |  46 --
 .../files/avogadro-libs-0.6.0-underlinking.patch   |  14 -
 sci-libs/avogadro-libs/metadata.xml                |  14 -
 sci-libs/cblas-reference/ChangeLog                 |   6 +-
 .../cblas-reference-20110218.ebuild                |   5 +-
 sci-libs/chemkit/ChangeLog                         |  10 -
 sci-libs/chemkit/Manifest                          |   1 -
 sci-libs/chemkit/chemkit-0.1.ebuild                |  55 --
 sci-libs/chemkit/metadata.xml                      |  11 -
 sci-libs/coinhsl/ChangeLog                         |  18 -
 sci-libs/coinhsl/Manifest                          |   2 -
 sci-libs/coinhsl/coinhsl-2012.12.21.ebuild         |  36 --
 sci-libs/coinhsl/coinhsl-2013.06.18.ebuild         |  32 --
 sci-libs/coinhsl/metadata.xml                      |  12 -
 sci-libs/coinor-alps/ChangeLog                     |  30 --
 sci-libs/coinor-alps/Manifest                      |   1 -
 sci-libs/coinor-alps/coinor-alps-1.4.7.ebuild      |  67 ---
 sci-libs/coinor-alps/metadata.xml                  |  13 -
 sci-libs/coinor-bcp/ChangeLog                      |  21 -
 sci-libs/coinor-bcp/Manifest                       |   1 -
 sci-libs/coinor-bcp/coinor-bcp-1.3.7.ebuild        |  56 ---
 sci-libs/coinor-bcp/metadata.xml                   |  13 -
 sci-libs/coinor-bcps/ChangeLog                     |  21 -
 sci-libs/coinor-bcps/Manifest                      |   1 -
 sci-libs/coinor-bcps/coinor-bcps-0.93.8.ebuild     |  67 ---
 sci-libs/coinor-bcps/metadata.xml                  |  13 -
 sci-libs/coinor-blis/ChangeLog                     |  30 --
 sci-libs/coinor-blis/Manifest                      |   1 -
 sci-libs/coinor-blis/coinor-blis-0.93.8.ebuild     |  65 ---
 sci-libs/coinor-blis/metadata.xml                  |  12 -
 sci-libs/coinor-bonmin/ChangeLog                   |  24 -
 sci-libs/coinor-bonmin/Manifest                    |   1 -
 sci-libs/coinor-bonmin/coinor-bonmin-1.7.3.ebuild  |  72 ---
 sci-libs/coinor-bonmin/metadata.xml                |  13 -
 sci-libs/coinor-buildtools/ChangeLog               |  15 -
 .../coinor-buildtools-0.7.9.ebuild                 |  38 --
 sci-libs/coinor-buildtools/metadata.xml            |   9 -
 sci-libs/coinor-cbc/ChangeLog                      |  39 --
 sci-libs/coinor-cbc/Manifest                       |   1 -
 sci-libs/coinor-cbc/coinor-cbc-2.8.7.ebuild        |  83 ---
 sci-libs/coinor-cbc/metadata.xml                   |  11 -
 sci-libs/coinor-cgl/ChangeLog                      |  36 --
 sci-libs/coinor-cgl/Manifest                       |   1 -
 sci-libs/coinor-cgl/coinor-cgl-0.58.4.ebuild       |  73 ---
 sci-libs/coinor-cgl/metadata.xml                   |  12 -
 sci-libs/coinor-clp/ChangeLog                      |  43 --
 sci-libs/coinor-clp/Manifest                       |   1 -
 sci-libs/coinor-clp/coinor-clp-1.15.5.ebuild       | 112 -----
 .../files/coinor-clp-1.15.1-mpi-header.patch       |  12 -
 sci-libs/coinor-clp/metadata.xml                   |  20 -
 sci-libs/coinor-couenne/ChangeLog                  |  21 -
 sci-libs/coinor-couenne/Manifest                   |   1 -
 .../coinor-couenne/coinor-couenne-0.4.6.ebuild     |  59 ---
 sci-libs/coinor-couenne/metadata.xml               |  12 -
 sci-libs/coinor-cppad/ChangeLog                    |  37 --
 sci-libs/coinor-cppad/Manifest                     |   1 -
 sci-libs/coinor-cppad/coinor-cppad-20131207.ebuild |  54 --
 sci-libs/coinor-cppad/metadata.xml                 |  14 -
 sci-libs/coinor-csdp/ChangeLog                     |  12 -
 sci-libs/coinor-csdp/Manifest                      |   1 -
 sci-libs/coinor-csdp/coinor-csdp-6.1.1.ebuild      | 100 ----
 sci-libs/coinor-csdp/metadata.xml                  |  16 -
 sci-libs/coinor-dip/ChangeLog                      |   9 -
 sci-libs/coinor-dip/Manifest                       |   1 -
 sci-libs/coinor-dip/coinor-dip-0.83.2.ebuild       |  62 ---
 sci-libs/coinor-dip/metadata.xml                   |  14 -
 sci-libs/coinor-dylp/ChangeLog                     |  21 -
 sci-libs/coinor-dylp/Manifest                      |   1 -
 sci-libs/coinor-dylp/coinor-dylp-1.9.3.ebuild      |  66 ---
 sci-libs/coinor-dylp/metadata.xml                  |  12 -
 sci-libs/coinor-flopcpp/ChangeLog                  |  21 -
 sci-libs/coinor-flopcpp/Manifest                   |   1 -
 .../coinor-flopcpp/coinor-flopcpp-1.1.6.ebuild     |  67 ---
 sci-libs/coinor-flopcpp/metadata.xml               |  14 -
 sci-libs/coinor-mp/ChangeLog                       |  24 -
 sci-libs/coinor-mp/Manifest                        |   1 -
 sci-libs/coinor-mp/coinor-mp-1.7.5.ebuild          |  56 ---
 sci-libs/coinor-mp/metadata.xml                    |  11 -
 sci-libs/coinor-netlib/ChangeLog                   |  25 -
 sci-libs/coinor-netlib/Manifest                    |   1 -
 sci-libs/coinor-netlib/coinor-netlib-1.2.6.ebuild  |  23 -
 sci-libs/coinor-netlib/metadata.xml                |   9 -
 sci-libs/coinor-os/ChangeLog                       |  15 -
 sci-libs/coinor-os/Manifest                        |   1 -
 sci-libs/coinor-os/coinor-os-2.8.2.ebuild          |  67 ---
 sci-libs/coinor-os/metadata.xml                    |  11 -
 sci-libs/coinor-osi/ChangeLog                      |  33 --
 sci-libs/coinor-osi/Manifest                       |   1 -
 sci-libs/coinor-osi/coinor-osi-0.106.4.ebuild      |  76 ---
 sci-libs/coinor-osi/metadata.xml                   |  15 -
 sci-libs/coinor-sample/ChangeLog                   |  43 --
 sci-libs/coinor-sample/Manifest                    |   1 -
 sci-libs/coinor-sample/coinor-sample-1.2.9.ebuild  |  23 -
 sci-libs/coinor-sample/metadata.xml                |   9 -
 sci-libs/coinor-smi/ChangeLog                      |   9 -
 sci-libs/coinor-smi/Manifest                       |   1 -
 sci-libs/coinor-smi/coinor-smi-0.93.3.ebuild       |  69 ---
 sci-libs/coinor-smi/metadata.xml                   |  18 -
 sci-libs/coinor-symphony/ChangeLog                 |  33 --
 sci-libs/coinor-symphony/Manifest                  |   1 -
 .../coinor-symphony/coinor-symphony-5.5.6.ebuild   |  89 ----
 sci-libs/coinor-symphony/metadata.xml              |  18 -
 sci-libs/coinor-utils/ChangeLog                    |  39 --
 sci-libs/coinor-utils/Manifest                     |   1 -
 sci-libs/coinor-utils/coinor-utils-2.9.10.ebuild   |  85 ----
 sci-libs/coinor-utils/metadata.xml                 |  15 -
 sci-libs/coinor-vol/ChangeLog                      |  24 -
 sci-libs/coinor-vol/Manifest                       |   1 -
 sci-libs/coinor-vol/coinor-vol-1.4.3.ebuild        |  71 ---
 sci-libs/coinor-vol/metadata.xml                   |  10 -
 sci-libs/ipopt/ChangeLog                           |  40 --
 sci-libs/ipopt/Manifest                            |   1 -
 sci-libs/ipopt/files/ipopt-3.11.2-mpi-header.patch |  14 -
 sci-libs/ipopt/ipopt-3.11.6.ebuild                 | 100 ----
 sci-libs/ipopt/metadata.xml                        |  18 -
 sci-libs/lemon/ChangeLog                           |  30 --
 sci-libs/lemon/Manifest                            |   1 -
 sci-libs/lemon/lemon-1.3.ebuild                    |  75 ---
 sci-libs/lemon/metadata.xml                        |  23 -
 sci-libs/libgeodecomp/Manifest                     |   1 +
 ...comp-0.2.0.ebuild => libgeodecomp-0.3.1.ebuild} |   0
 sci-libs/libxc/ChangeLog                           |   2 +-
 sci-libs/magma/ChangeLog                           |  52 --
 sci-libs/magma/Manifest                            |   1 -
 .../magma/files/magma-1.2.1-no-cuda-driver.patch   |  38 --
 sci-libs/magma/magma-1.4.0.ebuild                  | 126 -----
 sci-libs/magma/metadata.xml                        |  15 -
 sci-libs/mkl/ChangeLog                             |   2 +-
 sci-libs/msms/ChangeLog                            |   4 +-
 sci-libs/openlibm/ChangeLog                        |   4 +
 .../openlibm/files/openlibm-extras-soname.patch    |  11 -
 sci-libs/openlibm/files/openlibm-soname.patch      |  11 -
 sci-libs/openlibm/openlibm-9999.ebuild             |  10 +-
 sci-libs/scalapack/ChangeLog                       |   8 +-
 ...pack-2.0.2.ebuild => scalapack-2.0.2-r1.ebuild} |   4 +-
 sci-libs/silo/Manifest                             |   1 +
 sci-libs/silo/files/silo-4.9.1-qtlibs.patch        |  66 +++
 sci-libs/silo/metadata.xml                         |  18 +
 sci-libs/silo/silo-4.9.1.ebuild                    |  35 ++
 .../gappalib-coq/gappalib-coq-0.18.0.ebuild        |   2 +-
 sci-mathematics/mdp/ChangeLog                      |   2 +-
 sci-misc/nltk/ChangeLog                            |   2 +-
 skel.ChangeLog                                     |   2 +-
 skel.ebuild                                        |   2 +-
 skel.metadata.xml                                  |   1 -
 sys-cluster/openmpi/Manifest                       |   1 +
 sys-cluster/openmpi/metadata.xml                   |   2 +
 .../{openmpi-1.6.5.ebuild => openmpi-1.7.3.ebuild} |  27 +-
 sys-cluster/pyslice/ChangeLog                      |   2 +-
 virtual/blas/ChangeLog                             |   6 +-
 .../blas/{blas-2.1.ebuild => blas-2.1-r1.ebuild}   |  19 +-
 virtual/lapack/ChangeLog                           |   6 +-
 .../{lapack-3.4.ebuild => lapack-3.4-r1.ebuild}    |  18 +-
 virtual/lapack/metadata.xml                        |   4 +-
 223 files changed, 916 insertions(+), 4253 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Reinis Danne]

commit:     a04ca120483d242ed26af549324473df23a941de
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 21 21:09:11 2014 +0000
Commit:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Tue Jan 21 21:09:11 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a04ca120

Add initial contribution FAQ

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 CONTRIBUTING.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 0000000..7579f6d
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,7 @@
+#Contributions to the Gentoo Science Overlay
+
+##Prerequisite
+
+###For Contributors
+
+###For Maintainers

[gentoo-commits] proj/sci:master commit in: /

[Reinis Danne]

commit:     4f944448ca95b985e4270f35d05822023f7ce7f0
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Tue Jan 21 22:04:28 2014 +0000
Commit:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Tue Jan 21 22:04:28 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4f944448

Merge pull request #177 from Reinis/alternatives-2

alternatives-2.eclass updates


 eclass/alternatives-2.eclass | 138 +++++++++++++++++++++++++++++++------------
 1 file changed, 100 insertions(+), 38 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Reinis Danne]

commit:     83bd255e6aacd81a436b001623a67b91f877cf16
Author:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
AuthorDate: Tue Jan 21 18:01:46 2014 +0000
Commit:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Tue Jan 21 18:01:46 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=83bd255e

Merge github.com:gentoo-science/sci


 app-admin/eselect/ChangeLog                        |   7 +-
 ...elect-1.3.8-r100.ebuild => eselect-9999.ebuild} |  26 ++-
 eclass/alternatives-2.eclass                       |  19 +-
 licenses/HSL                                       | 222 ---------------------
 profiles/package.mask                              |   1 +
 5 files changed, 31 insertions(+), 244 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     29aa84626a9605fbc6009c0ce820c2a96d5a5a12
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Mon Jan 20 08:51:43 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan 20 08:51:43 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=29aa8462

Merge https://github.com/gentoo-science/sci


 dev-cpp/eigen/ChangeLog                            |   8 +-
 dev-cpp/eigen/Manifest                             |   1 +
 .../{eigen-9999.ebuild => eigen-3.2.0-r1.ebuild}   |  11 +-
 dev-cpp/eigen/metadata.xml                         |  14 +--
 dev-lang/julia/julia-9999.ebuild                   |  18 ++-
 profiles/package.use.mask                          |   3 +
 sci-chemistry/avogadro2/ChangeLog                  |  13 +++
 sci-chemistry/avogadro2/Manifest                   |   1 +
 sci-chemistry/avogadro2/avogadro2-0.7.2.ebuild     |  48 ++++++++
 sci-chemistry/{coot => avogadro2}/metadata.xml     |   4 +-
 sci-libs/avogadro-libs/ChangeLog                   |  18 ---
 sci-libs/avogadro-libs/Manifest                    |   1 -
 sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild  |  46 --------
 .../files/avogadro-libs-0.6.0-underlinking.patch   |  14 ---
 sci-libs/avogadro-libs/metadata.xml                |  14 ---
 sci-libs/chemkit/ChangeLog                         |  10 --
 sci-libs/chemkit/Manifest                          |   1 -
 sci-libs/chemkit/chemkit-0.1.ebuild                |  55 ---------
 sci-libs/chemkit/metadata.xml                      |  11 --
 sci-libs/coinhsl/ChangeLog                         |  18 ---
 sci-libs/coinhsl/Manifest                          |   2 -
 sci-libs/coinhsl/coinhsl-2012.12.21.ebuild         |  36 ------
 sci-libs/coinhsl/coinhsl-2013.06.18.ebuild         |  32 ------
 sci-libs/coinhsl/metadata.xml                      |  12 --
 sci-libs/coinor-alps/ChangeLog                     |  30 -----
 sci-libs/coinor-alps/Manifest                      |   1 -
 sci-libs/coinor-alps/coinor-alps-1.4.7.ebuild      |  67 -----------
 sci-libs/coinor-alps/metadata.xml                  |  13 ---
 sci-libs/coinor-bcp/ChangeLog                      |  21 ----
 sci-libs/coinor-bcp/Manifest                       |   1 -
 sci-libs/coinor-bcp/coinor-bcp-1.3.7.ebuild        |  56 ---------
 sci-libs/coinor-bcp/metadata.xml                   |  13 ---
 sci-libs/coinor-bcps/ChangeLog                     |  21 ----
 sci-libs/coinor-bcps/Manifest                      |   1 -
 sci-libs/coinor-bcps/coinor-bcps-0.93.8.ebuild     |  67 -----------
 sci-libs/coinor-bcps/metadata.xml                  |  13 ---
 sci-libs/coinor-blis/ChangeLog                     |  30 -----
 sci-libs/coinor-blis/Manifest                      |   1 -
 sci-libs/coinor-blis/coinor-blis-0.93.8.ebuild     |  65 -----------
 sci-libs/coinor-blis/metadata.xml                  |  12 --
 sci-libs/coinor-bonmin/ChangeLog                   |  24 ----
 sci-libs/coinor-bonmin/Manifest                    |   1 -
 sci-libs/coinor-bonmin/coinor-bonmin-1.7.3.ebuild  |  72 ------------
 sci-libs/coinor-bonmin/metadata.xml                |  13 ---
 sci-libs/coinor-buildtools/ChangeLog               |  15 ---
 .../coinor-buildtools-0.7.9.ebuild                 |  38 -------
 sci-libs/coinor-buildtools/metadata.xml            |   9 --
 sci-libs/coinor-cbc/ChangeLog                      |  39 -------
 sci-libs/coinor-cbc/Manifest                       |   1 -
 sci-libs/coinor-cbc/coinor-cbc-2.8.7.ebuild        |  83 --------------
 sci-libs/coinor-cbc/metadata.xml                   |  11 --
 sci-libs/coinor-cgl/ChangeLog                      |  36 ------
 sci-libs/coinor-cgl/Manifest                       |   1 -
 sci-libs/coinor-cgl/coinor-cgl-0.58.4.ebuild       |  73 ------------
 sci-libs/coinor-cgl/metadata.xml                   |  12 --
 sci-libs/coinor-clp/ChangeLog                      |  43 -------
 sci-libs/coinor-clp/Manifest                       |   1 -
 sci-libs/coinor-clp/coinor-clp-1.15.5.ebuild       | 112 ------------------
 .../files/coinor-clp-1.15.1-mpi-header.patch       |  12 --
 sci-libs/coinor-clp/metadata.xml                   |  20 ----
 sci-libs/coinor-couenne/ChangeLog                  |  21 ----
 sci-libs/coinor-couenne/Manifest                   |   1 -
 .../coinor-couenne/coinor-couenne-0.4.6.ebuild     |  59 ----------
 sci-libs/coinor-couenne/metadata.xml               |  12 --
 sci-libs/coinor-cppad/ChangeLog                    |  37 ------
 sci-libs/coinor-cppad/Manifest                     |   1 -
 sci-libs/coinor-cppad/coinor-cppad-20131207.ebuild |  54 ---------
 sci-libs/coinor-cppad/metadata.xml                 |  14 ---
 sci-libs/coinor-csdp/ChangeLog                     |  12 --
 sci-libs/coinor-csdp/Manifest                      |   1 -
 sci-libs/coinor-csdp/coinor-csdp-6.1.1.ebuild      | 100 ----------------
 sci-libs/coinor-csdp/metadata.xml                  |  16 ---
 sci-libs/coinor-dip/ChangeLog                      |   9 --
 sci-libs/coinor-dip/Manifest                       |   1 -
 sci-libs/coinor-dip/coinor-dip-0.83.2.ebuild       |  62 ----------
 sci-libs/coinor-dip/metadata.xml                   |  14 ---
 sci-libs/coinor-dylp/ChangeLog                     |  21 ----
 sci-libs/coinor-dylp/Manifest                      |   1 -
 sci-libs/coinor-dylp/coinor-dylp-1.9.3.ebuild      |  66 -----------
 sci-libs/coinor-dylp/metadata.xml                  |  12 --
 sci-libs/coinor-flopcpp/ChangeLog                  |  21 ----
 sci-libs/coinor-flopcpp/Manifest                   |   1 -
 .../coinor-flopcpp/coinor-flopcpp-1.1.6.ebuild     |  67 -----------
 sci-libs/coinor-flopcpp/metadata.xml               |  14 ---
 sci-libs/coinor-mp/ChangeLog                       |  24 ----
 sci-libs/coinor-mp/Manifest                        |   1 -
 sci-libs/coinor-mp/coinor-mp-1.7.5.ebuild          |  56 ---------
 sci-libs/coinor-mp/metadata.xml                    |  11 --
 sci-libs/coinor-netlib/ChangeLog                   |  25 ----
 sci-libs/coinor-netlib/Manifest                    |   1 -
 sci-libs/coinor-netlib/coinor-netlib-1.2.6.ebuild  |  23 ----
 sci-libs/coinor-netlib/metadata.xml                |   9 --
 sci-libs/coinor-os/ChangeLog                       |  15 ---
 sci-libs/coinor-os/Manifest                        |   1 -
 sci-libs/coinor-os/coinor-os-2.8.2.ebuild          |  67 -----------
 sci-libs/coinor-os/metadata.xml                    |  11 --
 sci-libs/coinor-osi/ChangeLog                      |  33 ------
 sci-libs/coinor-osi/Manifest                       |   1 -
 sci-libs/coinor-osi/coinor-osi-0.106.4.ebuild      |  76 -------------
 sci-libs/coinor-osi/metadata.xml                   |  15 ---
 sci-libs/coinor-sample/ChangeLog                   |  43 -------
 sci-libs/coinor-sample/Manifest                    |   1 -
 sci-libs/coinor-sample/coinor-sample-1.2.9.ebuild  |  23 ----
 sci-libs/coinor-sample/metadata.xml                |   9 --
 sci-libs/coinor-smi/ChangeLog                      |   9 --
 sci-libs/coinor-smi/Manifest                       |   1 -
 sci-libs/coinor-smi/coinor-smi-0.93.3.ebuild       |  69 -----------
 sci-libs/coinor-smi/metadata.xml                   |  18 ---
 sci-libs/coinor-symphony/ChangeLog                 |  33 ------
 sci-libs/coinor-symphony/Manifest                  |   1 -
 .../coinor-symphony/coinor-symphony-5.5.6.ebuild   |  89 ---------------
 sci-libs/coinor-symphony/metadata.xml              |  18 ---
 sci-libs/coinor-utils/ChangeLog                    |  39 -------
 sci-libs/coinor-utils/Manifest                     |   1 -
 sci-libs/coinor-utils/coinor-utils-2.9.10.ebuild   |  85 --------------
 sci-libs/coinor-utils/metadata.xml                 |  15 ---
 sci-libs/coinor-vol/ChangeLog                      |  24 ----
 sci-libs/coinor-vol/Manifest                       |   1 -
 sci-libs/coinor-vol/coinor-vol-1.4.3.ebuild        |  71 ------------
 sci-libs/coinor-vol/metadata.xml                   |  10 --
 sci-libs/ipopt/ChangeLog                           |  40 -------
 sci-libs/ipopt/Manifest                            |   1 -
 sci-libs/ipopt/files/ipopt-3.11.2-mpi-header.patch |  14 ---
 sci-libs/ipopt/ipopt-3.11.6.ebuild                 | 100 ----------------
 sci-libs/ipopt/metadata.xml                        |  18 ---
 sci-libs/lemon/ChangeLog                           |  38 -------
 sci-libs/lemon/Manifest                            |   1 -
 sci-libs/lemon/files/lemon-1.3-multilib.patch      |  18 ---
 sci-libs/lemon/files/lemon-1.3-underlinking.patch  |  47 --------
 sci-libs/lemon/lemon-1.3-r1.ebuild                 |  83 --------------
 sci-libs/lemon/metadata.xml                        |  23 ----
 sci-libs/magma/ChangeLog                           |  52 ---------
 sci-libs/magma/Manifest                            |   1 -
 .../magma/files/magma-1.2.1-no-cuda-driver.patch   |  38 -------
 sci-libs/magma/magma-1.4.0.ebuild                  | 126 ---------------------
 sci-libs/magma/metadata.xml                        |  15 ---
 sci-libs/scalapack/ChangeLog                       |   8 +-
 ...pack-2.0.2.ebuild => scalapack-2.0.2-r1.ebuild} |   4 +-
 .../gappalib-coq/gappalib-coq-0.18.0.ebuild        |   2 +-
 skel.ChangeLog                                     |   2 +-
 skel.ebuild                                        |   2 +-
 skel.metadata.xml                                  |   1 -
 virtual/blas/ChangeLog                             |   6 +-
 .../blas/{blas-2.1.ebuild => blas-2.1-r1.ebuild}   |  19 +++-
 virtual/lapack/ChangeLog                           |   6 +-
 .../{lapack-3.4.ebuild => lapack-3.4-r1.ebuild}    |  18 ++-
 virtual/lapack/metadata.xml                        |   4 +-
 147 files changed, 163 insertions(+), 3489 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     49e2019a54328c4a1ed1bdaf60f6d58d8eddd7b9
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Mon Jan 20 08:51:32 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan 20 08:51:32 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=49e2019a

Merge /usr/local/portage/andis_overlay


 sci-libs/libgeodecomp/Manifest                     |  1 +
 ...comp-0.2.0.ebuild => libgeodecomp-0.3.1.ebuild} |  0
 sci-libs/silo/Manifest                             |  1 +
 sci-libs/silo/files/silo-4.9.1-qtlibs.patch        | 66 ++++++++++++++++++++++
 sci-libs/silo/metadata.xml                         | 18 ++++++
 sci-libs/silo/silo-4.9.1.ebuild                    | 35 ++++++++++++
 6 files changed, 121 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5349078bd75ce915687988b6ba97c4c1920ab283
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 19 18:33:49 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 19 18:33:49 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5349078b

Update Copyright Year

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 skel.ChangeLog    | 2 +-
 skel.ebuild       | 2 +-
 skel.metadata.xml | 1 -
 3 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/skel.ChangeLog b/skel.ChangeLog
index 6a6f1d0..8075b07 100644
--- a/skel.ChangeLog
+++ b/skel.ChangeLog
@@ -1,5 +1,5 @@
 # ChangeLog for <CATEGORY>/<PACKAGE_NAME>
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
 *<PACKAGE_NAME>-<PACKAGE_VERSION>-<PACKAGE_RELEASE> (DD MMM YYYY)

diff --git a/skel.ebuild b/skel.ebuild
index 93f5e16..a547c22 100644
--- a/skel.ebuild
+++ b/skel.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 

diff --git a/skel.metadata.xml b/skel.metadata.xml
index 17b08b4..4c6550e 100644
--- a/skel.metadata.xml
+++ b/skel.metadata.xml
@@ -1,7 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-
 <herd>sci-blah</herd>
 <maintainer>
   <email>my.email@blah.doh</email>

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     dca9a2a3cfa7c47494d7af349d8056732558abde
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 18 07:39:08 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 18 07:39:08 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=dca9a2a3

Merge remote-tracking branch 'github/master'

* github/master: (30 commits)
  Fix typo in gappalib-coq-0.18.0.ebuild
  sci-chemistry/avogadro2: fix USE deps; don't install license file
  sci-libs/scalapack: Revbump to use alternatives vs. tree
  in main tree
  dev-cpp/eigen: Backport cmake fix
  sci-chemistry/avogadro2: New package, written by me
  inCvs
  sci-libs/avogadro-libs: Version BUmp
  inVCS
  sci-libs/chemkit: Fix multilib installation; fix test
  sci-libs/chemkit: Add missing eclass
  [sci-libs/openlibm] Remove extras and soname patch
  sci-chemistry/unio: Version BUmp
  removed superfluous die commands after emake
  sci-chemistry/chimera-bin: Version BUmp, #498154
  sci-chemistry/pymol: Readd argparse fix; fix icon installation
  sci-chemistry/pymol: Merge tree changes
  sci-libs/lemon: Import latest tree changes
  InCVS
  sci-libs/lemon: Fix for multilib-strict
  ...


 profiles/package.use.mask | 4 ++++
 1 file changed, 4 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     219da116e1447b49fa701947d16528c26976c902
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 16 12:15:14 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jan 16 12:15:14 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=219da116

Merge branch 'gentryx-master'

* gentryx-master:
  removed superfluous die commands after emake
  refactored CUDA use flag handling
  added ebuild for Open MPI 1.7.3


 profiles/package.use.mask                          |  6 ++++-
 sys-cluster/openmpi/Manifest                       |  1 +
 sys-cluster/openmpi/metadata.xml                   |  2 ++
 .../{openmpi-1.6.5.ebuild => openmpi-1.7.3.ebuild} | 27 ++++++++++------------
 4 files changed, 20 insertions(+), 16 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     cc8c047aa05d4b0ca5a044ab99b581daf3e3aaee
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 16 13:16:12 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jan 16 13:16:12 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cc8c047a

Merge branch 'xhochy-openlibm-9999-no-extras'

* xhochy-openlibm-9999-no-extras:
  [sci-libs/openlibm] Remove extras and soname patch


 sci-libs/openlibm/ChangeLog                          |  4 ++++
 sci-libs/openlibm/files/openlibm-extras-soname.patch | 11 -----------
 sci-libs/openlibm/files/openlibm-soname.patch        | 11 -----------
 sci-libs/openlibm/openlibm-9999.ebuild               | 10 +++-------
 4 files changed, 7 insertions(+), 29 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     de53f27d6c4332547312018d75ee7ffc7e905f8a
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Thu Jan 16 10:08:53 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jan 16 10:08:53 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=de53f27d

Merge https://github.com/gentoo-science/sci


 sci-chemistry/pesto/ChangeLog                      |   3 +
 sci-chemistry/pesto/pesto-9999.ebuild              |  13 +-
 sci-libs/cblas-reference/ChangeLog                 |   6 +-
 .../cblas-reference-20110218.ebuild                |   5 +-
 sci-libs/lemon/ChangeLog                           |   6 +-
 sci-libs/lemon/files/lemon-1.3-multilib.patch      |  18 +
 sci-libs/lemon/lemon-1.3.ebuild                    |   5 +-
 sci-libs/lemon/metadata.xml                        |  22 +-
 sci-libs/vtk/ChangeLog                             | 495 ---------------------
 sci-libs/vtk/Manifest                              |   2 -
 sci-libs/vtk/files/vtk-6.0.0-install.patch         |  19 -
 sci-libs/vtk/files/vtk-6.0.0-netcdf.patch          |  75 ----
 sci-libs/vtk/files/vtk-6.0.0-system.patch          |  27 --
 sci-libs/vtk/files/vtk-6.0.0-vtkpython.patch       |  12 -
 sci-libs/vtk/metadata.xml                          |  19 -
 sci-libs/vtk/vtk-6.0.0.ebuild                      | 321 -------------
 16 files changed, 60 insertions(+), 988 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     37c147172bcabefca0bad3163e9e54919a781336
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Thu Jan 16 10:05:29 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jan 16 10:05:29 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=37c14717

merge


 app-benchmarks/numbench/ChangeLog                  |   5 +-
 app-benchmarks/numbench/numbench-9999.ebuild       |   4 +-
 app-portage/g-octave/ChangeLog                     |   5 +-
 app-portage/g-octave/g-octave-9999.ebuild          |   5 +-
 app-text/jabref/ChangeLog                          |  51 ++-
 app-text/jabref/Manifest                           |   2 +
 app-text/jabref/jabref-2.10_beta-r1.ebuild         |  65 +++
 app-text/jabref/jabref-2.10_beta2-r1.ebuild        |  69 +++
 ...f-2.10_beta.ebuild => jabref-2.10_beta2.ebuild} |  12 +-
 ...ref-2.10_beta.ebuild => jabref-2.9.2-r1.ebuild} |  22 +-
 app-text/jabref/metadata.xml                       |   8 +-
 app-vim/vim-gromacs/ChangeLog                      |   6 +-
 app-vim/vim-gromacs/metadata.xml                   |   4 +-
 app-vim/vim-gromacs/vim-gromacs-9999.ebuild        |  10 +-
 dev-java/gluegen/ChangeLog                         |  16 +-
 dev-java/gluegen/Manifest                          |   1 +
 .../gluegen/files/2.1.4_rc1-dont-copy-jars.patch   |  17 +
 dev-java/gluegen/files/2.1.4_rc1-dont-strip.patch  |  22 +
 .../files/2.1.4_rc1-dont-test-archive.patch        |  16 +
 dev-java/gluegen/gluegen-2.1.4_rc1.ebuild          |  74 +++
 dev-java/jogl/ChangeLog                            |  12 +-
 dev-java/jogl/Manifest                             |   3 +-
 .../jogl/{jogl-1.1.1.ebuild => jogl-1.1.1a.ebuild} |  18 +-
 dev-java/jogl/jogl-2.1.4_rc1.ebuild                |  74 +++
 dev-lang/ispc/ChangeLog                            |   8 +-
 dev-lang/ispc/ispc-9999.ebuild                     |  16 +-
 dev-lang/julia/ChangeLog                           |   5 +-
 dev-lang/julia/julia-9999.ebuild                   |   9 +-
 dev-lang/julia/metadata.xml                        |   4 +-
 dev-lang/path64/ChangeLog                          |   5 +-
 dev-lang/path64/path64-9999.ebuild                 |  18 +-
 dev-libs/libcuda/ChangeLog                         |   8 +-
 dev-libs/libcuda/libcuda-9999.ebuild               |  25 +-
 dev-libs/libcuda/metadata.xml                      |   8 +-
 dev-libs/libgdev/ChangeLog                         |   8 +-
 dev-libs/libgdev/libgdev-9999.ebuild               |  28 +-
 dev-libs/libgdev/metadata.xml                      |   8 +-
 dev-python/RecSQL/ChangeLog                        |   5 +-
 dev-python/RecSQL/RecSQL-9999.ebuild               |   4 +-
 dev-python/astropy/ChangeLog                       |   5 +-
 dev-python/astropy/astropy-9999.ebuild             |   6 +-
 dev-python/astropysics/ChangeLog                   |   5 +-
 dev-python/astropysics/astropysics-9999.ebuild     |   4 +-
 dev-python/dimensionful/ChangeLog                  |   5 +-
 dev-python/dimensionful/dimensionful-9999.ebuild   |   4 +-
 dev-tex/pythontex/ChangeLog                        |   8 +
 .../pythontex}/metadata.xml                        |   2 +-
 dev-tex/pythontex/pythontex-0.12.ebuild            |  24 +-
 dev-tex/pythontex/pythontex-9999.ebuild            |  33 +-
 eclass/alternatives-2.eclass                       |   2 +-
 media-gfx/librecad/ChangeLog                       |   9 +-
 media-gfx/librecad/Manifest                        |   2 +-
 media-gfx/librecad/librecad-9999.ebuild            |   4 +-
 media-gfx/librecad/metadata.xml                    |  20 +-
 profiles/package.use.mask                          |   7 +
 sci-biology/BG7/BG7-9999.ebuild                    |  22 +-
 sci-biology/BG7/ChangeLog                          |   5 +-
 .../omniorbpy => sci-biology/BG7}/metadata.xml     |   0
 sci-biology/artemis/ChangeLog                      |   6 +-
 sci-biology/artemis/artemis-9999.ebuild            |  34 +-
 sci-biology/artemis/metadata.xml                   |  10 +-
 sci-biology/bamtools/ChangeLog                     |   6 +-
 sci-biology/bamtools/bamtools-9999.ebuild          |  10 +-
 sci-biology/bamtools/metadata.xml                  |  12 +-
 sci-biology/blasr/ChangeLog                        |   5 +-
 sci-biology/blasr/blasr-9999.ebuild                |   6 +-
 sci-biology/est2uni/ChangeLog                      |   6 +-
 sci-biology/est2uni/est2uni-9999.ebuild            |  23 +-
 sci-biology/est2uni/metadata.xml                   |  10 +-
 sci-biology/fastx_toolkit/ChangeLog                |   6 +-
 .../fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild    |   9 +-
 .../fastx_toolkit}/metadata.xml                    |   0
 sci-biology/genepop/ChangeLog                      |   6 +-
 sci-biology/genepop/Manifest                       |   2 +-
 ...{genepop-4.0.10.ebuild => genepop-4.2.1.ebuild} |  31 +-
 sci-biology/genepop/metadata.xml                   |  10 +-
 sci-biology/mira/ChangeLog                         |   7 +-
 sci-biology/mira/Manifest                          |   6 -
 sci-biology/mira/mira-3.4.0.1.ebuild               |  62 ---
 sci-biology/mira/mira-3.4.1.1.ebuild               |  61 ---
 sci-biology/mira/mira-3.9.15.ebuild                |  64 ---
 sci-biology/mira/mira-3.9.9.ebuild                 |  61 ---
 sci-biology/mira/mira-4.0_rc2.ebuild               |  80 ----
 sci-biology/mira/mira-4.0_rc4.ebuild               |   6 +-
 sci-biology/miranda/ChangeLog                      |   6 +-
 sci-biology/miranda/metadata.xml                   |  10 +-
 sci-biology/miranda/miranda-3.3a.ebuild            |   4 +-
 sci-biology/mne-python/ChangeLog                   |   8 +
 .../mne-python}/metadata.xml                       |   0
 sci-biology/mne-python/mne-python-0.7.ebuild       |  56 +--
 sci-biology/mne-python/mne-python-9999.ebuild      |  56 +--
 sci-biology/mosaik/ChangeLog                       |   6 +-
 sci-biology/mosaik/Manifest                        |   1 -
 sci-biology/mosaik/metadata.xml                    |  10 +-
 sci-biology/mosaik/mosaik-1.1.0021.ebuild          |  40 --
 sci-biology/mosaik/mosaik-2.1.33.ebuild            |  38 +-
 sci-biology/mosaik/mosaik-9999.ebuild              |  36 +-
 sci-biology/mrfast/ChangeLog                       |   9 +
 sci-biology/mrfast/Manifest                        |   2 +-
 .../mrfast-2.1.0.3-disc_buffer_overflow.patch      |  52 ---
 sci-biology/mrfast/metadata.xml                    |  10 +-
 ...mrfast-2.1.0.3.ebuild => mrfast-2.6.0.1.ebuild} |  23 +-
 sci-biology/mrsfast/ChangeLog                      |   8 +
 sci-biology/mrsfast/Manifest                       |   2 +-
 sci-biology/mrsfast/metadata.xml                   |  10 +-
 sci-biology/mrsfast/mrsfast-2.3.0.2.ebuild         |  30 --
 .../mrsfast-2.6.0.4.ebuild}                        |  25 +-
 sci-biology/psychopy/ChangeLog                     |   5 +-
 sci-biology/psychopy/psychopy-9999.ebuild          |  10 +-
 sci-biology/pybrain/ChangeLog                      |   5 +-
 sci-biology/pybrain/pybrain-9999.ebuild            |   7 +-
 sci-biology/pysurfer/ChangeLog                     |   8 +
 .../pysurfer}/metadata.xml                         |   0
 sci-biology/pysurfer/pysurfer-0.4.ebuild           |  14 +-
 sci-biology/pysurfer/pysurfer-9999.ebuild          |  16 +-
 sci-biology/staden/ChangeLog                       |   6 +-
 sci-biology/staden/metadata.xml                    |  10 +-
 sci-biology/staden/staden-2.0.0_beta9.ebuild       |   4 +-
 sci-biology/staden/staden-9999.ebuild              |  70 ++-
 sci-biology/symap/ChangeLog                        |   5 +-
 .../omniorbpy => sci-biology/symap}/metadata.xml   |   0
 sci-biology/symap/symap-4.0.ebuild                 |  19 +-
 sci-chemistry/GromacsWrapper/ChangeLog             |   5 +-
 .../GromacsWrapper/GromacsWrapper-9999.ebuild      |  10 +-
 sci-chemistry/ball/ChangeLog                       |   5 +-
 sci-chemistry/ball/ball-9999.ebuild                |   4 +-
 sci-chemistry/bist/ChangeLog                       |   6 +-
 sci-chemistry/bist/bist-0.5.1-r1.ebuild            |   6 +-
 sci-chemistry/bist/metadata.xml                    |   8 +-
 sci-chemistry/chemBuild/ChangeLog                  |   5 +-
 sci-chemistry/chemBuild/chemBuild-1.0.3.ebuild     |   4 +-
 sci-chemistry/drawxtl/ChangeLog                    |   9 +-
 sci-chemistry/drawxtl/Manifest                     |   4 +-
 .../{drawxtl-44.ebuild => drawxtl-45.ebuild}       |  40 +-
 .../{drawxtl-54.ebuild => drawxtl-55.ebuild}       |  30 +-
 sci-chemistry/drawxtl/files/54-gcc44.patch         |  11 -
 sci-chemistry/drawxtl/files/54-ldflags.patch       |  11 -
 .../{44-gentoo.patch => drawxtl-45-gentoo.patch}   |  40 +-
 .../{54-gentoo.patch => drawxtl-55-gentoo.patch}   |  35 +-
 sci-chemistry/drawxtl/metadata.xml                 |   4 +-
 sci-chemistry/freeon/ChangeLog                     |   6 +-
 sci-chemistry/freeon/freeon-9999.ebuild            |  13 +-
 sci-chemistry/freeon/metadata.xml                  |   2 +-
 sci-chemistry/gromacs/ChangeLog                    |  10 +-
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild      |  10 +-
 sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild     |   8 +-
 sci-chemistry/gromacs/gromacs-9999.ebuild          |   8 +-
 sci-chemistry/hydronmr/ChangeLog                   |   5 +-
 sci-chemistry/hydronmr/hydronmr-7c.ebuild          |   4 +-
 sci-chemistry/mtz2hkl/ChangeLog                    |   6 +-
 sci-chemistry/mtz2hkl/metadata.xml                 |   2 +-
 sci-chemistry/mtz2hkl/mtz2hkl-0.3.ebuild           |  17 +-
 sci-chemistry/mtz2sca/ChangeLog                    |   6 +-
 sci-chemistry/mtz2sca/metadata.xml                 |   2 +-
 sci-chemistry/mtz2sca/mtz2sca-0.3.ebuild           |  17 +-
 sci-chemistry/openbabel-java/ChangeLog             |   5 +-
 .../openbabel-java/openbabel-java-9999.ebuild      |  15 +-
 sci-chemistry/openbabel-perl/ChangeLog             |   5 +-
 .../openbabel-perl/openbabel-perl-9999.ebuild      |   6 +-
 sci-chemistry/openbabel-python/ChangeLog           |   5 +-
 .../openbabel-python/openbabel-python-9999.ebuild  |   5 +-
 sci-chemistry/openbabel-ruby/ChangeLog             |   5 +-
 .../openbabel-ruby/openbabel-ruby-9999.ebuild      |   7 +-
 sci-chemistry/openbabel/ChangeLog                  |   6 +-
 sci-chemistry/openbabel/metadata.xml               |  18 +-
 sci-chemistry/openbabel/openbabel-9999.ebuild      |   9 +-
 sci-chemistry/pesto/ChangeLog                      |   9 +
 sci-chemistry/{burrow-owl => pesto}/metadata.xml   |   0
 sci-chemistry/pesto/pesto-9999.ebuild              |  29 ++
 sci-chemistry/shiftx/ChangeLog                     |   5 +-
 sci-chemistry/shiftx/shiftx-1.1.ebuild             |  16 +-
 sci-chemistry/specView/ChangeLog                   |   5 +-
 sci-chemistry/specView/specView-1.0.3.ebuild       |   4 +-
 sci-chemistry/wxmacmolplt/ChangeLog                |  19 -
 sci-chemistry/wxmacmolplt/Manifest                 |   2 -
 .../wxmacmolplt/files/wxmacmolplt-7.4.3-glew.patch |  12 -
 sci-chemistry/wxmacmolplt/metadata.xml             |  11 -
 sci-chemistry/wxmacmolplt/wxmacmolplt-7.4.3.ebuild |  44 --
 sci-chemistry/wxmacmolplt/wxmacmolplt-7.5.ebuild   |  44 --
 sci-electronics/tnt/ChangeLog                      |   6 +-
 sci-electronics/tnt/Manifest                       |   2 +-
 .../tnt/files/tnt-1.2.2-autotools.patch            | 277 ++++++++++++
 sci-electronics/tnt/metadata.xml                   |   2 +-
 sci-electronics/tnt/tnt-1.2.2.ebuild               |  40 +-
 sci-libs/dealii/ChangeLog                          |   9 +
 sci-libs/dealii/Manifest                           |   2 +
 .../{dealii-8.0.0.ebuild => dealii-8.1.0.ebuild}   |   0
 sci-libs/dealii/dealii-9999.ebuild                 |  46 +-
 sci-libs/dealii/metadata.xml                       |  42 +-
 sci-libs/fftw/ChangeLog                            |   5 +-
 sci-libs/fftw/fftw-9999.ebuild                     |   4 +-
 sci-libs/fgsl/ChangeLog                            |   6 +-
 sci-libs/fgsl/fgsl-0.9.3.ebuild                    |  30 +-
 sci-libs/fgsl/fgsl-0.9.4.ebuild                    |  29 +-
 sci-libs/fgsl/metadata.xml                         |  12 +-
 sci-libs/itk/ChangeLog                             |   5 +-
 sci-libs/itk/metadata.xml                          |  20 +-
 sci-libs/nibabel/ChangeLog                         |   8 +
 sci-libs/nibabel/metadata.xml                      |  18 +-
 sci-libs/nibabel/nibabel-1.3.0.ebuild              |   4 +-
 sci-libs/nibabel/nibabel-9999.ebuild               |   8 +-
 sci-libs/nipy/ChangeLog                            |   8 +
 sci-libs/nipy/metadata.xml                         |  12 +-
 sci-libs/nipy/nipy-0.3.0.ebuild                    |  10 +-
 sci-libs/nipy/nipy-9999.ebuild                     |  12 +-
 sci-libs/nipype/ChangeLog                          |   8 +
 sci-libs/nipype/metadata.xml                       |  12 +-
 sci-libs/nipype/nipype-9999.ebuild                 |   9 +-
 sci-libs/openblas/ChangeLog                        |   6 +-
 sci-libs/openblas/metadata.xml                     |  12 +-
 sci-libs/openblas/openblas-9999.ebuild             |  19 +-
 sci-libs/openlibm/ChangeLog                        |   6 +-
 sci-libs/openlibm/metadata.xml                     |   4 +-
 sci-libs/openlibm/openlibm-9999.ebuild             |  16 +-
 sci-libs/pagmo/ChangeLog                           |   8 +-
 sci-libs/pagmo/metadata.xml                        |  10 +-
 sci-libs/pagmo/pagmo-9999.ebuild                   |  20 +-
 sci-libs/pmx/ChangeLog                             |  10 +
 sci-libs/pmx/metadata.xml                          |  13 +
 sci-libs/pmx/pmx-9999.ebuild                       |  26 ++
 sci-libs/pydicom/ChangeLog                         |   8 +
 .../omniorbpy => sci-libs/pydicom}/metadata.xml    |   0
 sci-libs/pydicom/pydicom-0.9.8.ebuild              |   6 +-
 sci-libs/trilinos/ChangeLog                        |   9 +-
 sci-libs/trilinos/metadata.xml                     |  64 +--
 sci-libs/trilinos/trilinos-11.0.3.ebuild           |  11 +-
 sci-libs/trilinos/trilinos-11.4.2.ebuild           |   4 +-
 sci-libs/vtk/ChangeLog                             | 495 +++++++++++++++++++++
 sci-libs/vtk/Manifest                              |   2 +
 sci-libs/vtk/files/vtk-6.0.0-install.patch         |  19 +
 sci-libs/vtk/files/vtk-6.0.0-netcdf.patch          |  75 ++++
 sci-libs/vtk/files/vtk-6.0.0-system.patch          |  27 ++
 sci-libs/vtk/files/vtk-6.0.0-vtkpython.patch       |  12 +
 sci-libs/vtk/metadata.xml                          |  19 +
 sci-libs/vtk/vtk-6.0.0.ebuild                      | 321 +++++++++++++
 sci-mathematics/cipi/ChangeLog                     |   5 +-
 sci-mathematics/cipi/Manifest                      |   1 +
 sci-mathematics/cipi/cipi-1.0.ebuild               |   9 +-
 sci-mathematics/cipi/metadata.xml                  |  12 +-
 sci-mathematics/petsc/ChangeLog                    |   6 +-
 sci-mathematics/petsc/Manifest                     |   1 -
 sci-mathematics/petsc/metadata.xml                 |   2 +
 sci-mathematics/petsc/petsc-3.3_p5.ebuild          | 223 ----------
 sci-mathematics/petsc/petsc-3.4.2.ebuild           |  22 +-
 .../scilab/files/scilab-5.5.0_beta1-nogui.patch    |  13 +
 sci-mathematics/scilab/scilab-5.5.0_beta1.ebuild   |  64 ++-
 sci-misc/elmer-meta/ChangeLog                      |   6 +-
 sci-misc/elmer-meta/elmer-meta-6.0_p4651.ebuild    |   5 +-
 sci-misc/elmer-meta/elmer-meta-9999.ebuild         |   5 +-
 sci-misc/simx/ChangeLog                            |   6 +-
 sci-misc/simx/metadata.xml                         |   2 +-
 sci-misc/simx/simx-0.1.ebuild                      |  16 +-
 sci-misc/simx/simx-9999.ebuild                     |  18 +-
 sci-physics/geant-vmc/ChangeLog                    |  13 +-
 sci-physics/geant-vmc/Manifest                     |   1 +
 sci-physics/geant-vmc/geant-vmc-4.2.14b.ebuild     |  14 +-
 ...-vmc-4.2.14b.ebuild => geant-vmc-4.2.15.ebuild} |  13 +-
 sci-physics/geant-vmc/metadata.xml                 |  10 +-
 sci-physics/root/ChangeLog                         |   5 +-
 sci-physics/root/root-9999.ebuild                  |   4 +-
 sci-visualization/labplot/ChangeLog                |   8 +
 sci-visualization/labplot/labplot-9999.ebuild      |   5 +-
 sci-visualization/labplot/metadata.xml             |   2 +-
 sys-cluster/charm/ChangeLog                        |  20 +-
 sys-cluster/charm/Manifest                         |   2 +-
 sys-cluster/charm/charm-6.5.1-r2.ebuild            | 209 ---------
 ...m-6.5.1-r3.ebuild => charm-6.6.0_rc1-r1.ebuild} |  48 +-
 sys-cluster/lustre/ChangeLog                       |   5 +-
 sys-cluster/lustre/lustre-9999.ebuild              |   6 +-
 sys-cluster/nullmpi/ChangeLog                      |   5 +-
 sys-cluster/nullmpi/nullmpi-9999.ebuild            |   8 +-
 x11-misc/envytools/ChangeLog                       |   5 +-
 x11-misc/envytools/envytools-9999.ebuild           |   4 +-
 273 files changed, 3174 insertions(+), 2143 deletions(-)

diff --cc profiles/package.use.mask
index 9e3e91a,136fec3..f7f1044
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@@ -16,10 -16,13 +16,17 @@@
  ## =media-video/mplayer-0.90_pre5-r1 foo
  #
  
+ # Justin Lecher <jlec@gntoo.org> (06 Jan 2014)
+ # Missing dep dev-python/scikits-cuda
+ sci-biology/mne-python cuda
+ 
 +# Andreas Schäfer <gentryx@gmx.de> (21 Nov 2013)
 +# cuda only works on x86 and amd64
 +sys-cluster/openmpi -cuda
 +
+ # sci-libs/parmetis-4* is masked
+ sci-libs/dealii metis
+ 
  # Christoph Junghans <ottxor@gentoo.org> (05 Nov 2013)
  # gui sandbox error
  dev-lang/conceptual gui

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     90d2fd647de416dd3008958efc135c016ee85f5f
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jan  8 11:20:50 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jan  8 11:20:50 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=90d2fd64

Merge remote-tracking branch 'github/master'

* github/master:
  Version bump of jogl
  It's actually a _rc not a _p


 dev-java/gluegen/Manifest                          |  2 +-
 ...y-jars.patch => 2.1.4_rc1-dont-copy-jars.patch} |  0
 ...dont-strip.patch => 2.1.4_rc1-dont-strip.patch} |  0
 ...ive.patch => 2.1.4_rc1-dont-test-archive.patch} |  0
 ...en-2.1.4_p1.ebuild => gluegen-2.1.4_rc1.ebuild} |  2 +-
 dev-java/jogl/ChangeLog                            |  6 +-
 dev-java/jogl/Manifest                             |  1 +
 dev-java/jogl/jogl-2.1.4_rc1.ebuild                | 74 ++++++++++++++++++++++
 8 files changed, 82 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     4a68d0ea640880df77c6dcefb8303275177fb8ef
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jan  7 07:45:17 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jan  7 07:45:17 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4a68d0ea

Merge remote-tracking branch 'github/master'

* github/master:
  sys-cluster/charm-6.6.0_rc1-r1: After ongoing problems with charm's git repository, I packaged the rc as a tar file and serve it from my personal dev webpage.


 sys-cluster/charm/ChangeLog                 | 5 +++++
 sys-cluster/charm/Manifest                  | 1 +
 sys-cluster/charm/charm-6.6.0_rc1-r1.ebuild | 9 ++-------
 3 files changed, 8 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b66ee1dc1d8549098d01178f9d585662d2cbc3a2
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan  6 17:41:15 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan  6 17:41:15 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b66ee1dc

Merge branch 'olifre-master'

* olifre-master:
  sci-physics/geant-vmc: Add missing die
  *geant-vmc-4.2.15 (06 Jan 2014)    06 Jan 2014; <o.freyermuth <AT> googlemail.com> geant-vmc-4.2.14b.ebuild,    +geant-vmc-4.2.15.ebuild:    Version bump to 2.15 which builds with Geant 4.10.00 (note #360287 and    #496678), make 2.14b DEPEND on <sci-physics/geant-4.10.00


 sci-physics/geant-vmc/ChangeLog                            | 13 ++++++++++++-
 sci-physics/geant-vmc/Manifest                             |  1 +
 sci-physics/geant-vmc/geant-vmc-4.2.14b.ebuild             | 14 ++++++++------
 .../{geant-vmc-4.2.14b.ebuild => geant-vmc-4.2.15.ebuild}  | 13 +++++++------
 sci-physics/geant-vmc/metadata.xml                         | 10 +++++-----
 5 files changed, 33 insertions(+), 18 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     1addd8ba473f3b574b491e82e97f55cfa716477a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan  5 18:37:38 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan  5 18:37:38 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1addd8ba

Merge branch 'ercpe-glue-jogl'

* ercpe-glue-jogl:
  Don't test the zip archive (thus avoid dep to 7z)
  Updated and polished ebuild for gluegen (dep of jogl) as per #171.


 dev-java/gluegen/ChangeLog                         | 16 ++++-
 dev-java/gluegen/Manifest                          |  1 +
 .../gluegen/files/2.1.4_p1-dont-copy-jars.patch    | 17 +++++
 dev-java/gluegen/files/2.1.4_p1-dont-strip.patch   | 22 +++++++
 .../gluegen/files/2.1.4_p1-dont-test-archive.patch | 16 +++++
 dev-java/gluegen/gluegen-2.1.4_p1.ebuild           | 74 ++++++++++++++++++++++
 6 files changed, 144 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     04018d62d56a533a863ced06d797b971d00169ae
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan  4 12:08:38 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan  4 12:08:38 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=04018d62

Merge remote-tracking branch 'github/master'

* github/master:
  app-text/jabref: Remove another bundled library.
  app-text/jabref: Remove another bundled lib.
  app-text/jabref: Do not remove unjarlib target yet.
  app-text/jabref: Fix bug in java-pkg_getjars; use a '-' instead of ':' to specify slot.
  app-text/jabref-2.10_beta-r1: Adding revised ebuild for first beta.
  app-text/jabref-2.10_beta2-r1: Added back slotted fontbox package, but fixed java-pkg_getjars.
  sys-cluster/charm-6.6.0_rc1-r1: Add non-shallow option to git to avoid breakage of checked out repository.


 app-text/jabref/ChangeLog                          | 29 ++++++++++++++++++++++
 ..._beta2-r1.ebuild => jabref-2.10_beta-r1.ebuild} | 11 ++++----
 app-text/jabref/jabref-2.10_beta2-r1.ebuild        | 15 ++++++-----
 sys-cluster/charm/ChangeLog                        |  4 +++
 sys-cluster/charm/charm-6.6.0_rc1-r1.ebuild        |  1 +
 5 files changed, 48 insertions(+), 12 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a6dfe3fa17554124d5963b26e9f0769908586d49
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan  4 12:08:26 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan  4 12:08:26 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a6dfe3fa

Merge branch 'tamiko-bump_dealii'

* tamiko-bump_dealii:
  sci-libs/dealii: Add missing die; shorten DESCRIPTION; add dummy locel USE description; Fix RDEPEND.suspect
  mask sci-libs/dealii[metis] due to masked deps
  sci-libs/dealii: Bump to version 8.1.0


 profiles/package.use.mask                          |  4 ++
 sci-libs/dealii/ChangeLog                          |  9 +++++
 sci-libs/dealii/Manifest                           |  2 +
 .../{dealii-8.0.0.ebuild => dealii-8.1.0.ebuild}   |  0
 sci-libs/dealii/dealii-9999.ebuild                 | 46 ++++++++++++----------
 sci-libs/dealii/metadata.xml                       | 42 +++++++++++---------
 6 files changed, 64 insertions(+), 39 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c058b90b7bbe833bcdc363af12bdf4d585871e0e
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 29 10:11:09 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Dec 29 10:11:09 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c058b90b

Merge branch 'ustcscgy-openaxiom'

* ustcscgy-openaxiom:
  sci-mathematics/open-axiom: Drop src_install in favour of default and use DOCS
  sci-mathematics/open-axiom: version bump to 1.4.2


 sci-mathematics/open-axiom/ChangeLog                        |  6 +++++-
 sci-mathematics/open-axiom/Manifest                         |  1 +
 sci-mathematics/open-axiom/metadata.xml                     |  4 ++--
 .../{open-axiom-1.3.0.ebuild => open-axiom-1.4.2.ebuild}    | 13 +++++--------
 4 files changed, 13 insertions(+), 11 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f0d1d8f2aac32a63bca67315a135131999f4454c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 28 23:17:01 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Dec 28 23:17:01 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f0d1d8f2

Merge remote-tracking branch 'github/master'

* github/master:
  media-gfx/librecad: version bump, 2.0.0


 media-gfx/librecad/ChangeLog                 |  3 ++
 media-gfx/librecad/Manifest                  |  2 +-
 media-gfx/librecad/librecad-2.0.0_rc2.ebuild | 45 ----------------------------
 3 files changed, 4 insertions(+), 46 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ca173d7bd3edfbbd73b906d978f7314e731c1f97
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 28 23:16:17 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Dec 28 23:16:17 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ca173d7b

Merge branch 'mahnmut-patch-1'

* mahnmut-patch-1:
  sci-biology/velvet: Some improvements regarding die and optional enviromental variables; respect CC, CFLAGS
  Create velvet-1.2.1O.ebuild


 sci-biology/velvet/ChangeLog                       | 11 ++++
 sci-biology/velvet/Manifest                        |  1 +
 .../velvet}/metadata.xml                           |  0
 sci-biology/velvet/velvet-1.2.10.ebuild            | 73 ++++++++++++++++++++++
 4 files changed, 85 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     cef461ff3cd290af1155d7cc9f3fc594bf5ec9e5
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Wed Dec 25 11:53:27 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Dec 25 11:53:27 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cef461ff

Merge pull request #164 from JohannesBuchner/cblasfix

sci-libs/cblas-reference: removed extra character that breaks make

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     be8a3c1b6a5aecafd24806c7048ddeed0989c4dc
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Sun Dec  8 04:47:48 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Sun Dec  8 04:47:48 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=be8a3c1b

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-chemistry/gromacs/ChangeLog                    |  4 +++
 sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild     | 11 +++----
 sci-chemistry/gromacs/metadata.xml                 | 34 +++++++++++-----------
 sci-chemistry/pyquante/ChangeLog                   |  6 +++-
 sci-chemistry/pyquante/Manifest                    |  1 +
 ...uante-1.6.3-r1.ebuild => pyquante-1.6.4.ebuild} |  0
 6 files changed, 33 insertions(+), 23 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a087e52198f8d9c9601adb3d9a614f8375d2d324
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Wed Dec  4 12:29:07 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Dec  4 12:29:07 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a087e521

Merge pull request #156 from xhochy/intel-ocl-sdk-3.1.1.11385

[dev-util/intel-ocl-sdk] Bump version to 3.1.1.11385

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     76c6f48d7044d924da9c03fa0ff12d8e7c2e3eb8
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Dec  3 08:46:44 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Dec  3 08:46:44 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=76c6f48d

Merge branch 'master' into asd

* master:
  make mdrun target work for gmx live
  More updates #2 to gmx live
  More updates to gmx live
  Slightly update live ebuild for master branch


 sci-chemistry/gromacs/ChangeLog           |  12 ++
 sci-chemistry/gromacs/gromacs-9999.ebuild | 264 +++++++++++++++++-------------
 2 files changed, 164 insertions(+), 112 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     9909afafdb9beef28ae10121c08e48105f3c51f0
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Dec  3 07:31:03 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Dec  3 07:31:03 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9909afaf

Merge branch 'billyonthemountain-master' into asd

* billyonthemountain-master:
  sci-libs/elmer-eio: Bump EAPI; fix license; fix DESCRIPTION; drop keywords from live ebuild; use correct phase functions; simplify configure
  dev-python/pythonqt: Add metadata.xml; bump to new pyhton eclasses; fix patch for multilib to do it the gentoo way; drop '.' from DESCRIPTION; add missing deps
  sci-misc/elmer-gui: Make x11-libs/qwt an optional dependency
  sci-libs/opencascade: Verion bump
  dev-python/pythonqt: New package
  sci-mathematics/netgen: Version bump
  sci-misc/elmer-meta: New ebuilds for Elmer FEM packages

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

Conflicts:
	dev-python/pythonqt/Manifest
	dev-python/pythonqt/files/pythonqt-2.1-lib_location.patch
	dev-python/pythonqt/files/pythonqt-9999-lib_location.patch
	dev-python/pythonqt/pythonqt-2.1.ebuild
	dev-python/pythonqt/pythonqt-9999.ebuild
	sci-libs/elmer-eio/Manifest
	sci-libs/elmer-eio/elmer-eio-9999.ebuild


 dev-python/pythonqt/ChangeLog                      | 11 ++++
 dev-python/pythonqt/Manifest                       |  1 -
 .../pythonqt/files/pythonqt-2.1-lib_location.patch |  6 +-
 .../files/pythonqt-9999-lib_location.patch         |  6 +-
 dev-python/{omniorbpy => pythonqt}/metadata.xml    |  0
 dev-python/pythonqt/pythonqt-1.1.ebuild            | 75 ----------------------
 dev-python/pythonqt/pythonqt-2.1.ebuild            | 29 +++++----
 dev-python/pythonqt/pythonqt-9999.ebuild           | 28 +++++---
 sci-libs/elmer-eio/ChangeLog                       | 11 ++++
 sci-libs/elmer-eio/Manifest                        |  2 -
 sci-libs/elmer-eio/elmer-eio-5.4.1.ebuild          | 30 +++++++++
 sci-libs/elmer-eio/elmer-eio-9999.ebuild           | 30 ++-------
 .../omniorbpy => sci-libs/elmer-eio}/metadata.xml  |  0
 13 files changed, 102 insertions(+), 127 deletions(-)

diff --cc dev-python/pythonqt/files/pythonqt-2.1-lib_location.patch
index 41d4dbf,1bba03a..dd3bcc6
--- a/dev-python/pythonqt/files/pythonqt-2.1-lib_location.patch
+++ b/dev-python/pythonqt/files/pythonqt-2.1-lib_location.patch
@@@ -1,22 -1,22 +1,22 @@@
  --- PythonQt2.1_Qt4.8/CMakeLists.txt.auto-diff-temp	2012-11-30 16:38:06.374358937 +0100
  +++ PythonQt2.1_Qt4.8/CMakeLists.txt	2012-11-30 16:39:37.421438916 +0100
  @@ -215,7 +215,7 @@
 - # See http://blog.onesadcookie.com/2008/01/installname-magic.html
 - #
 - set_target_properties(PythonQt  PROPERTIES
 --  INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/lib"
 -+  INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}"
 -   )
 - 
 - target_link_libraries(PythonQt
 + # See http://blog.onesadcookie.com/2008/01/installname-magic.html
 + #
 + set_target_properties(PythonQt  PROPERTIES
 +-  INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/lib"
- +  INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/lib64"
+++  INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}"
 +   )
 + 
 + target_link_libraries(PythonQt
  @@ -228,8 +228,8 @@
 - 
 - install(TARGETS PythonQt
 -         RUNTIME DESTINATION bin
 --        LIBRARY DESTINATION lib
 --        ARCHIVE DESTINATION lib)
 -+        LIBRARY DESTINATION lib${LIB_SUFFIX}
 -+        ARCHIVE DESTINATION lib${LIB_SUFFIX})
 - install(FILES ${headers} DESTINATION include/PythonQt)
 + 
 + install(TARGETS PythonQt
 +         RUNTIME DESTINATION bin
 +-        LIBRARY DESTINATION lib
 +-        ARCHIVE DESTINATION lib)
- +        LIBRARY DESTINATION lib64
- +        ARCHIVE DESTINATION lib64)
+++        LIBRARY DESTINATION lib${LIB_SUFFIX}
+++        ARCHIVE DESTINATION lib${LIB_SUFFIX})
 + install(FILES ${headers} DESTINATION include/PythonQt)
   
   MESSAGE(STATUS "<<< Gentoo configuration >>>

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     8a852e325b1693e4f289a5835aaac691c0ab752d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Dec  2 18:47:30 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec  2 18:47:30 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8a852e32

Merge branch 'master' into billyonthemountain-master

* master: (1752 commits)
  sci-mathematics/z3: Make build verbose; respect CXX, CXXFLAGS, LDFLAGS; use EPYTHON instead of a direct python call; check for openmp compatibility of the c++ compiler; add USE=gmp; drop unnecessary eclass; add missing metadata.xml
  Add MSR-LA
  xdrfile got added to gx86
  hpl: fix build with MKL blas and/or lapack libraries
  [sci-visualization/yt] provide workaround for latest Forthon
  [sci-visualization/yt] fix slots in CDEPEND
  Tentative prefixification
  Version bump: mne-python 0.7
  Masked live yt
  dev-python/Forthon: Version bump, keyworded for prefix
  [sci-visualization/yt] version bump
  sci-physics/geant-vmc: Version bump
  dev-python/emcee: Version bump
  sci-chemistry/coot: Update patch for current HEAD
  Update PyQtGraph to 0.9.8. Support of python 3.3
  sci-mathematics/z3-4.3.1: add z3-9999 using git-3 and fix some error
  sci-mathematics/z3-4.3.1: add z3-9999 using git-3
  sci-physics/lammps-20131123: Version bump.
  sys-cluster/charm-6.6.0-rc1: Reorganized some variables.
  sci-physics/tauola: new ebuild added
  ...

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

Conflicts:
	sci-mathematics/netgen/Manifest


 .gitignore                                         |    2 +
 README.md                                          |   12 +
 app-admin/eselect/ChangeLog                        |   40 +-
 app-admin/eselect/Manifest                         |    4 +-
 app-admin/eselect/eselect-1.3.2-r100.ebuild        |   80 -
 app-admin/eselect/eselect-1.3.3-r100.ebuild        |   79 -
 app-admin/eselect/eselect-1.3.7-r100.ebuild        |   72 +
 app-admin/eselect/eselect-1.3.8-r100.ebuild        |   72 +
 app-admin/eselect/files/eselect-1.3.2-eroot.patch  |   11 -
 .../eselect/files/eselect-1.3.8-alternatives.patch |  616 +++++++
 app-admin/eselect/files/eselect-alternatives.patch |    2 +-
 app-admin/eselect/metadata.xml                     |    6 +-
 app-benchmarks/btl/ChangeLog                       |    5 +-
 app-benchmarks/btl/btl-9999.ebuild                 |   11 +-
 app-benchmarks/btl/metadata.xml                    |   14 +-
 app-benchmarks/numbench/ChangeLog                  |    8 +-
 app-benchmarks/numbench/metadata.xml               |   14 +-
 app-benchmarks/numbench/numbench-0.2.ebuild        |   28 +-
 app-benchmarks/numbench/numbench-9999.ebuild       |   28 +-
 app-doc/blacs-docs/Manifest                        |    2 +-
 app-doc/blas-docs/Manifest                         |    6 +-
 app-doc/gromacs-manual/ChangeLog                   |   29 -
 .../gromacs-manual/gromacs-manual-4.6.9999.ebuild  |   50 -
 app-doc/gromacs-manual/gromacs-manual-9999.ebuild  |   49 -
 app-doc/gromacs-manual/metadata.xml                |    5 -
 app-doc/lapack-docs/ChangeLog                      |    6 +-
 app-doc/lapack-docs/Manifest                       |    4 +-
 app-doc/lapack-docs/lapack-docs-3.3-r1.ebuild      |    6 +-
 app-doc/root-docs/ChangeLog                        |   37 +-
 app-doc/root-docs/Manifest                         |    3 +-
 .../root-docs/files/root-docs-5.32-makehtml.patch  |   44 -
 app-doc/root-docs/root-docs-5.32.04.ebuild         |   96 -
 app-doc/root-docs/root-docs-5.34.03.ebuild         |   96 -
 app-doc/root-docs/root-docs-5.34.10.ebuild         |   77 +
 app-doc/root-docs/root-docs-9999.ebuild            |    3 +-
 app-doc/scalapack-docs/ChangeLog                   |    7 +-
 app-doc/scalapack-docs/metadata.xml                |    3 +-
 app-doc/scalapack-docs/scalapack-docs-2.0.ebuild   |    6 +-
 app-doc/votca-csg-manual/ChangeLog                 |   25 -
 .../votca-csg-manual/votca-csg-manual-9999.ebuild  |   38 -
 app-forensics/vine/ChangeLog                       |   11 +
 app-forensics/vine/Manifest                        |    1 +
 app-forensics/vine/files/vine-1.0-binutils.patch   |   16 +
 app-forensics/vine/files/vine-1.0-gcc46.patch      |   37 +
 app-forensics/vine/files/vine-1.0-install.patch    |   89 +
 .../vine/files/vine-1.0-ocamlgraph182.patch        |   68 +
 .../vine}/metadata.xml                             |    0
 app-forensics/vine/vine-1.0.ebuild                 |   40 +
 app-portage/g-cran/ChangeLog                       |   20 -
 app-portage/g-cran/g-cran-9999.ebuild              |   25 -
 app-portage/g-cran/metadata.xml                    |   10 -
 app-portage/g-octave/ChangeLog                     |    6 +-
 app-portage/g-octave/g-octave-9999.ebuild          |   44 +-
 app-portage/g-octave/metadata.xml                  |   10 +-
 app-text/dgs/Manifest                              |    2 +-
 app-text/dgs/metadata.xml                          |    3 -
 app-text/jabref/ChangeLog                          |   41 +
 app-text/jabref/Manifest                           |    2 +
 app-text/jabref/jabref-2.10_beta.ebuild            |   35 +
 app-text/jabref/jabref-2.9.2-r1.ebuild             |   31 +
 app-text/jabref/jabref-2.9.2.ebuild                |   28 +
 app-text/jabref/metadata.xml                       |    8 +
 app-vim/freefem++-syntax/Manifest                  |    2 +-
 app-vim/freefem++-syntax/metadata.xml              |    7 +-
 app-vim/vim-gromacs/metadata.xml                   |    5 +-
 dev-cpp/eigen/ChangeLog                            |   27 +-
 dev-cpp/eigen/Manifest                             |    4 +-
 dev-cpp/eigen/eigen-3.0.6-r1.ebuild                |   84 -
 .../{eigen-3.1.1-r1.ebuild => eigen-3.1.4.ebuild}  |    0
 .../{eigen-3.1.1-r1.ebuild => eigen-3.2.0.ebuild}  |    0
 dev-cpp/eigen/eigen-9999.ebuild                    |   11 +-
 dev-cpp/eigen/metadata.xml                         |   14 +-
 dev-cpp/growler-arch/Manifest                      |    4 +-
 dev-cpp/growler-arch/metadata.xml                  |   14 +-
 dev-cpp/growler-core/Manifest                      |    2 +-
 dev-cpp/growler-core/metadata.xml                  |   19 +-
 dev-cpp/growler-link/metadata.xml                  |    9 +-
 dev-cpp/growler-math/Manifest                      |    2 +-
 dev-cpp/growler-math/metadata.xml                  |   13 +-
 dev-cpp/growler-thread/Manifest                    |    2 +-
 dev-cpp/growler-thread/metadata.xml                |   17 +-
 dev-cpp/growler/metadata.xml                       |   13 +-
 dev-db/cppdb/ChangeLog                             |   26 +
 dev-db/cppdb/Manifest                              |    1 +
 dev-db/cppdb/cppdb-0.3.1-r1.ebuild                 |   50 +
 dev-db/cppdb/metadata.xml                          |   14 +
 dev-java/fits/ChangeLog                            |    9 +-
 dev-java/fits/Manifest                             |    2 +-
 dev-java/fits/fits-1.08.1.ebuild                   |   54 -
 dev-java/fits/fits-1.11.0.ebuild                   |   54 +
 dev-java/flexdock/ChangeLog                        |    4 +
 dev-java/flexdock/Manifest                         |    2 +-
 ....0-nodemo.patch => flexdock-1.2.4-nodemo.patch} |    0
 dev-java/flexdock/flexdock-1.1.1.ebuild            |    2 +-
 dev-java/flexdock/flexdock-1.2.0.ebuild            |   51 -
 dev-java/flexdock/flexdock-1.2.4.ebuild            |   45 +
 dev-java/gluegen/ChangeLog                         |   12 +-
 dev-java/gluegen/Manifest                          |    2 +
 dev-java/gluegen/gluegen-2.0_rc8.ebuild            |   87 +
 dev-java/gluegen/gluegen-2.1.2.ebuild              |   83 +
 dev-java/gluegen/metadata.xml                      |    4 +-
 dev-java/hdf-java/ChangeLog                        |   12 +-
 dev-java/hdf-java/Manifest                         |    3 +-
 dev-java/hdf-java/files/hdf-java-2.7-shared.patch  |  112 --
 dev-java/hdf-java/files/hdf-java-2.8-shared.patch  |  107 --
 dev-java/hdf-java/files/hdf-java-2.9-shared.patch  |  118 ++
 dev-java/hdf-java/hdf-java-2.7.ebuild              |   85 -
 .../{hdf-java-2.8.ebuild => hdf-java-2.9.ebuild}   |    0
 dev-java/jcip-annotations/ChangeLog                |    9 +-
 dev-java/jcip-annotations/Manifest                 |    2 +-
 .../jcip-annotations-1.0-r1.ebuild                 |    9 +-
 dev-java/jcip-annotations/metadata.xml             |    9 +-
 dev-java/jeuclid-core/Manifest                     |    2 +-
 dev-java/jgraphx/ChangeLog                         |    7 +-
 dev-java/jgraphx/Manifest                          |    4 +-
 dev-java/jgraphx/jgraphx-1.2.0.7.ebuild            |   44 -
 dev-java/jgraphx/jgraphx-1.3.0.2.ebuild            |   44 -
 dev-java/jgraphx/jgraphx-1.4.1.0.ebuild            |   18 +-
 dev-java/jgraphx/jgraphx-1.4.1.2.ebuild            |   44 -
 dev-java/jgraphx/jgraphx-1.8.0.6.ebuild            |   20 +-
 dev-java/jgraphx/jgraphx-2.1.0.8.ebuild            |   42 +
 dev-java/jgraphx/metadata.xml                      |    4 +-
 dev-java/jhealpix/ChangeLog                        |    9 +
 dev-java/jhealpix/Manifest                         |    1 +
 dev-java/jhealpix/jhealpix-3.11.ebuild             |   43 +
 dev-java/jhealpix/metadata.xml                     |   11 +
 dev-java/jlatexmath-fop/Manifest                   |    3 +-
 .../files/jlatexmath-fop-1.0.2-fixpaths.patch      |   13 +
 dev-java/jlatexmath-fop/files/version.xml          |    5 +
 .../jlatexmath-fop/jlatexmath-fop-0.9.7.ebuild     |   52 -
 .../jlatexmath-fop/jlatexmath-fop-1.0.0.ebuild     |   52 -
 .../jlatexmath-fop/jlatexmath-fop-1.0.2.ebuild     |   45 +
 dev-java/jlatexmath/Manifest                       |    3 +-
 dev-java/jlatexmath/jlatexmath-0.9.7.ebuild        |   32 -
 dev-java/jlatexmath/jlatexmath-1.0.0.ebuild        |   32 -
 dev-java/jlatexmath/jlatexmath-1.0.2.ebuild        |   32 +
 dev-java/joda-convert/Manifest                     |    2 +-
 dev-java/jogl/ChangeLog                            |   12 +-
 dev-java/jogl/Manifest                             |    4 +-
 dev-java/jogl/jogl-2.0_rc8-r1.ebuild               |  100 ++
 dev-java/jogl/jogl-2.1.2.ebuild                    |  100 ++
 dev-java/jogl/metadata.xml                         |   10 +-
 dev-java/jrosetta/files/engine-build.xml           |    2 +-
 dev-java/jrosetta/files/metadata.xml               |    6 -
 dev-java/jrosetta/jrosetta-1.0.4.ebuild            |   12 +-
 dev-java/jrosetta/metadata.xml                     |    3 +-
 dev-java/netcdf/Manifest                           |    2 +-
 dev-java/scirenderer/Manifest                      |    2 +-
 dev-java/scirenderer/scirenderer-1.0.2.ebuild      |   40 -
 dev-java/scirenderer/scirenderer-1.1.0.ebuild      |   40 +
 dev-java/vecmath/Manifest                          |    4 +-
 dev-java/vecmath/metadata.xml                      |    9 +-
 dev-lang/berkeley_upc/ChangeLog                    |   22 +
 dev-lang/berkeley_upc/Manifest                     |    2 +
 dev-lang/berkeley_upc/berkeley_upc-2.16.2.ebuild   |   58 +
 dev-lang/berkeley_upc/berkeley_upc-2.18.0.ebuild   |   58 +
 dev-lang/berkeley_upc/metadata.xml                 |   25 +
 dev-lang/berkeley_upc_translator/ChangeLog         |   27 +
 dev-lang/berkeley_upc_translator/Manifest          |    2 +
 .../berkeley_upc_translator-2.16.2.ebuild          |   31 +
 .../berkeley_upc_translator-2.18.0.ebuild          |   31 +
 .../berkeley_upc_translator-2.16.2-check-abi.patch |   10 +
 dev-lang/berkeley_upc_translator/metadata.xml      |    8 +
 dev-lang/conceptual/ChangeLog                      |   12 +
 dev-lang/conceptual/Manifest                       |    1 +
 dev-lang/conceptual/conceptual-1.4.ebuild          |   38 +
 dev-lang/conceptual/metadata.xml                   |   11 +
 dev-lang/ispc/ChangeLog                            |   17 +-
 dev-lang/ispc/ispc-9999.ebuild                     |   17 +-
 dev-lang/ispc/metadata.xml                         |    8 +-
 dev-lang/julia/ChangeLog                           |   24 +
 dev-lang/julia/files/63julia-gentoo.el             |    2 +
 dev-lang/julia/files/julia-nopatchelf.patch        |   14 +
 dev-lang/julia/julia-9999.ebuild                   |  105 ++
 dev-lang/julia/metadata.xml                        |   17 +
 dev-lang/path64/ChangeLog                          |    6 +-
 dev-lang/path64/metadata.xml                       |   22 +-
 dev-lang/path64/path64-9999.ebuild                 |    4 +-
 dev-lang/pgi/Manifest                              |    1 +
 dev-lang/pgi/files/pgi-13.5-glibc.patch            |   31 +
 dev-lang/pgi/files/pgi-13.5-terminal.patch         |   39 +
 dev-lang/pgi/metadata.xml                          |   16 +
 dev-lang/pgi/pgi-13.5.ebuild                       |  115 ++
 dev-lang/vtune/ChangeLog                           |   22 +-
 dev-lang/vtune/Manifest                            |    3 +-
 dev-lang/vtune/metadata.xml                        |    8 +-
 dev-lang/vtune/vtune-11.0.7.221625.ebuild          |   69 -
 dev-lang/vtune/vtune-13.1.10.298370.ebuild         |   34 +
 dev-lang/vtune/vtune-13.1.12.305106.ebuild         |   43 +
 dev-libs/asmjit/ChangeLog                          |    8 +-
 dev-libs/asmjit/Manifest                           |    2 +-
 dev-libs/asmjit/asmjit-1.0_beta4.ebuild            |   43 +
 dev-libs/asmjit/asmjit-1.0_beta_p2.ebuild          |   43 -
 dev-libs/asmjit/metadata.xml                       |   12 +-
 dev-libs/double-conversion/ChangeLog               |   10 +-
 dev-libs/double-conversion/Manifest                |    2 +-
 .../double-conversion-1.1.1.ebuild                 |   46 +
 .../double-conversion/double-conversion-1.1.ebuild |   46 -
 ...s.patch => double-conversion-1.1.1-scons.patch} |    0
 dev-libs/fortrancl/ChangeLog                       |    8 +
 dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild     |    5 +-
 dev-libs/fortrancl/metadata.xml                    |   12 +-
 dev-libs/libpfm/ChangeLog                          |   12 +
 dev-libs/libpfm/Manifest                           |    1 +
 dev-libs/libpfm/libpfm-4.3.0.ebuild                |   35 +
 .../envytools => dev-libs/libpfm}/metadata.xml     |    0
 dev-libs/libunzip/Manifest                         |    2 +-
 dev-libs/libunzip/metadata.xml                     |    1 -
 dev-libs/mathjax/ChangeLog                         |   10 -
 dev-libs/mathjax/Manifest                          |    1 -
 dev-libs/mathjax/mathjax-2.0.ebuild                |   50 -
 dev-libs/mathjax/metadata.xml                      |   17 -
 dev-libs/papi/ChangeLog                            |    9 +
 dev-libs/papi/Manifest                             |    1 +
 {x11-misc/envytools => dev-libs/papi}/metadata.xml |    0
 dev-libs/papi/papi-5.1.0.2.ebuild                  |   30 +
 dev-libs/simclist/Manifest                         |    5 +-
 dev-libs/simclist/metadata.xml                     |   17 +-
 dev-ml/lacaml/ChangeLog                            |    6 +-
 dev-ml/lacaml/lacaml-7.0.3.ebuild                  |   12 +-
 dev-ml/lacaml/metadata.xml                         |    4 +-
 dev-ml/mlgmpidl/Manifest                           |    6 +-
 dev-ml/mlgmpidl/metadata.xml                       |   23 +-
 dev-ml/ocamlgraph/ChangeLog                        |    6 +-
 dev-ml/ocamlgraph/Manifest                         |    6 +-
 dev-ml/ocamlgraph/metadata.xml                     |   41 +-
 dev-ml/ocamlgraph/ocamlgraph-1.8.1.ebuild          |   47 -
 dev-ml/ocamlgraph/ocamlgraph-1.8.2.ebuild          |   47 +
 dev-ml/zarith/ChangeLog                            |   20 +-
 dev-ml/zarith/metadata.xml                         |   12 +-
 dev-ml/zarith/zarith-1.1.ebuild                    |   55 +-
 dev-perl/BTLib/Manifest                            |    2 +-
 dev-perl/Bio-BigFile/Bio-BigFile-1.06.ebuild       |   28 -
 dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild       |   31 +
 dev-perl/Bio-BigFile/ChangeLog                     |    6 +-
 dev-perl/Bio-BigFile/Manifest                      |    2 +-
 dev-perl/Bio-BigFile/metadata.xml                  |   10 +-
 dev-perl/DBIx-DBStag/ChangeLog                     |    6 +-
 dev-perl/DBIx-DBStag/DBIx-DBStag-0.12.ebuild       |    9 +-
 dev-perl/DBIx-DBStag/Manifest                      |    2 +-
 dev-perl/DBIx-DBStag/metadata.xml                  |   10 +-
 dev-perl/Lab-Instrument/Manifest                   |    2 +-
 dev-perl/Lab-Tools/Manifest                        |    2 +-
 dev-perl/Lab-VISA/Manifest                         |    2 +-
 dev-perl/Log-Cabin/ChangeLog                       |    9 +-
 dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild           |    9 +-
 dev-perl/Log-Cabin/Manifest                        |    2 +-
 dev-perl/Log-Cabin/metadata.xml                    |   10 +-
 dev-perl/Text-ParseWords/ChangeLog                 |    6 +-
 dev-perl/Text-ParseWords/Manifest                  |    2 +-
 .../Text-ParseWords/Text-ParseWords-3.27.ebuild    |    6 +-
 dev-perl/Text-ParseWords/metadata.xml              |   10 +-
 dev-perl/Time-Progress/ChangeLog                   |    6 +-
 dev-perl/Time-Progress/Manifest                    |    2 +-
 dev-perl/Time-Progress/Time-Progress-1.7.ebuild    |    6 +-
 dev-perl/Time-Progress/metadata.xml                |   10 +-
 dev-perl/go-db-perl/Manifest                       |    2 +-
 dev-perl/go-perl/ChangeLog                         |    6 +-
 dev-perl/go-perl/Manifest                          |    2 +-
 dev-perl/go-perl/go-perl-0.13.ebuild               |   10 +-
 dev-perl/go-perl/metadata.xml                      |   10 +-
 dev-perl/opal-client/Manifest                      |    2 +-
 dev-perl/opal-client/metadata.xml                  |    3 -
 dev-python/Forthon/ChangeLog                       |   14 +
 dev-python/Forthon/Forthon-0.8.10.ebuild           |   33 -
 dev-python/Forthon/Forthon-0.8.13.ebuild           |   31 +
 dev-python/Forthon/Manifest                        |    2 +-
 dev-python/Forthon/metadata.xml                    |   19 +-
 dev-python/GOGrapher/ChangeLog                     |    9 +-
 dev-python/GOGrapher/GOGrapher-9999.ebuild         |   27 +-
 dev-python/GOGrapher/metadata.xml                  |   10 +-
 dev-python/RecSQL/ChangeLog                        |   18 +
 dev-python/RecSQL/RecSQL-9999.ebuild               |   33 +
 dev-python/RecSQL/metadata.xml                     |    9 +
 dev-python/asciidata/ChangeLog                     |   28 -
 dev-python/asciidata/Manifest                      |    1 -
 dev-python/asciidata/asciidata-1.1.1-r1.ebuild     |   41 -
 dev-python/asciidata/metadata.xml                  |   13 -
 dev-python/astlib/ChangeLog                        |    8 +-
 dev-python/astlib/Manifest                         |    2 +-
 dev-python/astlib/astlib-0.17.1.ebuild             |   45 -
 dev-python/astlib/astlib-0.7.0.ebuild              |   38 +
 .../astlib/files/astlib-0.17.1-wcstools.patch      |   75 -
 dev-python/astlib/metadata.xml                     |    3 +-
 dev-python/astropy/ChangeLog                       |    8 +
 dev-python/astropy/astropy-9999.ebuild             |   40 +-
 dev-python/astropy/metadata.xml                    |   10 +-
 dev-python/astropysics/ChangeLog                   |    6 +-
 dev-python/astropysics/astropysics-9999.ebuild     |   55 +-
 dev-python/astropysics/metadata.xml                |    4 +-
 dev-python/coards/ChangeLog                        |    8 +-
 dev-python/coards/Manifest                         |    2 +-
 dev-python/coards/coards-0.2.2.ebuild              |   22 -
 dev-python/coards/coards-1.0.5.ebuild              |   23 +
 dev-python/coards/metadata.xml                     |   10 +-
 dev-python/coords/ChangeLog                        |    6 +-
 dev-python/coords/Manifest                         |    2 +-
 dev-python/coords/coords-0.37.ebuild               |   22 +-
 dev-python/coords/metadata.xml                     |    4 +-
 dev-python/cosmocalc/ChangeLog                     |    6 +-
 dev-python/cosmocalc/Manifest                      |    2 +-
 dev-python/cosmocalc/cosmocalc-0.1.2-r1.ebuild     |   23 +-
 dev-python/cosmocalc/metadata.xml                  |    4 +-
 dev-python/dimensionful/ChangeLog                  |    6 +-
 dev-python/dimensionful/dimensionful-9999.ebuild   |   37 +-
 dev-python/dimensionful/metadata.xml               |    8 +-
 dev-python/emcee/ChangeLog                         |   15 +-
 dev-python/emcee/Manifest                          |    3 +-
 dev-python/emcee/emcee-1.0.1.ebuild                |   35 -
 dev-python/emcee/emcee-1.2.0.ebuild                |   27 +
 dev-python/emcee/emcee-2.0.0.ebuild                |   27 +
 dev-python/ffc/ChangeLog                           |    8 +-
 dev-python/ffc/Manifest                            |    2 +-
 dev-python/ffc/ffc-0.9.4.ebuild                    |   23 -
 dev-python/ffc/ffc-1.2.0.ebuild                    |   18 +
 dev-python/ffc/metadata.xml                        |   14 +-
 dev-python/fiat/ChangeLog                          |    8 +-
 dev-python/fiat/Manifest                           |    2 +-
 dev-python/fiat/fiat-0.9.2.ebuild                  |   23 -
 dev-python/fiat/fiat-1.1.ebuild                    |   21 +
 dev-python/fiat/metadata.xml                       |   16 +-
 dev-python/go-parser/ChangeLog                     |    6 +-
 dev-python/go-parser/Manifest                      |    2 +-
 dev-python/go-parser/go-parser-9999.ebuild         |   13 +-
 dev-python/go-parser/metadata.xml                  |   10 +-
 dev-python/healpy/ChangeLog                        |   12 +
 dev-python/healpy/Manifest                         |    1 +
 dev-python/healpy/healpy-1.6.2.ebuild              |   34 +
 dev-python/healpy/metadata.xml                     |   10 +
 dev-python/inference/ChangeLog                     |    7 +-
 dev-python/inference/inference-0.4.ebuild          |   31 +-
 dev-python/inference/metadata.xml                  |    4 +-
 dev-python/instant/ChangeLog                       |    8 +-
 dev-python/instant/Manifest                        |    2 +-
 dev-python/instant/instant-0.9.8.ebuild            |   23 -
 dev-python/instant/instant-1.2.0.ebuild            |   18 +
 dev-python/instant/metadata.xml                    |   11 +-
 dev-python/meshpy/ChangeLog                        |    8 +-
 dev-python/meshpy/Manifest                         |    2 +-
 dev-python/meshpy/meshpy-0.91.2.ebuild             |   36 -
 dev-python/meshpy/meshpy-2013.1.2.ebuild           |   39 +
 dev-python/meshpy/metadata.xml                     |    5 +-
 dev-python/numpydoc/ChangeLog                      |   11 +-
 dev-python/numpydoc/Manifest                       |    2 +-
 dev-python/numpydoc/metadata.xml                   |    9 +-
 dev-python/numpydoc/numpydoc-0.4.ebuild            |   28 +-
 dev-python/omniorbpy/ChangeLog                     |    9 +-
 dev-python/omniorbpy/Manifest                      |    2 +-
 dev-python/omniorbpy/metadata.xml                  |    2 +-
 dev-python/omniorbpy/omniorbpy-3.4.ebuild          |   94 +-
 dev-python/opal-client/ChangeLog                   |   12 +-
 dev-python/opal-client/Manifest                    |    2 +-
 dev-python/opal-client/metadata.xml                |    5 +-
 dev-python/opal-client/opal-client-2.2-r1.ebuild   |   55 -
 dev-python/opal-client/opal-client-2.4.1.ebuild    |   41 +
 dev-python/pyhdf/ChangeLog                         |    8 +
 dev-python/pyhdf/Manifest                          |    2 +-
 dev-python/pyhdf/metadata.xml                      |   16 +-
 dev-python/pyhdf/pyhdf-0.8.3.ebuild                |   29 +-
 dev-python/pymvpa/ChangeLog                        |    6 +-
 dev-python/pymvpa/metadata.xml                     |    4 +-
 dev-python/pymvpa/pymvpa-0.4.4.ebuild              |   30 +-
 dev-python/pyqtgraph/ChangeLog                     |   23 +
 dev-python/pyqtgraph/Manifest                      |    1 +
 dev-python/pyqtgraph/metadata.xml                  |   14 +
 dev-python/pyqtgraph/pyqtgraph-0.9.8.ebuild        |   32 +
 dev-python/pysolar/ChangeLog                       |   13 +-
 dev-python/pysolar/Manifest                        |    3 +-
 dev-python/pysolar/metadata.xml                    |    3 +
 dev-python/pysolar/pysolar-0.4.3.ebuild            |   66 -
 dev-python/pysolar/pysolar-0.4.4.ebuild            |   66 -
 dev-python/pysolar/pysolar-0.5.ebuild              |   50 +
 dev-python/pysparse/ChangeLog                      |   11 +-
 dev-python/pysparse/Manifest                       |    3 +-
 dev-python/pysparse/metadata.xml                   |    4 +-
 dev-python/pysparse/pysparse-1.1.1-r1.ebuild       |   60 +
 dev-python/pysparse/pysparse-1.1.1.ebuild          |   53 -
 dev-python/pysparse/pysparse-1.1.ebuild            |   53 -
 dev-python/pythoncgns/ChangeLog                    |    6 +-
 dev-python/pythoncgns/Manifest                     |    2 +-
 dev-python/pythoncgns/metadata.xml                 |    2 +-
 dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild |   10 +-
 dev-python/pythonocc/ChangeLog                     |   17 +-
 dev-python/pythonocc/Manifest                      |    2 +-
 dev-python/pythonocc/metadata.xml                  |    2 +-
 dev-python/pythonocc/pythonocc-0.4.ebuild          |   30 -
 dev-python/pythonocc/pythonocc-0.5.ebuild          |   27 +
 dev-python/theano/ChangeLog                        |   12 +
 dev-python/theano/Manifest                         |    1 +
 dev-python/theano/metadata.xml                     |   13 +
 dev-python/theano/theano-0.6.0_rc3.ebuild          |   33 +
 dev-python/ufl/ChangeLog                           |    5 +-
 dev-python/ufl/Manifest                            |    2 +-
 dev-python/ufl/metadata.xml                        |   13 +-
 dev-python/ufl/ufl-0.5.4.ebuild                    |   17 +-
 dev-python/viper/ChangeLog                         |    8 +-
 dev-python/viper/Manifest                          |    2 +-
 dev-python/viper/metadata.xml                      |   11 +-
 dev-python/viper/viper-0.4.6.ebuild                |   23 -
 dev-python/viper/viper-1.0.1.ebuild                |   18 +
 dev-tcltk/img_rotate/ChangeLog                     |    6 +-
 dev-tcltk/img_rotate/Manifest                      |    2 +-
 dev-tcltk/img_rotate/img_rotate-1.1.ebuild         |   14 +-
 dev-tcltk/img_rotate/metadata.xml                  |    3 -
 dev-tcltk/togl/Manifest                            |    2 +-
 dev-tcltk/togl/metadata.xml                        |    3 -
 dev-tex/pythontex/Manifest                         |    1 +
 dev-tex/pythontex/pythontex-0.12.ebuild            |   68 +
 dev-tex/pythontex/pythontex-9999.ebuild            |   67 +
 dev-util/VampirTrace/Manifest                      |    1 +
 dev-util/VampirTrace/VampirTrace-5.14.3.ebuild     |   37 +
 dev-util/VampirTrace/metadata.xml                  |   16 +
 dev-util/amdapp/Manifest                           |    2 +
 dev-util/amdapp/amdapp-2.8.ebuild                  |   76 +
 dev-util/amdapp/metadata.xml                       |   15 +
 dev-util/ccache-clang/ChangeLog                    |   10 -
 dev-util/ccache-clang/ccache-clang-0.1.ebuild      |   29 -
 dev-util/ccache-icc/ChangeLog                      |   13 -
 dev-util/ccache-icc/ccache-icc-0.1.ebuild          |   29 -
 dev-util/ccache-icc/metadata.xml                   |    8 -
 dev-util/f90cache/ChangeLog                        |    6 +
 dev-util/f90cache/Manifest                         |    2 +-
 dev-util/f90cache/f90cache-0.93.7.ebuild           |   41 -
 dev-util/f90cache/f90cache-0.94.ebuild             |   38 +
 dev-util/intel-ocl-sdk/Manifest                    |    1 +
 .../intel-ocl-sdk/intel-ocl-sdk-3.0.67279.ebuild   |   65 +
 dev-util/intel-ocl-sdk/metadata.xml                |   17 +
 dev-util/ndiff/ChangeLog                           |    7 +-
 dev-util/ndiff/metadata.xml                        |    2 +-
 dev-util/ndiff/ndiff-2.00.ebuild                   |    8 +-
 dev-util/numdiff/Manifest                          |    1 +
 dev-util/numdiff/metadata.xml                      |   16 +
 dev-util/numdiff/numdiff-5.8.1.ebuild              |   44 +
 dev-util/nvidia-cuda-sdk/ChangeLog                 |  188 --
 dev-util/nvidia-cuda-sdk/Manifest                  |    1 -
 .../files/nvidia-cuda-sdk-4.2.9-asneeded.patch     |   89 -
 dev-util/nvidia-cuda-sdk/metadata.xml              |   15 -
 .../nvidia-cuda-sdk/nvidia-cuda-sdk-4.2.9.ebuild   |   69 -
 dev-util/nvidia-cuda-toolkit/ChangeLog             |  293 ---
 dev-util/nvidia-cuda-toolkit/Manifest              |    2 -
 dev-util/nvidia-cuda-toolkit/metadata.xml          |   15 -
 .../nvidia-cuda-toolkit-4.2.9.ebuild               |   73 -
 dev-util/smartgit/Manifest                         |    2 +-
 eclass/alternatives-2.eclass                       |   27 +-
 eclass/mpi.eclass                                  |   16 +-
 eclass/numeric.eclass                              |  114 ++
 licenses/{Artistic-IGS => Artistic-Manatee}        |    0
 licenses/CPC                                       |   41 +
 licenses/CeCILL-2.0                                |  505 ------
 licenses/CeCILL-2.1                                |  519 ++++++
 licenses/ECL-2.0                                   |   97 +
 licenses/GRL                                       |   15 +
 licenses/HSL                                       |  222 +++
 licenses/LNLL-BSD                                  |   57 +
 licenses/MSR-LA                                    |  104 ++
 licenses/PGI                                       |  262 +++
 licenses/STFC                                      |   67 +
 licenses/Tablet                                    |    8 +-
 licenses/blasr                                     |   65 +
 licenses/cdfplayer                                 |  143 ++
 licenses/mddnmr                                    |  185 +-
 licenses/nmrpipe                                   |   23 +
 licenses/vampir                                    |   36 +
 media-gfx/PhiloGL/ChangeLog                        |    6 +-
 media-gfx/PhiloGL/PhiloGL-1.4.3.ebuild             |    6 +-
 media-gfx/PhiloGL/metadata.xml                     |    8 +-
 media-gfx/brlcad/ChangeLog                         |   14 +-
 media-gfx/brlcad/Manifest                          |    2 +
 media-gfx/brlcad/brlcad-7.22.0.ebuild              |  112 ++
 media-gfx/brlcad/brlcad-9999.ebuild                |   10 +-
 media-gfx/brlcad/metadata.xml                      |   26 +-
 media-gfx/librecad/ChangeLog                       |   32 +-
 media-gfx/librecad/Manifest                        |    8 +-
 media-gfx/librecad/files/1.0.0_rc2-gcc4.6.patch    |   38 -
 .../files/librecad-1.0.0_rc2-version.patch         |   11 -
 media-gfx/librecad/librecad-1.0.1.ebuild           |   42 -
 media-gfx/librecad/librecad-1.0.2.ebuild           |   45 -
 media-gfx/librecad/librecad-1.0.3.ebuild           |   45 +
 media-gfx/librecad/librecad-1.0.4.ebuild           |   45 +
 media-gfx/librecad/librecad-2.0.0_alpha3.ebuild    |   48 -
 media-gfx/librecad/librecad-2.0.0_alpha4.ebuild    |   48 -
 media-gfx/librecad/librecad-2.0.0_rc2.ebuild       |   45 +
 media-gfx/librecad/librecad-2.0.0_rc3.ebuild       |   45 +
 media-gfx/librecad/librecad-9999.ebuild            |   40 +-
 media-gfx/librecad/metadata.xml                    |   21 +-
 media-libs/OpenMOIV/Manifest                       |    2 +-
 media-libs/OpenMOIV/metadata.xml                   |    3 -
 media-libs/avbin-bin/Manifest                      |    4 +-
 media-libs/libgfx/Manifest                         |    2 +-
 media-libs/libgfx/metadata.xml                     |    3 -
 metadata/layout.conf                               |    6 +
 net-firewall/gcb/Manifest                          |    2 +-
 net-ftp/bbftp-client/Manifest                      |    2 +-
 net-ftp/bbftp-server/Manifest                      |    2 +-
 net-misc/bbscp/Manifest                            |    2 +-
 net-misc/dhcp/ChangeLog                            |   61 -
 net-misc/dhcp/Manifest                             |    1 -
 net-misc/dhcp/dhcp-4.2.3_p2-r1.ebuild              |  245 ---
 net-misc/dhcp/files/dhcp-3.0-fix-perms.patch       |   15 -
 net-misc/dhcp/files/dhcp-3.0.3-dhclient-dbus.patch |   84 -
 .../dhcp/files/dhcp-3.0.3-dhclient-no-down.patch   |   70 -
 net-misc/dhcp/files/dhcp-4.0-dhclient-ntp.patch    |  216 ---
 net-misc/dhcp/files/dhcp-4.2.0-PPP.patch           |  150 --
 .../dhcp/files/dhcp-4.2.0-errwarn-message.patch    |   31 -
 .../dhcp/files/dhcp-4.2.2-bind-build-flags.patch   |   14 -
 net-misc/dhcp/files/dhcp-4.2.2-bind-disable.patch  |   13 -
 .../files/dhcp-4.2.2-bind-parallel-build.patch     |   14 -
 .../files/dhcp-4.2.2-dhclient-resolvconf.patch     |  409 -----
 .../files/dhcp-4.2.2-dhclient-stdin-conf.patch     |  113 --
 net-misc/dhcp/files/dhcp-4.2.2-gpxe-cid.patch      |  132 --
 net-misc/dhcp/files/dhcp-4.2.2-improved-xid.patch  |  138 --
 net-misc/dhcp/files/dhcp-4.2.2-lpf-ib.patch        |  538 ------
 net-misc/dhcp/files/dhcp-4.2.2-nogateway.patch     |   46 -
 net-misc/dhcp/files/dhcp-4.2.2-xen-checksum.patch  |  249 ---
 net-misc/dhcp/files/dhcp-4.2.3-options.patch       |  391 ----
 net-misc/dhcp/files/dhcpd.conf2                    |   28 -
 net-misc/dhcp/files/dhcpd.init2                    |   94 -
 net-misc/dhcp/files/dhcpd.init5                    |  114 --
 net-misc/dhcp/files/dhcrelay.conf                  |   13 -
 net-misc/dhcp/files/dhcrelay.init2                 |   29 -
 net-misc/dhcp/metadata.xml                         |   11 -
 perl-core/encoding-warnings/Manifest               |    2 +-
 profiles/arch.list                                 |   44 +
 profiles/arch/amd64/no-multilib/package.mask       |   23 -
 profiles/arch/amd64/package.use.mask               |   23 -
 profiles/hardened/package.mask                     |   23 -
 profiles/package.mask                              |  173 +-
 profiles/package.use.mask                          |    4 +
 sci-astronomy/astrometry/ChangeLog                 |   29 +-
 sci-astronomy/astrometry/Manifest                  |    2 +-
 sci-astronomy/astrometry/astrometry-0.38.ebuild    |   58 -
 sci-astronomy/astrometry/astrometry-0.43.ebuild    |   87 +
 .../astrometry/files/0.38-array-bounds.patch       |   11 -
 .../astrometry/files/0.38-as-needed.patch          |  694 --------
 .../astrometry/files/0.38-missing-headers.patch    |   11 -
 .../astrometry/files/0.38-respect-user-flags.patch |   11 -
 .../astrometry/files/0.38-strict-aliasing.patch    |   30 -
 .../astrometry/files/0.38-system-libs.patch        |   48 -
 .../astrometry/files/0.43-as-needed.patch          |  366 ++++
 .../astrometry/files/0.43-respect-user-flags.patch |   14 +
 .../astrometry/files/0.43-system-libs.patch        |  742 ++++++++
 sci-astronomy/astrometry/metadata.xml              |    3 +
 sci-astronomy/bpz/ChangeLog                        |    5 +-
 sci-astronomy/bpz/bpz-1.99.3.ebuild                |   57 +-
 sci-astronomy/bpz/metadata.xml                     |    4 +-
 sci-astronomy/chealpix/ChangeLog                   |    9 +
 sci-astronomy/chealpix/Manifest                    |    1 +
 sci-astronomy/chealpix/chealpix-3.11.ebuild        |   30 +
 sci-astronomy/chealpix/metadata.xml                |   11 +
 sci-astronomy/eazy/ChangeLog                       |    5 +-
 sci-astronomy/eazy/eazy-1.00.ebuild                |   16 +-
 sci-astronomy/eazy/metadata.xml                    |    4 +-
 sci-astronomy/eye/ChangeLog                        |    4 +-
 sci-astronomy/eye/eye-9999.ebuild                  |    3 +-
 sci-astronomy/eye/metadata.xml                     |    4 +-
 sci-astronomy/galfit-bin/ChangeLog                 |   15 +-
 sci-astronomy/galfit-bin/Manifest                  |    6 +-
 sci-astronomy/galfit-bin/galfit-bin-3.0.4.ebuild   |   51 -
 sci-astronomy/galfit-bin/galfit-bin-3.0.5.ebuild   |   46 +
 sci-astronomy/galfit-bin/metadata.xml              |    4 +-
 sci-astronomy/healpix_cxx/ChangeLog                |    9 +
 sci-astronomy/healpix_cxx/Manifest                 |    1 +
 sci-astronomy/healpix_cxx/healpix_cxx-3.11.ebuild  |   54 +
 sci-astronomy/healpix_cxx/metadata.xml             |   12 +
 sci-astronomy/healpix_idl/ChangeLog                |    9 +
 sci-astronomy/healpix_idl/Manifest                 |    1 +
 sci-astronomy/healpix_idl/healpix_idl-3.11.ebuild  |   37 +
 sci-astronomy/healpix_idl/metadata.xml             |   12 +
 sci-astronomy/lephare/ChangeLog                    |    6 +-
 sci-astronomy/lephare/Manifest                     |    2 +-
 .../lephare/files/lephare-2.2-read-int.patch       |   11 -
 sci-astronomy/lephare/lephare-2.2.ebuild           |    3 +-
 sci-astronomy/psfex/ChangeLog                      |    5 +-
 sci-astronomy/psfex/metadata.xml                   |   10 +-
 sci-astronomy/psfex/psfex-9999.ebuild              |    3 +-
 sci-astronomy/scamp/ChangeLog                      |    5 +-
 sci-astronomy/scamp/Manifest                       |    2 +-
 sci-astronomy/scamp/metadata.xml                   |   10 +-
 sci-astronomy/scamp/scamp-9999.ebuild              |    3 +-
 sci-astronomy/sextractor/Manifest                  |    2 +-
 sci-astronomy/skymaker/Manifest                    |    2 +-
 sci-astronomy/starlink-bin/ChangeLog               |   15 +-
 sci-astronomy/starlink-bin/Manifest                |    4 +-
 .../starlink-bin/starlink-bin-20110517.ebuild      |   30 -
 .../starlink-bin/starlink-bin-20130413.ebuild      |   30 +
 sci-astronomy/stiff/ChangeLog                      |    5 +-
 sci-astronomy/stiff/metadata.xml                   |    4 +-
 sci-astronomy/stiff/stiff-9999.ebuild              |   23 +-
 sci-astronomy/stilts/ChangeLog                     |   15 +-
 sci-astronomy/stilts/Manifest                      |    2 +-
 sci-astronomy/stilts/stilts-2.4.ebuild             |   26 -
 sci-astronomy/stilts/stilts-2.5.1.ebuild           |   28 +
 sci-astronomy/stuff/Manifest                       |    2 +-
 sci-astronomy/topcat/ChangeLog                     |   14 +-
 sci-astronomy/topcat/Manifest                      |    4 +-
 sci-astronomy/topcat/topcat-3.9.ebuild             |   35 -
 sci-astronomy/topcat/topcat-4.0.1.ebuild           |   36 +
 sci-astronomy/zebra/ChangeLog                      |    5 +-
 sci-astronomy/zebra/metadata.xml                   |    4 +-
 sci-astronomy/zebra/zebra-1.01.ebuild              |   16 +-
 sci-biology/BG7/BG7-9999.ebuild                    |   28 +
 sci-biology/BG7/ChangeLog                          |    9 +
 sci-biology/Gambit/ChangeLog                       |    8 +
 sci-biology/Gambit/Gambit-0.4.145.ebuild           |    6 +-
 sci-biology/Gambit/Manifest                        |    4 +-
 sci-biology/Gambit/metadata.xml                    |   10 +-
 sci-biology/ONTO-PERL/Manifest                     |    2 +-
 sci-biology/YASRA/ChangeLog                        |    9 +-
 sci-biology/YASRA/Manifest                         |    2 +-
 sci-biology/YASRA/YASRA-2.1.ebuild                 |   24 -
 sci-biology/YASRA/YASRA-2.32.ebuild                |   17 +
 sci-biology/YASRA/metadata.xml                     |   10 +-
 sci-biology/align_to_scf/Manifest                  |    2 +-
 sci-biology/amos-short/Manifest                    |    2 +-
 sci-biology/amos/ChangeLog                         |   18 +-
 sci-biology/amos/Manifest                          |    1 +
 sci-biology/amos/amos-3.1.0-r1.ebuild              |   30 +
 sci-biology/amos/amos-9999.ebuild                  |   47 +-
 sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch    |   15 +
 ...mos-3.1.0-goBambus2.py-indent-and-cleanup.patch |   25 +
 sci-biology/amos/metadata.xml                      |   17 +-
 sci-biology/argo-bin/Manifest                      |    2 +-
 sci-biology/argo/Manifest                          |    2 +-
 sci-biology/artemis-bin/ChangeLog                  |    6 +-
 sci-biology/artemis-bin/Manifest                   |    2 +-
 sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild |    3 +-
 sci-biology/artemis-bin/metadata.xml               |   10 +-
 sci-biology/autoeditor/Manifest                    |    4 +-
 sci-biology/bambus/Manifest                        |    2 +-
 sci-biology/biopython/ChangeLog                    |  346 ++++
 sci-biology/biopython/Manifest                     |    1 +
 sci-biology/biopython/biopython-1.62-r1.ebuild     |   51 +
 .../biopython/files/biopython-1.62-SffIO.patch     |   36 +
 sci-biology/{dawg => biopython}/metadata.xml       |    0
 sci-biology/blasr/ChangeLog                        |    8 +-
 sci-biology/blasr/Manifest                         |    3 -
 sci-biology/blasr/blasr-9999.ebuild                |   13 +-
 sci-biology/blasr/metadata.xml                     |   10 +-
 sci-biology/bowtie/ChangeLog                       |    7 +
 sci-biology/bowtie/Manifest                        |    1 +
 sci-biology/bowtie/bowtie-2.1.0.ebuild             |   56 +
 .../bowtie/files/bowtie-2.1.0-buildsystem.patch    |   20 +
 sci-biology/{dawg => bowtie}/metadata.xml          |    0
 sci-biology/brat/Manifest                          |    2 +-
 sci-biology/caftools/ChangeLog                     |    8 +
 sci-biology/caftools/Manifest                      |    4 +-
 sci-biology/caftools/caftools-2.0.2.ebuild         |   36 +-
 sci-biology/caftools/caftools-2.0.ebuild           |   38 -
 sci-biology/caftools/metadata.xml                  |   16 +-
 sci-biology/cap3-bin/Manifest                      |    4 +-
 sci-biology/cdbfasta/Manifest                      |    2 +-
 sci-biology/clover/ChangeLog                       |    6 +-
 sci-biology/clover/Manifest                        |    4 +-
 sci-biology/clover/clover-2010.02.19.ebuild        |   43 -
 sci-biology/clover/clover-2011.10.24.ebuild        |   40 +
 sci-biology/clover/metadata.xml                    |    6 +-
 sci-biology/cluster/ChangeLog                      |    6 +-
 sci-biology/cluster/cluster-1.50-r1.ebuild         |    4 +-
 sci-biology/cluster/cluster-1.50.ebuild            |    4 +-
 sci-biology/cluster/metadata.xml                   |   12 +-
 sci-biology/clview/Manifest                        |    4 +-
 sci-biology/codonw/Manifest                        |    2 +-
 sci-biology/consed-bin/ChangeLog                   |    8 +
 sci-biology/consed-bin/Manifest                    |    4 +-
 sci-biology/consed-bin/consed-bin-20.ebuild        |    4 +-
 sci-biology/consed-bin/metadata.xml                |   10 +-
 sci-biology/cutadapt/ChangeLog                     |    6 +-
 sci-biology/cutadapt/Manifest                      |    2 +-
 sci-biology/cutadapt/cutadapt-1.0.ebuild           |   21 -
 sci-biology/cutadapt/cutadapt-1.2.1.ebuild         |   18 +
 sci-biology/cutadapt/metadata.xml                  |   10 +-
 sci-biology/dawg/Manifest                          |    2 +-
 sci-biology/embassy-cbstools/Manifest              |    2 +-
 sci-biology/embassy-domainatrix/Manifest           |    2 +-
 sci-biology/embassy-domalign/Manifest              |    2 +-
 sci-biology/embassy-domsearch/Manifest             |    2 +-
 sci-biology/embassy-emnu/Manifest                  |    2 +-
 sci-biology/embassy-esim4/Manifest                 |    2 +-
 sci-biology/embassy-hmmer/Manifest                 |    2 +-
 sci-biology/embassy-iprscan/Manifest               |    2 +-
 sci-biology/embassy-mse/Manifest                   |    2 +-
 sci-biology/embassy-phylipnew/Manifest             |    2 +-
 sci-biology/embassy-signature/Manifest             |    2 +-
 sci-biology/embassy-structure/Manifest             |    2 +-
 sci-biology/embassy-topo/Manifest                  |    2 +-
 sci-biology/embassy-vienna/Manifest                |    2 +-
 sci-biology/emboss/ChangeLog                       |   37 +-
 sci-biology/emboss/Manifest                        |    4 +-
 sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild       |   77 -
 sci-biology/emboss/emboss-6.3.1_p4-r2.ebuild       |   88 +
 sci-biology/emboss/emboss-6.5.7.ebuild             |   79 +
 sci-biology/emboss/emboss-6.6.0.ebuild             |   83 +
 sci-biology/emboss/files/ax_lib_mysql.m4           |  147 ++
 .../emboss/files/emboss-6.3.1_p4-r2_Makefile.patch |   47 +
 .../emboss-6.3.1_p4-r2_compilations-paths.patch    |  315 ++++
 .../emboss/files/emboss-6.3.1_p4-r2_libtool.patch  |   18 +
 ..._plcol.patch => emboss-6.3.1_p4-r2_plcol.patch} |    0
 ..._p4-r1_plcol.patch => emboss-6.6.0_plcol.patch} |    0
 sci-biology/erpin/ChangeLog                        |    5 +-
 sci-biology/erpin/Manifest                         |    4 +-
 sci-biology/erpin/erpin-5.5b.ebuild                |   23 +-
 sci-biology/erpin/metadata.xml                     |   10 +-
 sci-biology/est2uni/Manifest                       |   10 +-
 sci-biology/estscan/ChangeLog                      |    5 +-
 sci-biology/estscan/Manifest                       |   18 +-
 sci-biology/estscan/metadata.xml                   |   16 +-
 sci-biology/fastdnaml/Manifest                     |    4 +-
 sci-biology/fastx_toolkit/ChangeLog                |   10 +
 sci-biology/fastx_toolkit/Manifest                 |    1 +
 .../fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild    |   26 +
 sci-biology/gap2caf/ChangeLog                      |    8 +
 sci-biology/gap2caf/Manifest                       |    4 +-
 sci-biology/gap2caf/gap2caf-2.1.0.ebuild           |   45 +-
 sci-biology/gap2caf/metadata.xml                   |   10 +-
 sci-biology/gbench/Manifest                        |    2 +-
 sci-biology/genepop/Manifest                       |    2 +-
 sci-biology/generecon/Manifest                     |    2 +-
 sci-biology/genseed/Manifest                       |    2 +-
 sci-biology/grappa/Manifest                        |    2 +-
 sci-biology/hydra-sv/ChangeLog                     |    8 +
 sci-biology/hydra-sv/Manifest                      |    2 +-
 sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild         |   11 +-
 .../pythonqt => sci-biology/hydra-sv}/metadata.xml |    0
 sci-biology/jalview/Manifest                       |    2 +-
 sci-biology/lastz/ChangeLog                        |   12 +-
 sci-biology/lastz/Manifest                         |    3 +-
 sci-biology/lastz/files/lastz-1.03.34-build.patch  |   43 +
 sci-biology/lastz/lastz-1.02.00.ebuild             |   27 -
 sci-biology/lastz/lastz-1.03.34.ebuild             |   33 +
 sci-biology/lastz/metadata.xml                     |   10 +-
 sci-biology/libgtextutils/ChangeLog                |    8 +-
 sci-biology/libgtextutils/Manifest                 |    2 +-
 .../libgtextutils/libgtextutils-0.6.1.ebuild       |   21 +
 sci-biology/libgtextutils/libgtextutils-0.6.ebuild |   21 -
 sci-biology/lucy/Manifest                          |    2 +-
 sci-biology/manatee-igs/ChangeLog                  |   19 +-
 sci-biology/manatee-igs/Manifest                   |    4 +-
 sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild  |    7 +-
 sci-biology/manatee-igs/metadata.xml               |   10 +-
 sci-biology/manatee-jcvi/ChangeLog                 |   11 +
 sci-biology/manatee-jcvi/Manifest                  |    1 +
 sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild |   53 +
 .../{phylobayes => manatee-jcvi}/metadata.xml      |    0
 sci-biology/mavid/Manifest                         |    2 +-
 sci-biology/merlin/Manifest                        |    2 +-
 sci-biology/mira/ChangeLog                         |   33 +-
 sci-biology/mira/Manifest                          |   10 +-
 .../mira/files/mira-3.4.0.2-boost-1.50.patch       |   24 +
 sci-biology/mira/metadata.xml                      |   10 +-
 sci-biology/mira/mira-3.4.0.1.ebuild               |    2 +-
 sci-biology/mira/mira-3.4.1.1.ebuild               |   61 +
 sci-biology/mira/mira-3.9.15.ebuild                |   64 +
 sci-biology/mira/mira-3.9.9.ebuild                 |   61 +
 sci-biology/mira/mira-4.0_rc2.ebuild               |   80 +
 sci-biology/mira/mira-4.0_rc4.ebuild               |   76 +
 sci-biology/miranda/Manifest                       |    2 +-
 sci-biology/mne-python/Manifest                    |    1 +
 sci-biology/mne-python/mne-python-0.7.ebuild       |   55 +
 sci-biology/mne-python/mne-python-9999.ebuild      |   53 +
 sci-biology/mrbayes/Manifest                       |    2 +-
 sci-biology/mreps/Manifest                         |    2 +-
 sci-biology/mrfast/Manifest                        |    2 +-
 sci-biology/mrsfast/Manifest                       |    2 +-
 sci-biology/ncbi-tools++/ChangeLog                 |  108 ++
 sci-biology/ncbi-tools++/Manifest                  |    2 +
 sci-biology/ncbi-tools++/files/curl-types.patch    |   24 +
 .../files/disable-testsuite-compilation.txt        |    3 +
 sci-biology/ncbi-tools++/files/make_install.patch  |   14 +
 .../files/malloc_initialize_upstream_fix.patch     |  100 ++
 .../files/ncbi-tools++-12.0.0-as-needed.patch      | 1864 ++++++++++++++++++++
 .../files/ncbi-tools++-12.0.0-conf-opts.patch      |  213 +++
 .../ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch |   19 +
 .../ncbi-tools++-12.0.0-fix-creaders-linking.patch |   11 +
 .../ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch |   10 +
 .../files/ncbi-tools++-9.0.0-as-needed.patch       | 1864 ++++++++++++++++++++
 .../files/ncbi-tools++-9.0.0-conf-opts.patch       |  213 +++
 .../ncbi-tools++-9.0.0-disable_test_compress.patch |   15 +
 .../ncbi-tools++-9.0.0-fix-creaders-linking.patch  |   10 +
 .../ncbi-tools++-9.0.0-fix-order-of-libs.patch     |   24 +
 .../ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch  |   10 +
 ...-reference-to-GenBankReaders_Register_Id1.patch |   10 +
 ...ls++-9.0.0-remove-LZO-definition-upstream.patch |   10 +
 .../report_project_settings_configure.ac.patch     |   64 +
 .../files/report_project_settings_configure.patch  |   66 +
 .../files/respect_CXXFLAGS_configure.ac.patch      |   54 +
 .../files/respect_CXXFLAGS_configure.patch         |   53 +
 sci-biology/ncbi-tools++/metadata.xml              |   39 +
 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        |  311 ++++
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |  328 ++++
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild |  308 ++++
 sci-biology/nrcl/Manifest                          |    4 +-
 sci-biology/perlprimer/Manifest                    |    2 +-
 sci-biology/perlprimer/metadata.xml                |    3 -
 sci-biology/phylobayes/ChangeLog                   |   10 -
 sci-biology/phylobayes/Manifest                    |    2 -
 sci-biology/phylobayes/phylobayes-3.3b.ebuild      |   37 -
 sci-biology/proda/Manifest                         |    2 +-
 sci-biology/psx/Manifest                           |    2 +-
 sci-biology/psychopy/ChangeLog                     |    8 +
 sci-biology/psychopy/Manifest                      |    2 +
 sci-biology/psychopy/metadata.xml                  |    8 +
 sci-biology/psychopy/psychopy-1.75.01.ebuild       |   58 +-
 sci-biology/psychopy/psychopy-1.77.02.ebuild       |   56 +
 sci-biology/psychopy/psychopy-1.78.00.ebuild       |   56 +
 sci-biology/psychopy/psychopy-9999.ebuild          |   53 +-
 sci-biology/pybrain/ChangeLog                      |   12 +
 .../pythonqt => sci-biology/pybrain}/metadata.xml  |    0
 sci-biology/pybrain/pybrain-9999.ebuild            |   30 +
 sci-biology/pysurfer/Manifest                      |    1 +
 .../pysurfer/files/0.4-headless_build.patch        |   22 +
 sci-biology/pysurfer/pysurfer-0.4.ebuild           |   27 +
 sci-biology/pysurfer/pysurfer-9999.ebuild          |   25 +
 sci-biology/quicktree/ChangeLog                    |    6 +-
 sci-biology/quicktree/Manifest                     |    2 +-
 sci-biology/quicktree/metadata.xml                 |   10 +-
 sci-biology/quicktree/quicktree-1.1-r1.ebuild      |   17 +-
 sci-biology/rnaplex/Manifest                       |    2 +-
 sci-biology/roche454ace2caf/Manifest               |    2 +-
 sci-biology/sclust/Manifest                        |    4 +-
 sci-biology/sequin/ChangeLog                       |    9 +-
 sci-biology/sequin/Manifest                        |    4 +-
 sci-biology/sequin/sequin-20090722.ebuild          |   32 -
 sci-biology/sequin/sequin-20121202.ebuild          |   44 +
 sci-biology/sff_dump/Manifest                      |    2 +-
 sci-biology/signalp/Manifest                       |    2 +-
 sci-biology/smalt-bin/ChangeLog                    |    8 +-
 sci-biology/smalt-bin/Manifest                     |    2 +-
 sci-biology/smalt-bin/metadata.xml                 |   10 +-
 sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild       |   25 -
 sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild       |   31 +
 sci-biology/sra_sdk/ChangeLog                      |   15 +-
 sci-biology/sra_sdk/Manifest                       |    1 +
 sci-biology/sra_sdk/metadata.xml                   |   10 +-
 sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild           |    6 +-
 sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild          |  102 ++
 sci-biology/ssaha2-bin/ChangeLog                   |    6 +-
 sci-biology/ssaha2-bin/Manifest                    |    9 +-
 sci-biology/ssaha2-bin/metadata.xml                |   10 +-
 sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild     |   34 -
 sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild     |   40 +
 sci-biology/staden/ChangeLog                       |   10 +-
 sci-biology/staden/Manifest                        |    4 +-
 sci-biology/staden/files/rpath.patch               |  123 --
 .../staden/files/staden-2.0.0_beta9-ldflags.patch  |   30 +
 .../files/staden-2.0.0_beta9-libpng-1.5.patch      |   16 +
 .../staden/files/staden-2.0.0_beta9-zlib.patch     |   16 +
 sci-biology/staden/staden-2.0.0_beta8.ebuild       |   73 -
 sci-biology/staden/staden-2.0.0_beta9.ebuild       |   84 +
 sci-biology/swissknife/Manifest                    |    2 +-
 sci-biology/symap/ChangeLog                        |    9 +
 sci-biology/symap/Manifest                         |    1 +
 sci-biology/symap/symap-4.0.ebuild                 |   31 +
 sci-biology/tablet-bin/ChangeLog                   |    9 +-
 sci-biology/tablet-bin/Manifest                    |    3 +-
 sci-biology/tablet-bin/metadata.xml                |   10 +-
 .../tablet-bin/tablet-bin-1.11.05.03.ebuild        |   62 -
 .../tablet-bin/tablet-bin-1.11.11.01.ebuild        |   73 -
 .../tablet-bin/tablet-bin-1.13.05.17.ebuild        |   89 +
 sci-biology/tclust/Manifest                        |    4 +-
 sci-biology/tgicl/Manifest                         |    2 +-
 sci-biology/tigr-assembler/Manifest                |    2 +-
 sci-biology/tigr-foundation-libs/Manifest          |    2 +-
 sci-biology/tmhmm/Manifest                         |    2 +-
 sci-biology/twinscan/ChangeLog                     |    6 +-
 sci-biology/twinscan/Manifest                      |    2 +-
 sci-biology/twinscan/metadata.xml                  |   10 +-
 sci-biology/twinscan/twinscan-4.1.2.ebuild         |   30 +-
 sci-biology/wcd/ChangeLog                          |    8 +-
 sci-biology/wcd/Manifest                           |    2 +-
 sci-biology/wcd/files/wcd-0.6.0-impl-decl.patch    |   15 +
 sci-biology/wcd/files/wcd-0.6.0-ldflags.patch      |   16 +
 sci-biology/wcd/metadata.xml                       |   10 +-
 sci-biology/wcd/wcd-0.6.0.ebuild                   |   41 +-
 sci-biology/wgs-assembler/ChangeLog                |   12 -
 sci-biology/wgs-assembler/Manifest                 |    1 -
 sci-biology/wgs-assembler/metadata.xml             |    9 -
 sci-biology/wgs-assembler/wgs-assembler-7.0.ebuild |   70 -
 sci-biology/zmsort/Manifest                        |    4 +-
 sci-chemistry/GromacsWrapper/ChangeLog             |   25 +
 .../GromacsWrapper/GromacsWrapper-9999.ebuild      |   41 +
 .../files/0001-Drop-chmod-hack.patch               |   28 +
 sci-chemistry/GromacsWrapper/metadata.xml          |    9 +
 sci-chemistry/almost/Manifest                      |    2 +-
 sci-chemistry/ambertools/ChangeLog                 |   18 +-
 sci-chemistry/ambertools/ambertools-1.5-r2.ebuild  |  156 --
 sci-chemistry/ambertools/ambertools-1.5-r3.ebuild  |  158 --
 sci-chemistry/ambertools/ambertools-1.5-r4.ebuild  |   10 +-
 sci-chemistry/ambertools/ambertools-12.ebuild      |   18 +-
 sci-chemistry/ambertools/metadata.xml              |   10 +-
 sci-chemistry/avogadro/ChangeLog                   |   16 -
 sci-chemistry/avogadro/Manifest                    |    1 -
 sci-chemistry/avogadro/avogadro-1.1.0.ebuild       |   52 -
 sci-chemistry/avogadro/avogadro-9999.ebuild        |   53 -
 sci-chemistry/avogadro/metadata.xml                |   17 -
 sci-chemistry/ball/ChangeLog                       |    8 +-
 sci-chemistry/ball/ball-9999.ebuild                |   28 +-
 sci-chemistry/ball/metadata.xml                    |   20 +-
 sci-chemistry/bist/Manifest                        |    2 +-
 sci-chemistry/burrow-owl/ChangeLog                 |    6 +-
 sci-chemistry/burrow-owl/burrow-owl-9999.ebuild    |    6 +-
 sci-chemistry/burrow-owl/metadata.xml              |    5 +-
 sci-chemistry/camshift/ChangeLog                   |    6 +-
 sci-chemistry/camshift/Manifest                    |    2 +-
 sci-chemistry/camshift/camshift-1.35.0.ebuild      |   45 +-
 sci-chemistry/camshift/files/1.35.0-gcc47.patch    |  148 ++
 sci-chemistry/camshift/files/1.35.0-gentoo.patch   |   38 +
 sci-chemistry/camshift/metadata.xml                |    3 -
 sci-chemistry/chemBuild/ChangeLog                  |   11 +-
 sci-chemistry/chemBuild/Manifest                   |    1 +
 sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild     |   33 +-
 sci-chemistry/chemBuild/chemBuild-1.0.3.ebuild     |   57 +
 sci-chemistry/chemBuild/files/chemBuild            |    2 +-
 sci-chemistry/chemBuild/metadata.xml               |    2 +-
 sci-chemistry/chimera-bin/ChangeLog                |    8 +-
 sci-chemistry/chimera-bin/Manifest                 |    2 +
 sci-chemistry/chimera-bin/chimera-bin-1.6.2.ebuild |    8 +-
 sci-chemistry/chimera-bin/chimera-bin-1.8.ebuild   |   94 +
 sci-chemistry/chimera-bin/metadata.xml             |    2 +-
 sci-chemistry/chooch/ChangeLog                     |    7 +-
 sci-chemistry/chooch/Manifest                      |    2 +-
 sci-chemistry/chooch/chooch-5.0.2-r1.ebuild        |   47 +-
 sci-chemistry/chooch/metadata.xml                  |    3 -
 sci-chemistry/cnsface/ChangeLog                    |    6 +-
 sci-chemistry/cnsface/Manifest                     |    2 +-
 sci-chemistry/cnsface/cnsface-0.0.12.ebuild        |   19 +-
 sci-chemistry/cnsface/metadata.xml                 |    3 -
 sci-chemistry/concoord/ChangeLog                   |    8 +-
 sci-chemistry/concoord/Manifest                    |    2 +
 sci-chemistry/concoord/concoord-2.1.2.ebuild       |   33 +
 sci-chemistry/concoord/concoord-2.1.ebuild         |    4 +-
 sci-chemistry/concoord/metadata.xml                |    8 +-
 sci-chemistry/coot/ChangeLog                       |   40 +-
 sci-chemistry/coot/Manifest                        |    2 +-
 sci-chemistry/coot/coot-9999.ebuild                |   40 +-
 sci-chemistry/coot/files/9999-clipper-config.patch |   17 -
 sci-chemistry/coot/files/9999-goocanvas.patch      |   25 -
 sci-chemistry/coot/files/9999-mmdb-config.patch    |   18 -
 sci-chemistry/coot/files/9999-pc.patch             | 1047 +++++++++++
 sci-chemistry/coot/files/9999-ssm.patch            |   56 -
 sci-chemistry/coot/metadata.xml                    |   13 +-
 sci-chemistry/cs-rosetta/ChangeLog                 |   18 +
 sci-chemistry/cs-rosetta/Manifest                  |    3 +
 .../cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild |  104 ++
 sci-chemistry/cs-rosetta/metadata.xml              |    5 +
 sci-chemistry/curvefit/ChangeLog                   |    9 +-
 sci-chemistry/curvefit/curvefit-1.40.ebuild        |   12 +-
 sci-chemistry/curvefit/metadata.xml                |    2 +-
 sci-chemistry/direx/Manifest                       |    2 +-
 sci-chemistry/direx/metadata.xml                   |    3 -
 sci-chemistry/dl_poly/ChangeLog                    |   14 +
 sci-chemistry/dl_poly/Manifest                     |    2 +
 sci-chemistry/dl_poly/dl_poly-1.9.ebuild           |   35 +
 sci-chemistry/dl_poly/dl_poly-4.05.ebuild          |   41 +
 .../dl_poly}/metadata.xml                          |    0
 sci-chemistry/drawxtl/Manifest                     |    4 +-
 sci-chemistry/dssp2pdb/Manifest                    |    2 +-
 sci-chemistry/dssp2pdb/metadata.xml                |    3 -
 sci-chemistry/freeon/ChangeLog                     |  128 +-
 sci-chemistry/freeon/Manifest                      |    9 +
 sci-chemistry/freeon/freeon-1.0.1.ebuild           |   26 +
 sci-chemistry/freeon/freeon-1.0.2.ebuild           |   26 +
 sci-chemistry/freeon/freeon-1.0.3.ebuild           |   33 +
 sci-chemistry/freeon/freeon-1.0.4.ebuild           |   33 +
 sci-chemistry/freeon/freeon-1.0.5.ebuild           |   33 +
 sci-chemistry/freeon/freeon-1.0.6.ebuild           |   33 +
 sci-chemistry/freeon/freeon-1.0.7.ebuild           |   25 +
 sci-chemistry/freeon/freeon-1.0.8-r1.ebuild        |   27 +
 sci-chemistry/freeon/freeon-1.0.8.ebuild           |   25 +
 sci-chemistry/freeon/freeon-1.0.ebuild             |   27 +
 sci-chemistry/freeon/freeon-9999.ebuild            |   36 +-
 sci-chemistry/freeon/metadata.xml                  |   15 +-
 sci-chemistry/gamess/ChangeLog                     |   12 +-
 sci-chemistry/gamess/Manifest                      |    1 +
 .../gamess/files/gamess-20120501.1.gentoo.patch    |    4 +-
 .../gamess/files/gamess-20130501.1.gentoo.patch    |  206 +++
 sci-chemistry/gamess/gamess-20120501.1.ebuild      |    3 +-
 sci-chemistry/gamess/gamess-20130501.1.ebuild      |  338 ++++
 sci-chemistry/gamess/metadata.xml                  |   20 +-
 sci-chemistry/gnome-chemistry-utils/ChangeLog      |   45 +
 sci-chemistry/gnome-chemistry-utils/Manifest       |    1 +
 .../gnome-chemistry-utils-0.14.2-extern-c.patch    |   84 +
 .../gnome-chemistry-utils-0.14.2-r1.ebuild         |   46 +
 .../gnome-chemistry-utils-9999.ebuild              |   53 +
 sci-chemistry/gnome-chemistry-utils/metadata.xml   |   11 +
 sci-chemistry/gromacs/ChangeLog                    |  105 +-
 sci-chemistry/gromacs/Manifest                     |    2 +-
 .../files/gromacs-4.5.7-cmake-cpp-asm.patch        |   43 +
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild      |   40 +-
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild      |  234 ++-
 sci-chemistry/gromacs/gromacs-9999.ebuild          |   40 +-
 sci-chemistry/gromacs/metadata.xml                 |    6 +-
 sci-chemistry/hydronmr/ChangeLog                   |   13 +
 sci-chemistry/hydronmr/Manifest                    |   13 +
 sci-chemistry/hydronmr/hydronmr-7c.ebuild          |   56 +
 sci-chemistry/hydronmr/metadata.xml                |    5 +
 sci-chemistry/jana2000/Manifest                    |    2 +-
 sci-chemistry/jana2000/metadata.xml                |    3 -
 sci-chemistry/jligand/ChangeLog                    |    6 +-
 sci-chemistry/jligand/Manifest                     |    2 +-
 sci-chemistry/jligand/jligand-1.0.19.ebuild        |    4 +-
 sci-chemistry/jligand/metadata.xml                 |    5 +-
 sci-chemistry/jmol/ChangeLog                       |   54 -
 sci-chemistry/jmol/Manifest                        |    1 -
 .../jmol/files/12.0.45/jmol-manifest.patch         |   96 -
 sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch |  313 ----
 sci-chemistry/jmol/files/caffeine.xyz              |   26 -
 sci-chemistry/jmol/files/index.html                |   14 -
 .../jmol/files/selfSignedCertificate.store         |  Bin 1516 -> 0 bytes
 sci-chemistry/jmol/jmol-12.0.45-r1.ebuild          |  122 --
 sci-chemistry/jmol/metadata.xml                    |   13 -
 sci-chemistry/ligplot+/metadata.xml                |    2 +-
 sci-chemistry/mage/Manifest                        |    2 +-
 sci-chemistry/mage/metadata.xml                    |    3 -
 sci-chemistry/mddnmr/ChangeLog                     |   13 +-
 sci-chemistry/mddnmr/Manifest                      |    3 +-
 sci-chemistry/mddnmr/mddnmr-1.6.ebuild             |   43 -
 sci-chemistry/mddnmr/mddnmr-2.1.ebuild             |   59 +
 sci-chemistry/mddnmr/mddnmr-2.2.ebuild             |   59 +
 sci-chemistry/mddnmr/metadata.xml                  |    3 -
 sci-chemistry/mdsctk/ChangeLog                     |   19 +
 sci-chemistry/mdsctk/Manifest                      |    1 +
 sci-chemistry/mdsctk/mdsctk-1.1.0.ebuild           |   46 +
 sci-chemistry/mdsctk/metadata.xml                  |   12 +
 sci-chemistry/mgltools-autodocktools/ChangeLog     |   43 +-
 sci-chemistry/mgltools-autodocktools/Manifest      |    3 +-
 sci-chemistry/mgltools-autodocktools/metadata.xml  |    2 +-
 .../mgltools-autodocktools-1.5.4-r2.ebuild         |   77 -
 .../mgltools-autodocktools-1.5.6.ebuild            |   68 +
 .../mgltools-autodocktools-1.5.6_rc2.ebuild        |   71 -
 sci-chemistry/mgltools-bhtree/ChangeLog            |   26 +-
 sci-chemistry/mgltools-bhtree/Manifest             |    3 +-
 sci-chemistry/mgltools-bhtree/metadata.xml         |    2 +-
 .../mgltools-bhtree-1.5.4-r1.ebuild                |   54 -
 .../mgltools-bhtree/mgltools-bhtree-1.5.6.ebuild   |   46 +
 .../mgltools-bhtree-1.5.6_rc2.ebuild               |   48 -
 sci-chemistry/mgltools-cadd/ChangeLog              |   20 +-
 sci-chemistry/mgltools-cadd/Manifest               |    2 +-
 sci-chemistry/mgltools-cadd/metadata.xml           |    2 +-
 .../mgltools-cadd/mgltools-cadd-1.5.6.ebuild       |   45 +
 .../mgltools-cadd/mgltools-cadd-1.5.6_rc2.ebuild   |   48 -
 sci-chemistry/mgltools-cmolkit/ChangeLog           |   26 +-
 sci-chemistry/mgltools-cmolkit/Manifest            |    3 +-
 sci-chemistry/mgltools-cmolkit/metadata.xml        |    2 +-
 .../mgltools-cmolkit-1.5.4-r1.ebuild               |   55 -
 .../mgltools-cmolkit/mgltools-cmolkit-1.5.6.ebuild |   45 +
 .../mgltools-cmolkit-1.5.6_rc2.ebuild              |   48 -
 sci-chemistry/mgltools-dejavu/ChangeLog            |   26 +-
 sci-chemistry/mgltools-dejavu/Manifest             |    3 +-
 sci-chemistry/mgltools-dejavu/metadata.xml         |    2 +-
 .../mgltools-dejavu-1.5.4-r1.ebuild                |   55 -
 .../mgltools-dejavu/mgltools-dejavu-1.5.6.ebuild   |   48 +
 .../mgltools-dejavu-1.5.6_rc2.ebuild               |   51 -
 sci-chemistry/mgltools-geomutils/ChangeLog         |   26 +-
 sci-chemistry/mgltools-geomutils/Manifest          |    3 +-
 sci-chemistry/mgltools-geomutils/metadata.xml      |    2 +-
 .../mgltools-geomutils-1.5.4-r1.ebuild             |   57 -
 .../mgltools-geomutils-1.5.6.ebuild                |   45 +
 .../mgltools-geomutils-1.5.6_rc2.ebuild            |   49 -
 sci-chemistry/mgltools-gle/ChangeLog               |   25 +-
 sci-chemistry/mgltools-gle/Manifest                |    3 +-
 sci-chemistry/mgltools-gle/metadata.xml            |    2 +-
 .../mgltools-gle/mgltools-gle-1.5.4-r1.ebuild      |   53 -
 .../mgltools-gle/mgltools-gle-1.5.6.ebuild         |   46 +
 .../mgltools-gle/mgltools-gle-1.5.6_rc2.ebuild     |   48 -
 sci-chemistry/mgltools-mglutil/ChangeLog           |   26 +-
 sci-chemistry/mgltools-mglutil/Manifest            |    3 +-
 sci-chemistry/mgltools-mglutil/metadata.xml        |    2 +-
 .../mgltools-mglutil-1.5.4-r1.ebuild               |   57 -
 .../mgltools-mglutil/mgltools-mglutil-1.5.6.ebuild |   48 +
 .../mgltools-mglutil-1.5.6_rc2.ebuild              |   51 -
 sci-chemistry/mgltools-molkit/ChangeLog            |   26 +-
 sci-chemistry/mgltools-molkit/Manifest             |    3 +-
 sci-chemistry/mgltools-molkit/metadata.xml         |    2 +-
 .../mgltools-molkit-1.5.4-r1.ebuild                |   56 -
 .../mgltools-molkit/mgltools-molkit-1.5.6.ebuild   |   47 +
 .../mgltools-molkit-1.5.6_rc2.ebuild               |   50 -
 sci-chemistry/mgltools-networkeditor/ChangeLog     |   28 +-
 sci-chemistry/mgltools-networkeditor/Manifest      |    3 +-
 sci-chemistry/mgltools-networkeditor/metadata.xml  |    2 +-
 .../mgltools-networkeditor-1.5.4-r1.ebuild         |   56 -
 .../mgltools-networkeditor-1.5.6.ebuild            |   47 +
 .../mgltools-networkeditor-1.5.6_rc2.ebuild        |   50 -
 sci-chemistry/mgltools-opengltk/ChangeLog          |   26 +-
 sci-chemistry/mgltools-opengltk/Manifest           |    3 +-
 sci-chemistry/mgltools-opengltk/metadata.xml       |    2 +-
 .../mgltools-opengltk-1.5.4-r2.ebuild              |   63 -
 .../mgltools-opengltk-1.5.6.ebuild                 |   63 +
 .../mgltools-opengltk-1.5.6_rc2.ebuild             |   68 -
 sci-chemistry/mgltools-pmv/ChangeLog               |   25 +-
 sci-chemistry/mgltools-pmv/Manifest                |    3 +-
 sci-chemistry/mgltools-pmv/metadata.xml            |    2 +-
 .../mgltools-pmv/mgltools-pmv-1.5.4-r1.ebuild      |   63 -
 .../mgltools-pmv/mgltools-pmv-1.5.6.ebuild         |   48 +
 .../mgltools-pmv/mgltools-pmv-1.5.6_rc2.ebuild     |   52 -
 sci-chemistry/mgltools-pyautodock/ChangeLog        |   27 +-
 sci-chemistry/mgltools-pyautodock/Manifest         |    3 +-
 sci-chemistry/mgltools-pyautodock/metadata.xml     |    2 +-
 .../mgltools-pyautodock-1.5.4-r1.ebuild            |   54 -
 .../mgltools-pyautodock-1.5.6.ebuild               |   45 +
 .../mgltools-pyautodock-1.5.6_rc2.ebuild           |   48 -
 sci-chemistry/mgltools-pybabel/ChangeLog           |   26 +-
 sci-chemistry/mgltools-pybabel/Manifest            |    3 +-
 sci-chemistry/mgltools-pybabel/metadata.xml        |    2 +-
 .../mgltools-pybabel-1.5.4-r1.ebuild               |   56 -
 .../mgltools-pybabel/mgltools-pybabel-1.5.6.ebuild |   47 +
 .../mgltools-pybabel-1.5.6_rc2.ebuild              |   50 -
 sci-chemistry/mgltools-pyglf/ChangeLog             |   26 +-
 sci-chemistry/mgltools-pyglf/Manifest              |    3 +-
 sci-chemistry/mgltools-pyglf/metadata.xml          |    2 +-
 .../mgltools-pyglf/mgltools-pyglf-1.5.4-r1.ebuild  |   54 -
 .../mgltools-pyglf/mgltools-pyglf-1.5.6.ebuild     |   45 +
 .../mgltools-pyglf/mgltools-pyglf-1.5.6_rc2.ebuild |   48 -
 sci-chemistry/mgltools-qslimlib/ChangeLog          |   26 +-
 sci-chemistry/mgltools-qslimlib/Manifest           |    3 +-
 sci-chemistry/mgltools-qslimlib/metadata.xml       |    2 +-
 .../mgltools-qslimlib-1.5.4-r1.ebuild              |   56 -
 .../mgltools-qslimlib-1.5.6.ebuild                 |   49 +
 .../mgltools-qslimlib-1.5.6_rc2.ebuild             |   52 -
 sci-chemistry/mgltools-scenario/ChangeLog          |   27 -
 sci-chemistry/mgltools-scenario/Manifest           |    1 -
 sci-chemistry/mgltools-scenario/metadata.xml       |    5 -
 .../mgltools-scenario-1.5.4-r1.ebuild              |   58 -
 sci-chemistry/mgltools-scenario2/ChangeLog         |   21 +-
 sci-chemistry/mgltools-scenario2/Manifest          |    2 +-
 sci-chemistry/mgltools-scenario2/metadata.xml      |    2 +-
 .../mgltools-scenario2-1.5.6.ebuild                |   47 +
 .../mgltools-scenario2-1.5.6_rc2.ebuild            |   50 -
 sci-chemistry/mgltools-sff/ChangeLog               |   25 +-
 sci-chemistry/mgltools-sff/Manifest                |    3 +-
 sci-chemistry/mgltools-sff/metadata.xml            |    2 +-
 .../mgltools-sff/mgltools-sff-1.5.4-r1.ebuild      |   55 -
 .../mgltools-sff/mgltools-sff-1.5.6.ebuild         |   46 +
 .../mgltools-sff/mgltools-sff-1.5.6_rc2.ebuild     |   49 -
 sci-chemistry/mgltools-stride/ChangeLog            |   26 -
 sci-chemistry/mgltools-stride/Manifest             |    1 -
 sci-chemistry/mgltools-stride/metadata.xml         |    5 -
 .../mgltools-stride-1.5.4-r1.ebuild                |   54 -
 sci-chemistry/mgltools-support/ChangeLog           |   26 +-
 sci-chemistry/mgltools-support/Manifest            |    3 +-
 sci-chemistry/mgltools-support/metadata.xml        |    2 +-
 .../mgltools-support-1.5.4-r1.ebuild               |   56 -
 .../mgltools-support/mgltools-support-1.5.6.ebuild |   45 +
 .../mgltools-support-1.5.6_rc2.ebuild              |   49 -
 sci-chemistry/mgltools-symserv/ChangeLog           |   24 +-
 sci-chemistry/mgltools-symserv/Manifest            |    3 +-
 sci-chemistry/mgltools-symserv/metadata.xml        |    2 +-
 .../mgltools-symserv-1.5.4-r1.ebuild               |   54 -
 .../mgltools-symserv/mgltools-symserv-1.5.6.ebuild |   45 +
 .../mgltools-symserv-1.5.6_rc2.ebuild              |   48 -
 sci-chemistry/mgltools-utpackages/ChangeLog        |   27 +-
 sci-chemistry/mgltools-utpackages/Manifest         |    3 +-
 sci-chemistry/mgltools-utpackages/metadata.xml     |    2 +-
 .../mgltools-utpackages-1.5.4-r1.ebuild            |   56 -
 .../mgltools-utpackages-1.5.6.ebuild               |   45 +
 .../mgltools-utpackages-1.5.6_rc2.ebuild           |   49 -
 sci-chemistry/mgltools-viewer-framework/ChangeLog  |   30 +-
 sci-chemistry/mgltools-viewer-framework/Manifest   |    3 +-
 .../mgltools-viewer-framework/metadata.xml         |    2 +-
 .../mgltools-viewer-framework-1.5.4-r2.ebuild      |   58 -
 .../mgltools-viewer-framework-1.5.6.ebuild         |   50 +
 .../mgltools-viewer-framework-1.5.6_rc2.ebuild     |   53 -
 sci-chemistry/mgltools-vision/ChangeLog            |   26 +-
 sci-chemistry/mgltools-vision/Manifest             |    3 +-
 sci-chemistry/mgltools-vision/metadata.xml         |    2 +-
 .../mgltools-vision-1.5.4-r1.ebuild                |   64 -
 .../mgltools-vision/mgltools-vision-1.5.6.ebuild   |   56 +
 .../mgltools-vision-1.5.6_rc2.ebuild               |   59 -
 sci-chemistry/mgltools-visionlib/ChangeLog         |   26 +-
 sci-chemistry/mgltools-visionlib/Manifest          |    3 +-
 sci-chemistry/mgltools-visionlib/metadata.xml      |    2 +-
 .../mgltools-visionlib-1.5.4-r1.ebuild             |   53 -
 .../mgltools-visionlib-1.5.6.ebuild                |   45 +
 .../mgltools-visionlib-1.5.6_rc2.ebuild            |   48 -
 sci-chemistry/mgltools-volume/ChangeLog            |   26 +-
 sci-chemistry/mgltools-volume/Manifest             |    3 +-
 sci-chemistry/mgltools-volume/metadata.xml         |    2 +-
 .../mgltools-volume-1.5.4-r1.ebuild                |   55 -
 .../mgltools-volume/mgltools-volume-1.5.6.ebuild   |   47 +
 .../mgltools-volume-1.5.6_rc2.ebuild               |   50 -
 sci-chemistry/mgltools-webservices/ChangeLog       |   23 +-
 sci-chemistry/mgltools-webservices/Manifest        |    3 +-
 sci-chemistry/mgltools-webservices/metadata.xml    |    2 +-
 .../mgltools-webservices-1.5.4-r2.ebuild           |   50 -
 .../mgltools-webservices-1.5.6.ebuild              |   45 +
 .../mgltools-webservices-1.5.6_rc2.ebuild          |   49 -
 sci-chemistry/mgltools/ChangeLog                   |   34 +-
 sci-chemistry/mgltools/Manifest                    |    3 +-
 sci-chemistry/mgltools/metadata.xml                |    2 +-
 sci-chemistry/mgltools/mgltools-1.5.4.ebuild       |   42 -
 sci-chemistry/mgltools/mgltools-1.5.6.ebuild       |   47 +
 sci-chemistry/mgltools/mgltools-1.5.6_rc2.ebuild   |   39 -
 sci-chemistry/mics/ChangeLog                       |   10 +
 sci-chemistry/mics/Manifest                        |    1 +
 sci-chemistry/mics/metadata.xml                    |    5 +
 sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild |   51 +
 sci-chemistry/modelfree/ChangeLog                  |   18 +-
 sci-chemistry/modelfree/metadata.xml               |    8 +-
 sci-chemistry/modelfree/modelfree-4.20.ebuild      |   39 +-
 sci-chemistry/modeller/ChangeLog                   |   20 +-
 sci-chemistry/modeller/Manifest                    |    2 +-
 sci-chemistry/modeller/metadata.xml                |    2 +-
 sci-chemistry/modeller/modeller-9.12-r3.ebuild     |  149 ++
 sci-chemistry/modeller/modeller-9.8.ebuild         |  149 --
 sci-chemistry/mtz2hkl/Manifest                     |    2 +-
 sci-chemistry/mtz2hkl/metadata.xml                 |    3 -
 sci-chemistry/mtz2sca/Manifest                     |    2 +-
 sci-chemistry/mtz2sca/metadata.xml                 |    3 -
 sci-chemistry/nMOLDYN/ChangeLog                    |   12 +
 sci-chemistry/nMOLDYN/Manifest                     |    1 +
 sci-chemistry/{xdrfile => nMOLDYN}/metadata.xml    |    0
 sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild        |   24 +
 sci-chemistry/nmrpipe/ChangeLog                    |   69 +-
 sci-chemistry/nmrpipe/Manifest                     |    6 +-
 sci-chemistry/nmrpipe/files/extract.M              |   37 +
 ....patch => nmrpipe-8.1.2013.218.23.09-lib.patch} |    0
 sci-chemistry/nmrpipe/metadata.xml                 |   10 +-
 .../nmrpipe/nmrpipe-7.8.2012.295.14.58.ebuild      |  203 ---
 .../nmrpipe/nmrpipe-8.1.2013.218.23.09-r1.ebuild   |  214 +++
 sci-chemistry/nmrview/ChangeLog                    |    6 +-
 sci-chemistry/nmrview/metadata.xml                 |   10 +-
 sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild      |   15 +-
 sci-chemistry/nwchem/ChangeLog                     |   54 +
 sci-chemistry/nwchem/Manifest                      |    2 +
 .../files/nwchem-6.1.1-adjust-dir-length.patch     |   22 +
 .../nwchem/files/nwchem-6.1.1-makefile.patch       |   14 +
 .../nwchem/files/nwchem-6.1.1-nwchemrc.patch       |   13 +
 .../files/nwchem-6.1.1-python_makefile.patch       |   12 +
 .../nwchem/files/nwchem-6.3-r1-html_doc.patch      |   13 +
 sci-chemistry/nwchem/metadata.xml                  |   12 +
 sci-chemistry/nwchem/nwchem-6.3-r1.ebuild          |  150 ++
 sci-chemistry/nwchem/nwchem-6.3-r2.ebuild          |  157 ++
 sci-chemistry/openbabel-java/ChangeLog             |   10 +
 sci-chemistry/openbabel-java/metadata.xml          |   12 +
 .../openbabel-java/openbabel-java-9999.ebuild      |   63 +
 sci-chemistry/openbabel-perl/ChangeLog             |   11 +-
 sci-chemistry/openbabel-perl/Manifest              |    1 -
 .../files/openbabel-perl-2.3.2-bindings_only.patch |  108 --
 .../files/openbabel-perl-2.3.2-trunk_cmake.patch   |   41 -
 sci-chemistry/openbabel-perl/metadata.xml          |   16 +-
 .../openbabel-perl/openbabel-perl-2.3.2.ebuild     |   66 -
 .../openbabel-perl/openbabel-perl-9999.ebuild      |   64 +
 sci-chemistry/openbabel-python/ChangeLog           |   16 +-
 sci-chemistry/openbabel-python/Manifest            |    1 -
 .../openbabel-python-2.3.2-bindings_only.patch     |  209 ---
 .../files/openbabel-python-2.3.2-testpybel.patch   |   28 -
 sci-chemistry/openbabel-python/metadata.xml        |   16 +-
 .../openbabel-python/openbabel-python-2.3.2.ebuild |   94 -
 .../openbabel-python/openbabel-python-9999.ebuild  |   83 +
 sci-chemistry/openbabel-ruby/ChangeLog             |   10 +
 sci-chemistry/openbabel-ruby/metadata.xml          |   12 +
 .../openbabel-ruby/openbabel-ruby-9999.ebuild      |   78 +
 sci-chemistry/openbabel/ChangeLog                  |   13 +-
 sci-chemistry/openbabel/Manifest                   |    1 -
 .../files/openbabel-2.3.2-test_lib_path.patch      |   27 -
 sci-chemistry/openbabel/metadata.xml               |   26 +-
 sci-chemistry/openbabel/openbabel-2.3.2.ebuild     |   69 -
 sci-chemistry/openbabel/openbabel-9999.ebuild      |   87 +
 sci-chemistry/panav/ChangeLog                      |   10 +
 sci-chemistry/panav/Manifest                       |    1 +
 sci-chemistry/panav/metadata.xml                   |   30 +
 sci-chemistry/panav/panav-0.20130730.ebuild        |   34 +
 sci-chemistry/phaser/ChangeLog                     |   21 -
 sci-chemistry/phaser/Manifest                      |    1 -
 sci-chemistry/phaser/files/2.1.4-sadf.patch        |   64 -
 .../phaser/files/phaser-2.1.4-chmod.patch          |   11 -
 sci-chemistry/phaser/metadata.xml                  |   30 -
 sci-chemistry/phaser/phaser-2.1.4-r1.ebuild        |  138 --
 sci-chemistry/phaser/phaser-2.1.4.ebuild           |  114 --
 sci-chemistry/phenix-bin/ChangeLog                 |   23 +-
 sci-chemistry/phenix-bin/Manifest                  |    6 +-
 sci-chemistry/phenix-bin/metadata.xml              |    2 +-
 .../phenix-bin/phenix-bin-1.8.1.1168.ebuild        |  122 --
 .../phenix-bin/phenix-bin-1.8.2.1309.ebuild        |  110 ++
 .../phenix-bin/phenix-bin-1.8.4.1496.ebuild        |  110 ++
 sci-chemistry/polygon/ChangeLog                    |    7 +-
 sci-chemistry/polygon/Manifest                     |    4 +-
 sci-chemistry/polygon/files/0612-db.patch          |   11 +
 sci-chemistry/polygon/files/0710-db.patch          |   11 -
 sci-chemistry/polygon/metadata.xml                 |    3 -
 sci-chemistry/polygon/polygon-0612.ebuild          |   43 +
 sci-chemistry/polygon/polygon-0710.ebuild          |   37 -
 sci-chemistry/pymol-apbs-plugin/ChangeLog          |    9 +-
 sci-chemistry/pymol-apbs-plugin/metadata.xml       |    3 -
 .../pymol-apbs-plugin-9999.ebuild                  |   53 +-
 sci-chemistry/pymol-plugins-ezviz/ChangeLog        |   18 +-
 sci-chemistry/pymol-plugins-ezviz/Manifest         |    2 +-
 sci-chemistry/pymol-plugins-ezviz/metadata.xml     |   11 +-
 .../pymol-plugins-ezviz-1.0.2005-r1.ebuild         |   56 +
 .../pymol-plugins-ezviz-1.0.2005.ebuild            |   63 -
 sci-chemistry/pymol-plugins-psico/ChangeLog        |   12 +-
 sci-chemistry/pymol-plugins-psico/metadata.xml     |    8 +-
 .../pymol-plugins-psico-9999.ebuild                |   17 +-
 sci-chemistry/pymol/ChangeLog                      |   34 +-
 .../pymol/files/pymol-9999-data-path.patch         |  151 --
 sci-chemistry/pymol/files/pymol-9999-flags.patch   |   19 -
 .../pymol/files/pymol-9999-nosplash.patch          |   15 -
 sci-chemistry/pymol/files/pymol-9999-prefix.patch  |   57 -
 .../pymol/files/pymol-9999-setup.py.patch          |   39 -
 sci-chemistry/pymol/files/pymol-9999-vmd.patch     |   36 -
 sci-chemistry/pymol/files/pymol-9999-web.patch     |   16 -
 sci-chemistry/pymol/metadata.xml                   |   19 +-
 sci-chemistry/pymol/pymol-9999.ebuild              |   98 +-
 sci-chemistry/pyquante/ChangeLog                   |    6 +-
 sci-chemistry/pyquante/Manifest                    |    2 +-
 sci-chemistry/pyquante/metadata.xml                |    2 +-
 sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild    |   11 +-
 sci-chemistry/rosetta-tools/Manifest               |    2 +-
 sci-chemistry/rosetta-tools/metadata.xml           |    3 -
 sci-chemistry/rosetta/ChangeLog                    |   32 +-
 sci-chemistry/rosetta/Manifest                     |    3 +-
 .../rosetta/files/3.0-user-settings.patch          |   26 -
 .../{3.0-boinc.patch => rosetta-3.4-boinc.patch}   |    0
 .../rosetta/files/rosetta-3.4-boost.patch          |   16 +
 ....patch => rosetta-3.4-fix-scons-warnings.patch} |    0
 ...lgrind.patch => rosetta-3.4-fix-valgrind.patch} |    0
 .../rosetta/files/rosetta-3.4-gcc4.7.patch         |   32 +
 .../rosetta/files/rosetta-3.4-gcc4.78.patch        |   32 +
 .../rosetta/files/rosetta-3.4-lange-fix.patch      |   22 +
 ...0-platform.patch => rosetta-3.4-platform.patch} |    0
 .../rosetta/files/rosetta-3.4-unbundle.patch       |   47 +
 .../rosetta/files/rosetta-3.4-user-settings.patch  |   29 +
 .../{3.0-zlib.patch => rosetta-3.4-zlib.patch}     |    0
 sci-chemistry/rosetta/metadata.xml                 |   21 +-
 sci-chemistry/rosetta/rosetta-3.0-r1.ebuild        |  148 --
 sci-chemistry/rosetta/rosetta-3.4.ebuild           |  171 ++
 sci-chemistry/shiftx/ChangeLog                     |   12 +-
 sci-chemistry/shiftx/Manifest                      |    2 +-
 sci-chemistry/shiftx/files/1.1-Makefile.patch      |   15 +-
 sci-chemistry/shiftx/files/1.1-bfr-overflow.patch  |   16 +
 sci-chemistry/shiftx/metadata.xml                  |    5 +-
 sci-chemistry/shiftx/shiftx-1.1.ebuild             |   25 +-
 sci-chemistry/shiftx2/ChangeLog                    |   20 +
 sci-chemistry/shiftx2/Manifest                     |    1 +
 .../files/shiftx2-1.07_p20120106-java.patch        |  227 +++
 .../files/shiftx2-1.07_p20120106-system.patch      |  231 +++
 sci-chemistry/shiftx2/metadata.xml                 |   39 +
 .../shiftx2/shiftx2-1.07_p20120106.ebuild          |  129 ++
 sci-chemistry/simpson/ChangeLog                    |   11 +-
 sci-chemistry/simpson/files/3.0.1-gentoo.patch     |    2 +-
 sci-chemistry/simpson/files/3.1.0-gentoo.patch     |    2 +-
 sci-chemistry/simpson/files/3.1.2-gentoo.patch     |    2 +-
 sci-chemistry/simpson/metadata.xml                 |    2 +-
 sci-chemistry/simpson/simpson-3.0.1.ebuild         |    8 +-
 sci-chemistry/simpson/simpson-3.1.0.ebuild         |    8 +-
 sci-chemistry/simpson/simpson-3.1.2.ebuild         |    8 +-
 sci-chemistry/smmp/ChangeLog                       |    8 +-
 sci-chemistry/smmp/Manifest                        |    2 +-
 sci-chemistry/smmp/metadata.xml                    |    5 +-
 sci-chemistry/smmp/smmp-3.0.5.ebuild               |   44 +-
 sci-chemistry/specView/ChangeLog                   |   23 +-
 sci-chemistry/specView/Manifest                    |    1 +
 sci-chemistry/specView/metadata.xml                |    2 +-
 sci-chemistry/specView/specView-1.0.2.ebuild       |   70 +-
 sci-chemistry/specView/specView-1.0.3.ebuild       |   88 +
 sci-chemistry/ssp/ChangeLog                        |    5 +-
 sci-chemistry/ssp/metadata.xml                     |    8 +-
 sci-chemistry/ssp/ssp-09.11.ebuild                 |    6 +-
 sci-chemistry/talosn/ChangeLog                     |   16 +
 sci-chemistry/talosn/Manifest                      |    1 +
 sci-chemistry/talosn/metadata.xml                  |    5 +
 .../talosn/talosn-4.01.2013.148.15.55-r2.ebuild    |   68 +
 sci-chemistry/ucsf-tools/ChangeLog                 |   11 +
 sci-chemistry/ucsf-tools/Manifest                  |    2 +
 sci-chemistry/ucsf-tools/metadata.xml              |   31 +-
 sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild    |   19 +-
 sci-chemistry/unio/ChangeLog                       |    9 +-
 sci-chemistry/unio/Manifest                        |    3 +-
 sci-chemistry/unio/metadata.xml                    |    5 +-
 sci-chemistry/unio/unio-2.0.1-r1.ebuild            |   71 -
 sci-chemistry/unio/unio-2.0.2-r1.ebuild            |   67 +
 sci-chemistry/unio/unio-2.0.2.ebuild               |   71 -
 sci-chemistry/usf-tools/ChangeLog                  |    8 +-
 sci-chemistry/usf-tools/metadata.xml               |    5 +-
 sci-chemistry/usf-tools/usf-tools-9999.ebuild      |    4 +-
 sci-chemistry/votca-csg-tutorials/ChangeLog        |   17 -
 sci-chemistry/votca-csg-tutorials/metadata.xml     |    9 -
 .../votca-csg-tutorials-9999.ebuild                |   29 -
 sci-chemistry/votca-csg/ChangeLog                  |   11 +-
 sci-chemistry/votca-csg/votca-csg-9999.ebuild      |   49 +-
 sci-chemistry/votca-csgapps/ChangeLog              |    3 +
 .../votca-csgapps/votca-csgapps-9999.ebuild        |    4 +-
 sci-chemistry/wxmacmolplt/ChangeLog                |    7 +-
 sci-chemistry/wxmacmolplt/Manifest                 |    1 +
 sci-chemistry/wxmacmolplt/wxmacmolplt-7.5.ebuild   |   44 +
 sci-chemistry/xdrfile/ChangeLog                    |   15 -
 sci-chemistry/xdrfile/Manifest                     |    1 -
 sci-chemistry/xdrfile/xdrfile-1.1.ebuild           |   28 -
 sci-chemistry/xdsstat-bin/ChangeLog                |   10 -
 sci-chemistry/xdsstat-bin/Manifest                 |    1 -
 sci-chemistry/xdsstat-bin/metadata.xml             |    8 -
 .../xdsstat-bin/xdsstat-bin-100513.ebuild          |   29 -
 sci-electronics/player/Manifest                    |    2 +-
 sci-electronics/stage/Manifest                     |    2 +-
 sci-electronics/tnt/Manifest                       |    2 +-
 sci-geosciences/cdat-lite/Manifest                 |    4 +-
 sci-geosciences/congen/Manifest                    |    2 +-
 sci-geosciences/fullprof-bin/ChangeLog             |   10 +
 sci-geosciences/fullprof-bin/Manifest              |    1 +
 .../fullprof-bin/fullprof-bin-2012.11.ebuild       |   66 +
 sci-geosciences/fullprof-bin/metadata.xml          |   16 +
 .../harmonics-dwf-free-noncomm/Manifest            |    2 +-
 sci-geosciences/harmonics-dwf-free/Manifest        |    4 +-
 sci-geosciences/libtcd/Manifest                    |    4 +-
 sci-geosciences/pydap/ChangeLog                    |    8 +-
 sci-geosciences/pydap/Manifest                     |    2 +-
 sci-geosciences/pydap/metadata.xml                 |   12 +-
 sci-geosciences/pydap/pydap-3.0.3.ebuild           |   34 -
 sci-geosciences/pydap/pydap-3.1.ebuild             |   38 +
 sci-geosciences/qgis/ChangeLog                     |   11 +-
 sci-geosciences/qgis/Manifest                      |    2 +-
 sci-geosciences/qgis/metadata.xml                  |   11 +-
 sci-geosciences/qgis/qgis-9999.ebuild              |   58 +-
 sci-geosciences/seawater/Manifest                  |    2 +-
 sci-geosciences/swmm/Manifest                      |    2 +-
 sci-geosciences/tappy/Manifest                     |    2 +-
 sci-geosciences/tcd-utils/Manifest                 |    4 +-
 sci-geosciences/xtide/Manifest                     |    4 +-
 sci-libs/Cgraph/Cgraph-2.04.ebuild                 |    5 +-
 sci-libs/Cgraph/ChangeLog                          |    6 +-
 sci-libs/Cgraph/Manifest                           |    2 +-
 sci-libs/Cgraph/metadata.xml                       |    3 -
 sci-libs/acml/ChangeLog                            |   15 +-
 sci-libs/acml/Manifest                             |   30 +-
 sci-libs/acml/acml-4.4.0-r1.ebuild                 |  121 --
 sci-libs/acml/acml-5.2.0.ebuild                    |  109 --
 sci-libs/acml/acml-5.3.1.ebuild                    |  113 ++
 sci-libs/acml/metadata.xml                         |    4 +-
 sci-libs/amdlibm/ChangeLog                         |    9 +-
 sci-libs/amdlibm/amdlibm-3.0.2.ebuild              |   23 +-
 sci-libs/amdlibm/metadata.xml                      |    4 +-
 sci-libs/armadillo/ChangeLog                       |   61 +-
 sci-libs/armadillo/Manifest                        |    2 +-
 sci-libs/armadillo/armadillo-3.2.4-r1.ebuild       |   71 -
 sci-libs/armadillo/armadillo-3.910.0.ebuild        |   91 +
 .../files/armadillo-3.820.1-example-makefile.patch |   33 +
 .../armadillo/files/armadillo-3.820.1-hdf5.patch   |   19 +
 sci-libs/armadillo/metadata.xml                    |   20 +-
 sci-libs/atlas/ChangeLog                           |   31 +-
 sci-libs/atlas/Manifest                            |    6 +-
 sci-libs/atlas/atlas-3.10.0.ebuild                 |  280 ---
 sci-libs/atlas/atlas-3.10.1-r1.ebuild              |  270 +++
 sci-libs/atlas/atlas-3.8.4.ebuild                  |  281 ---
 sci-libs/atlas/files/3.9.39-bfr-overflow.patch     |   72 -
 sci-libs/atlas/metadata.xml                        |   23 +-
 sci-libs/avogadro-libs/ChangeLog                   |   18 +
 sci-libs/avogadro-libs/Manifest                    |    1 +
 sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild  |   46 +
 .../files/avogadro-libs-0.6.0-underlinking.patch   |   14 +
 sci-libs/avogadro-libs/metadata.xml                |   14 +
 sci-libs/bigdft-abi/ChangeLog                      |   48 +
 sci-libs/bigdft-abi/Manifest                       |    1 +
 sci-libs/bigdft-abi/bigdft-abi-1.0.4-r2.ebuild     |  171 ++
 .../files/bigdft-abi-1.0.4-CUDA_gethostname.patch  |   22 +
 .../files/bigdft-abi-1.0.4-tests.tar.bz2           |  Bin 0 -> 402968 bytes
 sci-libs/bigdft-abi/metadata.xml                   |   24 +
 sci-libs/bigdft/ChangeLog                          |  113 --
 sci-libs/bigdft/Manifest                           |    2 -
 sci-libs/bigdft/bigdft-1.6.0-r2.ebuild             |  122 --
 sci-libs/bigdft/bigdft-1.6_pre1-r4.ebuild          |  130 --
 .../bigdft/files/bigdft-1.6-tuto.1-GPUlibs-1.patch |   26 -
 .../files/bigdft-1.6-tuto.1-bigdft.pc-1.patch      |  207 ---
 .../bigdft/files/bigdft-1.6-tuto.1-gcc-4.6.patch   |   67 -
 .../bigdft-1.6-tuto.1-libxc_dir_include.patch      |   50 -
 .../files/bigdft-1.6.0-libxc_dir_include.patch     |   50 -
 sci-libs/bigdft/metadata.xml                       |   11 -
 sci-libs/blas-reference/ChangeLog                  |   22 +-
 sci-libs/blas-reference/Manifest                   |    1 -
 .../blas-reference/blas-reference-20120423.ebuild  |   67 -
 .../blas-reference/blas-reference-20120925.ebuild  |   74 +-
 .../blas-reference/blas-reference-99999999.ebuild  |   74 +-
 .../blas-reference/files/lapack-3.4.1-cmake.patch  |  208 ---
 sci-libs/blas-reference/metadata.xml               |    4 +-
 sci-libs/blastdb/ChangeLog                         |    8 +
 sci-libs/blastdb/blastdb-9999.ebuild               |   27 +
 .../pythonqt => sci-libs/blastdb}/metadata.xml     |    0
 sci-libs/bliss/ChangeLog                           |   14 +
 sci-libs/bliss/Manifest                            |    1 +
 sci-libs/bliss/bliss-0.72.ebuild                   |   43 +
 sci-libs/bliss/files/bliss-0.72-autotools.patch    |  159 ++
 sci-libs/bliss/files/bliss-0.72-fedora.patch       |  648 +++++++
 sci-libs/bliss/metadata.xml                        |    9 +
 sci-libs/calculix-ccx/ChangeLog                    |    8 +-
 sci-libs/calculix-ccx/Manifest                     |    6 +-
 sci-libs/calculix-ccx/calculix-ccx-2.2.ebuild      |   19 +-
 sci-libs/calculix-ccx/metadata.xml                 |    8 +-
 sci-libs/calculix-cgx/Manifest                     |    4 +-
 sci-libs/cblas-reference/ChangeLog                 |    4 +
 .../cblas-reference-20110218.ebuild                |    7 +-
 sci-libs/cgnsfoam/Manifest                         |    2 +-
 sci-libs/cgnslib/Manifest                          |    2 +-
 sci-libs/cgnstools/Manifest                        |    2 +-
 sci-libs/cgnstools/cgnstools-2.5.4-r1.ebuild       |    1 +
 .../cgnstools/files/cgnstools-2.5.4_tcltk.patch    |  114 ++
 sci-libs/chemkit/ChangeLog                         |   10 +
 sci-libs/chemkit/Manifest                          |    1 +
 sci-libs/chemkit/chemkit-0.1.ebuild                |   55 +
 sci-libs/chemkit/metadata.xml                      |   11 +
 sci-libs/cnsface-scripts/ChangeLog                 |   10 -
 sci-libs/cnsface-scripts/Manifest                  |    1 -
 .../cnsface-scripts/cnsface-scripts-0.1.ebuild     |   22 -
 sci-libs/cnsface-scripts/metadata.xml              |    8 -
 sci-libs/coinhsl/ChangeLog                         |   18 +
 sci-libs/coinhsl/Manifest                          |    2 +
 sci-libs/coinhsl/coinhsl-2012.12.21.ebuild         |   36 +
 sci-libs/coinhsl/coinhsl-2013.06.18.ebuild         |   32 +
 sci-libs/coinhsl/metadata.xml                      |   12 +
 sci-libs/coinor-alps/ChangeLog                     |   17 +-
 sci-libs/coinor-alps/Manifest                      |    2 +-
 sci-libs/coinor-alps/coinor-alps-1.4.2.ebuild      |   66 -
 sci-libs/coinor-alps/coinor-alps-1.4.4.ebuild      |   67 +
 sci-libs/coinor-bcp/ChangeLog                      |    8 +-
 sci-libs/coinor-bcp/Manifest                       |    2 +-
 sci-libs/coinor-bcp/coinor-bcp-1.3.4.ebuild        |   56 -
 sci-libs/coinor-bcp/coinor-bcp-1.3.5.ebuild        |   56 +
 sci-libs/coinor-bcps/ChangeLog                     |    8 +-
 sci-libs/coinor-bcps/Manifest                      |    2 +-
 sci-libs/coinor-bcps/coinor-bcps-0.93.4.ebuild     |   67 -
 sci-libs/coinor-bcps/coinor-bcps-0.93.5.ebuild     |   67 +
 sci-libs/coinor-blis/ChangeLog                     |   17 +-
 sci-libs/coinor-blis/Manifest                      |    2 +-
 sci-libs/coinor-blis/coinor-blis-0.93.3.ebuild     |   67 -
 sci-libs/coinor-blis/coinor-blis-0.93.5.ebuild     |   65 +
 sci-libs/coinor-bonmin/ChangeLog                   |   11 +-
 sci-libs/coinor-bonmin/Manifest                    |    2 +-
 sci-libs/coinor-bonmin/coinor-bonmin-1.6.0.ebuild  |   65 -
 sci-libs/coinor-bonmin/coinor-bonmin-1.7.0.ebuild  |   65 +
 sci-libs/coinor-bonmin/metadata.xml                |    7 +-
 sci-libs/coinor-buildtools/ChangeLog               |    9 +
 .../coinor-buildtools-0.7.4.ebuild                 |   38 +
 sci-libs/coinor-buildtools/metadata.xml            |    9 +
 sci-libs/coinor-cbc/ChangeLog                      |   26 +-
 sci-libs/coinor-cbc/Manifest                       |    2 +-
 sci-libs/coinor-cbc/coinor-cbc-2.7.7.ebuild        |   83 -
 sci-libs/coinor-cbc/coinor-cbc-2.8.3.ebuild        |   83 +
 sci-libs/coinor-cbc/metadata.xml                   |    4 +-
 sci-libs/coinor-cgl/ChangeLog                      |   23 +-
 sci-libs/coinor-cgl/Manifest                       |    2 +-
 sci-libs/coinor-cgl/coinor-cgl-0.57.3.ebuild       |   69 -
 sci-libs/coinor-cgl/coinor-cgl-0.58.1.ebuild       |   73 +
 sci-libs/coinor-clp/ChangeLog                      |   30 +-
 sci-libs/coinor-clp/Manifest                       |    2 +-
 sci-libs/coinor-clp/coinor-clp-1.14.6.ebuild       |  111 --
 sci-libs/coinor-clp/coinor-clp-1.15.2.ebuild       |  112 ++
 .../files/coinor-clp-1.15.1-mpi-header.patch       |   12 +
 sci-libs/coinor-couenne/ChangeLog                  |    8 +-
 sci-libs/coinor-couenne/Manifest                   |    2 +-
 .../coinor-couenne/coinor-couenne-0.4.2.ebuild     |   65 -
 .../coinor-couenne/coinor-couenne-0.4.3.ebuild     |   65 +
 sci-libs/coinor-cppad/ChangeLog                    |   24 +-
 sci-libs/coinor-cppad/Manifest                     |    2 +-
 sci-libs/coinor-cppad/coinor-cppad-20120719.ebuild |   56 -
 sci-libs/coinor-cppad/coinor-cppad-20130717.ebuild |   54 +
 sci-libs/coinor-cppad/metadata.xml                 |    4 +-
 sci-libs/coinor-csdp/ChangeLog                     |    5 +-
 sci-libs/coinor-csdp/coinor-csdp-6.1.1.ebuild      |    8 +-
 sci-libs/coinor-dip/coinor-dip-0.83.2.ebuild       |    6 +-
 sci-libs/coinor-dylp/ChangeLog                     |    8 +-
 sci-libs/coinor-dylp/Manifest                      |    2 +-
 sci-libs/coinor-dylp/coinor-dylp-1.8.3.ebuild      |   66 -
 sci-libs/coinor-dylp/coinor-dylp-1.9.0.ebuild      |   66 +
 sci-libs/coinor-flopcpp/ChangeLog                  |   15 +
 sci-libs/coinor-flopcpp/Manifest                   |    1 +
 .../coinor-flopcpp/coinor-flopcpp-1.1.3.ebuild     |   67 +
 sci-libs/coinor-flopcpp/metadata.xml               |   14 +
 sci-libs/coinor-mp/ChangeLog                       |   11 +-
 sci-libs/coinor-mp/Manifest                        |    2 +-
 sci-libs/coinor-mp/coinor-mp-1.6.0.ebuild          |   55 -
 sci-libs/coinor-mp/coinor-mp-1.7.0.ebuild          |   55 +
 sci-libs/coinor-netlib/ChangeLog                   |   12 +-
 sci-libs/coinor-netlib/Manifest                    |    2 +-
 sci-libs/coinor-netlib/coinor-netlib-1.2.2.ebuild  |   29 -
 sci-libs/coinor-netlib/coinor-netlib-1.2.4.ebuild  |   23 +
 sci-libs/coinor-os/coinor-os-2.6.0.ebuild          |    6 +-
 sci-libs/coinor-osi/ChangeLog                      |   20 +-
 sci-libs/coinor-osi/Manifest                       |    2 +-
 sci-libs/coinor-osi/coinor-osi-0.105.3.ebuild      |   75 -
 sci-libs/coinor-osi/coinor-osi-0.106.1.ebuild      |   76 +
 sci-libs/coinor-sample/ChangeLog                   |   30 +-
 sci-libs/coinor-sample/Manifest                    |    2 +-
 sci-libs/coinor-sample/coinor-sample-1.2.1.ebuild  |   29 -
 sci-libs/coinor-sample/coinor-sample-1.2.6.ebuild  |   23 +
 sci-libs/coinor-symphony/ChangeLog                 |   20 +-
 sci-libs/coinor-symphony/Manifest                  |    2 +-
 .../coinor-symphony/coinor-symphony-5.4.4.ebuild   |   94 -
 .../coinor-symphony/coinor-symphony-5.5.0.ebuild   |   89 +
 sci-libs/coinor-utils/ChangeLog                    |   26 +-
 sci-libs/coinor-utils/Manifest                     |    2 +-
 sci-libs/coinor-utils/coinor-utils-2.8.6.ebuild    |   84 -
 sci-libs/coinor-utils/coinor-utils-2.9.3.ebuild    |   85 +
 sci-libs/coinor-vol/ChangeLog                      |    8 +-
 sci-libs/coinor-vol/Manifest                       |    2 +-
 sci-libs/coinor-vol/coinor-vol-1.3.3.ebuild        |   71 -
 sci-libs/coinor-vol/coinor-vol-1.4.0.ebuild        |   71 +
 sci-libs/cs-rosetta-db/ChangeLog                   |   14 +
 sci-libs/cs-rosetta-db/Manifest                    |    7 +
 .../cs-rosetta-db-1.01.2009.1109.11.ebuild         |   61 +
 .../cs-rosetta-db}/metadata.xml                    |    0
 sci-libs/csrosetta-angless/ChangeLog               |   14 -
 sci-libs/csrosetta-angless/Manifest                |    1 -
 .../csrosetta-angless-2009.05.01.ebuild            |   24 -
 sci-libs/csrosetta-angless/metadata.xml            |    8 -
 sci-libs/csrosetta-cs/ChangeLog                    |   14 -
 sci-libs/csrosetta-cs/Manifest                     |    1 -
 .../csrosetta-cs/csrosetta-cs-2009.05.01.ebuild    |   24 -
 sci-libs/csrosetta-cs/metadata.xml                 |    8 -
 sci-libs/csrosetta-pdbh/ChangeLog                  |   14 -
 sci-libs/csrosetta-pdbh/Manifest                   |    1 -
 .../csrosetta-pdbh-2009.05.01.ebuild               |   24 -
 sci-libs/csrosetta-pdbh/metadata.xml               |    8 -
 sci-libs/dcmtk/Manifest                            |    6 +-
 sci-libs/dealii/Manifest                           |    2 +
 sci-libs/dealii/dealii-8.0.0.ebuild                |    1 +
 sci-libs/dealii/dealii-9999.ebuild                 |  128 ++
 sci-libs/dealii/metadata.xml                       |   28 +
 sci-libs/driftwood/Manifest                        |    2 +-
 sci-libs/driftwood/metadata.xml                    |    5 +-
 sci-libs/etsf_io/ChangeLog                         |   13 +-
 sci-libs/etsf_io/Manifest                          |    2 +-
 sci-libs/etsf_io/etsf_io-1.0.3-r1.ebuild           |   36 -
 sci-libs/etsf_io/etsf_io-1.0.3-r2.ebuild           |   36 +
 sci-libs/etsf_io/metadata.xml                      |    5 +-
 sci-libs/exodusii/ChangeLog                        |   22 -
 sci-libs/exodusii/Manifest                         |    1 -
 sci-libs/exodusii/exodusii-5.22.ebuild             |   31 -
 .../exodusii/files/exodusii-5.22-multilib.patch    |   20 -
 sci-libs/exodusii/metadata.xml                     |    8 -
 sci-libs/factory/Manifest                          |    2 +-
 sci-libs/fftw/ChangeLog                            |   22 +
 sci-libs/fftw/fftw-9999.ebuild                     |  187 ++
 .../fftw/files/fftw-3.3.3-install-header.patch     |   35 +
 sci-libs/fftw/metadata.xml                         |   23 +
 sci-libs/fgsl/Manifest                             |    4 +-
 sci-libs/fox/ChangeLog                             |   14 +-
 sci-libs/fox/Manifest                              |   12 +-
 .../fox/files/4.0.4-install-customizations.patch   |   27 -
 .../files/4.1.2-r2-install-customizations.patch    |   27 +
 sci-libs/fox/fox-4.1.2-r1.ebuild                   |   69 -
 sci-libs/fox/fox-4.1.2-r2.ebuild                   |   69 +
 sci-libs/fox/metadata.xml                          |   19 +-
 sci-libs/fplll/ChangeLog                           |    7 -
 sci-libs/fplll/Manifest                            |    1 -
 sci-libs/fplll/fplll-2.1.6.ebuild                  |   40 -
 sci-libs/fplll/metadata.xml                        |    6 -
 sci-libs/framewave/Manifest                        |    2 +-
 sci-libs/geom/Manifest                             |    2 +-
 sci-libs/givaro/Manifest                           |    4 +-
 sci-libs/gmsh/ChangeLog                            |    5 +-
 sci-libs/gmsh/gmsh-2.5.0.ebuild                    |    3 +-
 sci-libs/gmsh/metadata.xml                         |   24 +-
 sci-libs/gsl/ChangeLog                             |   20 +-
 sci-libs/gsl/Manifest                              |    2 +-
 sci-libs/gsl/files/gsl-1.15-cblas.patch            |   75 -
 sci-libs/gsl/files/gsl-1.16-cblas-external.patch   |  294 +++
 sci-libs/gsl/gsl-1.15-r2.ebuild                    |   42 -
 sci-libs/gsl/gsl-1.16-r1.ebuild                    |   60 +
 sci-libs/gsl/metadata.xml                          |    8 +-
 sci-libs/ipopt/ChangeLog                           |   27 +-
 sci-libs/ipopt/Manifest                            |    2 +-
 sci-libs/ipopt/files/ipopt-3.11.2-mpi-header.patch |   14 +
 sci-libs/ipopt/ipopt-3.10.2.ebuild                 |   85 -
 sci-libs/ipopt/ipopt-3.11.2.ebuild                 |  100 ++
 sci-libs/ipopt/metadata.xml                        |   11 +-
 sci-libs/itk/ChangeLog                             |    9 +
 sci-libs/itk/Manifest                              |    2 +
 sci-libs/itk/itk-4.4.2-r1.ebuild                   |  134 ++
 sci-libs/itk/itk-4.4.2.ebuild                      |  116 ++
 sci-libs/itk/metadata.xml                          |   18 +
 sci-libs/k3match/ChangeLog                         |    2 +-
 sci-libs/k3match/metadata.xml                      |    2 +-
 sci-libs/lapack-reference/ChangeLog                |   21 +-
 sci-libs/lapack-reference/Manifest                 |    2 -
 .../lapack-reference-3.3.1-r1.ebuild               |   84 -
 .../lapack-reference/lapack-reference-3.4.1.ebuild |   62 -
 .../lapack-reference/lapack-reference-3.4.2.ebuild |   75 +-
 .../lapack-reference/lapack-reference-9999.ebuild  |   86 +-
 sci-libs/lapack-reference/metadata.xml             |   11 +-
 sci-libs/lapacke-reference/ChangeLog               |   16 +-
 sci-libs/lapacke-reference/Manifest                |    1 -
 .../files/lapack-3.4.1-cmake.patch                 |  208 ---
 .../lapacke-reference-3.4.1.ebuild                 |   77 -
 .../lapacke-reference-3.4.2.ebuild                 |   93 +-
 .../lapacke-reference-9999.ebuild                  |  103 ++
 sci-libs/lapacke-reference/metadata.xml            |   12 +-
 sci-libs/lapackpp/ChangeLog                        |    4 +-
 sci-libs/lapackpp/lapackpp-2.5.4.ebuild            |   14 +-
 sci-libs/lemon/ChangeLog                           |   12 +-
 sci-libs/lemon/files/lemon-1.2.3-gcc47.patch       |   59 +
 sci-libs/lemon/lemon-1.2.3.ebuild                  |   51 +-
 sci-libs/lemon/metadata.xml                        |   21 +-
 sci-libs/levmar/ChangeLog                          |    4 +-
 sci-libs/levmar/levmar-2.6.ebuild                  |   13 +-
 sci-libs/libcgnsoo/Manifest                        |    2 +-
 sci-libs/libfac/Manifest                           |    4 +-
 sci-libs/libgeodecomp/Manifest                     |    2 +
 sci-libs/libgeodecomp/files/cmake.patch            |   17 +
 sci-libs/libgeodecomp/libgeodecomp-0.1.0.ebuild    |   26 +
 sci-libs/libgeodecomp/libgeodecomp-0.2.0.ebuild    |   36 +
 sci-libs/libgeodecomp/libgeodecomp-9999.ebuild     |   45 +
 sci-libs/libgeodecomp/metadata.xml                 |   14 +
 sci-libs/libmatheval/ChangeLog                     |   10 +
 sci-libs/libmatheval/Manifest                      |    1 +
 sci-libs/libmatheval/libmatheval-1.1.10.ebuild     |   17 +
 sci-libs/libmatheval/metadata.xml                  |   18 +
 sci-libs/libspatialindex/ChangeLog                 |    6 +-
 sci-libs/libspatialindex/Manifest                  |    2 +-
 .../libspatialindex/libspatialindex-1.6.1.ebuild   |   17 +-
 sci-libs/libspatialindex/metadata.xml              |    2 +-
 sci-libs/libsufr/ChangeLog                         |   19 +-
 sci-libs/libsufr/Manifest                          |    4 +-
 sci-libs/libsufr/libsufr-0.3.3.ebuild              |   29 -
 sci-libs/libsufr/libsufr-0.4.1.ebuild              |   28 +
 sci-libs/libsufr/libsufr-0.5.2.ebuild              |   28 +
 sci-libs/libsufr/libsufr-0.5.4.ebuild              |   28 +
 sci-libs/libxc/ChangeLog                           |   17 +-
 sci-libs/libxc/Manifest                            |    5 +-
 sci-libs/libxc/libxc-1.1.0-r1.ebuild               |   53 -
 sci-libs/libxc/libxc-1.2.0-r1.ebuild               |   55 +
 sci-libs/libxc/libxc-1.2.0.ebuild                  |   53 -
 sci-libs/libxc/libxc-2.0.1.ebuild                  |   59 +
 sci-libs/libxc/libxc-2.0.2.ebuild                  |   59 +
 sci-libs/libxc/libxc-9999.ebuild                   |   27 +-
 sci-libs/libxc/metadata.xml                        |    5 +-
 sci-libs/lwpr/ChangeLog                            |    9 +-
 sci-libs/lwpr/Manifest                             |    2 +-
 sci-libs/lwpr/files/lwpr-1.2.2-setup.py.patch      |   12 -
 sci-libs/lwpr/lwpr-1.2.2.ebuild                    |   83 -
 sci-libs/lwpr/lwpr-1.2.5.ebuild                    |   51 +
 sci-libs/lwpr/metadata.xml                         |   10 +-
 sci-libs/m4ri/Manifest                             |    4 +-
 sci-libs/magma/ChangeLog                           |   21 +-
 sci-libs/magma/Manifest                            |    3 +-
 .../files/magma-1.2.1-duplicate-symbols.patch      |  612 -------
 sci-libs/magma/magma-1.2.1.ebuild                  |  122 --
 sci-libs/magma/magma-1.3.0.ebuild                  |  142 ++
 sci-libs/magma/magma-1.4.0.ebuild                  |  122 ++
 sci-libs/magma/metadata.xml                        |   12 +-
 sci-libs/matio/Manifest                            |    2 +-
 sci-libs/med/metadata.xml                          |    5 +-
 sci-libs/mesquite/Manifest                         |    2 +-
 sci-libs/mkl/ChangeLog                             |   34 +-
 sci-libs/mkl/Manifest                              |   10 +-
 sci-libs/mkl/metadata.xml                          |    4 +-
 sci-libs/mkl/mkl-11.0.0.079.ebuild                 |  130 --
 sci-libs/mkl/mkl-11.0.3.163.ebuild                 |  131 ++
 sci-libs/mkl/mkl-11.0.5.192.ebuild                 |  131 ++
 sci-libs/mkl/mkl-11.1.0.080.ebuild                 |  140 ++
 sci-libs/mlpack/ChangeLog                          |   29 +
 sci-libs/mlpack/Manifest                           |    1 +
 sci-libs/mlpack/files/mlpack-1.0.4-libdir.patch    |   13 +
 sci-libs/mlpack/metadata.xml                       |   13 +
 sci-libs/mlpack/mlpack-1.0.6.ebuild                |   51 +
 sci-libs/mmdb/ChangeLog                            |   10 -
 sci-libs/mmdb/Manifest                             |    1 -
 .../mmdb/files/mmdb-1.24.20111208-pkg-config.patch |   49 -
 sci-libs/mmdb/metadata.xml                         |    8 -
 sci-libs/mmdb/mmdb-1.24.20111208.ebuild            |   25 -
 sci-libs/modglue/ChangeLog                         |   25 +-
 sci-libs/modglue/Manifest                          |    2 +-
 sci-libs/modglue/files/modglue-1.16-ldflags.patch  |   13 -
 sci-libs/modglue/files/modglue-1.16-lib64.patch    |   61 -
 .../modglue/files/modglue-1.16-parallelmake.patch  |   53 -
 .../modglue/files/modglue-1.19-Makefiles.patch     |  113 ++
 sci-libs/modglue/metadata.xml                      |   14 +-
 sci-libs/modglue/modglue-1.16.ebuild               |   46 -
 sci-libs/modglue/modglue-1.19.ebuild               |   40 +
 sci-libs/msms/ChangeLog                            |   10 +-
 sci-libs/msms/Manifest                             |    3 +-
 sci-libs/msms/metadata.xml                         |    5 +-
 sci-libs/msms/msms-1.5.4-r1.ebuild                 |   54 -
 sci-libs/msms/msms-1.5.6.ebuild                    |   44 +
 sci-libs/msms/msms-1.5.6_rc2.ebuild                |   45 -
 sci-libs/mumps/ChangeLog                           |   13 +-
 sci-libs/mumps/metadata.xml                        |    4 +-
 sci-libs/mumps/mumps-4.10.0-r1.ebuild              |  171 --
 sci-libs/mumps/mumps-4.10.0-r2.ebuild              |  184 ++
 sci-libs/nfft/ChangeLog                            |   28 -
 sci-libs/nfft/Manifest                             |    1 -
 sci-libs/nfft/metadata.xml                         |    9 -
 sci-libs/nfft/nfft-3.2.2.ebuild                    |   32 -
 sci-libs/ni-visa/Manifest                          |    2 +-
 sci-libs/nibabel/Manifest                          |    1 +
 sci-libs/nibabel/metadata.xml                      |   19 +
 sci-libs/nibabel/nibabel-1.3.0.ebuild              |   42 +
 sci-libs/nibabel/nibabel-9999.ebuild               |   40 +
 sci-libs/nipy/Manifest                             |    1 +
 sci-libs/nipy/metadata.xml                         |   12 +
 sci-libs/nipy/nipy-0.3.0.ebuild                    |   37 +
 sci-libs/nipy/nipy-9999.ebuild                     |   36 +
 sci-libs/nipype/metadata.xml                       |   21 +
 sci-libs/nipype/nipype-9999.ebuild                 |   33 +
 sci-libs/o2scl/ChangeLog                           |   21 +
 sci-libs/o2scl/Manifest                            |    1 +
 sci-libs/o2scl/metadata.xml                        |   12 +
 sci-libs/o2scl/o2scl-0.913.ebuild                  |   47 +
 sci-libs/oasa/Manifest                             |    2 +-
 sci-libs/omalloc/Manifest                          |    2 +-
 sci-libs/openblas/ChangeLog                        |   33 +-
 sci-libs/openblas/Manifest                         |    5 +-
 sci-libs/openblas/files/openblas-aliasing.patch    |   11 -
 .../openblas/files/openblas-sharedlibs-0.2.patch   |   45 -
 sci-libs/openblas/metadata.xml                     |    1 -
 sci-libs/openblas/openblas-0.2.2.ebuild            |    1 -
 sci-libs/openblas/openblas-0.2.3.ebuild            |  131 --
 sci-libs/openblas/openblas-0.2.4-r1.ebuild         |  131 --
 sci-libs/openblas/openblas-0.2.4.ebuild            |  131 --
 sci-libs/openblas/openblas-0.2.8.ebuild            |  126 ++
 sci-libs/openblas/openblas-9999.ebuild             |  156 +-
 sci-libs/openlibm/ChangeLog                        |   16 +
 .../openlibm/files/openlibm-extras-soname.patch    |   11 +
 .../files/openlibm-respect-toolchain.patch         |   42 +
 sci-libs/openlibm/files/openlibm-soname.patch      |   11 +
 sci-libs/openlibm/metadata.xml                     |   18 +
 sci-libs/openlibm/openlibm-9999.ebuild             |   48 +
 sci-libs/optpp/ChangeLog                           |   11 +-
 sci-libs/optpp/metadata.xml                        |    2 +-
 sci-libs/optpp/optpp-2.4.ebuild                    |   15 +-
 sci-libs/p4est/Manifest                            |    1 +
 sci-libs/p4est/files/p4est-libtool-fix.patch       |   59 +
 sci-libs/p4est/metadata.xml                        |   18 +
 sci-libs/p4est/p4est-0.3.4.2.ebuild                |   73 +
 sci-libs/pagmo/metadata.xml                        |   13 +-
 sci-libs/parmetis/ChangeLog                        |   13 +-
 sci-libs/parmetis/Manifest                         |    4 +-
 sci-libs/parmetis/metadata.xml                     |    4 +-
 sci-libs/parmetis/parmetis-4.0.2.ebuild            |  152 --
 sci-libs/parmetis/parmetis-4.0.3.ebuild            |  152 ++
 sci-libs/pg2plplot/ChangeLog                       |   10 +
 sci-libs/pg2plplot/Manifest                        |    1 +
 sci-libs/pg2plplot/metadata.xml                    |    9 +
 sci-libs/pg2plplot/pg2plplot-0.2.0.ebuild          |   34 +
 sci-libs/plasma/ChangeLog                          |   14 +-
 sci-libs/plasma/Manifest                           |    3 +-
 sci-libs/plasma/plasma-2.4.5.ebuild                |  116 --
 sci-libs/plasma/plasma-2.4.6.ebuild                |  125 ++
 sci-libs/plasma/plasma-2.5.1.ebuild                |  134 ++
 sci-libs/pydicom/Manifest                          |    1 +
 sci-libs/pydicom/pydicom-0.9.8.ebuild              |   20 +
 sci-libs/scalapack/ChangeLog                       |    5 +
 .../scalapack/files/scalapack-2.0.1-link.patch     |   18 -
 .../files/scalapack-2.0.1-multipledefs.patch       |  163 --
 sci-libs/scalapack/scalapack-2.0.2.ebuild          |    8 +-
 sci-libs/scikits_image/ChangeLog                   |   19 +
 sci-libs/scikits_image/metadata.xml                |   17 +
 sci-libs/scikits_image/scikits_image-9999.ebuild   |   47 +
 sci-libs/starparse/ChangeLog                       |    6 +-
 sci-libs/starparse/Manifest                        |    2 +-
 sci-libs/starparse/metadata.xml                    |    5 +-
 sci-libs/starparse/starparse-1.0.ebuild            |   25 +-
 sci-libs/starparse/starparse-9999.ebuild           |    8 +-
 sci-libs/starparse/starparse-9999_pre10.ebuild     |   22 +-
 sci-libs/superlu_dist/ChangeLog                    |   13 +
 sci-libs/superlu_dist/Manifest                     |    1 +
 .../files/superlu_dist-3.3-duplicate-symbols.patch |   70 +
 sci-libs/superlu_dist/metadata.xml                 |   23 +
 sci-libs/superlu_dist/superlu_dist-3.3.ebuild      |   82 +
 sci-libs/superlu_mt/ChangeLog                      |   17 +
 sci-libs/superlu_mt/Manifest                       |    1 +
 .../files/superlu_mt-2.1-duplicate-symbols.patch   |  900 ++++++++++
 .../files/superlu_mt-2.1-missing-includes.patch    |   44 +
 sci-libs/superlu_mt/metadata.xml                   |   23 +
 sci-libs/superlu_mt/superlu_mt-2.1.ebuild          |  110 ++
 sci-libs/symmetrica/Manifest                       |    2 +-
 sci-libs/tmglib/ChangeLog                          |   13 +
 sci-libs/tmglib/Manifest                           |    1 +
 sci-libs/tmglib/metadata.xml                       |    9 +
 sci-libs/tmglib/tmglib-3.4.2.ebuild                |   61 +
 sci-libs/trilinos/ChangeLog                        |   23 +-
 sci-libs/trilinos/Manifest                         |    4 +-
 .../files/trilinos-11.0.3-fix-install-paths.patch  |   76 +
 .../files/trilinos-11.2.3-fix-install-paths.patch  |   62 +
 .../files/trilinos-11.4.2-fix-install-paths.patch  |   60 +
 sci-libs/trilinos/metadata.xml                     |   45 +-
 sci-libs/trilinos/trilinos-10.10.1.ebuild          |  122 --
 sci-libs/trilinos/trilinos-11.0.3.ebuild           |  129 ++
 sci-libs/trilinos/trilinos-11.2.3-r1.ebuild        |    1 +
 sci-libs/trilinos/trilinos-11.4.2.ebuild           |  202 +++
 sci-libs/votca-tools/ChangeLog                     |    3 +
 sci-libs/votca-tools/votca-tools-9999.ebuild       |    4 +-
 sci-libs/wannier90/ChangeLog                       |   20 +-
 sci-libs/wannier90/Manifest                        |    2 +-
 sci-libs/wannier90/metadata.xml                    |    3 -
 sci-libs/wannier90/wannier90-1.2-r2.ebuild         |   76 +
 sci-libs/wannier90/wannier90-1.2.ebuild            |   78 -
 sci-libs/xblas/ChangeLog                           |    6 +-
 sci-libs/xblas/metadata.xml                        |    4 +-
 sci-libs/xblas/xblas-1.0.248.ebuild                |    8 +-
 sci-libs/zarja/ChangeLog                           |    7 +-
 sci-libs/zarja/Manifest                            |    2 +-
 sci-libs/zarja/metadata.xml                        |    4 +-
 sci-libs/zarja/zarja-1.1.1.ebuild                  |   22 +-
 sci-mathematics/Macaulay2/ChangeLog                |   19 +-
 sci-mathematics/Macaulay2/Macaulay2-9999.ebuild    |   79 +-
 sci-mathematics/Macaulay2/Manifest                 |    5 +-
 sci-mathematics/Macaulay2/files/9999-lapack.patch  |    2 +-
 sci-mathematics/Macaulay2/metadata.xml             |   18 +-
 sci-mathematics/Oid/Manifest                       |    4 +-
 sci-mathematics/acl2/Manifest                      |    2 +-
 sci-mathematics/algae/ChangeLog                    |   18 -
 sci-mathematics/algae/Manifest                     |    1 -
 sci-mathematics/algae/algae-4.3.6.ebuild           |   55 -
 sci-mathematics/algae/files/Makefile.in-doc.patch  |    5 -
 sci-mathematics/algae/files/Makefile.in-src.patch  |    4 -
 sci-mathematics/algae/files/configure.in.patch     |   10 -
 sci-mathematics/algae/metadata.xml                 |   16 -
 sci-mathematics/alt-ergo/ChangeLog                 |   19 +
 sci-mathematics/alt-ergo/Manifest                  |    1 +
 sci-mathematics/alt-ergo/alt-ergo-0.95.1.ebuild    |   37 +
 sci-mathematics/alt-ergo/metadata.xml              |   11 +
 sci-mathematics/apron/Manifest                     |    5 +-
 sci-mathematics/apron/metadata.xml                 |   31 +-
 sci-mathematics/aribas/Manifest                    |    2 +-
 sci-mathematics/axiom/Manifest                     |    2 +-
 sci-mathematics/bertini/ChangeLog                  |   13 -
 sci-mathematics/bertini/Manifest                   |    2 -
 sci-mathematics/bertini/bertini-1.3.1.ebuild       |   55 -
 sci-mathematics/bertini/metadata.xml               |   29 -
 sci-mathematics/burrtools/Manifest                 |    4 +-
 sci-mathematics/cadabra/ChangeLog                  |   21 +-
 sci-mathematics/cadabra/Manifest                   |    4 +-
 sci-mathematics/cadabra/cadabra-1.25.ebuild        |   89 -
 sci-mathematics/cadabra/cadabra-1.28.ebuild        |   87 -
 sci-mathematics/cadabra/cadabra-1.29.ebuild        |   87 -
 sci-mathematics/cadabra/cadabra-1.33.ebuild        |   87 +
 .../cadabra/files/cadabra-1.21-no-stripping.patch  |   30 -
 .../files/cadabra-1.25-xcadabra-flags.patch        |   11 -
 .../cadabra/files/cadabra-1.33-FLAGS.patch         |  171 ++
 sci-mathematics/cadabra/metadata.xml               |    4 +-
 sci-mathematics/cdfplayer/ChangeLog                |   25 +
 sci-mathematics/cdfplayer/Manifest                 |    1 +
 sci-mathematics/cdfplayer/cdfplayer-9.0.1.ebuild   |   54 +
 .../files/cdfplayer-9.0.1-installer.patch          |   19 +
 sci-mathematics/cdfplayer/metadata.xml             |   12 +
 sci-mathematics/dolfin/Manifest                    |    2 +-
 sci-mathematics/dsfmt/ChangeLog                    |    5 +-
 sci-mathematics/dsfmt/dsfmt-2.2.ebuild             |   11 +-
 sci-mathematics/dsfmt/metadata.xml                 |    4 +-
 sci-mathematics/flocq/ChangeLog                    |   10 +-
 sci-mathematics/flocq/Manifest                     |    5 +-
 sci-mathematics/flocq/flocq-1.4.0.ebuild           |   26 -
 sci-mathematics/flocq/flocq-2.1.0.ebuild           |   21 +
 sci-mathematics/flocq/metadata.xml                 |   17 +-
 sci-mathematics/frama-c/ChangeLog                  |    8 +-
 sci-mathematics/frama-c/Manifest                   |    5 +-
 sci-mathematics/frama-c/frama-c-20111001.ebuild    |   66 -
 sci-mathematics/frama-c/frama-c-20120901.ebuild    |   63 +
 sci-mathematics/frama-c/metadata.xml               |   28 +-
 sci-mathematics/freefem++/ChangeLog                |    8 +-
 sci-mathematics/freefem++/Manifest                 |    3 +-
 .../files/freefem++-3.4.2-no-doc-autobuild.patch   |   30 -
 sci-mathematics/freefem++/freefem++-3.5.ebuild     |  156 --
 sci-mathematics/freefem++/freefem++-3.8.ebuild     |   18 +-
 sci-mathematics/freefem++/metadata.xml             |    4 +-
 sci-mathematics/gambit/ChangeLog                   |    6 +-
 sci-mathematics/gambit/Manifest                    |    2 +-
 sci-mathematics/gambit/gambit-0.2010.09.01.ebuild  |    4 +-
 sci-mathematics/gambit/metadata.xml                |   16 +-
 sci-mathematics/gap-guava/Manifest                 |    2 +-
 sci-mathematics/gap-guava/metadata.xml             |    5 +-
 sci-mathematics/gap/Manifest                       |    4 +-
 sci-mathematics/gappa/ChangeLog                    |   13 +-
 sci-mathematics/gappa/Manifest                     |    5 +-
 sci-mathematics/gappa/gappa-0.15.1.ebuild          |   56 -
 sci-mathematics/gappa/gappa-1.0.0.ebuild           |   37 +
 sci-mathematics/gappa/metadata.xml                 |   19 +-
 sci-mathematics/gappalib-coq/ChangeLog             |   10 +-
 sci-mathematics/gappalib-coq/Manifest              |    5 +-
 .../gappalib-coq/files/gappalib-coq-coq84.patch    |   71 +
 .../gappalib-coq/gappalib-coq-0.16.0.ebuild        |   34 -
 .../gappalib-coq/gappalib-coq-0.18.0.ebuild        |   35 +
 sci-mathematics/gappalib-coq/metadata.xml          |   15 +-
 sci-mathematics/giac/ChangeLog                     |   11 +-
 sci-mathematics/giac/Manifest                      |    5 +-
 sci-mathematics/giac/giac-0.9.2.ebuild             |   57 -
 sci-mathematics/giac/giac-1.0.0.ebuild             |   59 +
 sci-mathematics/giac/metadata.xml                  |   22 +-
 sci-mathematics/htk/Manifest                       |    4 +-
 sci-mathematics/kayali/Manifest                    |    2 +-
 sci-mathematics/lattE-macchiato/ChangeLog          |    6 +-
 sci-mathematics/lattE-macchiato/Manifest           |    2 +-
 .../lattE-macchiato/lattE-macchiato-0.9.3.ebuild   |    5 +-
 sci-mathematics/lattE-macchiato/metadata.xml       |   12 +-
 sci-mathematics/libsfmt/Manifest                   |    2 +-
 sci-mathematics/lie/Manifest                       |    2 +-
 sci-mathematics/ltl2ba/Manifest                    |   25 +-
 sci-mathematics/ltl2ba/metadata.xml                |    3 -
 sci-mathematics/mdp/ChangeLog                      |    5 +-
 sci-mathematics/mdp/mdp-9999.ebuild                |   12 +-
 sci-mathematics/mdp/metadata.xml                   |   12 +-
 sci-mathematics/netgen/Manifest                    |    3 +-
 sci-mathematics/open-axiom/Manifest                |    2 +-
 sci-mathematics/pest/Manifest                      |    6 +-
 sci-mathematics/petsc/ChangeLog                    |   14 +-
 sci-mathematics/petsc/Manifest                     |    5 +-
 .../petsc/files/petsc-3.1_p8-configure-pic.patch   |   11 -
 .../petsc/files/petsc-3.1_p8-disable-rpath.patch   |   16 -
 .../petsc/files/petsc-3.2_p6-configure-pic.patch   |   11 -
 .../files/petsc-3.2_p6-disable-env-warnings.patch  |   13 -
 .../petsc/files/petsc-3.2_p6-disable-rpath.patch   |   16 -
 .../petsc/files/petsc-3.2_p6-fix-afterimage.patch  |   71 -
 .../petsc/files/petsc-3.2_p6-fix-imagemagick.patch |   24 -
 .../petsc/files/petsc-3.2_p6-fix-xops.patch        |   21 -
 .../files/petsc-3.3-disable-env-warnings.patch     |   13 -
 .../files/petsc-3.3-fix-complex-threads.patch      |   62 +
 .../petsc/files/petsc-3.4.2-disable-rpath.patch    |   16 +
 sci-mathematics/petsc/metadata.xml                 |   19 +-
 sci-mathematics/petsc/petsc-3.1_p8-r1.ebuild       |  202 ---
 sci-mathematics/petsc/petsc-3.2_p6.ebuild          |  217 ---
 sci-mathematics/petsc/petsc-3.3_p1.ebuild          |  215 ---
 sci-mathematics/petsc/petsc-3.3_p5.ebuild          |  223 +++
 sci-mathematics/petsc/petsc-3.4.2.ebuild           |  239 +++
 sci-mathematics/pff/ChangeLog                      |    9 +-
 sci-mathematics/pff/Manifest                       |    5 +-
 sci-mathematics/pff/metadata.xml                   |   17 +-
 sci-mathematics/pff/pff-8.3.ebuild                 |   33 -
 sci-mathematics/pff/pff-8.4.ebuild                 |   30 +
 sci-mathematics/polymake/ChangeLog                 |    8 +
 sci-mathematics/polymake/metadata.xml              |   18 +-
 sci-mathematics/polymake/polymake-2.11-r1.ebuild   |    4 +-
 sci-mathematics/pulp/ChangeLog                     |    9 +-
 sci-mathematics/pulp/Manifest                      |    2 +-
 sci-mathematics/pulp/metadata.xml                  |    3 +-
 sci-mathematics/pulp/pulp-1.4.9.ebuild             |   41 -
 sci-mathematics/pulp/pulp-1.5.3.ebuild             |   43 +
 sci-mathematics/rstudio/ChangeLog                  |   12 -
 sci-mathematics/rstudio/Manifest                   |    5 -
 .../rstudio/files/rstudio-linker_flags.patch       |   13 -
 sci-mathematics/rstudio/files/rstudio-paths.patch  |  106 --
 sci-mathematics/rstudio/files/rstudio-prefs.patch  |   20 -
 .../rstudio/files/rstudio-rserver.initd            |   15 -
 .../rstudio/files/rstudio.desktop.patch            |   16 -
 sci-mathematics/rstudio/metadata.xml               |   13 -
 sci-mathematics/rstudio/rstudio-0.96.316.ebuild    |  141 --
 sci-mathematics/rstudio/rstudio-0.96.331.ebuild    |  141 --
 sci-mathematics/scilab/ChangeLog                   |    6 +-
 sci-mathematics/scilab/Manifest                    |    3 +-
 .../files/scilab-5.3.3-java-version-check.patch    |   23 +
 .../scilab/files/scilab-5.4.0-fortran-link.patch   |   22 -
 .../scilab/files/scilab-5.4.0-java-heap.patch      |   12 -
 ... scilab-5.4.1-fix-random-runtime-failure.patch} |    0
 ...wlinks.patch => scilab-5.4.1-followlinks.patch} |    0
 ....0-gluegen.patch => scilab-5.4.1-gluegen.patch} |    0
 .../scilab/files/scilab-5.4.1-java-heap.patch      |   14 +
 .../files/scilab-5.5.0_beta1-accessviolation.patch |   21 +
 ...ilab-5.5.0_beta1-always-use-dynamic-stack.patch |   33 +
 ...ilab-5.5.0_beta1-disable-static-systemlib.patch |   20 +
 ...b-5.5.0_beta1-fix-random-runtime-failure.patch} |    0
 ....patch => scilab-5.5.0_beta1-followlinks.patch} |    0
 ...egen.patch => scilab-5.5.0_beta1-gluegen.patch} |    0
 .../files/scilab-5.5.0_beta1-java-heap.patch       |   13 +
 sci-mathematics/scilab/metadata.xml                |   16 +-
 sci-mathematics/scilab/scilab-5.3.3-r1.ebuild      |  249 ---
 sci-mathematics/scilab/scilab-5.3.3-r2.ebuild      |  252 +++
 sci-mathematics/scilab/scilab-5.4.0.ebuild         |  235 ---
 sci-mathematics/scilab/scilab-5.4.1.ebuild         |  243 +++
 sci-mathematics/scilab/scilab-5.5.0_beta1.ebuild   |  249 +++
 sci-mathematics/surfer/ChangeLog                   |    6 +-
 sci-mathematics/surfer/Manifest                    |    2 +-
 sci-mathematics/surfer/metadata.xml                |    2 +-
 sci-mathematics/surfer/surfer-0.0.197.ebuild       |   21 +-
 sci-mathematics/ufc/ChangeLog                      |    5 +-
 sci-mathematics/ufc/Manifest                       |    2 +-
 sci-mathematics/ufc/ufc-1.4.2.ebuild               |    4 +-
 sci-mathematics/why/ChangeLog                      |    5 +-
 sci-mathematics/why/Manifest                       |    6 +-
 sci-mathematics/why/metadata.xml                   |   34 +-
 sci-mathematics/why/why-2.30.ebuild                |   74 +-
 sci-mathematics/yorick/ChangeLog                   |    6 +-
 sci-mathematics/yorick/Manifest                    |    2 +-
 sci-mathematics/yorick/metadata.xml                |   12 +-
 sci-mathematics/yorick/yorick-2.1.06.ebuild        |   29 +-
 sci-mathematics/z3/ChangeLog                       |   10 +
 sci-mathematics/z3/Manifest                        |    1 +
 .../pythonqt => sci-mathematics/z3}/metadata.xml   |    0
 sci-mathematics/z3/z3-4.3.1.ebuild                 |   75 +
 sci-mathematics/z3/z3-9999.ebuild                  |   81 +
 sci-misc/finomaton/Manifest                        |    2 +-
 sci-misc/fitscut/Manifest                          |    2 +-
 sci-misc/foma/ChangeLog                            |    6 +-
 sci-misc/foma/foma-0.9.14_alpha.ebuild             |    4 +-
 sci-misc/foma/foma-0.9.16_alpha.ebuild             |    4 +-
 sci-misc/foma/metadata.xml                         |    6 +-
 sci-misc/hfst/ChangeLog                            |    6 +-
 sci-misc/hfst/hfst-3.0.2.ebuild                    |    4 +-
 sci-misc/hfst/hfst-3.3.12.ebuild                   |    6 +-
 sci-misc/hfst/metadata.xml                         |   16 +-
 sci-misc/jwnl/Manifest                             |    4 +-
 sci-misc/kotus-sanalista/Manifest                  |    2 +-
 sci-misc/nltk/Manifest                             |    2 +-
 sci-misc/omorfi/Manifest                           |    2 +-
 sci-misc/openfst/ChangeLog                         |   12 +-
 sci-misc/openfst/Manifest                          |    2 +-
 sci-misc/openfst/files/kaldi.patch                 |  599 +++++++
 sci-misc/openfst/metadata.xml                      |    6 +-
 sci-misc/openfst/openfst-1.2.7.ebuild              |    4 +-
 sci-misc/openfst/openfst-1.3.2.ebuild              |   30 -
 sci-misc/openfst/openfst-1.3.4.ebuild              |   24 +
 sci-misc/opennlp-maxent/Manifest                   |    2 +-
 sci-misc/opennlp-tools/Manifest                    |   88 +-
 sci-misc/praat/ChangeLog                           |    6 +-
 sci-misc/praat/Manifest                            |    4 +-
 sci-misc/praat/metadata.xml                        |    8 +-
 sci-misc/praat/praat-5.1.00.ebuild                 |   23 +-
 sci-misc/praat/praat-5.1.15.ebuild                 |   23 +-
 sci-misc/pywordnet/Manifest                        |    2 +-
 sci-misc/salome-component/ChangeLog                |    6 +-
 sci-misc/salome-component/Manifest                 |    4 +-
 sci-misc/salome-component/metadata.xml             |    2 +-
 .../salome-component/salome-component-5.1.3.ebuild |    8 +-
 .../salome-component/salome-component-5.1.4.ebuild |    8 +-
 sci-misc/salome-geom/ChangeLog                     |    6 +-
 sci-misc/salome-geom/Manifest                      |    4 +-
 sci-misc/salome-geom/metadata.xml                  |    2 +-
 sci-misc/salome-geom/salome-geom-5.1.3.ebuild      |   10 +-
 sci-misc/salome-geom/salome-geom-5.1.4.ebuild      |   10 +-
 sci-misc/salome-gui/ChangeLog                      |    6 +-
 sci-misc/salome-gui/Manifest                       |    4 +-
 sci-misc/salome-gui/metadata.xml                   |    2 +-
 sci-misc/salome-gui/salome-gui-5.1.3.ebuild        |   10 +-
 sci-misc/salome-gui/salome-gui-5.1.4.ebuild        |   10 +-
 sci-misc/salome-kernel/Manifest                    |    4 +-
 sci-misc/salome-med/ChangeLog                      |    6 +-
 sci-misc/salome-med/Manifest                       |    4 +-
 sci-misc/salome-med/metadata.xml                   |   10 +-
 sci-misc/salome-med/salome-med-5.1.3.ebuild        |    8 +-
 sci-misc/salome-med/salome-med-5.1.4.ebuild        |    8 +-
 sci-misc/salome-pycalculator/Manifest              |    4 +-
 sci-misc/salome-smesh/ChangeLog                    |    6 +-
 sci-misc/salome-smesh/Manifest                     |    4 +-
 sci-misc/salome-smesh/metadata.xml                 |    2 +-
 sci-misc/salome-smesh/salome-smesh-5.1.3.ebuild    |    8 +-
 sci-misc/salome-smesh/salome-smesh-5.1.4.ebuild    |    8 +-
 sci-misc/salome-visu/ChangeLog                     |    6 +-
 sci-misc/salome-visu/Manifest                      |    4 +-
 sci-misc/salome-visu/metadata.xml                  |    2 +-
 sci-misc/salome-visu/salome-visu-5.1.3.ebuild      |    8 +-
 sci-misc/salome-visu/salome-visu-5.1.4.ebuild      |    8 +-
 sci-misc/salome-yacs/ChangeLog                     |    6 +-
 sci-misc/salome-yacs/Manifest                      |    4 +-
 sci-misc/salome-yacs/metadata.xml                  |    2 +-
 sci-misc/salome-yacs/salome-yacs-5.1.3.ebuild      |    8 +-
 sci-misc/salome-yacs/salome-yacs-5.1.4.ebuild      |    8 +-
 sci-misc/sfst/ChangeLog                            |    6 +-
 sci-misc/sfst/Manifest                             |    2 +-
 sci-misc/sfst/metadata.xml                         |   10 +-
 sci-misc/sfst/sfst-1.4.2.ebuild                    |    4 +-
 sci-misc/sfst/sfst-1.4.6g.ebuild                   |    4 +-
 sci-misc/simx/ChangeLog                            |   22 +
 sci-misc/simx/Manifest                             |    1 +
 sci-misc/simx/files/simx-0.1-python-check.patch    |   27 +
 .../omniorbpy => sci-misc/simx}/metadata.xml       |    0
 sci-misc/simx/simx-0.1.ebuild                      |   38 +
 sci-misc/simx/simx-9999.ebuild                     |   36 +
 sci-misc/stanford-parser/Manifest                  |    2 +-
 sci-misc/stanford-tagger/Manifest                  |    2 +-
 sci-physics/LoopTools/ChangeLog                    |    6 +-
 sci-physics/LoopTools/LoopTools-2.8.ebuild         |    8 +-
 sci-physics/LoopTools/Manifest                     |    2 +-
 sci-physics/LoopTools/metadata.xml                 |    2 +-
 sci-physics/abinit/ChangeLog                       |   73 +-
 sci-physics/abinit/Manifest                        |    2 +-
 sci-physics/abinit/abinit-6.12.3-r2.ebuild         |  335 ----
 sci-physics/abinit/abinit-7.4.2.ebuild             |  350 ++++
 sci-physics/abinit/files/6.0.3-fftw.patch          |   14 -
 .../abinit/files/6.12.1-libabinit_options.patch    |   57 -
 sci-physics/abinit/files/6.12.3-gui-makefiles.tbz  |  Bin 0 -> 14600 bytes
 sci-physics/abinit/files/7.0.4-test_dirs.patch     |   12 +
 .../abinit/files/7.4.2-cuda_link_stdc++.patch      |   21 +
 .../abinit/files/7.4.2-levmar_diag_scaling.patch   |   21 +
 sci-physics/abinit/files/7.4.2-syntax.patch        |   21 +
 sci-physics/abinit/metadata.xml                    |  104 +-
 sci-physics/atompaw/ChangeLog                      |   20 +-
 sci-physics/atompaw/Manifest                       |    2 +-
 sci-physics/atompaw/atompaw-3.0.1.4.ebuild         |   70 -
 sci-physics/atompaw/atompaw-3.0.1.9-r1.ebuild      |   67 +
 sci-physics/atompaw/metadata.xml                   |   11 +-
 sci-physics/atompaw2abinit/ChangeLog               |    7 +-
 sci-physics/atompaw2abinit/Manifest                |    2 +-
 .../atompaw2abinit/atompaw2abinit-3.3.0-r1.ebuild  |   19 +-
 sci-physics/atompaw2abinit/metadata.xml            |    3 -
 sci-physics/bigdft/ChangeLog                       |  160 ++
 sci-physics/bigdft/Manifest                        |    1 +
 sci-physics/bigdft/bigdft-1.7_pre24.ebuild         |  142 ++
 .../files/bigdft-1.7-dev.24-nolib_mods.patch       |   25 +
 sci-physics/elk/ChangeLog                          |   17 +-
 sci-physics/elk/Manifest                           |    1 +
 sci-physics/elk/elk-1.4.22.ebuild                  |   94 +-
 sci-physics/elk/elk-2.1.25.ebuild                  |  131 ++
 sci-physics/elk/metadata.xml                       |   20 +-
 sci-physics/espresso++/ChangeLog                   |   18 +-
 sci-physics/espresso++/espresso++-9999.ebuild      |   42 +-
 sci-physics/espresso++/metadata.xml                |   16 +-
 sci-physics/espresso/ChangeLog                     |    9 +-
 sci-physics/espresso/espresso-9999.ebuild          |   38 +-
 sci-physics/espresso/metadata.xml                  |   10 +-
 sci-physics/geant-vmc/ChangeLog                    |   26 +
 sci-physics/geant-vmc/Manifest                     |    2 +
 sci-physics/geant-vmc/geant-vmc-3.1.15a.ebuild     |   39 +
 sci-physics/geant-vmc/geant-vmc-4.2.14b.ebuild     |   60 +
 sci-physics/geant-vmc/metadata.xml                 |   19 +
 sci-physics/geant/ChangeLog                        |  353 ++++
 sci-physics/geant/Manifest                         |    2 +
 sci-physics/geant/geant-3.21.14-r4.ebuild          |   70 +
 sci-physics/geant/metadata.xml                     |   14 +
 sci-physics/herwig++/ChangeLog                     |   22 +-
 sci-physics/herwig++/Manifest                      |    3 +-
 ...ptools.patch => herwig++-2.6.3-looptools.patch} |    0
 sci-physics/herwig++/herwig++-2.6.1b.ebuild        |   50 -
 sci-physics/herwig++/herwig++-2.6.3.ebuild         |   50 +
 sci-physics/herwig++/herwig++-2.7.0.ebuild         |   51 +
 sci-physics/herwig++/metadata.xml                  |    4 +-
 sci-physics/lammps/ChangeLog                       |   63 +
 sci-physics/lammps/Manifest                        |    7 +
 sci-physics/lammps/lammps-20130816.ebuild          |  115 ++
 sci-physics/lammps/lammps-20130830.ebuild          |  115 ++
 sci-physics/lammps/lammps-20130917.ebuild          |  115 ++
 sci-physics/lammps/lammps-20130923.ebuild          |  115 ++
 sci-physics/lammps/lammps-20130930.ebuild          |  115 ++
 sci-physics/lammps/lammps-20131111.ebuild          |  115 ++
 sci-physics/lammps/lammps-20131123.ebuild          |  115 ++
 sci-physics/lammps/metadata.xml                    |   31 +
 sci-physics/mc-tester/ChangeLog                    |   11 +
 sci-physics/mc-tester/Manifest                     |    1 +
 .../files/mc-tester-1.25.0-compare.sh.patch        |   30 +
 sci-physics/mc-tester/mc-tester-1.25.0.ebuild      |   65 +
 sci-physics/mc-tester/metadata.xml                 |   16 +
 sci-physics/openmx/ChangeLog                       |   40 +
 sci-physics/openmx/Manifest                        |    4 +
 sci-physics/openmx/files/3.7-fortran_objects.patch |   15 +
 sci-physics/openmx/metadata.xml                    |    5 +
 sci-physics/openmx/openmx-3.6.ebuild               |   97 +
 sci-physics/openmx/openmx-3.7.6.ebuild             |  171 ++
 sci-physics/qcl/Manifest                           |    8 +-
 sci-physics/root/ChangeLog                         |   79 +-
 sci-physics/root/Manifest                          |    7 +-
 .../root/files/root-5.28.00b-nobyte-compile.patch  |  138 --
 .../root/files/root-5.32.00-prop-flags.patch       |   15 +
 .../root/files/root-5.34.05-nobyte-compile.patch   |  137 ++
 sci-physics/root/files/root-9999-cling.patch       |   13 -
 sci-physics/root/metadata.xml                      |   41 +-
 sci-physics/root/root-5.32.04.ebuild               |   34 +-
 sci-physics/root/root-5.34.03.ebuild               |  378 ----
 sci-physics/root/root-5.34.10-r2.ebuild            |  408 +++++
 sci-physics/root/root-9999.ebuild                  |  219 ++-
 sci-physics/tauola/ChangeLog                       |   12 +
 sci-physics/tauola/Manifest                        |    1 +
 .../tauola/files/tauola-1.1.3-makefile.patch       |   12 +
 .../files/tauola-1.1.3-tau-spinner-makefile.patch  |   11 +
 sci-physics/tauola/metadata.xml                    |   17 +
 sci-physics/tauola/tauola-1.1.3.ebuild             |   69 +
 sci-physics/tauola/tauola-9999.ebuild              |   75 +
 sci-physics/thepeg/ChangeLog                       |   27 +-
 sci-physics/thepeg/Manifest                        |    7 +-
 ...eg-1.8.1-java.patch => thepeg-1.8.3-java.patch} |    0
 sci-physics/thepeg/metadata.xml                    |    3 +-
 sci-physics/thepeg/thepeg-1.8.1.ebuild             |   92 -
 sci-physics/thepeg/thepeg-1.8.3.ebuild             |   92 +
 sci-physics/thepeg/thepeg-1.9.0-r1.ebuild          |   94 +
 sci-physics/vgm/ChangeLog                          |   13 +
 sci-physics/vgm/metadata.xml                       |   13 +
 sci-physics/vgm/vgm-3.06.ebuild                    |   64 +
 sci-visualization/ferret-bin/ChangeLog             |    7 +-
 sci-visualization/ferret-bin/Manifest              |   10 +-
 .../ferret-bin/ferret-bin-6.6.4.ebuild             |   52 +-
 sci-visualization/ferret-bin/metadata.xml          |   12 +-
 sci-visualization/gnuplot/ChangeLog                |   32 +-
 sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild  |  217 +--
 sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild  |  214 +--
 sci-visualization/gnuplot/metadata.xml             |   26 +-
 sci-visualization/labplot/metadata.xml             |    3 +-
 sci-visualization/nodemon/Manifest                 |    2 +-
 sci-visualization/paraview/ChangeLog               |  144 --
 sci-visualization/paraview/Manifest                |    3 -
 .../paraview/files/paraview-3.10.1-gcc46.patch     |   20 -
 .../paraview/files/paraview-3.12.0-gcc46.patch     |   10 -
 .../paraview/files/paraview-3.12.0-protobuf.patch  |   53 -
 .../files/paraview-3.14.1-ffmpeg-noinstall.patch   |   27 -
 .../paraview/files/paraview-3.14.1-gcc-4.7.patch   |   28 -
 .../paraview/files/paraview-3.14.1-mpi4py.patch    |   15 -
 .../files/paraview-3.14.1-python-exit.patch        |   46 -
 .../files/paraview-3.14.1-removesqlite.patch       |  526 ------
 .../paraview/files/paraview-3.14.1-vtknetcd.patch  |   75 -
 .../files/paraview-3.14.1-xdmf-linking.patch       |   16 -
 .../paraview/files/paraview-3.8.0-h5part.patch     |   12 -
 .../files/paraview-3.8.0-installpath.patch         |   33 -
 ...araview-3.8.0-pointsprite-example-install.patch |    9 -
 .../files/paraview-3.8.0-pointsprite-example.patch |   25 -
 .../paraview/files/paraview-3.8.0-xdmf-bc.patch    |   13 -
 .../files/paraview-3.8.0-xdmf-cstring.patch        |   10 -
 .../paraview/files/vtk-5.6.0-cg-path.patch         |   36 -
 .../paraview/files/vtk-5.6.0-libpng14.patch        |   22 -
 .../paraview/files/vtk-5.6.0-odbc.patch            |   12 -
 .../paraview/files/vtk-5.6.1-ffmpeg.patch          |   42 -
 .../paraview/files/vtk-5.6.1-libav-0.8.patch       |   66 -
 .../paraview/files/vtk-boost1.49.patch             |   27 -
 sci-visualization/paraview/metadata.xml            |   22 -
 sci-visualization/paraview/paraview-3.10.1.ebuild  |  214 ---
 sci-visualization/paraview/paraview-3.12.0.ebuild  |  214 ---
 .../paraview/paraview-3.14.1-r4.ebuild             |  254 ---
 sci-visualization/v_sim/ChangeLog                  |    6 +-
 sci-visualization/v_sim/Manifest                   |    4 +-
 sci-visualization/v_sim/metadata.xml               |   23 +-
 sci-visualization/v_sim/v_sim-3.5.1.ebuild         |   80 -
 sci-visualization/v_sim/v_sim-3.5.2.ebuild         |   87 -
 sci-visualization/v_sim/v_sim-3.6.0.ebuild         |    4 +-
 sci-visualization/yt/Manifest                      |    1 +
 sci-visualization/yt/yt-2.6.ebuild                 |   51 +
 sci-visualization/yt/yt-9999.ebuild                |   65 +-
 skel.ChangeLog                                     |    2 +-
 skel.ebuild                                        |    7 +-
 skel.metadata.xml                                  |   38 +-
 sys-apps/likwid/Manifest                           |    1 +
 sys-apps/likwid/files/likwid.patch                 |   27 +
 sys-apps/likwid/files/use_access_daemon.patch      |   27 +
 sys-apps/likwid/files/use_uncore.patch             |   12 +
 sys-apps/likwid/likwid-3.0.ebuild                  |   33 +
 sys-apps/likwid/metadata.xml                       |   22 +
 sys-cluster/blcr/ChangeLog                         |    5 +-
 sys-cluster/blcr/blcr-0.8.4.ebuild                 |    3 +-
 sys-cluster/blcr/metadata.xml                      |    4 +-
 sys-cluster/charm/ChangeLog                        |  125 ++
 sys-cluster/charm/Manifest                         |    1 +
 sys-cluster/charm/charm-6.5.1-r2.ebuild            |  209 +++
 sys-cluster/charm/charm-6.5.1-r3.ebuild            |  204 +++
 sys-cluster/charm/charm-6.6.0_rc1.ebuild           |  222 +++
 .../charm/files/charm-6.5.0-charmc-gentoo.patch    |   25 +
 .../charm/files/charm-6.5.1-CkReductionMgr.patch   |   34 +
 .../charm/files/charm-6.5.1-charmc-gentoo.patch    |   39 +
 .../charm/files/charm-6.5.1-cleanup-config.patch   |   58 +
 .../files/charm-6.5.1-fix-markupSanitizer.patch    |  203 +++
 .../files/charm-6.5.1-fix-navmenuGenerator.patch   |   30 +
 .../files/charm-6.5.1-fix-string-parsing.patch     |   50 +
 .../files/charm-6.5.1-static-library-fix.patch     |  396 +++++
 .../files/charm-6.6.0-static-library-fix.patch     |  403 +++++
 sys-cluster/charm/metadata.xml                     |   18 +
 sys-cluster/charmdebug/ChangeLog                   |   27 +
 sys-cluster/charmdebug/Manifest                    |    1 +
 sys-cluster/charmdebug/charmdebug-6.2.0-r1.ebuild  |   31 +
 .../charmdebug}/metadata.xml                       |    0
 sys-cluster/condor/Manifest                        |    2 -
 sys-cluster/condor/condor-7.5.2.ebuild             |  160 --
 sys-cluster/condor/condor-7.5.4.ebuild             |  160 --
 sys-cluster/condor/metadata.xml                    |   26 -
 sys-cluster/empi/ChangeLog                         |   32 +-
 sys-cluster/empi/empi-0.10.ebuild                  |   32 +
 sys-cluster/empi/empi-0.7.ebuild                   |   28 -
 sys-cluster/empi/files/ChangeLog-0.10              |  121 ++
 sys-cluster/empi/files/ChangeLog-0.7               |  164 --
 sys-cluster/empi/files/empi-0.10                   |  497 ++++++
 sys-cluster/empi/files/empi-0.7                    |  408 -----
 sys-cluster/empi/files/eselect.mpi-0.10            |  274 +++
 sys-cluster/empi/files/eselect.mpi-0.7             |  274 ---
 sys-cluster/empi/metadata.xml                      |    8 +-
 sys-cluster/ganglia_jobmonarch/Manifest            |    2 +-
 sys-cluster/hpl/ChangeLog                          |   33 +-
 sys-cluster/hpl/Manifest                           |    3 +-
 sys-cluster/hpl/hpl-2.0-r1.ebuild                  |   20 +-
 sys-cluster/hpl/hpl-2.1.ebuild                     |   70 +
 sys-cluster/hpl/metadata.xml                       |   12 +-
 sys-cluster/hpx/Manifest                           |    2 +
 sys-cluster/hpx/files/hpx-0.9.5-install-path.patch |   39 +
 sys-cluster/hpx/hpx-0.9.5.ebuild                   |   29 +
 sys-cluster/hpx/hpx-0.9.6.ebuild                   |   29 +
 sys-cluster/hpx/metadata.xml                       |   17 +
 sys-cluster/{condor => htcondor}/ChangeLog         |    0
 sys-cluster/htcondor/Manifest                      |    1 +
 ...ser-s-condor_config-last-rather-than-firs.patch |   90 +
 .../{condor => htcondor}/files/condor.confd        |    0
 .../{condor => htcondor}/files/condor.initd        |    0
 .../htcondor/files/condor_config.generic.patch     |  257 +++
 .../{condor => htcondor}/files/condor_config.local |    0
 .../files/condor_shadow_dlopen-8.0.0.patch         |   11 +
 .../files/fix_sandbox_violations-8.0.0.patch       |   31 +
 .../files/packaging_directories-8.0.0.patch        |   32 +
 sys-cluster/htcondor/htcondor-8.0.0.ebuild         |  115 ++
 sys-cluster/htcondor/metadata.xml                  |   29 +
 sys-cluster/lustre/ChangeLog                       |  443 ++++-
 ...ld-make-AC-check-for-linux-arch-sandbox-f.patch |   95 +
 ...6-kernel-Kernel-update-for-3.7.2-201.fc18.patch |  169 ++
 ...rnel-3.9-hlist_for_each_entry-uses-3-args.patch |  117 ++
 ...79-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch |   82 +
 ...7-vfs-kernel-3.1-renames-lock-manager-ops.patch |  190 --
 ...37-vfs-kernel-3.1-kills-inode-i_alloc_sem.patch |  242 ---
 ...fs-kernel-3.1-changes-open_to_namei_flags.patch |   95 -
 ...7-vfs-provides-ll_get_acl-to-i_op-get_acl.patch |  150 --
 ...ck-kernel-3.2-make_request_fn-returns-voi.patch |  108 --
 ...337-vfs-kernel-3.2-protects-inode-i_nlink.patch |  194 --
 ...-3.3-changes-super_operations-inode_opera.patch |  217 ---
 ...nel-remove-unnecessary-includings-of-syst.patch |  211 ---
 ...-kernel-3.4-touch_atime-switchs-to-1-argu.patch |   89 -
 ...-kernel-3.4-converts-d_alloc_root-to-d_ma.patch |  128 --
 ...1-LU-1337-kernel-v3.5-defines-INVALID_UID.patch |   31 -
 ...te-kernel-3.5-renames-end_writeback-to-cl.patch |   90 -
 ...nel-3.5-kernel-encode_fh-passes-in-parent.patch |   88 -
 sys-cluster/lustre/lustre-9999.ebuild              |   97 +-
 sys-cluster/lustre/metadata.xml                    |   15 +-
 sys-cluster/modules/ChangeLog                      |   19 +-
 sys-cluster/modules/Manifest                       |    3 +-
 sys-cluster/modules/files/createmodule.py          |  186 ++
 sys-cluster/modules/files/createmodule.sh          |  166 ++
 .../modules/files/modules-3.2.10-avail.patch       |   12 +
 .../modules/files/modules-3.2.10-bindir.patch      |   11 +
 .../modules/files/modules-3.2.10-clear.patch       |   11 +
 .../modules/files/modules-3.2.10-errorline.patch   |   14 +
 .../modules/files/modules-3.2.10-versioning.patch  |   10 +
 .../modules/files/modules-3.2.9c-errorline.patch   |   14 +
 sys-cluster/modules/files/modules.sh.in            |    7 +
 sys-cluster/modules/metadata.xml                   |   20 +-
 sys-cluster/modules/modules-3.2.10-r1.ebuild       |   61 +
 sys-cluster/modules/modules-3.2.10.ebuild          |   49 +
 sys-cluster/modules/modules-3.2.9c-r1.ebuild       |    6 +-
 sys-cluster/mpe2/ChangeLog                         |   15 -
 sys-cluster/mpe2/Manifest                          |    1 -
 .../files/slog2sdk-trace_rlog-makefile-fixes.patch |   68 -
 .../slog2sdk-trace_sample-makefile-fixes.patch     |   68 -
 sys-cluster/mpe2/metadata.xml                      |   10 -
 sys-cluster/mpe2/mpe2-1.0.6_p1.ebuild              |  148 --
 sys-cluster/mpich/ChangeLog                        |   10 +
 sys-cluster/mpich/Manifest                         |    1 +
 .../files/eselect.mpi.mpich}                       |    0
 sys-cluster/{mpich2 => mpich}/metadata.xml         |    0
 sys-cluster/mpich/mpich-3.0.4.ebuild               |  122 ++
 sys-cluster/mvapich2/ChangeLog                     |    7 +
 sys-cluster/mvapich2/Manifest                      |    2 +-
 sys-cluster/mvapich2/mvapich2-1.6-r1.ebuild        |    4 +-
 sys-cluster/nullmpi/ChangeLog                      |    6 +-
 sys-cluster/nullmpi/Manifest                       |    2 +-
 sys-cluster/nullmpi/metadata.xml                   |   10 +-
 sys-cluster/nullmpi/nullmpi-0.7.ebuild             |    4 +-
 sys-cluster/nullmpi/nullmpi-9999.ebuild            |   16 +-
 sys-cluster/openmpi/ChangeLog                      |   35 +-
 sys-cluster/openmpi/Manifest                       |    2 +-
 ...le-malloc-override-inside-of-Gentoo-sandb.patch |   42 +
 sys-cluster/openmpi/metadata.xml                   |    2 -
 sys-cluster/openmpi/openmpi-1.5.3.ebuild           |  115 --
 sys-cluster/openmpi/openmpi-1.6.5.ebuild           |  162 ++
 sys-cluster/ovis/ChangeLog                         |    5 +-
 sys-cluster/ovis/metadata.xml                      |   10 +-
 sys-cluster/ovis/ovis-3.0.1.ebuild                 |    6 +-
 sys-cluster/projections/ChangeLog                  |   13 +
 sys-cluster/projections/Manifest                   |    1 +
 .../projections}/metadata.xml                      |    0
 sys-cluster/projections/projections-6.2.1.ebuild   |   30 +
 sys-cluster/pyslice/Manifest                       |    2 +-
 sys-devel/gdebugger/Manifest                       |    4 +-
 sys-infiniband/librxe/Manifest                     |    2 +-
 virtual/blas/ChangeLog                             |    5 +-
 virtual/blas/blas-2.1.ebuild                       |    4 +-
 virtual/blas/metadata.xml                          |    4 +-
 virtual/cblas/ChangeLog                            |   13 +-
 virtual/cblas/cblas-2.0.ebuild                     |   10 +-
 virtual/cblas/metadata.xml                         |    4 +-
 virtual/geant/ChangeLog                            |    9 +
 virtual/geant/geant-3.ebuild                       |   17 +
 virtual/geant/metadata.xml                         |    8 +
 virtual/lapack/ChangeLog                           |    8 +-
 virtual/lapack/lapack-3.3.ebuild                   |   23 -
 virtual/lapack/lapack-3.4.ebuild                   |   23 +
 virtual/lapack/metadata.xml                        |    3 +-
 virtual/mpi/ChangeLog                              |   15 +-
 virtual/mpi/mpi-2.0-r2.ebuild                      |   23 -
 virtual/mpi/mpi-2.0-r3.ebuild                      |   24 +
 virtual/scalapack/ChangeLog                        |    9 +-
 virtual/scalapack/metadata.xml                     |    4 +-
 virtual/scalapack/scalapack-1.8.ebuild             |   21 -
 virtual/scalapack/scalapack-2.0.ebuild             |   21 +
 www-apps/py-swish-e/ChangeLog                      |    6 +-
 www-apps/py-swish-e/Manifest                       |    2 +-
 www-apps/py-swish-e/metadata.xml                   |    3 -
 www-apps/py-swish-e/py-swish-e-0.5.ebuild          |   12 +-
 x11-libs/agg/ChangeLog                             |   27 +
 x11-libs/agg/Manifest                              |    1 +
 x11-libs/agg/agg-2.5-r3.ebuild                     |   69 +
 ...on-terminating-loop-conditions-when-len-1.patch |   81 +
 ...ion-by-aborting-if-the-co-ordinates-are-t.patch |   40 +
 ...ates-from-previous-vertex-if-last-command.patch |   30 +
 ...izer_outline_aa-ignore-close_polygon-when.patch |  138 ++
 .../files/2.5/0005-Remove-VC-6-workaround.patch    |   52 +
 ...-Implement-grain-merge-blending-mode-GIMP.patch |   85 +
 ...mplement-grain-extract-blending-mode-GIMP.patch |   85 +
 ...tiplication-and-division-operators-as-con.patch |   36 +
 ...0009-Add-a-static-identity-transformation.patch |   37 +
 .../2.5/0010-Add-renderer_scanline_aa_alpha.patch  |  193 ++
 ...Avoid-division-by-zero-in-color-burn-mode.patch |   58 +
 ...12-Avoid-pixel-artifacts-when-compositing.patch |   26 +
 ...conv-classes-to-allow-access-to-the-origi.patch |   93 +
 ...tial-zero-division-resulting-in-nan-in-ag.patch |   30 +
 ...t-value-in-the-gamma-table-is-always-zero.patch |   24 +
 x11-libs/agg/files/2.5/agg-2.4-depends.patch       |   48 +
 x11-libs/agg/files/2.5/agg-2.5-autotools.patch     |   11 +
 x11-libs/agg/files/2.5/agg-2.5-pkgconfig.patch     |   10 +
 x11-libs/agg/files/2.5/agg-2.5-sdl-automagic.patch |   26 +
 x11-libs/agg/files/2.5/agg-2.5-sdl-m4.patch        |  186 ++
 x11-libs/agg/metadata.xml                          |   14 +
 x11-libs/tr/Manifest                               |    2 +-
 x11-libs/tr/metadata.xml                           |    3 -
 x11-libs/xview-bin/ChangeLog                       |   12 +-
 x11-libs/xview-bin/Manifest                        |    2 +-
 x11-libs/xview-bin/metadata.xml                    |   10 +-
 x11-libs/xview-bin/xview-bin-3.2_p1428.ebuild      |    8 +-
 x11-libs/xview/ChangeLog                           |   12 +-
 x11-libs/xview/Manifest                            |    1 +
 x11-libs/xview/metadata.xml                        |   10 +-
 x11-libs/xview/xview-3.2-r6.ebuild                 |    4 +-
 x11-libs/xview/xview-3.2-r7.ebuild                 |    4 +-
 x11-libs/xview/xview-3.2-r8.ebuild                 |  108 ++
 x11-misc/envytools/ChangeLog                       |    6 +-
 x11-misc/envytools/envytools-9999.ebuild           |   18 +-
 x11-misc/envytools/metadata.xml                    |   10 +-
 2508 files changed, 57167 insertions(+), 38091 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     3ab3adea4f5b74d90d9df714c3f76d5ed48180cb
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Dec  2 16:20:22 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec  2 16:20:22 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3ab3adea

Merge branch 'master' into zhou13-master

* master: (25 commits)
  xdrfile got added to gx86
  hpl: fix build with MKL blas and/or lapack libraries
  [sci-visualization/yt] provide workaround for latest Forthon
  [sci-visualization/yt] fix slots in CDEPEND
  Tentative prefixification
  Version bump: mne-python 0.7
  Masked live yt
  dev-python/Forthon: Version bump, keyworded for prefix
  [sci-visualization/yt] version bump
  sci-physics/geant-vmc: Version bump
  dev-python/emcee: Version bump
  sci-chemistry/coot: Update patch for current HEAD
  Update PyQtGraph to 0.9.8. Support of python 3.3
  sci-physics/lammps-20131123: Version bump.
  sys-cluster/charm-6.6.0-rc1: Reorganized some variables.
  sci-physics/tauola: new ebuild added
  Add 1 more chunk for multifit/Makefile.am
  ebuild cleanup
  sci-misc/openfst: version bump, patch from Kaldi
  sci-physics/mc-tester: ebuild improvements, thanks to jlec
  ...


 dev-python/Forthon/ChangeLog                       |   8 +-
 ...Forthon-0.8.12.ebuild => Forthon-0.8.13.ebuild} |   4 +-
 dev-python/Forthon/Manifest                        |   2 +-
 .../files/Forthon-0.8.11-fix_options_parser.patch  |  17 -
 dev-python/Forthon/metadata.xml                    |  11 +
 dev-python/emcee/ChangeLog                         |   7 +-
 dev-python/emcee/Manifest                          |   1 +
 .../{emcee-1.2.0.ebuild => emcee-2.0.0.ebuild}     |   4 +-
 dev-python/emcee/metadata.xml                      |   4 +-
 dev-python/pyqtgraph/ChangeLog                     |   6 +
 dev-python/pyqtgraph/Manifest                      |   2 +-
 ...qtgraph-0.9.7.ebuild => pyqtgraph-0.9.8.ebuild} |   2 +-
 eclass/alternatives-2.eclass                       |   2 +-
 eclass/intel-sdp.eclass                            | 497 -----------------
 licenses/CPC                                       |  41 ++
 profiles/package.mask                              |   2 +
 sci-biology/mne-python/Manifest                    |   1 +
 ...ne-python-9999.ebuild => mne-python-0.7.ebuild} |   8 +-
 sci-chemistry/coot/ChangeLog                       |   3 +
 sci-chemistry/coot/files/9999-pc.patch             |  43 +-
 sci-chemistry/xdrfile/ChangeLog                    |  21 -
 sci-chemistry/xdrfile/Manifest                     |   1 -
 sci-chemistry/xdrfile/metadata.xml                 |   9 -
 sci-chemistry/xdrfile/xdrfile-1.1.1.ebuild         |  23 -
 sci-libs/gsl/files/gsl-1.16-cblas-external.patch   |  13 +
 sci-misc/openfst/ChangeLog                         |   6 +
 sci-misc/openfst/Manifest                          |   2 +-
 sci-misc/openfst/files/kaldi.patch                 | 599 +++++++++++++++++++++
 .../{openfst-1.3.2.ebuild => openfst-1.3.4.ebuild} |  14 +-
 sci-physics/geant-vmc/ChangeLog                    |   6 +
 sci-physics/geant-vmc/Manifest                     |   2 +-
 ...vmc-4.2.14a.ebuild => geant-vmc-4.2.14b.ebuild} |   0
 sci-physics/lammps/ChangeLog                       |   5 +
 sci-physics/lammps/Manifest                        |   1 +
 ...mmps-20130930.ebuild => lammps-20131123.ebuild} |   0
 sci-physics/mc-tester/ChangeLog                    |  11 +
 sci-physics/mc-tester/Manifest                     |   1 +
 .../files/mc-tester-1.25.0-compare.sh.patch        |  30 ++
 sci-physics/mc-tester/mc-tester-1.25.0.ebuild      |  65 +++
 .../mc-tester}/metadata.xml                        |  10 +-
 sci-physics/tauola/ChangeLog                       |  12 +
 sci-physics/tauola/Manifest                        |   1 +
 .../tauola/files/tauola-1.1.3-makefile.patch       |  12 +
 .../files/tauola-1.1.3-tau-spinner-makefile.patch  |  11 +
 .../cdfplayer => sci-physics/tauola}/metadata.xml  |  11 +-
 sci-physics/tauola/tauola-1.1.3.ebuild             |  69 +++
 sci-physics/tauola/tauola-9999.ebuild              |  75 +++
 sci-visualization/yt/Manifest                      |   1 +
 .../yt/{yt-9999.ebuild => yt-2.6.ebuild}           |  34 +-
 sci-visualization/yt/yt-9999.ebuild                |  25 +-
 sys-cluster/charm/ChangeLog                        |  13 +
 ...harm-6.5.1-r3.ebuild => charm-6.6.0_rc1.ebuild} |  48 +-
 ....patch => charm-6.6.0-static-library-fix.patch} |  49 +-
 sys-cluster/hpl/ChangeLog                          |  16 +
 sys-cluster/hpl/hpl-2.1.ebuild                     |   3 +-
 55 files changed, 1188 insertions(+), 676 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     47fe52638187ad8f4e534a7519570d354b2e1306
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Mon Dec  2 14:41:10 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec  2 14:41:10 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=47fe5263

Merge pull request #157 from jauhien/tauola

sci-physics/tauola: new ebuild added


 profiles/package.mask                              |  1 +
 sci-physics/tauola/ChangeLog                       | 12 ++++
 sci-physics/tauola/Manifest                        |  1 +
 .../tauola/files/tauola-1.1.3-makefile.patch       | 12 ++++
 .../files/tauola-1.1.3-tau-spinner-makefile.patch  | 11 ++++
 sci-physics/{mc-tester => tauola}/metadata.xml     |  3 +-
 sci-physics/tauola/tauola-1.1.3.ebuild             | 69 ++++++++++++++++++++
 sci-physics/tauola/tauola-9999.ebuild              | 75 ++++++++++++++++++++++
 8 files changed, 183 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     e27f5c86e55b50e3a44e5ac5406520cc14c02364
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Mon Dec  2 13:11:27 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec  2 13:11:27 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e27f5c86

Merge pull request #146 from jauhien/mc-tester-1.25.0

sci-physics/mc-tester: ebuild added


 licenses/CPC                                       | 41 ++++++++++++++
 sci-physics/mc-tester/ChangeLog                    | 11 ++++
 sci-physics/mc-tester/Manifest                     |  1 +
 .../files/mc-tester-1.25.0-compare.sh.patch        | 30 ++++++++++
 sci-physics/mc-tester/mc-tester-1.25.0.ebuild      | 65 ++++++++++++++++++++++
 .../mc-tester}/metadata.xml                        | 10 +++-
 6 files changed, 155 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     b766758302f034d665def51d215d4fd4c6000175
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Mon Dec  2 13:10:01 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec  2 13:10:01 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b7667583

Merge pull request #149 from akreal/openfst

sci-misc/openfst: version bump, patch from Kaldi


 sci-misc/openfst/ChangeLog                         |   6 +
 sci-misc/openfst/Manifest                          |   2 +-
 sci-misc/openfst/files/kaldi.patch                 | 599 +++++++++++++++++++++
 .../{openfst-1.3.2.ebuild => openfst-1.3.4.ebuild} |  14 +-
 4 files changed, 610 insertions(+), 11 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     e5704d768e7ca2405f8df273d757815dc744b383
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Tue Nov 26 21:56:35 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Nov 26 21:56:35 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e5704d76

Merge pull request #155 from mluessi/bump_mne-python_0.7

Version bump: mne-python 0.7


 sci-biology/mne-python/Manifest                                   | 1 +
 .../mne-python/{mne-python-9999.ebuild => mne-python-0.7.ebuild}  | 8 +++++---
 2 files changed, 6 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     ddac3e96dc44f21d8714edf0f06d2fe6a11a6d94
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 26 22:30:40 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Nov 26 22:30:40 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ddac3e96

Merge github.com:gentoo-science/sci


 sci-biology/mne-python/Manifest                                   | 1 +
 .../mne-python/{mne-python-9999.ebuild => mne-python-0.7.ebuild}  | 8 +++++---
 2 files changed, 6 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     d0cb485952e12a6a23e8364a09499131d39ba3da
Author:     Kacper Kowalik (Xarthisius) <xarthisius <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 26 19:14:05 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Nov 26 19:14:05 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d0cb4859

Merge branch 'master' of github.com:gentoo-science/sci


 app-doc/root-docs/ChangeLog                        |   9 +
 app-doc/root-docs/Manifest                         |   2 +-
 ...ocs-5.34.09.ebuild => root-docs-5.34.10.ebuild} |   3 +-
 dev-cpp/eigen/ChangeLog                            |   3 +
 dev-cpp/eigen/eigen-9999.ebuild                    |   1 +
 dev-java/flexdock/Manifest                         |   2 +-
 ....3-nodemo.patch => flexdock-1.2.4-nodemo.patch} |   0
 ...flexdock-1.2.3.ebuild => flexdock-1.2.4.ebuild} |   0
 dev-java/gluegen/Manifest                          |   1 +
 dev-java/gluegen/gluegen-2.1.2.ebuild              |  83 ++++
 dev-java/jgraphx/Manifest                          |   1 +
 dev-java/jgraphx/jgraphx-2.1.0.8.ebuild            |  42 ++
 dev-java/jogl/Manifest                             |   1 +
 dev-java/jogl/jogl-2.1.2.ebuild                    | 100 ++++
 dev-java/scirenderer/scirenderer-1.1.0.ebuild      |   2 +-
 dev-lang/berkeley_upc/ChangeLog                    |   6 +
 dev-lang/berkeley_upc/Manifest                     |   1 +
 dev-lang/berkeley_upc/berkeley_upc-2.16.2.ebuild   |   2 +-
 ...pc-2.16.2.ebuild => berkeley_upc-2.18.0.ebuild} |   2 +-
 dev-lang/berkeley_upc_translator/ChangeLog         |   8 +
 dev-lang/berkeley_upc_translator/Manifest          |   1 +
 .../berkeley_upc_translator-2.16.2.ebuild          |   6 +-
 ...build => berkeley_upc_translator-2.18.0.ebuild} |   6 +-
 .../berkeley_upc_translator-2.16.2-check-abi.patch |  10 +
 dev-lang/conceptual/ChangeLog                      |  12 +
 dev-lang/conceptual/Manifest                       |   1 +
 dev-lang/conceptual/conceptual-1.4.ebuild          |  38 ++
 .../conceptual}/metadata.xml                       |   8 +-
 dev-lang/vtune/ChangeLog                           |   5 +
 dev-lang/vtune/Manifest                            |   1 +
 dev-lang/vtune/vtune-13.1.12.305106.ebuild         |  43 ++
 ...BigFile-1.06.ebuild => Bio-BigFile-1.07.ebuild} |   9 +-
 dev-perl/Bio-BigFile/ChangeLog                     |   6 +-
 dev-perl/Bio-BigFile/Manifest                      |   2 +-
 dev-perl/Bio-BigFile/metadata.xml                  |  10 +-
 dev-python/emcee/ChangeLog                         |   7 +-
 dev-python/emcee/Manifest                          |   1 +
 dev-python/emcee/emcee-2.0.0.ebuild                |  27 ++
 dev-python/emcee/metadata.xml                      |   4 +-
 dev-python/healpy/ChangeLog                        |   3 +
 dev-python/healpy/healpy-1.6.2.ebuild              |   8 +-
 dev-python/omniorbpy/ChangeLog                     |   3 +
 dev-python/omniorbpy/omniorbpy-3.4.ebuild          |   6 +-
 dev-python/opal-client/ChangeLog                   |   4 +
 dev-python/opal-client/metadata.xml                |   2 +-
 dev-python/opal-client/opal-client-2.4.1.ebuild    |  13 +-
 dev-python/pyqtgraph/ChangeLog                     |   6 +
 dev-python/pyqtgraph/Manifest                      |   2 +-
 ...qtgraph-0.9.7.ebuild => pyqtgraph-0.9.8.ebuild} |   2 +-
 dev-tex/pythontex/Manifest                         |   1 +
 dev-tex/pythontex/pythontex-0.12.ebuild            |  68 +++
 dev-tex/pythontex/pythontex-9999.ebuild            |  67 +++
 dev-util/ccache/ChangeLog                          |  31 --
 dev-util/ccache/Manifest                           |   1 -
 dev-util/ccache/ccache-3.1.9-r2.ebuild             |  64 ---
 dev-util/ccache/files/ccache-3.1.7-no-perl.patch   |  15 -
 .../ccache/files/ccache-3.1.9-test-gcc-4.8.patch   | 156 -------
 dev-util/ccache/files/ccache-config-2              |  98 ----
 dev-util/ccache/metadata.xml                       |  15 -
 dev-util/numdiff/Manifest                          |   1 +
 dev-util/numdiff/metadata.xml                      |  16 +
 dev-util/numdiff/numdiff-5.8.1.ebuild              |  44 ++
 eclass/alternatives-2.eclass                       |   2 +-
 eclass/intel-sdp.eclass                            | 497 --------------------
 licenses/CeCILL-2.1                                | 519 +++++++++++++++++++++
 licenses/mgltools                                  |  42 --
 media-gfx/librecad/ChangeLog                       |   3 +
 media-gfx/librecad/Manifest                        |   5 +-
 ...librecad-1.0.3.ebuild => librecad-1.0.4.ebuild} |   0
 ...-2.0.0_rc1.ebuild => librecad-2.0.0_rc3.ebuild} |   0
 profiles/package.mask                              |  22 +
 profiles/package.use.mask                          |   8 +-
 sci-biology/biopython/ChangeLog                    | 346 +++++++++++++-
 sci-biology/biopython/Manifest                     |   1 +
 ...python-1.62.ebuild => biopython-1.62-r1.ebuild} |  24 +-
 .../biopython/files/biopython-1.62-SffIO.patch     |  36 ++
 sci-biology/bowtie/ChangeLog                       |   7 +
 sci-biology/bowtie/Manifest                        |   1 +
 sci-biology/bowtie/bowtie-2.1.0.ebuild             |  56 +++
 .../bowtie/files/bowtie-2.1.0-buildsystem.patch    |  20 +
 sci-biology/{biopython => bowtie}/metadata.xml     |   0
 sci-biology/emboss/ChangeLog                       |  17 +
 sci-biology/emboss/emboss-6.6.0.ebuild             |  14 +-
 ..._p4-r2_plcol.patch => emboss-6.6.0_plcol.patch} |   0
 sci-biology/mira/ChangeLog                         |  16 +
 sci-biology/mira/Manifest                          |   2 +
 sci-biology/mira/metadata.xml                      |  10 +-
 sci-biology/mira/mira-3.4.0.1.ebuild               |   2 +-
 sci-biology/mira/mira-4.0_rc2.ebuild               |  80 ++++
 sci-biology/mira/mira-4.0_rc4.ebuild               |  76 +++
 sci-biology/mne-python/mne-python-9999.ebuild      |  53 +++
 sci-biology/pysurfer/Manifest                      |   1 +
 .../pysurfer/files/0.4-headless_build.patch        |  22 +
 sci-biology/pysurfer/pysurfer-0.4.ebuild           |  27 ++
 sci-biology/pysurfer/pysurfer-9999.ebuild          |  25 +
 sci-chemistry/ball/ball-9999.ebuild                |  15 +-
 sci-chemistry/coot/ChangeLog                       |  12 +
 sci-chemistry/coot/coot-9999.ebuild                |   8 +-
 sci-chemistry/coot/files/9999-pc.patch             | 101 ++--
 sci-chemistry/freeon/ChangeLog                     |  92 ++++
 sci-chemistry/freeon/Manifest                      |  11 +-
 .../files/freeon-2012.05.03-no_internal_hdf5.patch |  30 --
 .../files/freeon-9999-no_internal_hdf5.patch       |  25 -
 ...reeon-2013.09.12.ebuild => freeon-1.0.1.ebuild} |  18 +-
 ...reeon-2013.09.12.ebuild => freeon-1.0.2.ebuild} |  18 +-
 ...reeon-2013.09.12.ebuild => freeon-1.0.3.ebuild} |  15 +-
 ...reeon-2013.09.12.ebuild => freeon-1.0.4.ebuild} |  15 +-
 ...reeon-2013.09.12.ebuild => freeon-1.0.5.ebuild} |  15 +-
 ...reeon-2013.09.12.ebuild => freeon-1.0.6.ebuild} |  15 +-
 ...reeon-2013.09.12.ebuild => freeon-1.0.7.ebuild} |  23 +-
 sci-chemistry/freeon/freeon-1.0.8-r1.ebuild        |  27 ++
 ...reeon-2013.09.12.ebuild => freeon-1.0.8.ebuild} |  23 +-
 ...{freeon-2013.09.12.ebuild => freeon-1.0.ebuild} |  17 +-
 sci-chemistry/freeon/freeon-2012.05.03.ebuild      |  50 --
 sci-chemistry/freeon/freeon-9999.ebuild            |  29 +-
 sci-chemistry/freeon/metadata.xml                  |   3 +
 sci-chemistry/gamess/ChangeLog                     |   6 +
 sci-chemistry/gamess/Manifest                      |   1 +
 .../gamess/files/gamess-20130501.1.gentoo.patch    | 206 ++++++++
 sci-chemistry/gamess/gamess-20130501.1.ebuild      | 338 ++++++++++++++
 sci-chemistry/mgltools/ChangeLog                   |   3 +
 sci-chemistry/mgltools/mgltools-1.5.6.ebuild       |   3 +-
 sci-chemistry/modeller/ChangeLog                   |   4 +
 ...ller-9.12-r2.ebuild => modeller-9.12-r3.ebuild} |   7 +
 sci-chemistry/namd/ChangeLog                       |  11 -
 sci-chemistry/namd/Manifest                        |   1 -
 sci-chemistry/namd/files/namd-2.7-iml-dec.patch    |  24 -
 sci-chemistry/namd/files/namd-2.9-gentoo.patch     | 151 ------
 sci-chemistry/namd/metadata.xml                    |   5 -
 sci-chemistry/namd/namd-2.9.ebuild                 | 105 -----
 sci-chemistry/nmrpipe/ChangeLog                    |  10 +
 sci-chemistry/nmrpipe/files/extract.M              |  37 ++
 ...ebuild => nmrpipe-8.1.2013.218.23.09-r1.ebuild} |   3 +
 sci-chemistry/nwchem/ChangeLog                     |  11 +
 sci-chemistry/nwchem/Manifest                      |   1 +
 sci-chemistry/nwchem/nwchem-6.3-r2.ebuild          | 157 +++++++
 sci-chemistry/openbabel-java/ChangeLog             |  10 +
 sci-chemistry/openbabel-java/metadata.xml          |  12 +
 .../openbabel-java/openbabel-java-9999.ebuild      |  63 +++
 sci-chemistry/openbabel-perl/ChangeLog             |  10 +
 sci-chemistry/openbabel-perl/metadata.xml          |  12 +
 .../openbabel-perl/openbabel-perl-9999.ebuild      |  64 +++
 sci-chemistry/openbabel-python/ChangeLog           |  13 +
 sci-chemistry/openbabel-python/metadata.xml        |  12 +
 .../openbabel-python/openbabel-python-9999.ebuild  |  83 ++++
 sci-chemistry/openbabel-ruby/ChangeLog             |  10 +
 sci-chemistry/openbabel-ruby/metadata.xml          |  12 +
 .../openbabel-ruby/openbabel-ruby-9999.ebuild      |  78 ++++
 sci-chemistry/openbabel/ChangeLog                  |  13 +
 sci-chemistry/openbabel/metadata.xml               |  20 +
 sci-chemistry/openbabel/openbabel-9999.ebuild      |  87 ++++
 sci-chemistry/phenix-bin/ChangeLog                 |   5 +
 sci-chemistry/phenix-bin/Manifest                  |   2 +
 ....2.1309.ebuild => phenix-bin-1.8.4.1496.ebuild} |   0
 sci-chemistry/pymol-plugins-ezviz/ChangeLog        |   4 +
 .../pymol-plugins-ezviz-1.0.2005-r1.ebuild         |   6 +-
 sci-chemistry/pymol-plugins-psico/ChangeLog        |   3 +
 .../pymol-plugins-psico-9999.ebuild                |   2 +-
 sci-chemistry/shiftx2/ChangeLog                    |   6 +
 .../shiftx2/shiftx2-1.07_p20120106.ebuild          |   5 +-
 sci-chemistry/smmp/ChangeLog                       |   3 +
 sci-chemistry/smmp/metadata.xml                    |   2 +-
 sci-chemistry/smmp/smmp-3.0.5.ebuild               |  17 +-
 sci-chemistry/unio/ChangeLog                       |   3 +
 sci-chemistry/unio/unio-2.0.2-r1.ebuild            |   9 +-
 sci-chemistry/wxmacmolplt/ChangeLog                |   7 +-
 sci-chemistry/wxmacmolplt/Manifest                 |   1 +
 sci-chemistry/wxmacmolplt/wxmacmolplt-7.5.ebuild   |  44 ++
 sci-geosciences/qgis/ChangeLog                     |   6 +
 sci-geosciences/qgis/qgis-9999.ebuild              |  46 +-
 sci-libs/atlas/ChangeLog                           |   7 +
 sci-libs/atlas/atlas-3.10.1-r1.ebuild              |  29 +-
 sci-libs/atlas/metadata.xml                        |  10 +-
 sci-libs/bigdft-abi/ChangeLog                      |  11 +
 ...-1.0.4-r1.ebuild => bigdft-abi-1.0.4-r2.ebuild} |   5 +-
 sci-libs/bigdft-abi/metadata.xml                   |  24 +
 sci-libs/bigdft/ChangeLog                          | 139 ------
 sci-libs/bigdft/Manifest                           |   2 -
 sci-libs/bigdft/bigdft-1.6.0-r2.ebuild             | 122 -----
 sci-libs/bigdft/bigdft-1.7_pre12.ebuild            | 147 ------
 .../bigdft/files/bigdft-1.6-tuto.1-GPUlibs-1.patch |  26 --
 .../files/bigdft-1.6-tuto.1-bigdft.pc-1.patch      | 207 --------
 .../bigdft/files/bigdft-1.6-tuto.1-gcc-4.6.patch   |  67 ---
 .../bigdft-1.6-tuto.1-libxc_dir_include.patch      |  50 --
 .../files/bigdft-1.6.0-libxc_dir_include.patch     |  50 --
 .../bigdft/files/bigdft-1.7-dev.12-GPUlink.patch   |  12 -
 .../bigdft-1.7-dev.12-libxc_dir_include.patch      |  50 --
 .../files/bigdft-1.7-dev.12-nolib_mods.patch       |  25 -
 .../bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2   | Bin 22103 -> 0 bytes
 sci-libs/bigdft/metadata.xml                       |  10 -
 sci-libs/cnsface-scripts/ChangeLog                 |  10 -
 sci-libs/cnsface-scripts/Manifest                  |   1 -
 .../cnsface-scripts/cnsface-scripts-0.1.ebuild     |  22 -
 sci-libs/cnsface-scripts/metadata.xml              |   5 -
 sci-libs/fftw/ChangeLog                            |   4 +
 sci-libs/fftw/Manifest                             |   1 -
 sci-libs/fftw/fftw-3.3.3-r3.ebuild                 | 187 --------
 sci-libs/gsl/files/gsl-1.16-cblas-external.patch   |  13 +
 sci-libs/itk/Manifest                              |   1 +
 sci-libs/itk/itk-4.4.2-r1.ebuild                   | 134 ++++++
 sci-libs/libsufr/ChangeLog                         |   6 +
 sci-libs/libsufr/Manifest                          |   3 +-
 sci-libs/libsufr/libsufr-0.4.1.ebuild              |   2 +-
 sci-libs/libsufr/libsufr-0.5.2.ebuild              |   2 +-
 .../{libsufr-0.3.3.ebuild => libsufr-0.5.4.ebuild} |   4 +-
 sci-libs/libxc/ChangeLog                           |   6 +
 sci-libs/libxc/Manifest                            |   1 +
 sci-libs/libxc/libxc-2.0.1.ebuild                  |  17 +-
 .../{libxc-2.0.1.ebuild => libxc-2.0.2.ebuild}     |  17 +-
 sci-libs/libxc/metadata.xml                        |   2 +-
 sci-libs/magma/Manifest                            |   1 +
 sci-libs/magma/magma-1.4.0.ebuild                  | 122 +++++
 sci-libs/mkl/ChangeLog                             |   5 +
 sci-libs/mkl/Manifest                              |   1 +
 sci-libs/mkl/mkl-11.1.0.080.ebuild                 | 140 ++++++
 sci-libs/modglue/ChangeLog                         |  14 +
 sci-libs/modglue/Manifest                          |   2 +-
 sci-libs/modglue/files/modglue-1.16-ldflags.patch  |  13 -
 sci-libs/modglue/files/modglue-1.16-lib64.patch    |  61 ---
 .../modglue/files/modglue-1.16-parallelmake.patch  |  53 ---
 .../modglue/files/modglue-1.19-Makefiles.patch     | 113 +++++
 .../{modglue-1.16.ebuild => modglue-1.19.ebuild}   |  11 +-
 sci-libs/nibabel/Manifest                          |   1 +
 sci-libs/nibabel/nibabel-1.3.0.ebuild              |  42 ++
 sci-libs/p4est/Manifest                            |   2 +-
 sci-libs/p4est/metadata.xml                        |   3 +
 .../{p4est-0.3.4.1.ebuild => p4est-0.3.4.2.ebuild} |   8 +-
 sci-libs/plasma/Manifest                           |   2 +-
 sci-libs/scikits_image/ChangeLog                   |  12 +
 sci-libs/scikits_image/metadata.xml                |  17 +
 sci-libs/scikits_image/scikits_image-9999.ebuild   |  24 +-
 sci-libs/trilinos/Manifest                         |   1 +
 .../files/trilinos-11.2.3-fix-install-paths.patch  |  62 +++
 .../files/trilinos-11.4.2-fix-install-paths.patch  |  60 +++
 sci-libs/trilinos/trilinos-11.2.3-r1.ebuild        |   1 +
 ...ilinos-11.2.3.ebuild => trilinos-11.4.2.ebuild} |  16 +
 sci-libs/wannier90/ChangeLog                       |   6 +
 ...ier90-1.2-r1.ebuild => wannier90-1.2-r2.ebuild} |   5 +-
 sci-mathematics/cadabra/ChangeLog                  |   8 +
 sci-mathematics/cadabra/Manifest                   |   2 +-
 .../{cadabra-1.31.ebuild => cadabra-1.33.ebuild}   |  18 +-
 .../cadabra/files/cadabra-1.21-no-stripping.patch  |  30 --
 .../files/cadabra-1.25-xcadabra-flags.patch        |  11 -
 .../cadabra/files/cadabra-1.33-FLAGS.patch         | 171 +++++++
 sci-mathematics/cdfplayer/cdfplayer-9.0.1.ebuild   |   2 +-
 sci-mathematics/petsc/Manifest                     |   1 +
 .../petsc/files/petsc-3.4.2-disable-rpath.patch    |  16 +
 sci-mathematics/petsc/petsc-3.4.2.ebuild           | 239 ++++++++++
 sci-mathematics/scilab/Manifest                    |   1 +
 .../files/scilab-5.3.3-java-version-check.patch    |  23 +
 .../files/scilab-5.5.0_beta1-accessviolation.patch |  21 +
 ...ilab-5.5.0_beta1-always-use-dynamic-stack.patch |  33 ++
 ...ilab-5.5.0_beta1-disable-static-systemlib.patch |  20 +
 ...b-5.5.0_beta1-fix-random-runtime-failure.patch} |   0
 ....patch => scilab-5.5.0_beta1-followlinks.patch} |   0
 ...egen.patch => scilab-5.5.0_beta1-gluegen.patch} |   0
 .../files/scilab-5.5.0_beta1-java-heap.patch       |  13 +
 ...ilab-5.3.3-r1.ebuild => scilab-5.3.3-r2.ebuild} |   5 +-
 sci-mathematics/scilab/scilab-5.4.1.ebuild         |   7 +-
 ...ilab-5.4.1.ebuild => scilab-5.5.0_beta1.ebuild} |  67 +--
 sci-misc/simx/ChangeLog                            |  22 +
 sci-misc/simx/Manifest                             |   1 +
 sci-misc/simx/files/simx-0.1-python-check.patch    |  27 ++
 {dev-java/jrosetta => sci-misc/simx}/metadata.xml  |   0
 sci-misc/simx/simx-0.1.ebuild                      |  38 ++
 sci-misc/simx/simx-9999.ebuild                     |  36 ++
 sci-physics/LoopTools/LoopTools-2.8.ebuild         |   4 +-
 sci-physics/abinit/ChangeLog                       |  30 +-
 sci-physics/abinit/Manifest                        |   2 +-
 .../{abinit-7.2.2.ebuild => abinit-7.4.2.ebuild}   | 283 +++++------
 .../abinit/files/7.4.2-cuda_link_stdc++.patch      |  21 +
 .../abinit/files/7.4.2-levmar_diag_scaling.patch   |  21 +
 sci-physics/abinit/files/7.4.2-syntax.patch        |  21 +
 sci-physics/abinit/metadata.xml                    |  36 +-
 sci-physics/espresso++/ChangeLog                   |   3 +
 sci-physics/espresso++/espresso++-9999.ebuild      |  14 +-
 sci-physics/geant-vmc/ChangeLog                    |   6 +
 sci-physics/geant-vmc/Manifest                     |   2 +-
 ...vmc-4.2.14a.ebuild => geant-vmc-4.2.14b.ebuild} |   0
 sci-physics/herwig++/ChangeLog                     |   6 +
 sci-physics/herwig++/Manifest                      |   1 +
 sci-physics/herwig++/herwig++-2.6.3.ebuild         |   4 +-
 ...herwig++-2.6.3.ebuild => herwig++-2.7.0.ebuild} |   9 +-
 sci-physics/herwig++/metadata.xml                  |   2 +
 sci-physics/lammps/ChangeLog                       |  27 ++
 sci-physics/lammps/Manifest                        |   8 +-
 ...mmps-20130708.ebuild => lammps-20130917.ebuild} |   0
 ...mmps-20130711.ebuild => lammps-20130923.ebuild} |   0
 ...mmps-20130701.ebuild => lammps-20130930.ebuild} |  18 +-
 ...mmps-20130708.ebuild => lammps-20131111.ebuild} |   2 +-
 ...mmps-20130708.ebuild => lammps-20131123.ebuild} |   2 +-
 sci-physics/openmx/ChangeLog                       |   6 +
 sci-physics/openmx/Manifest                        |   2 +-
 .../{openmx-3.7.4.ebuild => openmx-3.7.6.ebuild}   |  12 +-
 sci-physics/root/ChangeLog                         |  35 ++
 sci-physics/root/Manifest                          |   9 +-
 .../root/files/root-5.28.00b-asneeded.patch        |  20 +
 .../root/files/root-5.28.00b-prop-ldflags.patch    |  13 +
 .../files/root-5.32.00-explicit-functions.patch    |  18 +
 sci-physics/root/files/root-9999-cling.patch       |  13 -
 sci-physics/root/metadata.xml                      |   5 +-
 .../{root-5.34.09.ebuild => root-5.32.04.ebuild}   | 103 ++--
 ...{root-5.34.09.ebuild => root-5.34.10-r2.ebuild} | 141 +++---
 sci-physics/root/root-9999.ebuild                  | 215 +++++----
 sci-physics/thepeg/ChangeLog                       |  11 +
 sci-physics/thepeg/Manifest                        |   1 +
 sci-physics/thepeg/metadata.xml                    |   1 +
 sci-physics/thepeg/thepeg-1.8.3.ebuild             |   2 +-
 ...{thepeg-1.8.3.ebuild => thepeg-1.9.0-r1.ebuild} |  10 +-
 sys-cluster/charm/ChangeLog                        |  70 +++
 .../{charm-6.5.1.ebuild => charm-6.5.1-r2.ebuild}  |  38 +-
 ...charm-6.5.1-r1.ebuild => charm-6.5.1-r3.ebuild} |  29 +-
 .../{charm-6.5.1.ebuild => charm-6.6.0_rc1.ebuild} |  65 ++-
 .../charm/files/charm-6.5.1-CkReductionMgr.patch   |  10 +-
 .../charm/files/charm-6.5.1-charmc-gentoo.patch    |  39 ++
 .../charm/files/charm-6.5.1-cleanup-config.patch   |  14 +-
 .../files/charm-6.5.1-fix-markupSanitizer.patch    | 203 ++++++++
 .../files/charm-6.5.1-fix-navmenuGenerator.patch   |  30 ++
 .../files/charm-6.5.1-fix-string-parsing.patch     |  14 +-
 .../files/charm-6.5.1-static-library-fix.patch     | 396 ++++++++++++++++
 .../files/charm-6.6.0-static-library-fix.patch     | 403 ++++++++++++++++
 321 files changed, 7300 insertions(+), 3533 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     338159615d2a9b2e67520c6a5cdc88a48934da07
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 26 05:28:36 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Nov 26 05:28:36 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=33815961

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-chemistry/coot/ChangeLog           |  3 +++
 sci-chemistry/coot/files/9999-pc.patch | 43 ++++++++++++++++++++--------------
 2 files changed, 29 insertions(+), 17 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     0ea2f80458d8854880509bfa9dfda40c09e37aa9
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Fri Nov 22 17:26:02 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Fri Nov 22 17:26:02 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0ea2f804

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-libs/gsl/files/gsl-1.16-cblas-external.patch   | 13 ++++++
 sys-cluster/charm/ChangeLog                        | 13 ++++++
 ...harm-6.5.1-r3.ebuild => charm-6.6.0_rc1.ebuild} | 48 ++++++++++++++-------
 ....patch => charm-6.6.0-static-library-fix.patch} | 49 ++++++++++++----------
 4 files changed, 87 insertions(+), 36 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     dd613c96653c84c8ba0aab9efa4cfdd9fc7d2958
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 19 18:14:50 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Nov 19 18:14:50 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=dd613c96

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-biology/mne-python/mne-python-9999.ebuild | 53 +++++++++++++++++++++++++++
 sci-chemistry/freeon/ChangeLog                |  7 ++++
 sci-chemistry/freeon/freeon-1.0.8-r1.ebuild   |  6 +--
 sci-chemistry/freeon/freeon-9999.ebuild       |  7 ++--
 4 files changed, 67 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     2c3b91fa81f613db5385c432b3fac83731bf5cc6
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 25 16:50:25 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Nov 25 16:50:25 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2c3b91fa

Merge github.com:gentoo-science/sci


 dev-python/pyqtgraph/ChangeLog                                      | 6 ++++++
 dev-python/pyqtgraph/Manifest                                       | 2 +-
 .../pyqtgraph/{pyqtgraph-0.9.7.ebuild => pyqtgraph-0.9.8.ebuild}    | 2 +-
 sci-physics/lammps/ChangeLog                                        | 5 +++++
 sci-physics/lammps/Manifest                                         | 1 +
 .../lammps/{lammps-20130930.ebuild => lammps-20131123.ebuild}       | 0
 6 files changed, 14 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     c71b89602518ff58b895a66fd6b219de1436417f
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 18 17:04:02 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Nov 18 17:04:02 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c71b8960

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 dev-java/gluegen/Manifest                          |  2 +-
 .../{gluegen-2.0.2.ebuild => gluegen-2.1.2.ebuild} |  2 +-
 dev-java/jogl/Manifest                             |  2 +-
 .../jogl/{jogl-2.0.2.ebuild => jogl-2.1.2.ebuild}  |  4 ++--
 sci-biology/pysurfer/Manifest                      |  1 +
 .../pysurfer/files/0.4-headless_build.patch        | 22 +++++++++++++++++
 sci-biology/pysurfer/pysurfer-0.4.ebuild           | 27 +++++++++++++++++++++
 sci-biology/pysurfer/pysurfer-9999.ebuild          | 25 +++++++++++++++++++
 sci-chemistry/openbabel-python/ChangeLog           |  3 +++
 .../openbabel-python/openbabel-python-9999.ebuild  |  3 +--
 sci-chemistry/openbabel/ChangeLog                  |  3 +++
 sci-chemistry/openbabel/openbabel-9999.ebuild      |  2 +-
 sci-chemistry/wxmacmolplt/ChangeLog                |  7 +++++-
 sci-chemistry/wxmacmolplt/Manifest                 |  1 +
 ...cmolplt-7.4.3.ebuild => wxmacmolplt-7.5.ebuild} | 10 ++++----
 sci-libs/itk/Manifest                              |  1 +
 .../itk/{itk-4.4.2.ebuild => itk-4.4.2-r1.ebuild}  | 26 ++++++++++++++++----
 sci-libs/magma/Manifest                            |  1 +
 .../{magma-1.3.0.ebuild => magma-1.4.0.ebuild}     | 28 ++++------------------
 .../files/scilab-5.5.0_beta1-accessviolation.patch |  2 +-
 sci-mathematics/scilab/scilab-5.5.0_beta1.ebuild   | 28 ++++++++++------------
 21 files changed, 142 insertions(+), 58 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     7d6151694aa673df86b03129633154dedf1f6e29
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 14 01:16:50 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Thu Nov 14 01:16:50 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7d615169

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-biology/mira/ChangeLog                         |  8 ++++++++
 sci-biology/mira/Manifest                          |  1 +
 sci-biology/mira/mira-3.4.0.1.ebuild               |  2 +-
 .../{mira-4.0_rc2.ebuild => mira-4.0_rc4.ebuild}   |  4 ----
 sci-chemistry/freeon/ChangeLog                     |  3 +++
 sci-chemistry/freeon/freeon-9999.ebuild            |  4 ++--
 sci-libs/cnsface-scripts/ChangeLog                 | 10 ----------
 sci-libs/cnsface-scripts/Manifest                  |  1 -
 .../cnsface-scripts/cnsface-scripts-0.1.ebuild     | 22 ----------------------
 sci-libs/cnsface-scripts/metadata.xml              |  5 -----
 10 files changed, 15 insertions(+), 45 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     e595de854f7596b2e85510dd52cc8a90df5b4c20
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Nov 12 16:33:48 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Nov 12 16:33:48 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e595de85

Merge github.com:gentoo-science/sci


 sci-chemistry/freeon/ChangeLog                     |  11 ++
 sci-chemistry/freeon/Manifest                      |   1 +
 ...{freeon-1.0.7.ebuild => freeon-1.0.8-r1.ebuild} |   6 +-
 .../{freeon-1.0.7.ebuild => freeon-1.0.8.ebuild}   |   0
 sci-libs/nibabel/Manifest                          |   1 +
 .../{nibabel-9999.ebuild => nibabel-1.3.0.ebuild}  |   6 +-
 sci-libs/trilinos/Manifest                         |   1 +
 .../files/trilinos-11.2.3-fix-install-paths.patch  |  62 ++++++
 .../files/trilinos-11.4.2-fix-install-paths.patch  |  60 ++++++
 sci-libs/trilinos/trilinos-11.2.3-r1.ebuild        |   1 +
 ...ilinos-11.2.3.ebuild => trilinos-11.4.2.ebuild} |  16 ++
 sci-physics/LoopTools/LoopTools-2.8.ebuild         |   4 +-
 sci-physics/herwig++/herwig++-2.7.0.ebuild         |   2 +-
 sci-physics/lammps/ChangeLog                       |   5 +
 sci-physics/lammps/Manifest                        |   1 +
 ...mmps-20130930.ebuild => lammps-20131111.ebuild} |   0
 sci-physics/root/ChangeLog                         |   7 +
 sci-physics/root/Manifest                          |   2 +
 .../root/files/root-5.28.00b-asneeded.patch        |  20 ++
 .../root/files/root-5.28.00b-prop-ldflags.patch    |  13 ++
 .../files/root-5.32.00-explicit-functions.patch    |  18 ++
 ...ile.patch => root-5.32.00-nobyte-compile.patch} |  20 +-
 sci-physics/root/metadata.xml                      |   3 +-
 ...{root-5.34.10-r2.ebuild => root-5.32.04.ebuild} | 216 +++++++++------------
 sci-physics/thepeg/ChangeLog                       |   6 +
 sci-physics/thepeg/metadata.xml                    |   1 +
 ...{thepeg-1.9.0.ebuild => thepeg-1.9.0-r1.ebuild} |   6 +-
 27 files changed, 346 insertions(+), 143 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     900bb308ae8db8ca2c5665ffa2854117d2c02667
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 14 16:32:00 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Thu Nov 14 16:32:00 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=900bb308

Merge github.com:gentoo-science/sci


 media-gfx/librecad/ChangeLog                                           | 3 +++
 media-gfx/librecad/Manifest                                            | 3 ++-
 media-gfx/librecad/{librecad-1.0.3.ebuild => librecad-1.0.4.ebuild}    | 0
 .../librecad/{librecad-2.0.0_rc1.ebuild => librecad-2.0.0_rc3.ebuild}  | 0
 sci-chemistry/mgltools/ChangeLog                                       | 3 +++
 sci-chemistry/mgltools/mgltools-1.5.6.ebuild                           | 3 ++-
 sci-chemistry/pymol-plugins-psico/ChangeLog                            | 3 +++
 sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-9999.ebuild      | 2 +-
 8 files changed, 14 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     dc3022b9bf2a8fa5c092a329db4b5eb752bc2e56
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Nov  6 21:14:51 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Nov  6 21:14:51 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=dc3022b9

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 dev-lang/conceptual/ChangeLog                      | 12 +++++++
 dev-lang/conceptual/Manifest                       |  1 +
 dev-lang/conceptual/conceptual-1.4.ebuild          | 38 ++++++++++++++++++++++
 .../f90cache => dev-lang/conceptual}/metadata.xml  |  3 ++
 profiles/package.use.mask                          |  8 ++---
 sci-libs/libxc/ChangeLog                           |  6 ++++
 sci-libs/libxc/Manifest                            |  1 +
 sci-libs/libxc/libxc-2.0.1.ebuild                  | 17 ++++++----
 .../{libxc-2.0.1.ebuild => libxc-2.0.2.ebuild}     | 17 ++++++----
 sci-libs/libxc/metadata.xml                        |  2 +-
 10 files changed, 88 insertions(+), 17 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     f43d31eacc77ecb610a07094693e3b705850bd3f
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Fri Nov  8 20:55:06 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Fri Nov  8 20:55:06 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f43d31ea

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 dev-java/scirenderer/scirenderer-1.1.0.ebuild      |   2 +-
 sci-chemistry/unio/ChangeLog                       |   3 +
 sci-chemistry/unio/unio-2.0.2-r1.ebuild            |   9 +-
 sci-mathematics/scilab/scilab-5.4.1.ebuild         |   2 +-
 sci-mathematics/scilab/scilab-5.5.0_beta1.ebuild   |   2 +-
 sci-physics/root/ChangeLog                         |   4 +
 sci-physics/root/root-5.34.10-r2.ebuild            |   8 +-
 sys-cluster/charm/ChangeLog                        |  10 +
 ...charm-6.5.1-r2.ebuild => charm-6.5.1-r3.ebuild} |  13 +-
 .../files/charm-6.5.1-fix-markupSanitizer.patch    | 203 +++++++++++++++++++++
 10 files changed, 238 insertions(+), 18 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     6283a3ea356d6b5d6a4e2590c8faa2e39ded94ec
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Mon Nov  4 18:19:11 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Nov  4 18:19:11 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6283a3ea

Merge pull request #130 from jauhien/thepeg-1.9.0_herwig++-2.7.0

Thepeg 1.9.0 herwig++ 2.7.0


 sci-physics/herwig++/ChangeLog                                     | 6 ++++++
 sci-physics/herwig++/Manifest                                      | 1 +
 .../herwig++/{herwig++-2.6.3.ebuild => herwig++-2.7.0.ebuild}      | 7 ++++---
 sci-physics/herwig++/metadata.xml                                  | 2 ++
 sci-physics/thepeg/ChangeLog                                       | 5 +++++
 sci-physics/thepeg/Manifest                                        | 1 +
 sci-physics/thepeg/{thepeg-1.8.3.ebuild => thepeg-1.9.0.ebuild}    | 2 +-
 7 files changed, 20 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     89ddfe84e224333ff1fc58696ee055cc4e837af4
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Nov  4 22:10:41 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Nov  4 22:10:41 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=89ddfe84

Merge github.com:gentoo-science/sci


 dev-java/scirenderer/scirenderer-1.1.0.ebuild      |  2 +-
 dev-lang/berkeley_upc/ChangeLog                    |  6 ++
 dev-lang/berkeley_upc/Manifest                     |  1 +
 dev-lang/berkeley_upc/berkeley_upc-2.16.2.ebuild   |  2 +-
 ...pc-2.16.2.ebuild => berkeley_upc-2.18.0.ebuild} |  2 +-
 dev-lang/berkeley_upc_translator/ChangeLog         |  8 +++
 dev-lang/berkeley_upc_translator/Manifest          |  1 +
 .../berkeley_upc_translator-2.16.2.ebuild          |  6 +-
 ...build => berkeley_upc_translator-2.18.0.ebuild} |  6 +-
 .../berkeley_upc_translator-2.16.2-check-abi.patch | 10 ++++
 dev-tex/pythontex/Manifest                         |  1 +
 dev-tex/pythontex/pythontex-0.12.ebuild            | 68 ++++++++++++++++++++++
 dev-tex/pythontex/pythontex-9999.ebuild            | 67 +++++++++++++++++++++
 sci-mathematics/scilab/scilab-5.3.3-r2.ebuild      |  2 +-
 sci-mathematics/scilab/scilab-5.4.1.ebuild         |  2 +-
 sci-mathematics/scilab/scilab-5.5.0_beta1.ebuild   |  4 +-
 sci-physics/herwig++/ChangeLog                     |  6 ++
 sci-physics/herwig++/Manifest                      |  1 +
 sci-physics/herwig++/herwig++-2.6.3.ebuild         |  4 +-
 ...herwig++-2.6.3.ebuild => herwig++-2.7.0.ebuild} |  9 +--
 sci-physics/herwig++/metadata.xml                  |  2 +
 sci-physics/thepeg/ChangeLog                       |  5 ++
 sci-physics/thepeg/Manifest                        |  1 +
 sci-physics/thepeg/thepeg-1.8.3.ebuild             |  2 +-
 .../{thepeg-1.8.3.ebuild => thepeg-1.9.0.ebuild}   |  4 +-
 25 files changed, 204 insertions(+), 18 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     427aacd6bdb48eedaf5d329ca985b7784ccaa23e
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Mon Nov  4 18:18:36 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Nov  4 18:18:36 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=427aacd6

Merge pull request #129 from jauhien/thepeg-1.8.3_herwig++-2.6.3

sci-physics/thepeg, sci-physics/herwig++: ~amd64 keyword added


 sci-physics/herwig++/herwig++-2.6.3.ebuild | 4 ++--
 sci-physics/thepeg/thepeg-1.8.3.ebuild     | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     5c11ba9f064ef163be8c05fb251659bc6068d537
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Thu Oct 31 15:39:02 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Thu Oct 31 15:39:02 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5c11ba9f

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 .../files/scilab-5.5.0_beta1-accessviolation.patch  | 21 +++++++++++++++++++++
 ...ilab-5.5.0_beta1-always-use-dynamic-stack.patch} |  0
 ...ilab-5.5.0_beta1-disable-static-systemlib.patch} |  0
 ...ab-5.5.0_beta1-fix-random-runtime-failure.patch} |  0
 ...s.patch => scilab-5.5.0_beta1-followlinks.patch} |  0
 ...uegen.patch => scilab-5.5.0_beta1-gluegen.patch} |  0
 ...eap.patch => scilab-5.5.0_beta1-java-heap.patch} |  0
 ...cilab-5.5.0.ebuild => scilab-5.5.0_beta1.ebuild} |  9 +++++----
 8 files changed, 26 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     bf500609a10b9aa2152512046b9660f58591a8a7
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 28 16:07:17 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Oct 28 16:07:17 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bf500609

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 dev-java/gluegen/Manifest                          |   1 +
 ...gluegen-2.0_rc8.ebuild => gluegen-2.0.2.ebuild} |  14 +-
 dev-java/jgraphx/Manifest                          |   1 +
 ...raphx-1.4.1.0.ebuild => jgraphx-2.1.0.8.ebuild} |  16 +-
 dev-java/jogl/Manifest                             |   1 +
 .../{jogl-2.0_rc8-r1.ebuild => jogl-2.0.2.ebuild}  |   6 +-
 licenses/CeCILL-2.1                                | 519 +++++++++++++++++++++
 profiles/package.mask                              |  16 +-
 sci-chemistry/freeon/ChangeLog                     |   9 +
 sci-chemistry/freeon/Manifest                      |   1 +
 .../{freeon-1.0.1.ebuild => freeon-1.0.7.ebuild}   |   5 +-
 sci-chemistry/nmrpipe/ChangeLog                    |  10 +
 sci-chemistry/nmrpipe/files/extract.M              |  37 ++
 ...ebuild => nmrpipe-8.1.2013.218.23.09-r1.ebuild} |   3 +
 sci-libs/libsufr/ChangeLog                         |   6 +
 sci-libs/libsufr/Manifest                          |   3 +-
 sci-libs/libsufr/libsufr-0.4.1.ebuild              |   2 +-
 sci-libs/libsufr/libsufr-0.5.2.ebuild              |   2 +-
 .../{libsufr-0.3.3.ebuild => libsufr-0.5.4.ebuild} |   4 +-
 sci-mathematics/scilab/Manifest                    |   1 +
 .../scilab-5.5.0-always-use-dynamic-stack.patch    |  33 ++
 .../scilab-5.5.0-disable-static-systemlib.patch    |  20 +
 ... scilab-5.5.0-fix-random-runtime-failure.patch} |   0
 ...wlinks.patch => scilab-5.5.0-followlinks.patch} |   0
 ....1-gluegen.patch => scilab-5.5.0-gluegen.patch} |   0
 ...ava-heap.patch => scilab-5.5.0-java-heap.patch} |   9 +-
 .../{scilab-5.4.1.ebuild => scilab-5.5.0.ebuild}   |  35 +-
 sci-misc/simx/ChangeLog                            |   4 +
 sci-misc/simx/simx-0.1.ebuild                      |   4 +-
 sci-misc/simx/simx-9999.ebuild                     |   4 +-
 30 files changed, 712 insertions(+), 54 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     51cc833c51f90e804418b96f9e0262fd59fb1df1
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Oct 29 15:28:38 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Oct 29 15:28:38 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=51cc833c

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 dev-java/flexdock/Manifest                                              | 2 +-
 .../files/{flexdock-1.2.3-nodemo.patch => flexdock-1.2.4-nodemo.patch}  | 0
 dev-java/flexdock/{flexdock-1.2.3.ebuild => flexdock-1.2.4.ebuild}      | 0
 3 files changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     4ac0efff27793e15428f1337d07042e95cff14bb
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Oct 23 15:29:51 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Oct 23 15:29:51 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4ac0efff

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 dev-util/ccache/ChangeLog                          |  31 ----
 dev-util/ccache/Manifest                           |   1 -
 dev-util/ccache/ccache-3.1.9-r2.ebuild             |  64 ---------
 dev-util/ccache/files/ccache-3.1.7-no-perl.patch   |  15 --
 .../ccache/files/ccache-3.1.9-test-gcc-4.8.patch   | 156 ---------------------
 dev-util/ccache/files/ccache-config-2              |  98 -------------
 dev-util/ccache/metadata.xml                       |  15 --
 licenses/mgltools                                  |  42 ------
 sci-chemistry/shiftx2/ChangeLog                    |   3 +
 .../shiftx2/shiftx2-1.07_p20120106.ebuild          |   1 +
 sci-misc/simx/ChangeLog                            |  18 +++
 sci-misc/simx/Manifest                             |   1 +
 sci-misc/simx/files/simx-0.1-python-check.patch    |  27 ++++
 {dev-java/jrosetta => sci-misc/simx}/metadata.xml  |   0
 sci-misc/simx/simx-0.1.ebuild                      |  38 +++++
 sci-misc/simx/simx-9999.ebuild                     |  36 +++++
 16 files changed, 124 insertions(+), 422 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     23727a99e9bd71ff797b9e8d3eb511932ea0161e
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 21 18:21:29 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Oct 21 18:21:29 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=23727a99

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 .../files/scilab-5.3.3-java-version-check.patch    | 23 ++++++++++++++++++++++
 ...ilab-5.3.3-r1.ebuild => scilab-5.3.3-r2.ebuild} |  3 ++-
 sci-mathematics/scilab/scilab-5.4.1.ebuild         |  3 ++-
 3 files changed, 27 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     3960ca36f2a302ef06bb40202a0330553daa5759
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 25 18:48:19 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 25 18:48:19 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3960ca36

Merge remote-tracking branch 'github/master'

* github/master:
  Update PyQtGraph to 0.9.8. Support of python 3.3


 dev-python/pyqtgraph/ChangeLog                                      | 6 ++++++
 dev-python/pyqtgraph/Manifest                                       | 2 +-
 .../pyqtgraph/{pyqtgraph-0.9.7.ebuild => pyqtgraph-0.9.8.ebuild}    | 2 +-
 3 files changed, 8 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f746fbc46d13c086f941500576af4f22440cf5d9
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Mon Nov 25 12:55:43 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 25 12:55:43 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f746fbc4

Merge pull request #154 from gpoulin/master

Update PyQtGraph to 0.9.8. Support of python 3.3


 dev-python/pyqtgraph/ChangeLog                                      | 6 ++++++
 dev-python/pyqtgraph/Manifest                                       | 2 +-
 .../pyqtgraph/{pyqtgraph-0.9.7.ebuild => pyqtgraph-0.9.8.ebuild}    | 2 +-
 3 files changed, 8 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     1333e4ae3d7a6a686ef5e597189ff1cadafa29d4
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Fri Nov 22 16:42:10 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Fri Nov 22 16:42:10 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1333e4ae

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-libs/gsl/files/gsl-1.16-cblas-external.patch | 13 +++++++++++++
 1 file changed, 13 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6c1c249794c2a3365a525c338ca62658e0a31992
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Mon Nov 18 20:00:10 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 18 20:00:10 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6c1c2497

Merge pull request #144 from mluessi/add_mne-python

ENH: mne-python ebuild


 sci-biology/mne-python/mne-python-9999.ebuild | 53 +++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     14c39963b5e81d6df890e80932fb9aaac15e7ad6
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Mon Nov 18 08:01:01 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 18 08:01:01 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=14c39963

Merge pull request #143 from gentryx/master

added Magma 1.4.0 ebuild


 sci-libs/magma/Manifest                            |  1 +
 .../{magma-1.3.0.ebuild => magma-1.4.0.ebuild}     | 28 ++++------------------
 2 files changed, 5 insertions(+), 24 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Guillaume Horel]

commit:     341f60aba205f8ddc0d608b44956c6a998c0ebfd
Author:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
AuthorDate: Sat Nov 16 17:02:08 2013 +0000
Commit:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
CommitDate: Sat Nov 16 17:02:08 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=341f60ab

Merge branch 'master' of github.com:gentoo-science/sci


 sci-biology/pysurfer/Manifest                      |  1 +
 .../pysurfer/files/0.4-headless_build.patch        | 22 ++++++++++++++++++
 sci-biology/pysurfer/pysurfer-0.4.ebuild           | 27 ++++++++++++++++++++++
 sci-biology/pysurfer/pysurfer-9999.ebuild          | 25 ++++++++++++++++++++
 sci-libs/itk/Manifest                              |  1 +
 .../itk/{itk-4.4.2.ebuild => itk-4.4.2-r1.ebuild}  | 26 +++++++++++++++++----
 6 files changed, 98 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Guillaume Horel]

commit:     205bb450e392f3d77964e430a83e59b1552e0097
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Fri Nov 15 07:28:40 2013 +0000
Commit:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
CommitDate: Fri Nov 15 07:28:40 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=205bb450

Merge pull request #136 from mluessi/pysurfer

WIP: PySurfer ebuild


 sci-biology/pysurfer/Manifest                      |  1 +
 .../pysurfer/files/0.4-headless_build.patch        | 22 ++++++++++++++++++
 sci-biology/pysurfer/pysurfer-0.4.ebuild           | 27 ++++++++++++++++++++++
 sci-biology/pysurfer/pysurfer-9999.ebuild          | 25 ++++++++++++++++++++
 4 files changed, 75 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Guillaume Horel]

commit:     4f2eb782c375ea85fc25356070c62567e78e9c07
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Fri Nov 15 22:44:55 2013 +0000
Commit:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
CommitDate: Fri Nov 15 22:44:55 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4f2eb782

Merge pull request #142 from shuber2/itk2

sci-libs/itk: add use flags vtkglue and doc


 sci-libs/itk/Manifest                              |  1 +
 .../itk/{itk-4.4.2.ebuild => itk-4.4.2-r1.ebuild}  | 26 ++++++++++++++++++----
 2 files changed, 23 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Guillaume Horel]

commit:     eada124e95f0c0a09db18e47017434389a57a8a4
Author:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
AuthorDate: Sat Nov 16 16:58:50 2013 +0000
Commit:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
CommitDate: Sat Nov 16 16:58:50 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=eada124e

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 dev-lang/berkeley_upc/ChangeLog                    |   6 +
 dev-lang/berkeley_upc/Manifest                     |   1 +
 dev-lang/berkeley_upc/berkeley_upc-2.16.2.ebuild   |   2 +-
 ...pc-2.16.2.ebuild => berkeley_upc-2.18.0.ebuild} |   2 +-
 dev-lang/berkeley_upc_translator/ChangeLog         |   8 +
 dev-lang/berkeley_upc_translator/Manifest          |   1 +
 .../berkeley_upc_translator-2.16.2.ebuild          |   6 +-
 ...build => berkeley_upc_translator-2.18.0.ebuild} |   6 +-
 .../berkeley_upc_translator-2.16.2-check-abi.patch |  10 +
 dev-tex/pythontex/Manifest                         |   1 +
 dev-tex/pythontex/pythontex-0.12.ebuild            |  68 +++++++
 dev-tex/pythontex/pythontex-9999.ebuild            |  67 +++++++
 media-gfx/librecad/ChangeLog                       |   3 +
 media-gfx/librecad/Manifest                        |   3 +-
 ...librecad-1.0.3.ebuild => librecad-1.0.4.ebuild} |   0
 ...-2.0.0_rc1.ebuild => librecad-2.0.0_rc3.ebuild} |   0
 sci-biology/mira/ChangeLog                         |   8 +
 sci-biology/mira/Manifest                          |   1 +
 sci-biology/mira/mira-3.4.0.1.ebuild               |   2 +-
 .../{mira-4.0_rc2.ebuild => mira-4.0_rc4.ebuild}   |   4 -
 sci-chemistry/freeon/ChangeLog                     |  14 ++
 sci-chemistry/freeon/Manifest                      |   1 +
 ...{freeon-1.0.7.ebuild => freeon-1.0.8-r1.ebuild} |   6 +-
 .../{freeon-1.0.7.ebuild => freeon-1.0.8.ebuild}   |   0
 sci-chemistry/freeon/freeon-9999.ebuild            |   4 +-
 sci-chemistry/mgltools/ChangeLog                   |   3 +
 sci-chemistry/mgltools/mgltools-1.5.6.ebuild       |   3 +-
 sci-chemistry/openbabel-python/ChangeLog           |   3 +
 .../openbabel-python/openbabel-python-9999.ebuild  |   3 +-
 sci-chemistry/openbabel/ChangeLog                  |   3 +
 sci-chemistry/openbabel/openbabel-9999.ebuild      |   2 +-
 sci-chemistry/pymol-plugins-psico/ChangeLog        |   3 +
 .../pymol-plugins-psico-9999.ebuild                |   2 +-
 sci-chemistry/unio/ChangeLog                       |   3 +
 sci-chemistry/unio/unio-2.0.2-r1.ebuild            |   9 +-
 sci-chemistry/wxmacmolplt/ChangeLog                |   7 +-
 sci-chemistry/wxmacmolplt/Manifest                 |   1 +
 ...cmolplt-7.4.3.ebuild => wxmacmolplt-7.5.ebuild} |  10 +-
 sci-libs/cnsface-scripts/ChangeLog                 |  10 -
 sci-libs/cnsface-scripts/Manifest                  |   1 -
 .../cnsface-scripts/cnsface-scripts-0.1.ebuild     |  22 ---
 sci-libs/cnsface-scripts/metadata.xml              |   5 -
 sci-libs/nibabel/Manifest                          |   1 +
 .../{nibabel-9999.ebuild => nibabel-1.3.0.ebuild}  |   6 +-
 sci-libs/trilinos/Manifest                         |   1 +
 .../files/trilinos-11.2.3-fix-install-paths.patch  |  62 ++++++
 .../files/trilinos-11.4.2-fix-install-paths.patch  |  60 ++++++
 sci-libs/trilinos/trilinos-11.2.3-r1.ebuild        |   1 +
 ...ilinos-11.2.3.ebuild => trilinos-11.4.2.ebuild} |  16 ++
 sci-physics/LoopTools/LoopTools-2.8.ebuild         |   4 +-
 sci-physics/herwig++/ChangeLog                     |   6 +
 sci-physics/herwig++/Manifest                      |   1 +
 sci-physics/herwig++/herwig++-2.6.3.ebuild         |   4 +-
 ...herwig++-2.6.3.ebuild => herwig++-2.7.0.ebuild} |   9 +-
 sci-physics/herwig++/metadata.xml                  |   2 +
 sci-physics/lammps/ChangeLog                       |   5 +
 sci-physics/lammps/Manifest                        |   1 +
 ...mmps-20130930.ebuild => lammps-20131111.ebuild} |   0
 sci-physics/root/ChangeLog                         |  11 ++
 sci-physics/root/Manifest                          |   2 +
 .../root/files/root-5.28.00b-asneeded.patch        |  20 ++
 .../root/files/root-5.28.00b-prop-ldflags.patch    |  13 ++
 .../files/root-5.32.00-explicit-functions.patch    |  18 ++
 ...ile.patch => root-5.32.00-nobyte-compile.patch} |  20 +-
 sci-physics/root/metadata.xml                      |   3 +-
 ...{root-5.34.10-r2.ebuild => root-5.32.04.ebuild} | 216 +++++++++------------
 sci-physics/root/root-5.34.10-r2.ebuild            |   8 +-
 sci-physics/thepeg/ChangeLog                       |  11 ++
 sci-physics/thepeg/Manifest                        |   1 +
 sci-physics/thepeg/metadata.xml                    |   1 +
 sci-physics/thepeg/thepeg-1.8.3.ebuild             |   2 +-
 ...{thepeg-1.8.3.ebuild => thepeg-1.9.0-r1.ebuild} |  10 +-
 sys-cluster/charm/ChangeLog                        |  10 +
 ...charm-6.5.1-r2.ebuild => charm-6.5.1-r3.ebuild} |  13 +-
 .../files/charm-6.5.1-fix-markupSanitizer.patch    | 203 +++++++++++++++++++
 75 files changed, 828 insertions(+), 227 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     4a64d59a05f7928ddc2a651574ab3c87e8e789c6
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Tue Nov 12 16:43:04 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Tue Nov 12 16:43:04 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4a64d59a

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     1a73be8826866a2f6577ec4dce4595c7e851a53b
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Tue Nov 12 16:30:12 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Tue Nov 12 16:30:12 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1a73be88

Merge pull request #139 from tamiko/fix_trilinos_ldpath

sci-libs/trilinos: Bugfixes:


 sci-libs/trilinos/Manifest               |  1 +
 sci-libs/trilinos/trilinos-11.4.2.ebuild | 11 +++++++++++
 2 files changed, 12 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     32327aad3f1b44b43383cc322c7e166413f07ca9
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Tue Nov 12 04:21:05 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Tue Nov 12 04:21:05 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=32327aad

Merge pull request #138 from tamiko/bump_trilinos

sci-libs/trilinos: Fix project config directory; version bump


 .../files/trilinos-11.2.3-fix-install-paths.patch  | 62 ++++++++++++++++++++++
 .../files/trilinos-11.4.2-fix-install-paths.patch  | 60 +++++++++++++++++++++
 sci-libs/trilinos/trilinos-11.2.3-r1.ebuild        |  1 +
 ...ilinos-11.2.3.ebuild => trilinos-11.4.2.ebuild} |  5 ++
 4 files changed, 128 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     3a027d513ea2c37dda50b6ac06df28e2eaac1fb8
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Mon Nov 11 06:53:22 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Mon Nov 11 06:53:22 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3a027d51

Merge pull request #137 from mluessi/nibabel_1.3.0

ENH: nibabel stable ebuild


 sci-libs/nibabel/Manifest                                      | 1 +
 sci-libs/nibabel/{nibabel-9999.ebuild => nibabel-1.3.0.ebuild} | 6 ++++--
 2 files changed, 5 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     83c5e617937d93aa3eb67dd174dca2d3676d67a2
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Sat Nov  9 13:07:50 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Nov  9 13:07:50 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=83c5e617

Merge pull request #135 from jauhien/master

sci-physics/herwig++: fix dependency on sci-physics/thepeg


 sci-physics/herwig++/herwig++-2.7.0.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     0b5f49db5f99d6e656d85982d3a41d42c5add636
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Nov  9 08:55:44 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Nov  9 08:55:44 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0b5f49db

Merge remote-tracking branch 'github/master'

* github/master:
  sci-physics/thepeg: USE flags fixed for ver. 1.9.0
  sci-physics/LoopTools: ~amd64 keyword added, EAPI=5


 sci-physics/LoopTools/LoopTools-2.8.ebuild                         | 4 ++--
 sci-physics/thepeg/ChangeLog                                       | 6 ++++++
 sci-physics/thepeg/metadata.xml                                    | 1 +
 sci-physics/thepeg/{thepeg-1.9.0.ebuild => thepeg-1.9.0-r1.ebuild} | 6 ++++--
 4 files changed, 13 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     06f89a3eca9b44cd8d5c3d0437721b8a2c2dc822
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Sat Nov  9 07:42:36 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Nov  9 07:42:36 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=06f89a3e

Merge pull request #134 from jauhien/master

sci-physics/thepeg: USE flags fixed for ver. 1.9.0


 sci-physics/thepeg/ChangeLog                                       | 6 ++++++
 sci-physics/thepeg/metadata.xml                                    | 1 +
 sci-physics/thepeg/{thepeg-1.9.0.ebuild => thepeg-1.9.0-r1.ebuild} | 6 ++++--
 3 files changed, 11 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     98dbec665a62daf6f886437c39857ff67b4898e1
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Fri Nov  8 17:50:23 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Nov  8 17:50:23 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=98dbec66

Merge pull request #133 from jauhien/master

sci-physics/LoopTools: ~amd64 keyword added, EAPI=5


 sci-physics/LoopTools/LoopTools-2.8.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Alexey Shvetsov]

commit:     4ac353d936feedf4ad42bb135a86ae6a0dc84532
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Thu Nov  7 17:14:54 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Nov  7 17:14:54 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4ac353d9

Merge pull request #131 from jauhien/master

Please, merge changes you've lost when synchronizing with http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git


 dev-lang/berkeley_upc/ChangeLog                    |  6 ++
 dev-lang/berkeley_upc/Manifest                     |  1 +
 dev-lang/berkeley_upc/berkeley_upc-2.16.2.ebuild   |  2 +-
 ...pc-2.16.2.ebuild => berkeley_upc-2.18.0.ebuild} |  2 +-
 dev-lang/berkeley_upc_translator/ChangeLog         |  8 +++
 dev-lang/berkeley_upc_translator/Manifest          |  1 +
 .../berkeley_upc_translator-2.16.2.ebuild          |  6 +-
 ...build => berkeley_upc_translator-2.18.0.ebuild} |  6 +-
 .../berkeley_upc_translator-2.16.2-check-abi.patch | 10 ++++
 dev-tex/pythontex/Manifest                         |  1 +
 dev-tex/pythontex/pythontex-0.12.ebuild            | 68 ++++++++++++++++++++++
 dev-tex/pythontex/pythontex-9999.ebuild            | 67 +++++++++++++++++++++
 sci-physics/herwig++/ChangeLog                     |  6 ++
 sci-physics/herwig++/Manifest                      |  1 +
 sci-physics/herwig++/herwig++-2.6.3.ebuild         |  4 +-
 ...herwig++-2.6.3.ebuild => herwig++-2.7.0.ebuild} |  9 +--
 sci-physics/herwig++/metadata.xml                  |  2 +
 sci-physics/thepeg/ChangeLog                       |  5 ++
 sci-physics/thepeg/Manifest                        |  1 +
 sci-physics/thepeg/thepeg-1.8.3.ebuild             |  2 +-
 .../{thepeg-1.8.3.ebuild => thepeg-1.9.0.ebuild}   |  4 +-
 21 files changed, 199 insertions(+), 13 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Alexey Shvetsov]

commit:     bb8ac6f572020cd21e3968781927fd6722956900
Author:     Jauhien Piatlicki <piatlicki <AT> gmail <DOT> com>
AuthorDate: Thu Nov  7 14:19:14 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Nov  7 14:19:14 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bb8ac6f5

Merge remote-tracking branch 'origin/thepeg-1.9.0_herwig++-2.7.0'


 sci-physics/herwig++/ChangeLog                                     | 6 ++++++
 sci-physics/herwig++/Manifest                                      | 1 +
 .../herwig++/{herwig++-2.6.3.ebuild => herwig++-2.7.0.ebuild}      | 7 ++++---
 sci-physics/herwig++/metadata.xml                                  | 2 ++
 sci-physics/thepeg/ChangeLog                                       | 5 +++++
 sci-physics/thepeg/Manifest                                        | 1 +
 sci-physics/thepeg/{thepeg-1.8.3.ebuild => thepeg-1.9.0.ebuild}    | 2 +-
 7 files changed, 20 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Alexey Shvetsov]

commit:     21d83f0680fd7a573034dffbe880472c12c4ffe7
Author:     Jauhien Piatlicki <piatlicki <AT> gmail <DOT> com>
AuthorDate: Thu Nov  7 14:23:45 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Nov  7 14:23:45 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=21d83f06

Merge remote-tracking branch 'upstream/master'


 dev-java/scirenderer/scirenderer-1.1.0.ebuild      |  2 +-
 dev-lang/conceptual/ChangeLog                      | 12 +++++++
 dev-lang/conceptual/Manifest                       |  1 +
 dev-lang/conceptual/conceptual-1.4.ebuild          | 38 ++++++++++++++++++++++
 .../f90cache => dev-lang/conceptual}/metadata.xml  |  3 ++
 profiles/package.use.mask                          |  8 ++---
 sci-libs/libxc/ChangeLog                           |  6 ++++
 sci-libs/libxc/Manifest                            |  1 +
 sci-libs/libxc/libxc-2.0.1.ebuild                  | 17 ++++++----
 .../{libxc-2.0.1.ebuild => libxc-2.0.2.ebuild}     | 17 ++++++----
 sci-libs/libxc/metadata.xml                        |  2 +-
 sci-mathematics/scilab/scilab-5.4.1.ebuild         |  2 +-
 sci-mathematics/scilab/scilab-5.5.0_beta1.ebuild   |  2 +-
 13 files changed, 91 insertions(+), 20 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Alexey Shvetsov]

commit:     d98c47a6b9f921c1a7253705a5354895dce1cde1
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Sun Nov  3 08:45:10 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Sun Nov  3 08:45:10 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d98c47a6

Merge pull request #128 from jauhien/berkeley_upc_translator-2.18.0

dev-lang/berkeley_upc_translator: version bump (2.18.0), ~amd64 keyword ...


 dev-lang/berkeley_upc_translator/ChangeLog                     |  8 ++++++++
 dev-lang/berkeley_upc_translator/Manifest                      |  1 +
 .../berkeley_upc_translator-2.16.2.ebuild                      |  6 +++++-
 ...tor-2.16.2.ebuild => berkeley_upc_translator-2.18.0.ebuild} |  6 +++++-
 .../files/berkeley_upc_translator-2.16.2-check-abi.patch       | 10 ++++++++++
 5 files changed, 29 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Alexey Shvetsov]

commit:     0c3efb8cd89968a20996d490b479ebf3196517a9
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Sat Nov  2 07:03:13 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Sat Nov  2 07:03:13 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0c3efb8c

Merge pull request #122 from TheChymera/pythontex

Pythontex ebuild


 dev-tex/pythontex/Manifest              |  1 +
 dev-tex/pythontex/pythontex-0.12.ebuild | 68 +++++++++++++++++++++++++++++++++
 dev-tex/pythontex/pythontex-9999.ebuild | 67 ++++++++++++++++++++++++++++++++
 3 files changed, 136 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Alexey Shvetsov]

commit:     3f05827170a1796e78961b0259cc04b80f5b492d
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Sun Nov  3 08:44:55 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Sun Nov  3 08:44:55 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3f058271

Merge pull request #127 from jauhien/berkeley_upc-2.18.0

dev-lang/berkeley_upc: version bump (2.18.0), ~amd64 keyword added


 dev-lang/berkeley_upc/ChangeLog                                     | 6 ++++++
 dev-lang/berkeley_upc/Manifest                                      | 1 +
 dev-lang/berkeley_upc/berkeley_upc-2.16.2.ebuild                    | 2 +-
 .../{berkeley_upc-2.16.2.ebuild => berkeley_upc-2.18.0.ebuild}      | 2 +-
 4 files changed, 9 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Guillaume Horel]

commit:     55e23f5a6a9ba09fd363bb086c527df332544455
Author:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
AuthorDate: Thu Nov  7 00:36:48 2013 +0000
Commit:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
CommitDate: Thu Nov  7 00:36:48 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=55e23f5a

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 dev-lang/conceptual/ChangeLog                      | 12 +++++++
 dev-lang/conceptual/Manifest                       |  1 +
 dev-lang/conceptual/conceptual-1.4.ebuild          | 38 ++++++++++++++++++++++
 .../f90cache => dev-lang/conceptual}/metadata.xml  |  3 ++
 profiles/package.use.mask                          |  8 ++---
 sci-libs/libxc/ChangeLog                           |  6 ++++
 sci-libs/libxc/Manifest                            |  1 +
 sci-libs/libxc/libxc-2.0.1.ebuild                  | 17 ++++++----
 .../{libxc-2.0.1.ebuild => libxc-2.0.2.ebuild}     | 17 ++++++----
 sci-libs/libxc/metadata.xml                        |  2 +-
 10 files changed, 88 insertions(+), 17 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Guillaume Horel]

commit:     68b20b256a5c75512a0a5428364d056ce785d684
Author:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
AuthorDate: Mon Oct 28 22:31:48 2013 +0000
Commit:     Guillaume Horel <guillaume.horel <AT> gmail <DOT> com>
CommitDate: Mon Oct 28 22:31:48 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=68b20b25

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-chemistry/nmrpipe/ChangeLog                    | 10 ++++++
 sci-chemistry/nmrpipe/files/extract.M              | 37 ++++++++++++++++++++++
 ...ebuild => nmrpipe-8.1.2013.218.23.09-r1.ebuild} |  3 ++
 3 files changed, 50 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     6ae20ea7c23960d83feb5f9b34659f2292cf0435
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Thu Oct 24 17:46:34 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Thu Oct 24 17:46:34 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6ae20ea7

Merge branch 'master' of github.com:gentoo-science/sci


 sci-misc/simx/ChangeLog        | 4 ++++
 sci-misc/simx/simx-0.1.ebuild  | 4 ++--
 sci-misc/simx/simx-9999.ebuild | 4 ++--
 3 files changed, 8 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     146e19ee8a7384b6a12dfda937f13710dc63be78
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 21 21:41:27 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Oct 21 21:41:27 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=146e19ee

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 .../files/scilab-5.3.3-java-version-check.patch    | 23 ++++++++++++++++++++++
 ...ilab-5.3.3-r1.ebuild => scilab-5.3.3-r2.ebuild} |  3 ++-
 sci-mathematics/scilab/scilab-5.4.1.ebuild         |  3 ++-
 3 files changed, 27 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     98ef4aa433f0c7012674fd3cb25cc5914a082cbf
Author:     Thrasibule <guillaume.horel <AT> gmail <DOT> com>
AuthorDate: Mon Oct 21 03:19:45 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Oct 21 03:19:45 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=98ef4aa4

Merge pull request #125 from laomaiweng/scilab-revdep-rebuild

Fix false positive from revdep-rebuild for scilab-5.4.1


 sci-mathematics/scilab/scilab-5.4.1.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     74bc4efaae4379476441101e4a82476cfaab7c31
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Sat Oct 19 09:45:17 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Oct 19 09:45:17 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=74bc4efa

Merge pull request #124 from laomaiweng/java-version-check

Fix broken minimum version check in scilab-5.3.3


 .../files/scilab-5.3.3-java-version-check.patch    | 23 ++++++++++++++++++++++
 ...ilab-5.3.3-r1.ebuild => scilab-5.3.3-r2.ebuild} |  3 ++-
 2 files changed, 25 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Honza Macháček]

commit:     4575c31e7a04d8c7f959301e32088ab77b559590
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Sat Oct 19 09:30:45 2013 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Sat Oct 19 09:30:45 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4575c31e

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

sci-chemistry/nwchem-6.3-r2 updated too long after the last pull, concurrent
commits have happened.


 media-libs/libafterimage/ChangeLog                 | 181 +++++++++++++++++++++
 media-libs/libafterimage/Manifest                  |   1 +
 .../libafterimage/files/libafterimage-config.patch |  15 ++
 .../libafterimage/files/libafterimage-gif.patch    |  18 ++
 .../libafterimage/files/libafterimage-giflib.patch |  15 ++
 .../files/libafterimage-libpng15.patch             |  31 ++++
 .../files/libafterimage-makefile.in.patch          |  62 +++++++
 media-libs/libafterimage/libafterimage-1.20.ebuild |  89 ++++++++++
 media-libs/libafterimage/metadata.xml              |  16 ++
 9 files changed, 428 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     cd9de4cacb12ff4f5f10ceba0a4b63c9c137ccad
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Wed Oct 16 10:01:56 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Oct 16 10:01:56 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cd9de4ca

Merge pull request #119 from tamiko/bump_petsc

Bump petsc to 3.4.2, include support for scotch and mumps


 sci-mathematics/petsc/Manifest                     |  1 +
 ...rpath.patch => petsc-3.4.2-disable-rpath.patch} |  8 ++---
 .../{petsc-3.3_p5.ebuild => petsc-3.4.2.ebuild}    | 34 ++++++++++++++++------
 3 files changed, 30 insertions(+), 13 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     bca8a77fb529a5f8510a6a6167a34f315d91b4a6
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Oct 18 16:19:05 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Oct 18 16:19:05 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bca8a77f

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 sci-libs/p4est/Manifest                            |  2 +-
 sci-libs/p4est/metadata.xml                        |  3 ++
 .../{p4est-0.3.4.1.ebuild => p4est-0.3.4.2.ebuild} |  8 +++--
 sci-mathematics/petsc/Manifest                     |  1 +
 ...rpath.patch => petsc-3.4.2-disable-rpath.patch} |  8 ++---
 .../{petsc-3.3_p5.ebuild => petsc-3.4.2.ebuild}    | 34 ++++++++++++++++------
 6 files changed, 39 insertions(+), 17 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     31567ef0d4d16c554c699a56f1864e06d3b85f82
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Wed Oct 16 10:01:04 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Oct 16 10:01:04 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=31567ef0

Merge pull request #120 from tamiko/bump_p4est

Bump p4est to version 0.3.4.2


 sci-libs/p4est/Manifest                                       | 2 +-
 sci-libs/p4est/metadata.xml                                   | 3 +++
 sci-libs/p4est/{p4est-0.3.4.1.ebuild => p4est-0.3.4.2.ebuild} | 8 +++++---
 3 files changed, 9 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     1a88ed9d98ba56a00d6047dc97f1c3a50c5d159f
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Wed Oct 16 04:49:36 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Wed Oct 16 04:49:36 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1a88ed9d

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     e006cc9a629d80e33b2f9bbfab25a7dd086e4e68
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Mon Oct 14 21:06:56 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Mon Oct 14 21:06:56 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e006cc9a

Merge branch 'master' of github.com:gentoo-science/sci


 app-doc/root-docs/ChangeLog                        |   9 ++
 app-doc/root-docs/Manifest                         |   2 +-
 ...ocs-5.34.09.ebuild => root-docs-5.34.10.ebuild} |   3 +-
 sci-chemistry/phenix-bin/ChangeLog                 |   5 +
 sci-chemistry/phenix-bin/Manifest                  |   2 +
 ....2.1309.ebuild => phenix-bin-1.8.4.1496.ebuild} |   0
 sci-libs/atlas/ChangeLog                           |   7 ++
 sci-libs/atlas/atlas-3.10.1-r1.ebuild              |  29 ++---
 sci-libs/atlas/metadata.xml                        |  10 +-
 sci-physics/abinit/ChangeLog                       |   4 +
 sci-physics/abinit/abinit-7.4.2.ebuild             |   3 +-
 .../abinit/files/7.4.2-cuda_link_stdc++.patch      |  21 ++++
 sci-physics/espresso++/ChangeLog                   |   3 +
 sci-physics/espresso++/espresso++-9999.ebuild      |  14 ++-
 sci-physics/root/ChangeLog                         |  19 +++
 sci-physics/root/Manifest                          |   6 +-
 sci-physics/root/metadata.xml                      |   2 +-
 ...{root-5.34.09.ebuild => root-5.34.10-r1.ebuild} |  17 ++-
 ...{root-5.34.09.ebuild => root-5.34.10-r2.ebuild} | 139 ++++++++++++---------
 .../{root-5.34.09.ebuild => root-5.34.10.ebuild}   |   8 +-
 20 files changed, 201 insertions(+), 102 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     a8bb0bdffff6d6375b41f23bf109d03c5a0f7457
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Oct  1 15:42:07 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Oct  1 15:42:07 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a8bb0bdf

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 media-gfx/librecad/Manifest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     acc4a5ee57b06ea09baa9a85d5a777e9f540eb34
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Tue Oct  1 03:58:50 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Tue Oct  1 03:58:50 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=acc4a5ee

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-libs/plasma/Manifest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     a5f6d81b77e4d5390144f3f22f9eb7d8b2b1c708
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Fri Sep 27 17:34:06 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Fri Sep 27 17:34:06 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a5f6d81b

Merge branch 'master' of github.com:gentoo-science/sci

Conflicts:
	sys-cluster/charm/ChangeLog


 sys-cluster/charm/ChangeLog | 4 ++++
 1 file changed, 4 insertions(+)

diff --cc sys-cluster/charm/ChangeLog
index ace12f1,2ff10b6..492cc96
--- a/sys-cluster/charm/ChangeLog
+++ b/sys-cluster/charm/ChangeLog
@@@ -2,14 -2,10 +2,18 @@@
  # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
  # $Header: $
  
 +  27 Sep 2013; Nicolas Bock <nicolasbock@gmail.com>
 +  +files/charm-6.5.1-charmc-gentoo.patch, charm-6.5.1-r1.ebuild,
 +  files/charm-6.5.1-CkReductionMgr.patch,
 +  files/charm-6.5.1-cleanup-config.patch,
 +  files/charm-6.5.1-fix-string-parsing.patch:
 +  sys-clyster/charm-6.5.1-r1: Fix missing DEPEND.  This addresses bug 486202.
 +  The ebuild had a missing DEPEND using the doc USE flag.
 +
+   27 Sep 2013; Christoph Junghans <ottxor@gentoo.org>
+   files/charm-6.5.1-fix-string-parsing.patch:
+   fix broken patch
+ 
    14 Sep 2013; Nicolas Bock <nicolasbock@gmail.com>
    files/charm-6.5.1-fix-string-parsing.patch:
    sys-cluster/charm-6.5.1: Small fix in patch to make printing less verbose.

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     ab0ec531115a2f8f46592210ed61ce02b91bf553
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Fri Sep 27 06:27:37 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Fri Sep 27 06:27:37 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ab0ec531

Merge pull request #116 from cel4/master

sci-biology/bowtie: Added ebuild for bowtie-2.1.0.


 sci-biology/bowtie/Manifest                        |  4 ++
 sci-biology/bowtie/bowtie-2.1.0.ebuild             | 56 ++++++++++++++++++++++
 .../bowtie/files/bowtie-2.1.0-buildsystem.patch    | 20 ++++++++
 sci-biology/{biopython => bowtie}/metadata.xml     |  0
 4 files changed, 80 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Honza Macháček]

commit:     8ed16bddd92f96ab022ec42f0513b153ed0065f2
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Mon Sep 23 07:42:36 2013 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Mon Sep 23 07:42:36 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8ed16bdd

Commits of sci-libs/bigdft-abi-1.0.4-r2 messed up, trying to clean up my mess.


 sci-libs/bigdft-abi/ChangeLog                  |  5 +++++
 sci-libs/bigdft-abi/bigdft-abi-1.0.4-r2.ebuild |  5 ++++-
 sci-libs/bigdft-abi/metadata.xml               | 24 ++++++++++++++++++++++++
 3 files changed, 33 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Honza Macháček]

commit:     d5bb620f967ea83ff4ae93cd591e254a530fb45b
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Mon Sep 23 06:49:37 2013 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Mon Sep 23 06:49:37 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d5bb620f

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 ...BigFile-1.06.ebuild => Bio-BigFile-1.07.ebuild} |   9 +-
 dev-perl/Bio-BigFile/ChangeLog                     |   6 +-
 dev-perl/Bio-BigFile/Manifest                      |   2 +-
 dev-perl/Bio-BigFile/metadata.xml                  |  10 +-
 sci-chemistry/coot/ChangeLog                       |   3 +
 sci-chemistry/coot/coot-9999.ebuild                |   8 +-
 sci-chemistry/freeon/ChangeLog                     |   9 ++
 sci-chemistry/freeon/Manifest                      |   1 +
 .../{freeon-1.0.ebuild => freeon-1.0.3.ebuild}     |  10 +-
 sci-chemistry/freeon/metadata.xml                  |   3 +
 sci-chemistry/modeller/ChangeLog                   |   4 +
 ...ller-9.12-r2.ebuild => modeller-9.12-r3.ebuild} |   7 ++
 sci-libs/modglue/ChangeLog                         |   6 ++
 sci-libs/modglue/files/modglue-1.16-lib64.patch    |  61 -----------
 .../modglue/files/modglue-1.19-Makefiles.patch     | 113 +++++++++++++++++++++
 sci-libs/modglue/files/modglue-1.19-ldflags.patch  |  14 ---
 .../modglue/files/modglue-1.19-parallelmake.patch  |  53 ----------
 sci-libs/modglue/modglue-1.19.ebuild               |   9 +-
 sci-libs/scikits_image/ChangeLog                   |   7 ++
 sci-libs/scikits_image/metadata.xml                |  16 +--
 sci-libs/scikits_image/scikits_image-9999.ebuild   |   6 +-
 21 files changed, 192 insertions(+), 165 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Honza Macháček]

commit:     8264cf578dd291cd44eed3ca3daa6eb37d4ecde8
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Thu Sep 26 09:31:28 2013 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Thu Sep 26 09:31:28 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8264cf57

There is apparently something wrong happenning with my commits. Trying to go on and get somewhere.


 sci-biology/biopython/ChangeLog                    | 346 +++++++++++++++++++++
 sci-biology/biopython/Manifest                     |   1 +
 sci-biology/biopython/biopython-1.62-r1.ebuild     |  51 +++
 .../biopython/files/biopython-1.62-SffIO.patch     |  36 +++
 sci-biology/{dawg => biopython}/metadata.xml       |   0
 sci-biology/mira/ChangeLog                         |   4 +
 sci-biology/mira/Manifest                          |   1 +
 sci-biology/mira/metadata.xml                      |  10 +-
 .../{mira-3.9.15.ebuild => mira-4.0_rc2.ebuild}    |  32 +-
 9 files changed, 467 insertions(+), 14 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     30141b35ea5b62b066b29bcc7c903097990777a3
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Sep 25 12:30:09 2013 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Sep 25 12:30:09 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=30141b35

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 ...BigFile-1.06.ebuild => Bio-BigFile-1.07.ebuild} |   9 +-
 dev-perl/Bio-BigFile/ChangeLog                     |   6 +-
 dev-perl/Bio-BigFile/Manifest                      |   2 +-
 dev-perl/Bio-BigFile/metadata.xml                  |  10 +-
 sci-chemistry/coot/ChangeLog                       |   3 +
 sci-chemistry/coot/coot-9999.ebuild                |   8 +-
 sci-chemistry/freeon/ChangeLog                     |  14 ++
 sci-chemistry/freeon/Manifest                      |   2 +
 .../{freeon-1.0.1.ebuild => freeon-1.0.2.ebuild}   |   0
 .../{freeon-1.0.ebuild => freeon-1.0.3.ebuild}     |  10 +-
 sci-chemistry/freeon/metadata.xml                  |   3 +
 sci-chemistry/modeller/ChangeLog                   |   4 +
 ...ller-9.12-r2.ebuild => modeller-9.12-r3.ebuild} |   7 +
 sci-libs/bigdft-abi/ChangeLog                      |  11 +
 ...-1.0.4-r1.ebuild => bigdft-abi-1.0.4-r2.ebuild} |   5 +-
 sci-libs/bigdft-abi/metadata.xml                   |  24 ++
 sci-libs/bigdft/ChangeLog                          | 139 -----------
 sci-libs/bigdft/Manifest                           |   2 -
 sci-libs/bigdft/bigdft-1.6.0-r2.ebuild             | 122 ---------
 sci-libs/bigdft/bigdft-1.7_pre12.ebuild            | 147 -----------
 .../bigdft/files/bigdft-1.6-tuto.1-GPUlibs-1.patch |  26 --
 .../files/bigdft-1.6-tuto.1-bigdft.pc-1.patch      | 207 ---------------
 .../bigdft/files/bigdft-1.6-tuto.1-gcc-4.6.patch   |  67 -----
 .../bigdft-1.6-tuto.1-libxc_dir_include.patch      |  50 ----
 .../files/bigdft-1.6.0-libxc_dir_include.patch     |  50 ----
 .../bigdft/files/bigdft-1.7-dev.12-GPUlink.patch   |  12 -
 .../bigdft-1.7-dev.12-libxc_dir_include.patch      |  50 ----
 .../files/bigdft-1.7-dev.12-nolib_mods.patch       |  25 --
 .../bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2   | Bin 22103 -> 0 bytes
 sci-libs/bigdft/metadata.xml                       |  10 -
 sci-libs/modglue/ChangeLog                         |  14 ++
 sci-libs/modglue/Manifest                          |   2 +-
 sci-libs/modglue/files/modglue-1.16-ldflags.patch  |  13 -
 sci-libs/modglue/files/modglue-1.16-lib64.patch    |  61 -----
 .../modglue/files/modglue-1.16-parallelmake.patch  |  53 ----
 .../modglue/files/modglue-1.19-Makefiles.patch     | 113 +++++++++
 .../{modglue-1.16.ebuild => modglue-1.19.ebuild}   |  11 +-
 sci-libs/scikits_image/ChangeLog                   |   7 +
 sci-libs/scikits_image/metadata.xml                |  16 +-
 sci-libs/scikits_image/scikits_image-9999.ebuild   |   6 +-
 sci-libs/wannier90/ChangeLog                       |   6 +
 ...ier90-1.2-r1.ebuild => wannier90-1.2-r2.ebuild} |   5 +-
 sci-mathematics/cadabra/ChangeLog                  |   8 +
 sci-mathematics/cadabra/Manifest                   |   2 +-
 .../{cadabra-1.31.ebuild => cadabra-1.33.ebuild}   |  18 +-
 .../cadabra/files/cadabra-1.21-no-stripping.patch  |  30 ---
 .../files/cadabra-1.25-xcadabra-flags.patch        |  11 -
 .../cadabra/files/cadabra-1.33-FLAGS.patch         | 171 +++++++++++++
 sci-physics/abinit/ChangeLog                       |  15 +-
 sci-physics/abinit/Manifest                        |   2 +-
 .../{abinit-7.2.2.ebuild => abinit-7.4.2.ebuild}   | 277 ++++++++++-----------
 .../abinit/files/7.4.2-levmar_diag_scaling.patch   |  21 ++
 sci-physics/abinit/files/7.4.2-syntax.patch        |  21 ++
 sci-physics/abinit/metadata.xml                    |  36 ++-
 sci-physics/openmx/ChangeLog                       |   6 +
 sci-physics/openmx/Manifest                        |   2 +-
 .../{openmx-3.7.4.ebuild => openmx-3.7.6.ebuild}   |  12 +-
 57 files changed, 681 insertions(+), 1283 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     2b7c2c96e9f8797e04904c9ca8205aae954c0525
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Fri Sep 20 20:49:16 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Fri Sep 20 20:49:16 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2b7c2c96

Merge branch 'master' of github.com:gentoo-science/sci


 ...BigFile-1.06.ebuild => Bio-BigFile-1.07.ebuild} |   9 +-
 dev-perl/Bio-BigFile/ChangeLog                     |   6 +-
 dev-perl/Bio-BigFile/Manifest                      |   2 +-
 dev-perl/Bio-BigFile/metadata.xml                  |  10 +-
 sci-chemistry/modeller/ChangeLog                   |   4 +
 ...ller-9.12-r2.ebuild => modeller-9.12-r3.ebuild} |   7 +
 sci-libs/bigdft-abi/ChangeLog                      |   6 +
 ...-1.0.4-r1.ebuild => bigdft-abi-1.0.4-r2.ebuild} |   0
 sci-libs/bigdft/ChangeLog                          | 139 -----------
 sci-libs/bigdft/Manifest                           |   2 -
 sci-libs/bigdft/bigdft-1.6.0-r2.ebuild             | 122 ---------
 sci-libs/bigdft/bigdft-1.7_pre12.ebuild            | 147 -----------
 .../bigdft/files/bigdft-1.6-tuto.1-GPUlibs-1.patch |  26 --
 .../files/bigdft-1.6-tuto.1-bigdft.pc-1.patch      | 207 ---------------
 .../bigdft/files/bigdft-1.6-tuto.1-gcc-4.6.patch   |  67 -----
 .../bigdft-1.6-tuto.1-libxc_dir_include.patch      |  50 ----
 .../files/bigdft-1.6.0-libxc_dir_include.patch     |  50 ----
 .../bigdft/files/bigdft-1.7-dev.12-GPUlink.patch   |  12 -
 .../bigdft-1.7-dev.12-libxc_dir_include.patch      |  50 ----
 .../files/bigdft-1.7-dev.12-nolib_mods.patch       |  25 --
 .../bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2   | Bin 22103 -> 0 bytes
 sci-libs/bigdft/metadata.xml                       |  10 -
 sci-libs/modglue/ChangeLog                         |   6 +
 sci-libs/modglue/files/modglue-1.16-lib64.patch    |  61 -----
 .../modglue/files/modglue-1.19-Makefiles.patch     | 113 +++++++++
 sci-libs/modglue/files/modglue-1.19-ldflags.patch  |  14 --
 .../modglue/files/modglue-1.19-parallelmake.patch  |  53 ----
 sci-libs/modglue/modglue-1.19.ebuild               |   9 +-
 sci-libs/scikits_image/ChangeLog                   |   7 +
 sci-libs/scikits_image/metadata.xml                |  16 +-
 sci-libs/scikits_image/scikits_image-9999.ebuild   |   6 +-
 sci-libs/wannier90/ChangeLog                       |   6 +
 ...ier90-1.2-r1.ebuild => wannier90-1.2-r2.ebuild} |   5 +-
 sci-physics/abinit/ChangeLog                       |  15 +-
 sci-physics/abinit/Manifest                        |   2 +-
 .../{abinit-7.2.2.ebuild => abinit-7.4.2.ebuild}   | 277 ++++++++++-----------
 .../abinit/files/7.4.2-levmar_diag_scaling.patch   |  21 ++
 sci-physics/abinit/files/7.4.2-syntax.patch        |  21 ++
 sci-physics/abinit/metadata.xml                    |  36 ++-
 sci-physics/openmx/ChangeLog                       |   6 +
 sci-physics/openmx/Manifest                        |   2 +-
 .../{openmx-3.7.4.ebuild => openmx-3.7.6.ebuild}   |  12 +-
 42 files changed, 416 insertions(+), 1223 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     e87b5644c3da149bf6b34a7ea2c4b8a3846448ee
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Wed Sep 18 12:11:54 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Wed Sep 18 12:11:54 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e87b5644

Merge pull request #114 from jauhien/master

sci-mathematics/cdfplayer: add ~amd64 keyword


 sci-mathematics/cdfplayer/cdfplayer-9.0.1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     debc3c5c5328fccaed8269facb60628b08f0bbf3
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 17 19:13:36 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Sep 17 19:13:36 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=debc3c5c

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 sci-physics/root/root-9999.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     60f36f6993a51f7d5073909bd16c401daca7f605
Author:     Justin <jlec <AT> users <DOT> noreply <DOT> github <DOT> com>
AuthorDate: Tue Sep 17 18:55:30 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Sep 17 18:55:30 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=60f36f69

Merge pull request #112 from poletti-marco/master

Update root-9999.ebuild


 sci-physics/root/root-9999.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     071990a51a69ae821610c46cc04f319fe006c546
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Tue Sep 17 17:33:40 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Tue Sep 17 17:33:40 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=071990a5

Merge branch 'master' of github.com:gentoo-science/sci


 sci-libs/scikits_image/ChangeLog                 |  5 +++++
 sci-libs/scikits_image/metadata.xml              | 17 +++++++++++++++++
 sci-libs/scikits_image/scikits_image-9999.ebuild | 18 +++++++-----------
 3 files changed, 29 insertions(+), 11 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     593a634e321be682aecfeed7089cefa2beec462d
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 17 17:24:17 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Sep 17 17:24:17 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=593a634e

Merge github.com:gentoo-science/sci


 sci-biology/biopython/ChangeLog             | 10 ------
 sci-biology/biopython/biopython-1.62.ebuild | 49 -----------------------------
 sci-biology/biopython/metadata.xml          |  5 ---
 3 files changed, 64 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     61c929ce168524edbb0be7443371a925131f412d
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 17 15:47:12 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Sep 17 15:47:12 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=61c929ce

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 dev-python/healpy/ChangeLog           | 3 +++
 dev-python/healpy/healpy-1.6.2.ebuild | 8 ++++----
 2 files changed, 7 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     0bc136501f3e56a23e078f0cc035a740f7d7baa9
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 17 05:53:56 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Sep 17 05:53:56 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0bc13650

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 dev-util/numdiff/Manifest             |  1 +
 dev-util/numdiff/metadata.xml         | 16 +++++++++++++
 dev-util/numdiff/numdiff-5.8.1.ebuild | 44 +++++++++++++++++++++++++++++++++++
 3 files changed, 61 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     b0455245a9db91b711ec552aa183b839c2cf75a1
Author:     Kacper Kowalik <xarthisius.kk <AT> gmail <DOT> com>
AuthorDate: Tue Sep 17 09:05:11 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Tue Sep 17 09:05:11 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b0455245

Merge pull request #111 from mgorny/python-fixes

python-r1 fixes


 dev-python/healpy/ChangeLog                             |  3 +++
 dev-python/healpy/healpy-1.6.2.ebuild                   |  8 ++++----
 sci-biology/emboss/ChangeLog                            | 17 +++++++++++++++++
 sci-biology/emboss/emboss-6.6.0.ebuild                  | 14 +++++++++-----
 ...6.3.1_p4-r2_plcol.patch => emboss-6.6.0_plcol.patch} |  0
 5 files changed, 33 insertions(+), 9 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     2a0c2c75a01ce87a6785dd46d8fe1e9b081207b2
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Mon Sep 16 22:24:17 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Mon Sep 16 22:24:17 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2a0c2c75

Merge pull request #109 from tamiko/numdiff

An ebuild for numdiff (http://www.nongnu.org/numdiff/)


 dev-util/numdiff/Manifest             |  1 +
 dev-util/numdiff/metadata.xml         | 16 +++++++++++++
 dev-util/numdiff/numdiff-5.8.1.ebuild | 44 +++++++++++++++++++++++++++++++++++
 3 files changed, 61 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     66b75133458a140f67c294399aa6c5ef0e7cfcdc
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Sep 16 18:43:51 2013 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Sep 16 18:43:51 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=66b75133

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-chemistry/ball/ball-9999.ebuild                       | 15 +++++++--------
 sci-chemistry/freeon/ChangeLog                            |  9 +++++++++
 sci-chemistry/freeon/Manifest                             |  1 +
 ...{freeon-2013.09.12.ebuild => freeon-2013.09.16.ebuild} |  9 ---------
 4 files changed, 17 insertions(+), 17 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     9070dda0aeb8504be1b2f68dfafa3320e021709f
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Mon Sep 16 00:29:15 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Mon Sep 16 00:29:15 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9070dda0

Merge pull request #108 from ustcscgy/patch-1

fix ball-9999.ebuild upstream git uri and qt dependencies


 sci-chemistry/ball/ball-9999.ebuild | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     4ffb04de8cc4f64a6eb0582ceac43dbc2999cbbc
Author:     Kacper Kowalik (Xarthisius) <xarthisius <AT> gentoo <DOT> org>
AuthorDate: Sun Sep 15 05:18:11 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Sun Sep 15 05:18:11 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4ffb04de

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 app-admin/eselect/ChangeLog                        |  10 +
 app-admin/eselect/Manifest                         |   1 +
 app-admin/eselect/eselect-1.3.7-r100.ebuild        |   2 +-
 ...1.3.7-r100.ebuild => eselect-1.3.8-r100.ebuild} |   4 +-
 .../eselect/files/eselect-1.3.8-alternatives.patch | 616 +++++++++++++++++++++
 dev-python/pyqtgraph/ChangeLog                     |  17 +
 dev-python/pyqtgraph/Manifest                      |   1 +
 dev-python/pyqtgraph/metadata.xml                  |  14 +
 dev-python/pyqtgraph/pyqtgraph-0.9.7.ebuild        |  32 ++
 licenses/CeCILL-2.0                                | 505 -----------------
 licenses/STFC                                      |  67 +++
 media-gfx/librecad/ChangeLog                       |   3 +
 media-gfx/librecad/Manifest                        |   1 +
 ...-2.0.0_rc1.ebuild => librecad-2.0.0_rc2.ebuild} |   0
 profiles/package.mask                              |   1 +
 sci-biology/amos/ChangeLog                         |  10 +-
 sci-biology/amos/Manifest                          |   1 +
 sci-biology/amos/amos-3.1.0-r1.ebuild              |  30 +
 sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch    |  15 +
 ...mos-3.1.0-goBambus2.py-indent-and-cleanup.patch |  25 +
 sci-biology/biopython/ChangeLog                    |  10 +
 sci-biology/biopython/biopython-1.62.ebuild        |  49 ++
 sci-biology/{dawg => biopython}/metadata.xml       |   0
 sci-biology/emboss/ChangeLog                       |  20 +-
 sci-biology/emboss/Manifest                        |   4 +-
 ....3.1_p4-r1.ebuild => emboss-6.3.1_p4-r2.ebuild} |  15 +-
 ...boss-6.3.1_p4-r1.ebuild => emboss-6.5.7.ebuild} |  10 +-
 ...boss-6.3.1_p4-r1.ebuild => emboss-6.6.0.ebuild} |  10 +-
 sci-biology/emboss/files/ax_lib_mysql.m4           | 147 +++++
 .../emboss/files/emboss-6.3.1_p4-r2_Makefile.patch |  47 ++
 .../emboss-6.3.1_p4-r2_compilations-paths.patch    | 315 +++++++++++
 .../emboss/files/emboss-6.3.1_p4-r2_libtool.patch  |  18 +
 ..._plcol.patch => emboss-6.3.1_p4-r2_plcol.patch} |   0
 sci-biology/ncbi-tools++/ChangeLog                 |  81 +++
 sci-biology/ncbi-tools++/Manifest                  |   1 +
 ...d.patch => ncbi-tools++-12.0.0-as-needed.patch} |   2 +-
 ...s.patch => ncbi-tools++-12.0.0-conf-opts.patch} |   0
 .../ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch |  19 +
 .../ncbi-tools++-12.0.0-fix-creaders-linking.patch |  11 +
 .../ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch |  10 +
 .../files/ncbi-tools++-9.0.0-as-needed.patch       |   2 +-
 .../ncbi-tools++-9.0.0-fix-creaders-linking.patch  |  10 +
 .../ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch  |  10 +
 ...-reference-to-GenBankReaders_Register_Id1.patch |  10 +
 ...ls++-9.0.0-remove-LZO-definition-upstream.patch |  10 +
 ...-9.0.0-r1.ebuild => ncbi-tools++-12.0.0.ebuild} |  20 +-
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |  33 +-
 sci-biology/psychopy/Manifest                      |   2 +
 sci-biology/psychopy/psychopy-1.75.01.ebuild       |  12 +-
 ...hopy-1.75.01.ebuild => psychopy-1.77.02.ebuild} |  12 +-
 ...hopy-1.75.01.ebuild => psychopy-1.78.00.ebuild} |  14 +-
 sci-biology/psychopy/psychopy-9999.ebuild          |  12 +-
 sci-chemistry/freeon/ChangeLog                     |   5 +
 sci-chemistry/freeon/Manifest                      |   1 +
 sci-chemistry/freeon/freeon-20130912.ebuild        |  38 ++
 sci-chemistry/namd/ChangeLog                       |  11 +
 sci-chemistry/namd/Manifest                        |   1 +
 sci-chemistry/namd/files/namd-2.7-iml-dec.patch    |  24 +
 sci-chemistry/namd/files/namd-2.9-gentoo.patch     | 151 +++++
 sci-chemistry/{ligplot+ => namd}/metadata.xml      |   0
 sci-chemistry/namd/namd-2.9.ebuild                 | 105 ++++
 sci-libs/fftw/ChangeLog                            |  18 +
 sci-libs/fftw/Manifest                             |   1 +
 sci-libs/fftw/fftw-3.3.3-r3.ebuild                 | 187 +++++++
 sci-libs/fftw/fftw-9999.ebuild                     | 187 +++++++
 .../fftw/files/fftw-3.3.3-install-header.patch     |  35 ++
 sci-libs/fftw/metadata.xml                         |  23 +
 sci-libs/itk/ChangeLog                             |   9 +
 sci-libs/itk/Manifest                              |   1 +
 sci-libs/itk/itk-4.4.2.ebuild                      | 116 ++++
 sci-libs/itk/metadata.xml                          |  18 +
 sci-libs/modglue/ChangeLog                         |   5 +-
 sci-libs/modglue/Manifest                          |   2 +-
 sci-libs/modglue/modglue-1.16.ebuild               |   6 +-
 sci-libs/nibabel/metadata.xml                      |  19 +
 sci-libs/nibabel/nibabel-9999.ebuild               |  40 ++
 sci-libs/nipy/Manifest                             |   1 +
 sci-libs/nipy/metadata.xml                         |  12 +
 sci-libs/nipy/nipy-0.3.0.ebuild                    |  37 ++
 sci-libs/nipy/nipy-9999.ebuild                     |  36 ++
 sci-libs/nipype/metadata.xml                       |  21 +
 sci-libs/nipype/nipype-9999.ebuild                 |  33 ++
 sci-libs/pydicom/Manifest                          |   1 +
 sci-libs/pydicom/pydicom-0.9.8.ebuild              |  20 +
 sci-misc/sfst/Manifest                             |   2 +-
 sci-physics/lammps/ChangeLog                       |   5 +
 sci-physics/lammps/Manifest                        |   1 +
 ...mmps-20130708.ebuild => lammps-20130830.ebuild} |   0
 sys-cluster/charm/ChangeLog                        |  29 +
 sys-cluster/charm/charm-6.5.1-r1.ebuild            | 195 +++++++
 .../charm/files/charm-6.5.1-CkReductionMgr.patch   |  34 ++
 .../files/charm-6.5.1-fix-string-parsing.patch     |  50 ++
 92 files changed, 3193 insertions(+), 558 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     cee802e35ee7fda5e437b1e2d08e8526d2d67ccd
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Sat Sep 14 12:43:13 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Sat Sep 14 12:43:13 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cee802e3

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-biology/ncbi-tools++/ChangeLog                 | 81 ++++++++++++++++++++++
 sci-biology/ncbi-tools++/Manifest                  |  1 +
 ...d.patch => ncbi-tools++-12.0.0-as-needed.patch} |  2 +-
 ...s.patch => ncbi-tools++-12.0.0-conf-opts.patch} |  0
 .../ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch | 19 +++++
 .../ncbi-tools++-12.0.0-fix-creaders-linking.patch | 11 +++
 .../ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch | 10 +++
 .../files/ncbi-tools++-9.0.0-as-needed.patch       |  2 +-
 .../ncbi-tools++-9.0.0-fix-creaders-linking.patch  | 10 +++
 .../ncbi-tools++-9.0.0-fix-svn-URL-upstream.patch  | 10 +++
 ...-reference-to-GenBankReaders_Register_Id1.patch | 10 +++
 ...ls++-9.0.0-remove-LZO-definition-upstream.patch | 10 +++
 ...-9.0.0-r1.ebuild => ncbi-tools++-12.0.0.ebuild} | 20 ++++--
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      | 33 ++++++++-
 14 files changed, 209 insertions(+), 10 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     d67894628f31ad3ad6daf4645fccf8ccda275c87
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Sep 11 20:43:15 2013 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Sep 11 20:43:15 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d6789462

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sys-cluster/charm/ChangeLog                              |  4 ++++
 .../charm/files/charm-6.5.1-fix-string-parsing.patch     | 16 +++++++++-------
 2 files changed, 13 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     d102a96553e2c716b0f3815c369721e6706e52eb
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Wed Sep 11 20:31:56 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Wed Sep 11 20:31:56 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d102a965

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-biology/amos/ChangeLog                         |  10 +-
 sci-biology/amos/Manifest                          |   1 +
 sci-biology/amos/amos-3.1.0-r1.ebuild              |  30 ++
 sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch    |  15 +
 ...mos-3.1.0-goBambus2.py-indent-and-cleanup.patch |  25 ++
 sci-biology/emboss/ChangeLog                       |  20 +-
 sci-biology/emboss/Manifest                        |   4 +-
 ....3.1_p4-r1.ebuild => emboss-6.3.1_p4-r2.ebuild} |  15 +-
 ...boss-6.3.1_p4-r1.ebuild => emboss-6.5.7.ebuild} |  10 +-
 ...boss-6.3.1_p4-r1.ebuild => emboss-6.6.0.ebuild} |  10 +-
 sci-biology/emboss/files/ax_lib_mysql.m4           | 147 ++++++++++
 .../emboss/files/emboss-6.3.1_p4-r2_Makefile.patch |  47 +++
 .../emboss-6.3.1_p4-r2_compilations-paths.patch    | 315 +++++++++++++++++++++
 .../emboss/files/emboss-6.3.1_p4-r2_libtool.patch  |  18 ++
 ..._plcol.patch => emboss-6.3.1_p4-r2_plcol.patch} |   0
 15 files changed, 654 insertions(+), 13 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Martin Mokrejs]

commit:     af3019cf2540f9a4e5191b527b5ac897e33e1416
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Sep 11 20:19:09 2013 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Sep 11 20:19:09 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=af3019cf

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-libs/itk/Manifest                              |   4 +
 .../files/itk-4.4-v3compat_I2VI_const-fix.patch    |  12 ++
 sci-libs/itk/itk-4.4.0.ebuild                      | 172 +++++++++++++++++++++
 sci-libs/itk/metadata.xml                          |  17 ++
 sys-cluster/charm/ChangeLog                        |  21 +++
 .../{charm-6.5.1.ebuild => charm-6.5.1-r1.ebuild}  |   2 +
 .../charm/files/charm-6.5.1-CkReductionMgr.patch   |  34 ++++
 .../files/charm-6.5.1-fix-string-parsing.patch     |  49 ++++++
 8 files changed, 311 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     603eab0cab917c47d19bb35fdab92cd9e45556f9
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Tue Sep 10 17:45:58 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Tue Sep 10 17:45:58 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=603eab0c

Merge pull request #80 from gerddie/master

Add sci-libs/itk Closes: #124241 - merging will need work.


 sci-libs/itk/Manifest                              |   4 +
 .../files/itk-4.4-v3compat_I2VI_const-fix.patch    |  12 ++
 sci-libs/itk/itk-4.4.0.ebuild                      | 172 +++++++++++++++++++++
 sci-libs/itk/metadata.xml                          |  17 ++
 4 files changed, 205 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     e96ae4f713672cd0e72e5244aeccccd5ffe8b89c
Author:     Gert Wollny <gert <AT> die <DOT> upm <DOT> es>
AuthorDate: Mon Jun 10 13:52:45 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Mon Jun 10 13:52:45 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e96ae4f7

Merge branch 'master' of github.com:gerddie/sci

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     6022907caf50de6d0fadcdeebaf0ae509e872b85
Author:     Kacper Kowalik <xarthisius.kk <AT> gmail <DOT> com>
AuthorDate: Sat Sep  7 12:44:47 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Sat Sep  7 12:44:47 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6022907c

Merge pull request #106 from gpoulin/master

Add dev-python/pyqtgraph


 dev-python/pyqtgraph/ChangeLog              | 17 +++++++++++++++
 dev-python/pyqtgraph/Manifest               |  1 +
 dev-python/pyqtgraph/metadata.xml           | 14 +++++++++++++
 dev-python/pyqtgraph/pyqtgraph-0.9.7.ebuild | 32 +++++++++++++++++++++++++++++
 4 files changed, 64 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     8c59ec6819e350d668ef0858afa2239eb19c5806
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Thu Sep  5 00:31:52 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Thu Sep  5 00:31:52 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8c59ec68

Merge branch 'master' of git://github.com/gentoo-science/sci

Conflicts:
	sci-biology/psychopy/Manifest


 app-admin/eselect/ChangeLog                        |   6 +
 app-admin/eselect/Manifest                         |   7 +
 ...1.3.7-r100.ebuild => eselect-1.3.8-r100.ebuild} |   2 +-
 ...ives.patch => eselect-1.3.8-alternatives.patch} |   8 +-
 app-doc/lapack-docs/ChangeLog                      |   6 +-
 app-doc/lapack-docs/Manifest                       |   4 +-
 app-doc/lapack-docs/lapack-docs-3.3-r1.ebuild      |   6 +-
 dev-util/ccache/ChangeLog                          |   8 +
 ...ache-3.1.9-r1.ebuild => ccache-3.1.9-r2.ebuild} |   6 +-
 dev-util/ccache/files/ccache-config-2              |   7 +-
 licenses/{Artistic-IGS => Artistic-Manatee}        |   0
 media-gfx/librecad/ChangeLog                       |   3 +
 media-gfx/librecad/Manifest                        |   1 +
 ...-2.0.0_rc1.ebuild => librecad-2.0.0_rc2.ebuild} |   0
 profiles/package.mask                              |   1 +
 sci-biology/BG7/BG7-9999.ebuild                    |  28 +++
 sci-biology/BG7/ChangeLog                          |   9 +
 sci-biology/fastx_toolkit/ChangeLog                |  10 ++
 sci-biology/fastx_toolkit/Manifest                 |   1 +
 .../fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild    |  26 +++
 sci-biology/libgtextutils/ChangeLog                |   8 +-
 sci-biology/libgtextutils/Manifest                 |   2 +-
 ...utils-0.6.ebuild => libgtextutils-0.6.1.ebuild} |   4 +-
 sci-biology/manatee-igs/ChangeLog                  |  13 ++
 sci-biology/manatee-igs/Manifest                   |   4 +-
 sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild  |   5 +-
 sci-biology/manatee-jcvi/ChangeLog                 |  11 ++
 sci-biology/manatee-jcvi/Manifest                  |   1 +
 sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild |  53 ++++++
 .../manatee-jcvi}/metadata.xml                     |   0
 sci-biology/psychopy/Manifest                      |   4 +
 sci-biology/psychopy/psychopy-1.75.01.ebuild       |  12 +-
 ...hopy-1.75.01.ebuild => psychopy-1.77.02.ebuild} |  12 +-
 ...hopy-1.75.01.ebuild => psychopy-1.78.00.ebuild} |  14 +-
 sci-biology/psychopy/psychopy-9999.ebuild          |  12 +-
 sci-biology/symap/ChangeLog                        |   9 +
 sci-biology/symap/Manifest                         |   1 +
 sci-biology/symap/symap-4.0.ebuild                 |  31 ++++
 sci-chemistry/coot/ChangeLog                       |   6 +
 sci-chemistry/coot/coot-9999.ebuild                |   6 +
 sci-chemistry/coot/files/9999-pc.patch             |  51 +++---
 sci-libs/fftw/ChangeLog                            |  14 ++
 sci-libs/fftw/Manifest                             |   1 +
 sci-libs/fftw/fftw-3.3.3-r3.ebuild                 | 193 +++++++++++++++++++++
 sci-libs/fftw/fftw-9999.ebuild                     | 193 +++++++++++++++++++++
 .../fftw/files/fftw-3.3.3-install-header.patch     |  35 ++++
 sci-libs/fftw/metadata.xml                         |  23 +++
 sci-libs/modglue/ChangeLog                         |   5 +-
 sci-libs/modglue/Manifest                          |   2 +-
 sci-libs/modglue/modglue-1.16.ebuild               |   6 +-
 sci-mathematics/alt-ergo/ChangeLog                 |   7 +
 sci-mathematics/alt-ergo/Manifest                  |   2 +-
 ...alt-ergo-0.95.ebuild => alt-ergo-0.95.1.ebuild} |   2 +-
 sci-mathematics/alt-ergo/metadata.xml              |   3 +-
 sci-misc/sfst/Manifest                             |   2 +-
 sci-physics/lammps/ChangeLog                       |   5 +
 sci-physics/lammps/Manifest                        |   1 +
 ...mmps-20130708.ebuild => lammps-20130830.ebuild} |   0
 sci-visualization/yt/yt-9999.ebuild                |  45 ++---
 59 files changed, 832 insertions(+), 105 deletions(-)

diff --cc sci-biology/psychopy/Manifest
index 96fc24a,c306e02..d93b8e1
--- a/sci-biology/psychopy/Manifest
+++ b/sci-biology/psychopy/Manifest
@@@ -1,2 -1,3 +1,6 @@@
  DIST PsychoPy-1.75.01.zip 3512277 SHA256 c86c617bcd9a215f1fe3d1420563a9bc1c8c6707b477481f885437a68a56d211 SHA512 3a57dcff426d9bbeeababd7699d2fe99fc36025d45b4f52abb8ae4544454314dacb00b52b16f94168c86a255f9ac469fad297590b6e466931d5de12e7520f684 WHIRLPOOL a0f258c293937efbd6cbbc325663a1de93961de349e0113562c20d54a957c686590256d7c7a2e0ebea7a497090569ba0e2b777165e9cfe908af82a90991bb939
  DIST PsychoPy-1.77.02.zip 6313389 SHA256 37313ca13e6062146979dbc79dde79306377a08958b47ea1477957373914f1a1 SHA512 11c305d69763c7eca236c53ccef56780637ad2d53801764dada52565a4e07949422722cf7d8691b615d515c6eeee1c29e2ec44fc312fb299fc2bea17b5a15b44 WHIRLPOOL 568cd06a9ad511ceeb0f0293296d4a98549855960be82e25de57b576bbf6614f37253358dcc44909570a73b298df0651920ab2378e0145eb8bd69186922a745c
++<<<<<<< HEAD
++=======
+ DIST PsychoPy-1.78.00.zip 6376071 SHA256 ac74ea948f400a4a962a6abde7e7360fce5738a0f44aec4a0ff636d00976cc25 SHA512 ec2cd1c2094488d2b02c94070c7bc3d50e12e597c0107d2f64d49522e43a12c81b060b7a8abc15e83d50736776ee9d3d7190b78d39c58ee8f8be88b32330c5e2 WHIRLPOOL 9395a55bb820d2d326f4d95e12fb7513fbc4038eea25d0fd182e7e909e86d153374ac14293e89162761f0655b14bb8ca2abfa7fdf3df3e1951bec11e469db1f7
++>>>>>>> 21d8cdffa8697b00d3831a20b6a1c0335b7d8450

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     74c29aae4e5b31a6c6b7242ac05842449c80a006
Author:     Kacper Kowalik (Xarthisius) <xarthisius <AT> gentoo <DOT> org>
AuthorDate: Thu Sep  5 05:28:57 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Thu Sep  5 05:28:57 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=74c29aae

merging


 sci-libs/pydicom/Manifest             |  1 +
 sci-libs/pydicom/pydicom-0.9.8.ebuild | 23 +++++++++++++++++++++++
 2 files changed, 24 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     38ad37bb4760fa7b91bdc6a007c04ee8b920f45c
Author:     Kacper Kowalik (Xarthisius) <xarthisius <AT> gentoo <DOT> org>
AuthorDate: Wed Sep  4 05:13:06 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Wed Sep  4 05:13:06 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=38ad37bb

merging


 sci-libs/nibabel/metadata.xml           | 19 ++++++++++++++++
 sci-libs/nibabel/nibabel-9999.ebuild    | 40 +++++++++++++++++++++++++++++++++
 sci-libs/nipy/Manifest                  |  1 +
 sci-libs/{omalloc => nipy}/metadata.xml |  6 ++---
 sci-libs/nipy/nipy-0.3.0.ebuild         | 38 +++++++++++++++++++++++++++++++
 sci-libs/nipy/nipy-9999.ebuild          | 37 ++++++++++++++++++++++++++++++
 sci-libs/nipype/metadata.xml            | 21 +++++++++++++++++
 sci-libs/nipype/nipype-9999.ebuild      | 33 +++++++++++++++++++++++++++
 8 files changed, 192 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     8a94652fb3d26fdcbaebf3885fee795a6fae94bc
Author:     TheChymera <h.chr <AT> mail <DOT> ru>
AuthorDate: Thu Aug 22 00:18:51 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Thu Aug 22 00:18:51 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8a94652f

Merge branch 'master' of https://github.com/TheChymera/sci


 sci-libs/nipy/nipy-0.3.0.ebuild | 1 +
 sci-libs/nipy/nipy-9999.ebuild  | 1 +
 2 files changed, 2 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     236b1bee9a50b90b064e2726c9bc4ec54db98a91
Author:     TheChymera <h.chr <AT> mail <DOT> ru>
AuthorDate: Wed Aug 21 23:25:00 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Wed Aug 21 23:25:00 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=236b1bee

Merge branch 'master' of git://github.com/gentoo-science/sci

Conflicts:
	sci-libs/scikits_image/scikits_image-9999.ebuild


 dev-cpp/eigen/ChangeLog                            |   7 +
 dev-cpp/eigen/Manifest                             |   3 +-
 .../{eigen-3.1.3-r1.ebuild => eigen-3.1.4.ebuild}  |   0
 .../{eigen-3.1.3-r1.ebuild => eigen-3.2.0.ebuild}  |   0
 dev-util/nvidia-cuda-toolkit/ChangeLog             | 190 -------------
 dev-util/nvidia-cuda-toolkit/Manifest              |   2 -
 dev-util/nvidia-cuda-toolkit/files/cuda-config.in  |  28 --
 .../files/nvidia-cuda-toolkit-2.2-enum_fix.patch   |  42 ---
 .../files/nvidia-cuda-toolkit-3.0-enum_fix.patch   |  54 ----
 .../files/nvidia-cuda-toolkit-3.1-enum_fix.patch   |  24 --
 dev-util/nvidia-cuda-toolkit/metadata.xml          |  18 --
 .../nvidia-cuda-toolkit-5.5.11.ebuild              | 142 ----------
 licenses/nmrpipe                                   |  23 ++
 sci-chemistry/chemBuild/ChangeLog                  |   5 +
 sci-chemistry/chemBuild/Manifest                   |   1 +
 ...emBuild-1.0.2.ebuild => chemBuild-1.0.3.ebuild} |   0
 sci-chemistry/chimera-bin/ChangeLog                |   8 +-
 sci-chemistry/chimera-bin/Manifest                 |   2 +
 sci-chemistry/chimera-bin/chimera-bin-1.6.2.ebuild |   8 +-
 ...era-bin-1.6.2.ebuild => chimera-bin-1.8.ebuild} |   8 +-
 sci-chemistry/chimera-bin/metadata.xml             |   2 +-
 sci-chemistry/dl_poly/ChangeLog                    |  14 +
 sci-chemistry/dl_poly/Manifest                     |   2 +
 sci-chemistry/dl_poly/dl_poly-1.9.ebuild           |  35 +++
 sci-chemistry/dl_poly/dl_poly-4.05.ebuild          |  41 +++
 .../{votca-csgapps => dl_poly}/metadata.xml        |   0
 sci-chemistry/gnome-chemistry-utils/ChangeLog      |   4 +
 .../gnome-chemistry-utils-0.14.2-r1.ebuild         |   1 +
 sci-chemistry/jmol/ChangeLog                       |  54 ----
 sci-chemistry/jmol/Manifest                        |   1 -
 .../jmol/files/12.0.45/jmol-manifest.patch         |  96 -------
 sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch | 313 ---------------------
 sci-chemistry/jmol/files/caffeine.xyz              |  26 --
 sci-chemistry/jmol/files/index.html                |  14 -
 .../jmol/files/selfSignedCertificate.store         | Bin 1516 -> 0 bytes
 sci-chemistry/jmol/jmol-12.0.45-r1.ebuild          | 122 --------
 sci-chemistry/jmol/metadata.xml                    |  13 -
 sci-chemistry/nmrpipe/ChangeLog                    |   6 +
 sci-chemistry/nmrpipe/Manifest                     |   6 +-
 ....patch => nmrpipe-8.1.2013.218.23.09-lib.patch} |   0
 ...r3.ebuild => nmrpipe-8.1.2013.218.23.09.ebuild} |   2 +-
 sci-chemistry/panav/ChangeLog                      |  10 +
 sci-chemistry/panav/Manifest                       |   1 +
 sci-chemistry/panav/metadata.xml                   |  30 ++
 sci-chemistry/panav/panav-0.20130730.ebuild        |  34 +++
 sci-chemistry/phenix-bin/ChangeLog                 |   3 +
 .../phenix-bin/phenix-bin-1.8.2.1309.ebuild        |   4 +-
 sci-chemistry/specView/ChangeLog                   |   5 +
 sci-chemistry/specView/Manifest                    |   1 +
 ...specView-1.0.2.ebuild => specView-1.0.3.ebuild} |   0
 sci-chemistry/unio/ChangeLog                       |   6 +-
 sci-chemistry/unio/Manifest                        |   3 +-
 sci-chemistry/unio/metadata.xml                    |   2 +-
 sci-chemistry/unio/unio-2.0.1-r1.ebuild            |  71 -----
 sci-chemistry/unio/unio-2.0.2-r1.ebuild            |  62 ++++
 sci-chemistry/unio/unio-2.0.2.ebuild               |  71 -----
 sci-libs/armadillo/ChangeLog                       |   6 +
 sci-libs/armadillo/Manifest                        |   2 +-
 ...llo-3.900.6.ebuild => armadillo-3.910.0.ebuild} |   0
 sci-libs/avogadro-libs/ChangeLog                   |   8 +
 sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild  |  19 +-
 .../files/avogadro-libs-0.6.0-underlinking.patch   |  14 +
 sci-libs/avogadro-libs/metadata.xml                |   3 +
 sci-libs/coinor-mp/ChangeLog                       |   6 +
 sci-libs/coinor-mp/Manifest                        |   2 +-
 ...inor-mp-1.6.0.ebuild => coinor-mp-1.7.0.ebuild} |   4 +-
 sci-libs/gsl/ChangeLog                             |   7 +
 sci-libs/gsl/Manifest                              |   2 +-
 ...5-cblas.patch => gsl-1.16-cblas-external.patch} | 181 ++++++------
 .../gsl/{gsl-1.15-r3.ebuild => gsl-1.16-r1.ebuild} |  13 +-
 sci-libs/gsl/metadata.xml                          |  12 +-
 .../{libsufr-0.4.1.ebuild => libsufr-0.5.2.ebuild} |   0
 sci-libs/o2scl/ChangeLog                           |   6 +
 sci-libs/o2scl/Manifest                            |   2 +-
 .../{o2scl-0.912.ebuild => o2scl-0.913.ebuild}     |   3 +-
 sci-libs/openblas/ChangeLog                        |   6 +
 sci-libs/openblas/Manifest                         |   2 +-
 ...openblas-0.2.7.ebuild => openblas-0.2.8.ebuild} |  25 +-
 sci-libs/openblas/openblas-9999.ebuild             |  22 +-
 sci-libs/scikits_image/ChangeLog                   |   7 +
 sci-libs/scikits_image/scikits_image-9999.ebuild   |   8 +-
 sci-mathematics/bertini/ChangeLog                  |  17 --
 sci-mathematics/bertini/Manifest                   |   2 -
 sci-mathematics/bertini/bertini-1.3.1.ebuild       |  54 ----
 sci-mathematics/bertini/metadata.xml               |  29 --
 sci-mathematics/gappa/ChangeLog                    |   7 +-
 sci-mathematics/gappa/Manifest                     |   2 +-
 sci-mathematics/gappa/gappa-0.16.3.ebuild          |  50 ----
 sci-mathematics/gappa/gappa-1.0.0.ebuild           |  37 +++
 sci-physics/espresso++/ChangeLog                   |   3 +
 sci-physics/espresso++/espresso++-9999.ebuild      |   3 +
 sci-physics/lammps/ChangeLog                       |   5 +
 sci-physics/lammps/Manifest                        |   1 +
 ...mmps-20130708.ebuild => lammps-20130816.ebuild} |   0
 sys-cluster/charmdebug/ChangeLog                   |  15 +
 sys-cluster/charmdebug/Manifest                    |   2 +-
 ...bug-6.2.0.ebuild => charmdebug-6.2.0-r1.ebuild} |   2 +-
 sys-cluster/hpx/Manifest                           |   1 +
 sys-cluster/hpx/files/hpx-0.9.5-install-path.patch |  39 +++
 sys-cluster/hpx/hpx-0.9.5.ebuild                   |   1 +
 .../hpx/{hpx-0.9.5.ebuild => hpx-0.9.6.ebuild}     |   1 +
 virtual/cblas/ChangeLog                            |   3 +
 virtual/cblas/cblas-2.0.ebuild                     |   2 +-
 virtual/cblas/metadata.xml                         |   4 +-
 x11-libs/agg/ChangeLog                             |  27 ++
 x11-libs/agg/Manifest                              |   1 +
 x11-libs/agg/agg-2.5-r3.ebuild                     |  69 +++++
 ...on-terminating-loop-conditions-when-len-1.patch |  81 ++++++
 ...ion-by-aborting-if-the-co-ordinates-are-t.patch |  40 +++
 ...ates-from-previous-vertex-if-last-command.patch |  30 ++
 ...izer_outline_aa-ignore-close_polygon-when.patch | 138 +++++++++
 .../files/2.5/0005-Remove-VC-6-workaround.patch    |  52 ++++
 ...-Implement-grain-merge-blending-mode-GIMP.patch |  85 ++++++
 ...mplement-grain-extract-blending-mode-GIMP.patch |  85 ++++++
 ...tiplication-and-division-operators-as-con.patch |  36 +++
 ...0009-Add-a-static-identity-transformation.patch |  37 +++
 .../2.5/0010-Add-renderer_scanline_aa_alpha.patch  | 193 +++++++++++++
 ...Avoid-division-by-zero-in-color-burn-mode.patch |  58 ++++
 ...12-Avoid-pixel-artifacts-when-compositing.patch |  26 ++
 ...conv-classes-to-allow-access-to-the-origi.patch |  93 ++++++
 ...tial-zero-division-resulting-in-nan-in-ag.patch |  30 ++
 ...t-value-in-the-gamma-table-is-always-zero.patch |  24 ++
 x11-libs/agg/files/2.5/agg-2.4-depends.patch       |  48 ++++
 x11-libs/agg/files/2.5/agg-2.5-autotools.patch     |  11 +
 x11-libs/agg/files/2.5/agg-2.5-pkgconfig.patch     |  10 +
 x11-libs/agg/files/2.5/agg-2.5-sdl-automagic.patch |  26 ++
 x11-libs/agg/files/2.5/agg-2.5-sdl-m4.patch        | 186 ++++++++++++
 x11-libs/agg/metadata.xml                          |  14 +
 128 files changed, 2050 insertions(+), 1610 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     38140f79a7c2686029f955748296e39209d53949
Author:     TheChymera <h.chr <AT> mail <DOT> ru>
AuthorDate: Wed Aug 21 22:43:12 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Wed Aug 21 22:43:12 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=38140f79

Merge branch 'master' of https://github.com/TheChymera/sci

Conflicts:
	sci-libs/scikits_image/scikits_image-9999.ebuild


 dev-lang/vtune/ChangeLog                           |   4 +
 dev-lang/vtune/Manifest                            |   7 +-
 ...9.295420.ebuild => vtune-13.1.10.298370.ebuild} |  26 +-
 dev-lang/vtune/vtune-13.1.4.270817.ebuild          |  38 --
 eclass/intel-sdp.eclass                            |  29 +-
 profiles/package.mask                              |   5 -
 sci-biology/psychopy/Manifest                      |   1 +
 sci-chemistry/pymol/ChangeLog                      |   3 +
 sci-chemistry/pymol/pymol-9999.ebuild              |   1 +
 sci-libs/avogadro-libs/ChangeLog                   |  10 +
 sci-libs/avogadro-libs/Manifest                    |   1 +
 sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild  |  41 ++
 .../coot => sci-libs/avogadro-libs}/metadata.xml   |   4 +-
 sci-libs/chemkit/ChangeLog                         |  10 +
 sci-libs/chemkit/Manifest                          |   1 +
 sci-libs/chemkit/chemkit-0.1.ebuild                |  55 +++
 .../coot => sci-libs/chemkit}/metadata.xml         |   4 +-
 sci-libs/dealii/Manifest                           |   2 +
 sci-libs/dealii/dealii-8.0.0.ebuild                |   1 +
 sci-libs/dealii/dealii-9999.ebuild                 | 128 +++++
 sci-libs/dealii/metadata.xml                       |  28 ++
 sci-libs/nibabel/nibabel-9999.ebuild               |  40 ++
 sci-libs/nipy/Manifest                             |   1 +
 sci-libs/nipy/nipy-0.3.0.ebuild                    |  37 ++
 sci-libs/nipy/nipy-9999.ebuild                     |  34 ++
 sci-libs/nipype/nipype-9999.ebuild                 |  26 +
 sci-libs/openblas/ChangeLog                        |   8 +
 sci-libs/openblas/Manifest                         |   3 +-
 sci-libs/openblas/files/openblas-aliasing.patch    |  11 -
 .../openblas/files/openblas-sharedlibs-0.2.patch   |  45 --
 sci-libs/openblas/metadata.xml                     |   1 -
 sci-libs/openblas/openblas-0.2.6.ebuild            |   1 -
 sci-libs/openblas/openblas-0.2.7.ebuild            | 127 +++++
 sci-libs/openblas/openblas-9999.ebuild             | 148 +++---
 sci-libs/p4est/Manifest                            |   1 +
 sci-libs/p4est/files/p4est-libtool-fix.patch       |  59 +++
 sci-libs/p4est/metadata.xml                        |  15 +
 sci-libs/p4est/p4est-0.3.4.1.ebuild                |  71 +++
 sci-libs/scikits_image/scikits_image-9999.ebuild   |   4 +
 sci-visualization/paraview/ChangeLog               | 156 ------
 sci-visualization/paraview/Manifest                |   3 -
 .../paraview/files/paraview-3.10.1-gcc46.patch     |  20 -
 .../paraview/files/paraview-3.12.0-gcc46.patch     |  10 -
 .../paraview/files/paraview-3.12.0-protobuf.patch  |  53 ---
 .../files/paraview-3.14.1-ffmpeg-noinstall.patch   |  27 --
 .../paraview/files/paraview-3.14.1-gcc-4.7.patch   |  28 --
 .../paraview/files/paraview-3.14.1-mpi4py.patch    |  15 -
 .../files/paraview-3.14.1-python-exit.patch        |  46 --
 .../files/paraview-3.14.1-removesqlite.patch       | 526 ---------------------
 .../paraview/files/paraview-3.14.1-vtknetcd.patch  |  97 ----
 .../files/paraview-3.14.1-xdmf-linking.patch       |  16 -
 .../paraview/files/paraview-3.8.0-h5part.patch     |  12 -
 .../files/paraview-3.8.0-installpath.patch         |  33 --
 ...araview-3.8.0-pointsprite-example-install.patch |   9 -
 .../files/paraview-3.8.0-pointsprite-example.patch |  25 -
 .../paraview/files/paraview-3.8.0-xdmf-bc.patch    |  13 -
 .../files/paraview-3.8.0-xdmf-cstring.patch        |  10 -
 .../paraview/files/vtk-5.6.0-cg-path.patch         |  36 --
 .../paraview/files/vtk-5.6.0-libpng14.patch        |  22 -
 .../paraview/files/vtk-5.6.0-odbc.patch            |  12 -
 .../paraview/files/vtk-5.6.1-ffmpeg.patch          |  42 --
 .../paraview/files/vtk-5.6.1-libav-0.8.patch       |  66 ---
 .../paraview/files/vtk-boost1.49.patch             |  27 --
 sci-visualization/paraview/metadata.xml            |  22 -
 sci-visualization/paraview/paraview-3.10.1.ebuild  | 214 ---------
 sci-visualization/paraview/paraview-3.12.0.ebuild  | 214 ---------
 .../paraview/paraview-3.14.1-r4.ebuild             | 254 ----------
 virtual/cblas/ChangeLog                            |   6 +-
 virtual/cblas/cblas-2.0.ebuild                     |   6 +-
 69 files changed, 824 insertions(+), 2227 deletions(-)

diff --cc sci-libs/scikits_image/scikits_image-9999.ebuild
index 9515834,46a02c1..9c92ac4
--- a/sci-libs/scikits_image/scikits_image-9999.ebuild
+++ b/sci-libs/scikits_image/scikits_image-9999.ebuild
@@@ -42,9 -42,7 +42,13 @@@ S="${WORKDIR}/${MYPN}-${PV}
  DOCS=( CONTRIBUTORS.txt DEPENDS.txt RELEASE.txt TASKS.txt )
  
  python_test() {
++<<<<<<< HEAD
 +	distutils_install_for_testing.py \
 +		install --root="${T}/test-${EPYTHON}" \
 +		--no-compile || die "install test failed"
++=======
+ 	distutils_install_for_testing.py
++>>>>>>> e20cf96b7230e5bd7e2d5a7531754a84ba6a67df
  	cd "${T}/test-${EPYTHON}/$(python_get_sitedir)" || die
  	echo "backend: Agg" > matplotlibrc
  	MPLCONFIGDIR=. PYTHONPATH=. nosetests-"${EPYTHON}" || die

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     817bf7662037d4d9c6c3c96aca16eb8ad8d45b25
Author:     TheChymera <h.chr <AT> mail <DOT> ru>
AuthorDate: Wed Jul 24 03:09:10 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Wed Jul 24 03:09:10 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=817bf766

Merge branch 'master' of https://github.com/TheChymera/sci


 sci-libs/scikits_image/Manifest                  |  1 +
 sci-libs/scikits_image/scikits_image-9999.ebuild | 51 ++++++++++++++++++++++++
 2 files changed, 52 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     21d8cdffa8697b00d3831a20b6a1c0335b7d8450
Author:     Kacper Kowalik (Xarthisius) <xarthisius <AT> gentoo <DOT> org>
AuthorDate: Wed Sep  4 05:11:16 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Wed Sep  4 05:11:16 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=21d8cdff

Merge branch 'master' of github.com:gentoo-science/sci


 media-gfx/librecad/ChangeLog                               |  3 +++
 media-gfx/librecad/Manifest                                |  1 +
 ...librecad-2.0.0_rc1.ebuild => librecad-2.0.0_rc2.ebuild} |  0
 sci-biology/psychopy/Manifest                              |  2 ++
 sci-biology/psychopy/psychopy-1.75.01.ebuild               | 12 +++++++-----
 .../{psychopy-1.75.01.ebuild => psychopy-1.77.02.ebuild}   | 12 +++++++-----
 .../{psychopy-1.75.01.ebuild => psychopy-1.78.00.ebuild}   | 14 ++++++++------
 sci-biology/psychopy/psychopy-9999.ebuild                  | 12 +++++++-----
 sci-misc/sfst/Manifest                                     |  2 +-
 9 files changed, 36 insertions(+), 22 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     5e86d06ab1f3a19eb7e171f94c35d2d80d1c27fa
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Tue Sep  3 22:46:31 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Tue Sep  3 22:46:31 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5e86d06a

Merge pull request #104 from TheChymera/psychopy

New, updated Psychopy ebuilds


 sci-biology/psychopy/Manifest                              |  2 ++
 sci-biology/psychopy/psychopy-1.75.01.ebuild               | 12 +++++++-----
 .../{psychopy-1.75.01.ebuild => psychopy-1.77.02.ebuild}   | 12 +++++++-----
 .../{psychopy-1.75.01.ebuild => psychopy-1.78.00.ebuild}   | 14 ++++++++------
 sci-biology/psychopy/psychopy-9999.ebuild                  | 12 +++++++-----
 5 files changed, 31 insertions(+), 21 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     8d03803835688ac4e6837f57d8d98794a9388a8b
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Tue Sep  3 16:43:31 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Tue Sep  3 16:43:31 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8d038038

Merge pull request #105 from jhcloos/sfst

sci-misc/sfst: Fix Manifest for sci-misc/sfst1.4.6g.


 sci-misc/sfst/Manifest | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     d7175ca43809b905367b6925ac240b7feb9feadc
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Fri Aug 30 04:16:43 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Fri Aug 30 04:16:43 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d7175ca4

Merge branch 'master' of git://github.com/gentoo-science/sci into psychopy


 app-doc/lapack-docs/ChangeLog                      |   6 +-
 app-doc/lapack-docs/Manifest                       |   4 +-
 app-doc/lapack-docs/lapack-docs-3.3-r1.ebuild      |   6 +-
 dev-cpp/eigen/ChangeLog                            |   7 +
 dev-cpp/eigen/Manifest                             |   3 +-
 .../{eigen-3.1.3-r1.ebuild => eigen-3.1.4.ebuild}  |   0
 .../{eigen-3.1.3-r1.ebuild => eigen-3.2.0.ebuild}  |   0
 dev-util/ccache/ChangeLog                          |   8 +
 ...ache-3.1.9-r1.ebuild => ccache-3.1.9-r2.ebuild} |   6 +-
 dev-util/ccache/files/ccache-config-2              |   7 +-
 dev-util/nvidia-cuda-toolkit/ChangeLog             | 190 -------------
 dev-util/nvidia-cuda-toolkit/Manifest              |   2 -
 dev-util/nvidia-cuda-toolkit/files/cuda-config.in  |  28 --
 .../files/nvidia-cuda-toolkit-2.2-enum_fix.patch   |  42 ---
 .../files/nvidia-cuda-toolkit-3.0-enum_fix.patch   |  54 ----
 .../files/nvidia-cuda-toolkit-3.1-enum_fix.patch   |  24 --
 dev-util/nvidia-cuda-toolkit/metadata.xml          |  18 --
 .../nvidia-cuda-toolkit-5.5.11.ebuild              | 142 ----------
 licenses/nmrpipe                                   |  23 ++
 sci-chemistry/chemBuild/ChangeLog                  |   5 +
 sci-chemistry/chemBuild/Manifest                   |   1 +
 ...emBuild-1.0.2.ebuild => chemBuild-1.0.3.ebuild} |   0
 sci-chemistry/chimera-bin/ChangeLog                |   8 +-
 sci-chemistry/chimera-bin/Manifest                 |   2 +
 sci-chemistry/chimera-bin/chimera-bin-1.6.2.ebuild |   8 +-
 ...era-bin-1.6.2.ebuild => chimera-bin-1.8.ebuild} |   8 +-
 sci-chemistry/chimera-bin/metadata.xml             |   2 +-
 sci-chemistry/coot/ChangeLog                       |   6 +
 sci-chemistry/coot/coot-9999.ebuild                |   6 +
 sci-chemistry/coot/files/9999-pc.patch             |  51 ++--
 sci-chemistry/dl_poly/ChangeLog                    |  14 +
 sci-chemistry/dl_poly/Manifest                     |   2 +
 sci-chemistry/dl_poly/dl_poly-1.9.ebuild           |  35 +++
 sci-chemistry/dl_poly/dl_poly-4.05.ebuild          |  41 +++
 .../{votca-csgapps => dl_poly}/metadata.xml        |   0
 sci-chemistry/gnome-chemistry-utils/ChangeLog      |   4 +
 .../gnome-chemistry-utils-0.14.2-r1.ebuild         |   1 +
 sci-chemistry/jmol/ChangeLog                       |  54 ----
 sci-chemistry/jmol/Manifest                        |   1 -
 .../jmol/files/12.0.45/jmol-manifest.patch         |  96 -------
 sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch | 313 ---------------------
 sci-chemistry/jmol/files/caffeine.xyz              |  26 --
 sci-chemistry/jmol/files/index.html                |  14 -
 .../jmol/files/selfSignedCertificate.store         | Bin 1516 -> 0 bytes
 sci-chemistry/jmol/jmol-12.0.45-r1.ebuild          | 122 --------
 sci-chemistry/jmol/metadata.xml                    |  13 -
 sci-chemistry/nmrpipe/ChangeLog                    |   6 +
 sci-chemistry/nmrpipe/Manifest                     |   6 +-
 ....patch => nmrpipe-8.1.2013.218.23.09-lib.patch} |   0
 ...r3.ebuild => nmrpipe-8.1.2013.218.23.09.ebuild} |   2 +-
 sci-chemistry/panav/ChangeLog                      |  10 +
 sci-chemistry/panav/Manifest                       |   1 +
 sci-chemistry/panav/metadata.xml                   |  30 ++
 sci-chemistry/panav/panav-0.20130730.ebuild        |  34 +++
 sci-chemistry/phenix-bin/ChangeLog                 |   3 +
 .../phenix-bin/phenix-bin-1.8.2.1309.ebuild        |   4 +-
 sci-chemistry/specView/ChangeLog                   |   5 +
 sci-chemistry/specView/Manifest                    |   1 +
 ...specView-1.0.2.ebuild => specView-1.0.3.ebuild} |   0
 sci-chemistry/unio/ChangeLog                       |   6 +-
 sci-chemistry/unio/Manifest                        |   3 +-
 sci-chemistry/unio/metadata.xml                    |   2 +-
 sci-chemistry/unio/unio-2.0.1-r1.ebuild            |  71 -----
 sci-chemistry/unio/unio-2.0.2-r1.ebuild            |  62 ++++
 sci-chemistry/unio/unio-2.0.2.ebuild               |  71 -----
 sci-libs/armadillo/ChangeLog                       |   6 +
 sci-libs/armadillo/Manifest                        |   2 +-
 ...llo-3.900.6.ebuild => armadillo-3.910.0.ebuild} |   0
 sci-libs/avogadro-libs/ChangeLog                   |   8 +
 sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild  |  19 +-
 .../files/avogadro-libs-0.6.0-underlinking.patch   |  14 +
 sci-libs/avogadro-libs/metadata.xml                |   3 +
 sci-libs/coinor-mp/ChangeLog                       |   6 +
 sci-libs/coinor-mp/Manifest                        |   2 +-
 ...inor-mp-1.6.0.ebuild => coinor-mp-1.7.0.ebuild} |   4 +-
 sci-libs/gsl/ChangeLog                             |   7 +
 sci-libs/gsl/Manifest                              |   2 +-
 ...5-cblas.patch => gsl-1.16-cblas-external.patch} | 181 ++++++------
 .../gsl/{gsl-1.15-r3.ebuild => gsl-1.16-r1.ebuild} |  13 +-
 sci-libs/gsl/metadata.xml                          |  12 +-
 .../{libsufr-0.4.1.ebuild => libsufr-0.5.2.ebuild} |   0
 sci-libs/o2scl/ChangeLog                           |   6 +
 sci-libs/o2scl/Manifest                            |   2 +-
 .../{o2scl-0.912.ebuild => o2scl-0.913.ebuild}     |   3 +-
 sci-libs/openblas/ChangeLog                        |   6 +
 sci-libs/openblas/Manifest                         |   2 +-
 ...openblas-0.2.7.ebuild => openblas-0.2.8.ebuild} |  25 +-
 sci-libs/openblas/openblas-9999.ebuild             |  22 +-
 sci-libs/scikits_image/ChangeLog                   |   7 +
 sci-libs/scikits_image/scikits_image-9999.ebuild   |   6 +-
 sci-mathematics/alt-ergo/ChangeLog                 |   7 +
 sci-mathematics/alt-ergo/Manifest                  |   2 +-
 ...alt-ergo-0.95.ebuild => alt-ergo-0.95.1.ebuild} |   2 +-
 sci-mathematics/alt-ergo/metadata.xml              |   3 +-
 sci-mathematics/bertini/ChangeLog                  |  17 --
 sci-mathematics/bertini/Manifest                   |   2 -
 sci-mathematics/bertini/bertini-1.3.1.ebuild       |  54 ----
 sci-mathematics/bertini/metadata.xml               |  29 --
 sci-mathematics/gappa/ChangeLog                    |   7 +-
 sci-mathematics/gappa/Manifest                     |   2 +-
 sci-mathematics/gappa/gappa-0.16.3.ebuild          |  50 ----
 sci-mathematics/gappa/gappa-1.0.0.ebuild           |  37 +++
 sci-physics/espresso++/ChangeLog                   |   3 +
 sci-physics/espresso++/espresso++-9999.ebuild      |   3 +
 sci-physics/lammps/ChangeLog                       |   5 +
 sci-physics/lammps/Manifest                        |   1 +
 ...mmps-20130708.ebuild => lammps-20130816.ebuild} |   0
 sys-cluster/charmdebug/ChangeLog                   |  15 +
 sys-cluster/charmdebug/Manifest                    |   2 +-
 ...bug-6.2.0.ebuild => charmdebug-6.2.0-r1.ebuild} |   2 +-
 sys-cluster/hpx/Manifest                           |   1 +
 sys-cluster/hpx/files/hpx-0.9.5-install-path.patch |  39 +++
 sys-cluster/hpx/hpx-0.9.5.ebuild                   |   1 +
 .../hpx/{hpx-0.9.5.ebuild => hpx-0.9.6.ebuild}     |   1 +
 virtual/cblas/ChangeLog                            |   3 +
 virtual/cblas/cblas-2.0.ebuild                     |   2 +-
 virtual/cblas/metadata.xml                         |   4 +-
 x11-libs/agg/ChangeLog                             |  27 ++
 x11-libs/agg/Manifest                              |   1 +
 x11-libs/agg/agg-2.5-r3.ebuild                     |  69 +++++
 ...on-terminating-loop-conditions-when-len-1.patch |  81 ++++++
 ...ion-by-aborting-if-the-co-ordinates-are-t.patch |  40 +++
 ...ates-from-previous-vertex-if-last-command.patch |  30 ++
 ...izer_outline_aa-ignore-close_polygon-when.patch | 138 +++++++++
 .../files/2.5/0005-Remove-VC-6-workaround.patch    |  52 ++++
 ...-Implement-grain-merge-blending-mode-GIMP.patch |  85 ++++++
 ...mplement-grain-extract-blending-mode-GIMP.patch |  85 ++++++
 ...tiplication-and-division-operators-as-con.patch |  36 +++
 ...0009-Add-a-static-identity-transformation.patch |  37 +++
 .../2.5/0010-Add-renderer_scanline_aa_alpha.patch  | 193 +++++++++++++
 ...Avoid-division-by-zero-in-color-burn-mode.patch |  58 ++++
 ...12-Avoid-pixel-artifacts-when-compositing.patch |  26 ++
 ...conv-classes-to-allow-access-to-the-origi.patch |  93 ++++++
 ...tial-zero-division-resulting-in-nan-in-ag.patch |  30 ++
 ...t-value-in-the-gamma-table-is-always-zero.patch |  24 ++
 x11-libs/agg/files/2.5/agg-2.4-depends.patch       |  48 ++++
 x11-libs/agg/files/2.5/agg-2.5-autotools.patch     |  11 +
 x11-libs/agg/files/2.5/agg-2.5-pkgconfig.patch     |  10 +
 x11-libs/agg/files/2.5/agg-2.5-sdl-automagic.patch |  26 ++
 x11-libs/agg/files/2.5/agg-2.5-sdl-m4.patch        | 186 ++++++++++++
 x11-libs/agg/metadata.xml                          |  14 +
 141 files changed, 2124 insertions(+), 1648 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     8bc64e1bf29aafe4d04a3765213ba6242045b305
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Mon Sep  2 18:17:06 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Mon Sep  2 18:17:06 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8bc64e1b

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 app-admin/eselect/ChangeLog                                       | 6 ++++++
 app-admin/eselect/Manifest                                        | 7 +++++++
 .../{eselect-1.3.7-r100.ebuild => eselect-1.3.8-r100.ebuild}      | 2 +-
 ...select-alternatives.patch => eselect-1.3.8-alternatives.patch} | 8 +++-----
 4 files changed, 17 insertions(+), 6 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     1a21cdf6cdb90c46faf9beefcbe2809710b056af
Author:     Kacper Kowalik (Xarthisius) <xarthisius <AT> gentoo <DOT> org>
AuthorDate: Fri Aug 30 07:27:48 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Fri Aug 30 07:27:48 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1a21cdf6

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 licenses/{Artistic-IGS => Artistic-Manatee}        |  0
 sci-biology/BG7/BG7-9999.ebuild                    | 28 ++++++++++++
 sci-biology/BG7/ChangeLog                          |  9 ++++
 sci-biology/fastx_toolkit/ChangeLog                | 10 ++++
 sci-biology/fastx_toolkit/Manifest                 |  1 +
 .../fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild    | 26 +++++++++++
 sci-biology/libgtextutils/ChangeLog                |  8 +++-
 sci-biology/libgtextutils/Manifest                 |  2 +-
 ...utils-0.6.ebuild => libgtextutils-0.6.1.ebuild} |  4 +-
 sci-biology/manatee-igs/ChangeLog                  | 13 ++++++
 sci-biology/manatee-igs/Manifest                   |  4 +-
 sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild  |  5 +-
 sci-biology/manatee-jcvi/ChangeLog                 | 11 +++++
 sci-biology/manatee-jcvi/Manifest                  |  1 +
 sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild | 53 ++++++++++++++++++++++
 .../manatee-jcvi}/metadata.xml                     |  0
 sci-biology/symap/ChangeLog                        |  9 ++++
 sci-biology/symap/Manifest                         |  1 +
 sci-biology/symap/symap-4.0.ebuild                 | 31 +++++++++++++
 19 files changed, 208 insertions(+), 8 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     e355a3ea1ecf6d1ca9b75e0a4edde1045d924914
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Mon Aug 12 21:27:42 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Aug 12 21:27:42 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e355a3ea

Merge pull request #101 from gentryx/master

updates HPX ebuild to 0.9.6


 sys-cluster/hpx/Manifest                               | 1 +
 sys-cluster/hpx/{hpx-0.9.5.ebuild => hpx-0.9.6.ebuild} | 0
 2 files changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     b270be385d9e888d63b5f711e3d83d33e5bf88e3
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Mon Aug 12 14:55:01 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Aug 12 14:55:01 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b270be38

Merge /usr/local/portage/andis_overlay


 sys-cluster/hpx/Manifest                               | 1 +
 sys-cluster/hpx/{hpx-0.9.5.ebuild => hpx-0.9.6.ebuild} | 0
 2 files changed, 1 insertion(+)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     b6ca73c8c6022a33365a2f8a2a1b6ff807e747d8
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Mon Aug 12 09:35:34 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Aug 12 09:35:34 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b6ca73c8

merge


 dev-cpp/eigen/ChangeLog                            |   7 +
 dev-cpp/eigen/Manifest                             |   3 +-
 .../{eigen-3.1.3-r1.ebuild => eigen-3.1.4.ebuild}  |   0
 .../{eigen-3.1.3-r1.ebuild => eigen-3.2.0.ebuild}  |   0
 dev-util/nvidia-cuda-toolkit/ChangeLog             | 190 -------------
 dev-util/nvidia-cuda-toolkit/Manifest              |   2 -
 dev-util/nvidia-cuda-toolkit/files/cuda-config.in  |  28 --
 .../files/nvidia-cuda-toolkit-2.2-enum_fix.patch   |  42 ---
 .../files/nvidia-cuda-toolkit-3.0-enum_fix.patch   |  54 ----
 .../files/nvidia-cuda-toolkit-3.1-enum_fix.patch   |  24 --
 dev-util/nvidia-cuda-toolkit/metadata.xml          |  18 --
 sci-chemistry/gnome-chemistry-utils/ChangeLog      |   4 +
 .../gnome-chemistry-utils-0.14.2-r1.ebuild         |   1 +
 sci-chemistry/jmol/ChangeLog                       |  54 ----
 sci-chemistry/jmol/Manifest                        |   1 -
 .../jmol/files/12.0.45/jmol-manifest.patch         |  96 -------
 sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch | 313 ---------------------
 sci-chemistry/jmol/files/caffeine.xyz              |  26 --
 sci-chemistry/jmol/files/index.html                |  14 -
 .../jmol/files/selfSignedCertificate.store         | Bin 1516 -> 0 bytes
 sci-chemistry/jmol/jmol-12.0.45-r1.ebuild          | 122 --------
 sci-chemistry/jmol/metadata.xml                    |  13 -
 sci-libs/avogadro-libs/ChangeLog                   |   8 +
 sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild  |  19 +-
 .../files/avogadro-libs-0.6.0-underlinking.patch   |  14 +
 sci-libs/avogadro-libs/metadata.xml                |   3 +
 .../{libsufr-0.4.1.ebuild => libsufr-0.5.2.ebuild} |   0
 sci-libs/openblas/ChangeLog                        |   6 +
 sci-libs/openblas/Manifest                         |   2 +-
 ...openblas-0.2.7.ebuild => openblas-0.2.8.ebuild} |  25 +-
 sci-libs/openblas/openblas-9999.ebuild             |  22 +-
 sci-mathematics/bertini/ChangeLog                  |  17 --
 sci-mathematics/bertini/Manifest                   |   2 -
 sci-mathematics/bertini/bertini-1.3.1.ebuild       |  54 ----
 sci-mathematics/bertini/metadata.xml               |  29 --
 virtual/cblas/ChangeLog                            |   3 +
 virtual/cblas/cblas-2.0.ebuild                     |   2 +-
 virtual/cblas/metadata.xml                         |   4 +-
 x11-libs/agg/ChangeLog                             |  27 ++
 x11-libs/agg/Manifest                              |   1 +
 x11-libs/agg/agg-2.5-r3.ebuild                     |  69 +++++
 ...on-terminating-loop-conditions-when-len-1.patch |  81 ++++++
 ...ion-by-aborting-if-the-co-ordinates-are-t.patch |  40 +++
 ...ates-from-previous-vertex-if-last-command.patch |  30 ++
 ...izer_outline_aa-ignore-close_polygon-when.patch | 138 +++++++++
 .../files/2.5/0005-Remove-VC-6-workaround.patch    |  52 ++++
 ...-Implement-grain-merge-blending-mode-GIMP.patch |  85 ++++++
 ...mplement-grain-extract-blending-mode-GIMP.patch |  85 ++++++
 ...tiplication-and-division-operators-as-con.patch |  36 +++
 ...0009-Add-a-static-identity-transformation.patch |  37 +++
 .../2.5/0010-Add-renderer_scanline_aa_alpha.patch  | 193 +++++++++++++
 ...Avoid-division-by-zero-in-color-burn-mode.patch |  58 ++++
 ...12-Avoid-pixel-artifacts-when-compositing.patch |  26 ++
 ...conv-classes-to-allow-access-to-the-origi.patch |  93 ++++++
 ...tial-zero-division-resulting-in-nan-in-ag.patch |  30 ++
 ...t-value-in-the-gamma-table-is-always-zero.patch |  24 ++
 x11-libs/agg/files/2.5/agg-2.4-depends.patch       |  48 ++++
 x11-libs/agg/files/2.5/agg-2.5-autotools.patch     |  11 +
 x11-libs/agg/files/2.5/agg-2.5-pkgconfig.patch     |  10 +
 x11-libs/agg/files/2.5/agg-2.5-sdl-automagic.patch |  26 ++
 x11-libs/agg/files/2.5/agg-2.5-sdl-m4.patch        | 186 ++++++++++++
 x11-libs/agg/metadata.xml                          |  14 +
 62 files changed, 1487 insertions(+), 1135 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     5c6befde452048a11275e7a6b9fbc00fc25f9785
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Mon Aug 12 09:35:52 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Aug 12 09:35:52 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5c6befde

Merge https://github.com/gentoo-science/sci


 licenses/nmrpipe                                   | 23 ++++++++++++++++++++++
 sci-chemistry/chemBuild/ChangeLog                  |  5 +++++
 sci-chemistry/chemBuild/Manifest                   |  1 +
 ...emBuild-1.0.2.ebuild => chemBuild-1.0.3.ebuild} |  0
 sci-chemistry/nmrpipe/ChangeLog                    |  6 ++++++
 sci-chemistry/nmrpipe/Manifest                     |  6 +++---
 ....patch => nmrpipe-8.1.2013.218.23.09-lib.patch} |  0
 ...r3.ebuild => nmrpipe-8.1.2013.218.23.09.ebuild} |  2 +-
 sci-chemistry/specView/ChangeLog                   |  5 +++++
 sci-chemistry/specView/Manifest                    |  1 +
 ...specView-1.0.2.ebuild => specView-1.0.3.ebuild} |  0
 11 files changed, 45 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     d1ac10e85061b3d6c02796f956f4c371fe686b8b
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Mon Aug 12 09:33:48 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Aug 12 09:33:48 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d1ac10e8

Merge /usr/local/portage/andis_overlay


 dev-util/nvidia-cuda-toolkit/Manifest              |   4 +-
 ...11.ebuild => nvidia-cuda-toolkit-5.5.22.ebuild} |   8 +-
 x11-drivers/nvidia-drivers/Manifest                |   4 +
 .../nvidia-drivers/files/95-nvidia-settings        |   2 +
 x11-drivers/nvidia-drivers/files/nvidia-169.07     |  14 +
 x11-drivers/nvidia-drivers/files/nvidia-smi.init   |  25 ++
 x11-drivers/nvidia-drivers/files/nvidia-udev.sh    |  17 +
 x11-drivers/nvidia-drivers/files/nvidia.udev-rule  |   6 +
 .../nvidia-drivers/nvidia-drivers-325.15.ebuild    | 466 +++++++++++++++++++++
 9 files changed, 539 insertions(+), 7 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     fc58596b8a6d68defaf37a3924fd5d70b618e635
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Tue Aug  6 04:11:32 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Aug  6 04:11:32 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fc58596b

Merge pull request #99 from gentryx/master

Fixed HPX ebuild


 sys-cluster/hpx/files/hpx-0.9.5-install-path.patch | 39 ++++++++++++++++++++++
 sys-cluster/hpx/hpx-0.9.5.ebuild                   |  1 +
 2 files changed, 40 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     e0f5cb42b5415015a4a5f42e49db3974236bb712
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Sun Aug  4 11:03:43 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Sun Aug  4 11:03:43 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e0f5cb42

Merge https://github.com/gentoo-science/sci


 dev-lang/vtune/ChangeLog                           |   4 +
 dev-lang/vtune/Manifest                            |   7 +-
 ...9.295420.ebuild => vtune-13.1.10.298370.ebuild} |  26 +-
 dev-lang/vtune/vtune-13.1.4.270817.ebuild          |  38 --
 dev-python/numpydoc/ChangeLog                      |   5 +-
 dev-python/numpydoc/metadata.xml                   |   9 +-
 dev-python/numpydoc/numpydoc-0.4.ebuild            |   8 +-
 dev-python/pysolar/ChangeLog                       |   5 +-
 dev-python/pysolar/Manifest                        |   1 -
 dev-python/pysolar/metadata.xml                    |   7 +-
 dev-python/pysolar/pysolar-0.4.4.ebuild            |  52 --
 dev-python/pysolar/pysolar-0.5.ebuild              |  14 +-
 dev-python/theano/ChangeLog                        |  12 +
 dev-python/theano/Manifest                         |   1 +
 dev-python/theano/metadata.xml                     |  13 +
 dev-python/theano/theano-0.6.0_rc3.ebuild          |  33 ++
 eclass/intel-sdp.eclass                            |  78 +--
 profiles/package.mask                              |   5 -
 sci-chemistry/coot/ChangeLog                       |   3 +
 sci-chemistry/coot/files/9999-pc.patch             |   2 +-
 sci-chemistry/dl_poly/ChangeLog                    |  14 +
 sci-chemistry/dl_poly/Manifest                     |   2 +
 sci-chemistry/dl_poly/dl_poly-1.9.ebuild           |  35 ++
 sci-chemistry/dl_poly/dl_poly-4.05.ebuild          |  41 ++
 .../{votca-csgapps => dl_poly}/metadata.xml        |   0
 sci-chemistry/nwchem/ChangeLog                     |  10 +
 sci-chemistry/nwchem/Manifest                      |   2 +-
 .../files/nwchem-6.1.1-python_makefile.patch       |  10 +-
 .../nwchem/files/nwchem-6.3-html_doc.patch         |  82 ----
 .../nwchem/files/nwchem-6.3-r1-html_doc.patch      |  13 +
 .../{nwchem-6.3.ebuild => nwchem-6.3-r1.ebuild}    |  10 +-
 sci-chemistry/panav/ChangeLog                      |  10 +
 sci-chemistry/panav/Manifest                       |   1 +
 sci-chemistry/panav/metadata.xml                   |  30 ++
 sci-chemistry/panav/panav-0.20130730.ebuild        |  34 ++
 sci-chemistry/pymol/ChangeLog                      |   3 +
 sci-chemistry/pymol/pymol-9999.ebuild              |   1 +
 sci-chemistry/specView/ChangeLog                   |   3 +
 sci-chemistry/specView/specView-1.0.2.ebuild       |   2 +-
 sci-libs/avogadro-libs/ChangeLog                   |  10 +
 sci-libs/avogadro-libs/Manifest                    |   1 +
 sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild  |  41 ++
 .../coot => sci-libs/avogadro-libs}/metadata.xml   |   4 +-
 sci-libs/chemkit/ChangeLog                         |  10 +
 sci-libs/chemkit/Manifest                          |   1 +
 sci-libs/chemkit/chemkit-0.1.ebuild                |  55 +++
 .../coot => sci-libs/chemkit}/metadata.xml         |   4 +-
 sci-libs/dealii/Manifest                           |   2 +
 sci-libs/dealii/dealii-8.0.0.ebuild                |   1 +
 sci-libs/dealii/dealii-9999.ebuild                 | 128 +++++
 sci-libs/dealii/metadata.xml                       |  28 ++
 sci-libs/openblas/ChangeLog                        |   8 +
 sci-libs/openblas/Manifest                         |   3 +-
 sci-libs/openblas/files/openblas-aliasing.patch    |  11 -
 .../openblas/files/openblas-sharedlibs-0.2.patch   |  45 --
 sci-libs/openblas/metadata.xml                     |   1 -
 sci-libs/openblas/openblas-0.2.6.ebuild            |   1 -
 sci-libs/openblas/openblas-0.2.7.ebuild            | 127 +++++
 sci-libs/openblas/openblas-9999.ebuild             | 148 +++---
 sci-libs/p4est/Manifest                            |   1 +
 sci-libs/p4est/files/p4est-libtool-fix.patch       |  59 +++
 sci-libs/p4est/metadata.xml                        |  15 +
 sci-libs/p4est/p4est-0.3.4.1.ebuild                |  71 +++
 sci-libs/scikits_image/scikits_image-9999.ebuild   |  49 ++
 sci-physics/elk/ChangeLog                          |   7 +
 sci-physics/elk/Manifest                           |   1 +
 .../elk/{elk-1.4.22.ebuild => elk-2.1.25.ebuild}   |  34 +-
 sci-physics/elk/metadata.xml                       |  10 +
 sci-physics/espresso++/ChangeLog                   |   3 +
 sci-physics/espresso++/espresso++-9999.ebuild      |   3 +
 sci-visualization/paraview/ChangeLog               | 156 ------
 sci-visualization/paraview/Manifest                |   3 -
 .../paraview/files/paraview-3.10.1-gcc46.patch     |  20 -
 .../paraview/files/paraview-3.12.0-gcc46.patch     |  10 -
 .../paraview/files/paraview-3.12.0-protobuf.patch  |  53 ---
 .../files/paraview-3.14.1-ffmpeg-noinstall.patch   |  27 --
 .../paraview/files/paraview-3.14.1-gcc-4.7.patch   |  28 --
 .../paraview/files/paraview-3.14.1-mpi4py.patch    |  15 -
 .../files/paraview-3.14.1-python-exit.patch        |  46 --
 .../files/paraview-3.14.1-removesqlite.patch       | 526 ---------------------
 .../paraview/files/paraview-3.14.1-vtknetcd.patch  |  97 ----
 .../files/paraview-3.14.1-xdmf-linking.patch       |  16 -
 .../paraview/files/paraview-3.8.0-h5part.patch     |  12 -
 .../files/paraview-3.8.0-installpath.patch         |  33 --
 ...araview-3.8.0-pointsprite-example-install.patch |   9 -
 .../files/paraview-3.8.0-pointsprite-example.patch |  25 -
 .../paraview/files/paraview-3.8.0-xdmf-bc.patch    |  13 -
 .../files/paraview-3.8.0-xdmf-cstring.patch        |  10 -
 .../paraview/files/vtk-5.6.0-cg-path.patch         |  36 --
 .../paraview/files/vtk-5.6.0-libpng14.patch        |  22 -
 .../paraview/files/vtk-5.6.0-odbc.patch            |  12 -
 .../paraview/files/vtk-5.6.1-ffmpeg.patch          |  42 --
 .../paraview/files/vtk-5.6.1-libav-0.8.patch       |  66 ---
 .../paraview/files/vtk-boost1.49.patch             |  27 --
 sci-visualization/paraview/metadata.xml            |  22 -
 sci-visualization/paraview/paraview-3.10.1.ebuild  | 214 ---------
 sci-visualization/paraview/paraview-3.12.0.ebuild  | 214 ---------
 .../paraview/paraview-3.14.1-r4.ebuild             | 254 ----------
 sys-cluster/charm/ChangeLog                        |   6 +
 sys-cluster/charm/charm-6.5.1.ebuild               |   2 +
 .../charm/files/charm-6.5.1-cleanup-config.patch   |  58 +++
 sys-cluster/charmdebug/ChangeLog                   |   4 +
 sys-cluster/charmdebug/charmdebug-6.2.0.ebuild     |   2 +-
 virtual/cblas/ChangeLog                            |   6 +-
 virtual/cblas/cblas-2.0.ebuild                     |   6 +-
 105 files changed, 1178 insertions(+), 2422 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     27416f67200b63c098046f29a72f6a00e79cc3f5
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Fri Jul 26 06:12:55 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Fri Jul 26 06:12:55 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=27416f67

Merge pull request #94 from TheChymera/master

Scikits_image 9999 ebuild.


 sci-libs/scikits_image/scikits_image-9999.ebuild | 49 ++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     f42c85a9ade35247e3c9a917c7b318d88c6affa5
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Fri Jul 26 13:54:11 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Fri Jul 26 13:54:11 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f42c85a9

Merge pull request #96 from tamiko/package-dealii

An ebuild for deal.II [1]


 sci-libs/dealii/Manifest            |   2 +
 sci-libs/dealii/dealii-8.0.0.ebuild |   1 +
 sci-libs/dealii/dealii-9999.ebuild  | 128 ++++++++++++++++++++++++++++++++++++
 sci-libs/dealii/metadata.xml        |  28 ++++++++
 4 files changed, 159 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     53d7e1cd2f61e690ace9c02d651050803d67622d
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Thu Jul 25 22:51:19 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Thu Jul 25 22:51:19 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=53d7e1cd

Merge pull request #95 from tamiko/package-p4est

An ebuild for p4est [1]


 sci-libs/p4est/Manifest                      |  1 +
 sci-libs/p4est/files/p4est-libtool-fix.patch | 59 +++++++++++++++++++++++
 sci-libs/p4est/metadata.xml                  | 15 ++++++
 sci-libs/p4est/p4est-0.3.4.1.ebuild          | 71 ++++++++++++++++++++++++++++
 4 files changed, 146 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     0c47d0a2fe8ee1048667831fb4b7399545564fd6
Author:     root <root <AT> desktophost <DOT> fritz <DOT> box>
AuthorDate: Thu Jul 25 13:42:40 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Thu Jul 25 13:42:40 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0c47d0a2

Merge branch 'master' of git://github.com/gentoo-science/sci


 dev-lang/vtune/ChangeLog                           |   4 +
 dev-lang/vtune/Manifest                            |   7 +-
 ...9.295420.ebuild => vtune-13.1.10.298370.ebuild} |  26 ++--
 dev-lang/vtune/vtune-13.1.4.270817.ebuild          |  38 ------
 eclass/intel-sdp.eclass                            |  29 ++--
 sci-chemistry/pymol/ChangeLog                      |   3 +
 sci-chemistry/pymol/pymol-9999.ebuild              |   1 +
 sci-libs/avogadro-libs/ChangeLog                   |  10 ++
 sci-libs/avogadro-libs/Manifest                    |   1 +
 sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild  |  41 ++++++
 .../coot => sci-libs/avogadro-libs}/metadata.xml   |   4 +-
 sci-libs/chemkit/ChangeLog                         |  10 ++
 sci-libs/chemkit/Manifest                          |   1 +
 sci-libs/chemkit/chemkit-0.1.ebuild                |  55 ++++++++
 .../coot => sci-libs/chemkit}/metadata.xml         |   4 +-
 sci-libs/openblas/ChangeLog                        |   8 ++
 sci-libs/openblas/Manifest                         |   3 +-
 sci-libs/openblas/files/openblas-aliasing.patch    |  11 --
 .../openblas/files/openblas-sharedlibs-0.2.patch   |  45 -------
 sci-libs/openblas/metadata.xml                     |   1 -
 sci-libs/openblas/openblas-0.2.6.ebuild            |   1 -
 sci-libs/openblas/openblas-0.2.7.ebuild            | 127 ++++++++++++++++++
 sci-libs/openblas/openblas-9999.ebuild             | 148 ++++++++++-----------
 23 files changed, 369 insertions(+), 209 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     84e94e78a73a78f994e1b8fd32fc4857bf42006d
Author:     root <root <AT> desktophost <DOT> fritz <DOT> box>
AuthorDate: Wed Jul 24 03:42:05 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Wed Jul 24 03:42:05 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=84e94e78

Merge branch 'master' of git://github.com/gentoo-science/sci

[gentoo-commits] proj/sci:master commit in: /

[Alexey Shvetsov]

commit:     6ccaaed24dc8c695c6f215db81e0726c4e89b02e
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Fri Jul 19 18:26:26 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Jul 19 18:26:26 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6ccaaed2

Merge remote-tracking branch 'github/master'


 eclass/intel-sdp.eclass | 479 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 479 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Alexey Shvetsov]

commit:     138c86a63c0d75c6897c44bfeb25bca4dfb97934
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Fri Jul 19 18:24:23 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Jul 19 18:24:23 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=138c86a6

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-chemistry/gnome-chemistry-utils/ChangeLog            |  4 ++++
 .../gnome-chemistry-utils-0.14.2-r1.ebuild               |  5 -----
 sci-chemistry/specView/ChangeLog                         |  6 ++++++
 sci-chemistry/specView/specView-1.0.2.ebuild             | 16 ++++++++--------
 4 files changed, 18 insertions(+), 13 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     3450723c63ee6b9a34c3503c6a774017abb6a529
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 18 09:45:32 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jul 18 09:48:45 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3450723c

ignore dummy package

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index e43b0f9..14f4f8c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
 .DS_Store
+app-misc/dummy

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     9662285f61521020000d11ce4fcf1b4a7548eed5
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Wed Jul 17 09:14:58 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jul 17 09:14:58 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9662285f

Merge pull request #92 from jhcloos/fplll

sci-libs/fplll: Remove in favour of newer version in gx86.


 sci-libs/fplll/ChangeLog          |  7 -------
 sci-libs/fplll/Manifest           |  1 -
 sci-libs/fplll/fplll-2.1.6.ebuild | 40 ---------------------------------------
 sci-libs/fplll/metadata.xml       |  6 ------
 4 files changed, 54 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     15886679985e9cc4be651221a53d2f9b5c724df2
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Tue Jul 16 21:04:32 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Tue Jul 16 21:04:32 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=15886679

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 app-admin/eselect/ChangeLog                        |   3 +
 app-admin/eselect/Manifest                         |   2 +-
 ...1.3.6-r100.ebuild => eselect-1.3.7-r100.ebuild} |  10 +-
 dev-lang/vtune/ChangeLog                           |   5 +
 dev-lang/vtune/Manifest                            |   3 +
 ....4.270817.ebuild => vtune-13.1.9.295420.ebuild} |   4 +-
 sci-libs/coinhsl/ChangeLog                         |   6 +
 sci-libs/coinhsl/Manifest                          |   1 +
 ...2012.12.21.ebuild => coinhsl-2013.06.18.ebuild} |   4 -
 sci-libs/mkl/ChangeLog                             |   6 +
 sci-libs/mkl/Manifest                              |   3 +
 sci-libs/mkl/metadata.xml                          |   4 +-
 ...mkl-11.0.3.163.ebuild => mkl-11.0.5.192.ebuild} |   4 +-
 sci-libs/superlu_dist/ChangeLog                    |  10 +
 sci-libs/superlu_dist/Manifest                     |   1 +
 .../files/superlu_dist-3.3-duplicate-symbols.patch |  70 ++
 sci-libs/superlu_dist/metadata.xml                 |  23 +
 sci-libs/superlu_dist/superlu_dist-3.3.ebuild      |  82 ++
 sci-libs/superlu_mt/ChangeLog                      |  14 +
 sci-libs/superlu_mt/Manifest                       |   1 +
 .../files/superlu_mt-2.1-duplicate-symbols.patch   | 900 +++++++++++++++++++++
 .../files/superlu_mt-2.1-missing-includes.patch    |  44 +
 sci-libs/superlu_mt/metadata.xml                   |  23 +
 sci-libs/superlu_mt/superlu_mt-2.1.ebuild          | 105 +++
 sci-libs/vtk/ChangeLog                             | 484 +++++++++++
 sci-libs/vtk/Manifest                              |   3 +
 sci-libs/vtk/files/vtk-6.0.0-cg-path.patch         |  16 +
 sci-libs/vtk/metadata.xml                          |  18 +
 sci-libs/vtk/vtk-6.0.0.ebuild                      | 279 +++++++
 sci-physics/openmx/ChangeLog                       |  10 +
 sci-physics/openmx/Manifest                        |   2 +-
 .../{openmx-3.7.3.ebuild => openmx-3.7.4.ebuild}   |   8 +-
 32 files changed, 2128 insertions(+), 20 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a4d83b445f886298bfc1d25435bb0536f071ef98
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jul 16 20:13:04 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jul 16 20:13:04 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a4d83b44

Merge branch 'vtk'

* vtk:
  app-admin/eselect: Bump to latest eselect
  sci-libs/vtk: Version BUmp
  dev-lang/vtune: Version Bump
  sci-libs/mkl: Version Bump
  sci-libs/vtk: First working version


 app-admin/eselect/ChangeLog                        |   3 +
 app-admin/eselect/Manifest                         |   2 +-
 ...1.3.6-r100.ebuild => eselect-1.3.7-r100.ebuild} |  10 +-
 dev-lang/vtune/ChangeLog                           |   5 +
 dev-lang/vtune/Manifest                            |   3 +
 ....4.270817.ebuild => vtune-13.1.9.295420.ebuild} |   4 +-
 sci-libs/mkl/ChangeLog                             |   6 +
 sci-libs/mkl/Manifest                              |   3 +
 sci-libs/mkl/metadata.xml                          |   4 +-
 ...mkl-11.0.3.163.ebuild => mkl-11.0.5.192.ebuild} |   4 +-
 sci-libs/vtk/ChangeLog                             | 484 +++++++++++++++++++++
 sci-libs/vtk/Manifest                              |   3 +
 sci-libs/vtk/files/vtk-6.0.0-cg-path.patch         |  16 +
 sci-libs/vtk/metadata.xml                          |  18 +
 sci-libs/vtk/vtk-6.0.0.ebuild                      | 279 ++++++++++++
 15 files changed, 832 insertions(+), 12 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     009edaac5d6d10aabae9e2bc5e11fae02f11277f
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Jul 15 13:55:36 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Jul 15 13:55:36 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=009edaac

Merge github.com:gentoo-science/sci


 dev-lang/julia/ChangeLog                          |  3 +++
 dev-lang/julia/julia-9999.ebuild                  |  1 +
 sci-visualization/gnuplot/ChangeLog               |  3 +++
 sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild | 15 +--------------
 4 files changed, 8 insertions(+), 14 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     09bd07012c5b2863ffa7b6105128e4a4e373a12c
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Sun Jul 14 19:41:59 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Sun Jul 14 19:41:59 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=09bd0701

Merge pull request #91 from jhcloos/julia

dev-lang/julia: Use git-2.eclass’ submodule support.


 dev-lang/julia/ChangeLog         | 3 +++
 dev-lang/julia/julia-9999.ebuild | 1 +
 2 files changed, 4 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     2100d5094a194866d8cb3d9feea2c15f37df7c71
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Fri Jul 12 17:36:16 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Fri Jul 12 17:36:16 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2100d509

Merge github.com:gentoo-science/sci


 sys-cluster/htcondor/ChangeLog                     |  40 ++++
 sys-cluster/htcondor/Manifest                      |   1 +
 ...ser-s-condor_config-last-rather-than-firs.patch |  90 ++++++++
 sys-cluster/htcondor/files/condor.confd            |   2 +
 sys-cluster/htcondor/files/condor.initd            |  64 +++++
 .../htcondor/files/condor_config.generic.patch     | 257 +++++++++++++++++++++
 sys-cluster/htcondor/files/condor_config.local     |  11 +
 .../files/condor_shadow_dlopen-8.0.0.patch         |  11 +
 .../files/fix_sandbox_violations-8.0.0.patch       |  31 +++
 .../files/packaging_directories-8.0.0.patch        |  32 +++
 sys-cluster/htcondor/htcondor-8.0.0.ebuild         | 115 +++++++++
 sys-cluster/htcondor/metadata.xml                  |  29 +++
 12 files changed, 683 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     da85c2bb856e3c7461a2f49bf63104791ec98ff1
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Fri Jul 12 16:55:54 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Fri Jul 12 16:55:54 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=da85c2bb

Merge pull request #88 from chatcannon/HTCondor

Ebuild for htcondor (fixes #81)


 sys-cluster/htcondor/ChangeLog                     |  40 ++++
 sys-cluster/htcondor/Manifest                      |   1 +
 ...ser-s-condor_config-last-rather-than-firs.patch |  90 ++++++++
 sys-cluster/htcondor/files/condor.confd            |   2 +
 sys-cluster/htcondor/files/condor.initd            |  64 +++++
 .../htcondor/files/condor_config.generic.patch     | 257 +++++++++++++++++++++
 sys-cluster/htcondor/files/condor_config.local     |  11 +
 .../files/condor_shadow_dlopen-8.0.0.patch         |  11 +
 .../files/fix_sandbox_violations-8.0.0.patch       |  31 +++
 .../files/packaging_directories-8.0.0.patch        |  32 +++
 sys-cluster/htcondor/htcondor-8.0.0.ebuild         | 115 +++++++++
 sys-cluster/htcondor/metadata.xml                  |  29 +++
 12 files changed, 683 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     b58b842d105f935b1331be45c46c9c963128a68a
Author:     Chris Kerr <cjk34 <AT> cam <DOT> ac <DOT> uk>
AuthorDate: Tue Jul  2 20:17:13 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Jul  2 20:17:13 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b58b842d

Merge branch 'master' of https://github.com/gentoo-science/sci into HTCondor


 metadata/layout.conf                               |   6 +
 sci-chemistry/pymol-plugins-ezviz/ChangeLog        |   5 +
 ...uild => pymol-plugins-ezviz-1.0.2005-r1.ebuild} |   1 +
 sci-mathematics/ufc/ChangeLog                      |   5 +-
 sci-mathematics/ufc/ufc-1.4.2.ebuild               |   4 +-
 sys-cluster/charm/ChangeLog                        |  13 ++
 sys-cluster/charm/Manifest                         |   1 +
 sys-cluster/charm/charm-6.5.1.ebuild               | 181 +++++++++++++++++++++
 .../charm/files/charm-6.5.0-charmc-gentoo.patch    |  25 +++
 sys-cluster/charm/metadata.xml                     |  15 ++
 sys-cluster/empi/ChangeLog                         |  14 ++
 .../empi/{empi-0.8.ebuild => empi-0.9.ebuild}      |  14 +-
 .../empi/files/{ChangeLog-0.8 => ChangeLog-0.9}    |   0
 sys-cluster/empi/files/{empi-0.8 => empi-0.9}      |   4 +-
 .../files/{eselect.mpi-0.8 => eselect.mpi-0.9}     |   0
 sys-cluster/empi/metadata.xml                      |   8 +-
 sys-cluster/openmpi/ChangeLog                      |  11 +-
 ...le-malloc-override-inside-of-Gentoo-sandb.patch |  42 +++++
 ...penmpi-1.6.4.ebuild => openmpi-1.6.4-r1.ebuild} |   4 +-
 19 files changed, 338 insertions(+), 15 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     91e3f6c389cc9d273751b3eae3800e749876ec66
Author:     Chris Kerr <cjk34 <AT> cam <DOT> ac <DOT> uk>
AuthorDate: Mon Jul  1 12:10:38 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Jul  1 12:10:38 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=91e3f6c3

Merge branch 'master' of https://github.com/gentoo-science/sci into HTCondor


 app-doc/root-docs/ChangeLog                        |  6 +++
 app-doc/root-docs/Manifest                         |  2 +-
 ...ocs-5.34.08.ebuild => root-docs-5.34.09.ebuild} |  2 +-
 sci-libs/msms/ChangeLog                            | 10 +++-
 sci-libs/msms/Manifest                             |  3 +-
 sci-libs/msms/metadata.xml                         |  2 +-
 sci-libs/msms/msms-1.5.4-r1.ebuild                 | 54 ----------------------
 .../{msms-1.5.6_rc2.ebuild => msms-1.5.6.ebuild}   | 19 ++++----
 sci-physics/root/ChangeLog                         |  6 +++
 sci-physics/root/Manifest                          |  5 +-
 sci-physics/root/metadata.xml                      |  1 +
 .../{root-5.34.08.ebuild => root-5.34.09.ebuild}   | 15 +++---
 sys-cluster/hpl/ChangeLog                          |  8 ++++
 sys-cluster/hpl/Manifest                           |  3 +-
 .../hpl/{hpl-2.0-r1.ebuild => hpl-2.1.ebuild}      | 33 +++++++------
 15 files changed, 76 insertions(+), 93 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     9cd4154b07caff4b4e16de035492be7f6b244c26
Author:     Chris Kerr <cjk34 <AT> cam <DOT> ac <DOT> uk>
AuthorDate: Sat Jun 29 21:06:21 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Sat Jun 29 21:06:21 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9cd4154b

Merge branch 'master' of https://github.com/gentoo-science/sci into HTCondor


 sci-chemistry/ambertools/ChangeLog                 |   4 +-
 sci-chemistry/ambertools/ambertools-12.ebuild      |   2 +-
 sci-libs/bigdft-abi/ChangeLog                      |   8 +
 ...abi-1.0.4.ebuild => bigdft-abi-1.0.4-r1.ebuild} |   3 +
 .../files/bigdft-abi-1.0.4-CUDA_gethostname.patch  |  22 +++
 sci-physics/lammps/ChangeLog                       |  65 --------
 sci-physics/lammps/Manifest                        |   3 -
 sci-physics/lammps/lammps-20130512.ebuild          |  72 ---------
 sci-physics/lammps/lammps-20130514.ebuild          |  75 ---------
 sci-physics/lammps/lammps-20130526.ebuild          | 105 ------------
 sci-physics/lammps/metadata.xml                    |  30 ----
 sys-cluster/charm/ChangeLog                        |  43 -----
 sys-cluster/charm/Manifest                         |   1 -
 sys-cluster/charm/charm-6.5.0.ebuild               | 178 ---------------------
 .../charm/files/charm-6.5.0-charmc-gentoo.patch    |  25 ---
 sys-cluster/charm/metadata.xml                     |  12 --
 16 files changed, 37 insertions(+), 611 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     abcaad94ebb25bca3f799fce8be60a9174fbff43
Author:     Chris Kerr <cjk34 <AT> cam <DOT> ac <DOT> uk>
AuthorDate: Wed Jun 26 23:12:56 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Jun 26 23:12:56 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=abcaad94

Merge branch 'master' of https://github.com/gentoo-science/sci into HTCondor


 app-admin/eselect/ChangeLog                        |   6 +
 app-admin/eselect/Manifest                         |   2 +-
 ...1.3.4-r100.ebuild => eselect-1.3.5-r100.ebuild} |   0
 app-text/dgs/metadata.xml                          |   3 -
 app-text/jabref/ChangeLog                          |  10 +
 ...jabref-2.10b.ebuild => jabref-2.10_beta.ebuild} |   8 +-
 app-vim/freefem++-syntax/metadata.xml              |   7 +-
 app-vim/vim-gromacs/metadata.xml                   |   5 +-
 dev-db/cppdb/metadata.xml                          |  19 +-
 dev-java/fits/ChangeLog                            |   9 +-
 dev-java/fits/Manifest                             |   2 +-
 .../{fits-1.08.1.ebuild => fits-1.11.0.ebuild}     |   6 +-
 dev-java/jhealpix/ChangeLog                        |   9 +
 dev-java/jhealpix/Manifest                         |   1 +
 dev-java/jhealpix/jhealpix-3.11.ebuild             |  43 +++
 dev-java/jhealpix/metadata.xml                     |  11 +
 dev-lang/ispc/ChangeLog                            |   3 +
 dev-lang/ispc/ispc-9999.ebuild                     |   3 +-
 dev-libs/simclist/metadata.xml                     |  17 +-
 dev-ml/mlgmpidl/metadata.xml                       |  23 +-
 dev-ml/ocamlgraph/metadata.xml                     |  47 ++-
 dev-ml/zarith/metadata.xml                         |  20 +-
 dev-perl/opal-client/metadata.xml                  |   3 -
 dev-python/healpy/ChangeLog                        |   9 +
 dev-python/healpy/Manifest                         |   1 +
 dev-python/healpy/healpy-1.6.2.ebuild              |  34 ++
 dev-python/healpy/metadata.xml                     |  10 +
 dev-python/opal-client/ChangeLog                   |   8 +-
 dev-python/opal-client/Manifest                    |   2 +-
 dev-python/opal-client/metadata.xml                |   5 +-
 dev-python/opal-client/opal-client-2.2-r1.ebuild   |  55 ----
 dev-python/opal-client/opal-client-2.4.1.ebuild    |  42 +++
 dev-tcltk/img_rotate/metadata.xml                  |   5 +-
 dev-tcltk/togl/metadata.xml                        |   3 -
 licenses/GRL                                       |  15 +
 licenses/Tablet                                    |   8 +-
 media-gfx/librecad/ChangeLog                       |   6 +
 media-gfx/librecad/Manifest                        |   4 +-
 media-gfx/librecad/files/1.0.0_rc2-gcc4.6.patch    |  38 ---
 .../files/librecad-1.0.0_rc2-version.patch         |  11 -
 media-gfx/librecad/librecad-1.0.2.ebuild           |  45 ---
 media-gfx/librecad/librecad-2.0.0_beta5.ebuild     |  48 ---
 media-gfx/librecad/librecad-2.0.0_rc1.ebuild       |  27 +-
 media-gfx/librecad/metadata.xml                    |  23 +-
 media-libs/OpenMOIV/metadata.xml                   |   3 -
 media-libs/libgfx/metadata.xml                     |   3 -
 profiles/package.mask                              |  11 +
 sci-astronomy/astrometry/ChangeLog                 |   7 +
 sci-astronomy/astrometry/astrometry-0.43.ebuild    |  40 ++-
 .../astrometry/files/0.43-system-libs.patch        | 226 +++++++------
 sci-astronomy/astrometry/metadata.xml              |   7 +-
 sci-astronomy/chealpix/ChangeLog                   |   9 +
 sci-astronomy/chealpix/Manifest                    |   1 +
 sci-astronomy/chealpix/chealpix-3.11.ebuild        |  30 ++
 sci-astronomy/chealpix/metadata.xml                |  11 +
 sci-astronomy/healpix_cxx/ChangeLog                |   9 +
 sci-astronomy/healpix_cxx/Manifest                 |   1 +
 sci-astronomy/healpix_cxx/healpix_cxx-3.11.ebuild  |  54 ++++
 sci-astronomy/healpix_cxx/metadata.xml             |  12 +
 sci-astronomy/healpix_idl/ChangeLog                |   9 +
 sci-astronomy/healpix_idl/Manifest                 |   1 +
 sci-astronomy/healpix_idl/healpix_idl-3.11.ebuild  |  37 +++
 sci-astronomy/healpix_idl/metadata.xml             |  12 +
 sci-biology/YASRA/ChangeLog                        |   4 +
 sci-biology/YASRA/Manifest                         |   2 +-
 .../YASRA/{YASRA-2.1.ebuild => YASRA-2.32.ebuild}  |  15 +-
 sci-biology/caftools/ChangeLog                     |   8 +
 sci-biology/caftools/Manifest                      |   4 +-
 sci-biology/caftools/caftools-2.0.2.ebuild         |  36 +--
 sci-biology/caftools/caftools-2.0.ebuild           |  38 ---
 sci-biology/caftools/metadata.xml                  |  16 +-
 sci-biology/clover/ChangeLog                       |   6 +-
 sci-biology/clover/Manifest                        |   4 +-
 sci-biology/clover/clover-2010.02.19.ebuild        |  43 ---
 sci-biology/clover/clover-2011.10.24.ebuild        |  40 +++
 sci-biology/clover/metadata.xml                    |   6 +-
 sci-biology/cutadapt/ChangeLog                     |   6 +-
 sci-biology/cutadapt/Manifest                      |   2 +-
 .../{cutadapt-1.0.ebuild => cutadapt-1.2.1.ebuild} |  13 +-
 sci-biology/cutadapt/metadata.xml                  |  10 +-
 sci-biology/erpin/ChangeLog                        |   5 +-
 sci-biology/erpin/Manifest                         |   4 +-
 sci-biology/erpin/erpin-5.5b.ebuild                |  23 +-
 sci-biology/erpin/metadata.xml                     |  10 +-
 sci-biology/gap2caf/ChangeLog                      |   8 +
 sci-biology/gap2caf/Manifest                       |   4 +-
 sci-biology/gap2caf/gap2caf-2.1.0.ebuild           |  45 +--
 sci-biology/gap2caf/metadata.xml                   |  10 +-
 sci-biology/perlprimer/metadata.xml                |   3 -
 sci-biology/quicktree/ChangeLog                    |   6 +-
 sci-biology/quicktree/Manifest                     |   2 +-
 sci-biology/quicktree/metadata.xml                 |  10 +-
 sci-biology/quicktree/quicktree-1.1-r1.ebuild      |  17 +-
 sci-biology/sequin/ChangeLog                       |   9 +-
 sci-biology/sequin/Manifest                        |   4 +-
 sci-biology/sequin/sequin-20090722.ebuild          |  32 --
 sci-biology/sequin/sequin-20121202.ebuild          |  44 +++
 sci-biology/smalt-bin/ChangeLog                    |   8 +-
 sci-biology/smalt-bin/Manifest                     |   2 +-
 sci-biology/smalt-bin/metadata.xml                 |  10 +-
 sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild       |  25 --
 sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild       |  31 ++
 sci-biology/ssaha2-bin/ChangeLog                   |   6 +-
 sci-biology/ssaha2-bin/Manifest                    |   9 +-
 sci-biology/ssaha2-bin/metadata.xml                |  10 +-
 ...a2-bin-2.5.3.ebuild => ssaha2-bin-2.5.5.ebuild} |  26 +-
 sci-biology/tablet-bin/ChangeLog                   |   9 +-
 sci-biology/tablet-bin/Manifest                    |   3 +-
 sci-biology/tablet-bin/metadata.xml                |  10 +-
 .../tablet-bin/tablet-bin-1.11.11.01.ebuild        |  73 -----
 ...1.05.03.ebuild => tablet-bin-1.13.05.17.ebuild} |  57 +++-
 sci-biology/twinscan/ChangeLog                     |   6 +-
 sci-biology/twinscan/Manifest                      |   2 +-
 sci-biology/twinscan/metadata.xml                  |  10 +-
 sci-biology/twinscan/twinscan-4.1.2.ebuild         |  30 +-
 sci-chemistry/GromacsWrapper/metadata.xml          |   2 +-
 sci-chemistry/ball/metadata.xml                    |   2 +-
 sci-chemistry/burrow-owl/metadata.xml              |   5 +-
 sci-chemistry/camshift/metadata.xml                |   5 +-
 sci-chemistry/chemBuild/ChangeLog                  |   6 +-
 sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild     |  33 +-
 sci-chemistry/chemBuild/files/chemBuild            |   2 +-
 sci-chemistry/chemBuild/metadata.xml               |   2 +-
 sci-chemistry/chimera-bin/metadata.xml             |   2 +-
 sci-chemistry/chooch/metadata.xml                  |   5 +-
 sci-chemistry/cnsface/ChangeLog                    |   6 +-
 sci-chemistry/cnsface/Manifest                     |   2 +-
 sci-chemistry/cnsface/cnsface-0.0.12.ebuild        |  19 +-
 sci-chemistry/cnsface/metadata.xml                 |   3 -
 sci-chemistry/concoord/metadata.xml                |   2 +-
 sci-chemistry/coot/metadata.xml                    |   3 -
 sci-chemistry/cs-rosetta/metadata.xml              |   2 +-
 sci-chemistry/curvefit/metadata.xml                |   2 +-
 sci-chemistry/direx/metadata.xml                   |   3 -
 sci-chemistry/dssp2pdb/metadata.xml                |   3 -
 sci-chemistry/freeon/ChangeLog                     |   9 +
 ...ch => freeon-2012.05.03-no_internal_hdf5.patch} |  32 +-
 .../files/freeon-9999-no_internal_hdf5.patch       |  25 ++
 .../files/freeon-9999-no_internal_libs.patch       |  47 ---
 sci-chemistry/freeon/freeon-2012.05.03.ebuild      |   7 +-
 sci-chemistry/freeon/freeon-9999.ebuild            |   7 +-
 sci-chemistry/gnome-chemistry-utils/ChangeLog      |   4 +
 .../gnome-chemistry-utils-0.14.2.ebuild            |   2 +-
 sci-chemistry/gnome-chemistry-utils/metadata.xml   |   8 +-
 sci-chemistry/hydronmr/metadata.xml                |   2 +-
 sci-chemistry/jana2000/metadata.xml                |   3 -
 sci-chemistry/jligand/metadata.xml                 |   5 +-
 sci-chemistry/ligplot+/metadata.xml                |   2 +-
 sci-chemistry/mage/metadata.xml                    |   3 -
 sci-chemistry/mddnmr/metadata.xml                  |   5 +-
 sci-chemistry/mics/ChangeLog                       |  10 +
 sci-chemistry/mics/Manifest                        |   1 +
 .../{mgltools-autodocktools => mics}/metadata.xml  |   0
 sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild |  51 +++
 sci-chemistry/modelfree/metadata.xml               |   2 +-
 sci-chemistry/modeller/ChangeLog                   |  16 +-
 sci-chemistry/modeller/Manifest                    |   2 +-
 sci-chemistry/modeller/metadata.xml                |   2 +-
 ...modeller-9.8.ebuild => modeller-9.12-r2.ebuild} |  97 +++---
 sci-chemistry/mtz2hkl/metadata.xml                 |   3 -
 sci-chemistry/mtz2sca/metadata.xml                 |   3 -
 sci-chemistry/nMOLDYN/ChangeLog                    |  12 +
 sci-chemistry/nMOLDYN/Manifest                     |   1 +
 sci-chemistry/{trajng => nMOLDYN}/metadata.xml     |   0
 sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild        |  24 ++
 sci-chemistry/nmrpipe/ChangeLog                    |   8 +
 .../nmrpipe/nmrpipe-7.9.2013.021.23.09-r2.ebuild   |   4 +-
 sci-chemistry/nmrview/ChangeLog                    |   6 +-
 sci-chemistry/nmrview/metadata.xml                 |  10 +-
 sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild      |  15 +-
 sci-chemistry/nwchem/ChangeLog                     |   4 +
 sci-chemistry/nwchem/Manifest                      |   1 -
 sci-chemistry/nwchem/nwchem-6.1.1.ebuild           | 126 --------
 sci-chemistry/nwchem/nwchem-6.3.ebuild             |  10 +-
 sci-chemistry/phaser/ChangeLog                     |  21 --
 sci-chemistry/phaser/Manifest                      |   1 -
 sci-chemistry/phaser/files/2.1.4-sadf.patch        |  64 ----
 .../phaser/files/phaser-2.1.4-chmod.patch          |  11 -
 sci-chemistry/phaser/metadata.xml                  |  30 --
 sci-chemistry/phaser/phaser-2.1.4-r1.ebuild        | 138 --------
 sci-chemistry/phaser/phaser-2.1.4.ebuild           | 114 -------
 sci-chemistry/phenix-bin/metadata.xml              |   2 +-
 sci-chemistry/polygon/ChangeLog                    |   7 +-
 sci-chemistry/polygon/Manifest                     |   4 +-
 .../polygon/files/{0710-db.patch => 0612-db.patch} |  20 +-
 sci-chemistry/polygon/metadata.xml                 |   3 -
 .../{polygon-0710.ebuild => polygon-0612.ebuild}   |  18 +-
 sci-chemistry/pymol-apbs-plugin/ChangeLog          |   9 +-
 sci-chemistry/pymol-apbs-plugin/metadata.xml       |   3 -
 .../pymol-apbs-plugin-9999.ebuild                  |  53 ++-
 sci-chemistry/pymol-plugins-ezviz/ChangeLog        |   4 +
 sci-chemistry/pymol-plugins-ezviz/Manifest         |   2 +-
 .../pymol-plugins-ezviz-1.0.2005.ebuild            |  56 ++--
 sci-chemistry/pymol-plugins-psico/ChangeLog        |   3 +
 .../pymol-plugins-psico-9999.ebuild                |  15 +-
 sci-chemistry/pymol/ChangeLog                      |   3 +
 sci-chemistry/pymol/pymol-9999.ebuild              |   2 +-
 sci-chemistry/pyquante/ChangeLog                   |   6 +-
 sci-chemistry/pyquante/Manifest                    |   2 +-
 sci-chemistry/pyquante/metadata.xml                |   2 +-
 sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild    |  11 +-
 sci-chemistry/rosetta-tools/metadata.xml           |   3 -
 sci-chemistry/rosetta/metadata.xml                 |  23 +-
 sci-chemistry/shiftx/ChangeLog                     |  12 +-
 sci-chemistry/shiftx/Manifest                      |   2 +-
 sci-chemistry/shiftx/files/1.1-Makefile.patch      |  15 +-
 sci-chemistry/shiftx/files/1.1-bfr-overflow.patch  |  16 +
 sci-chemistry/shiftx/metadata.xml                  |   5 +-
 sci-chemistry/shiftx/shiftx-1.1.ebuild             |  25 +-
 sci-chemistry/shiftx2/ChangeLog                    |   8 +
 sci-chemistry/shiftx2/Manifest                     |   1 +
 sci-chemistry/shiftx2/files/gentoo-fixes.patch     | 194 +++++++++++
 sci-chemistry/shiftx2/metadata.xml                 |  39 +++
 .../shiftx2/shiftx2-1.07_p20120106.ebuild          | 112 +++++++
 sci-chemistry/simpson/metadata.xml                 |   2 +-
 sci-chemistry/smmp/ChangeLog                       |   5 +-
 sci-chemistry/smmp/Manifest                        |   2 +-
 sci-chemistry/smmp/metadata.xml                    |   3 -
 sci-chemistry/smmp/smmp-3.0.5.ebuild               |  41 +--
 sci-chemistry/specView/ChangeLog                   |   3 +
 sci-chemistry/specView/metadata.xml                |   2 +-
 sci-chemistry/specView/specView-1.0.2.ebuild       |  52 +--
 sci-chemistry/ssp/ChangeLog                        |   5 +-
 sci-chemistry/ssp/metadata.xml                     |   8 +-
 sci-chemistry/ssp/ssp-09.11.ebuild                 |   6 +-
 sci-chemistry/talosn/ChangeLog                     |  16 +
 sci-chemistry/talosn/Manifest                      |   1 +
 .../metadata.xml                                   |   0
 .../talosn/talosn-4.01.2013.148.15.55-r2.ebuild    |  68 ++++
 sci-chemistry/ucsf-tools/ChangeLog                 |   3 +
 sci-chemistry/ucsf-tools/metadata.xml              |   2 +-
 sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild    |  13 +-
 sci-chemistry/unio/metadata.xml                    |   5 +-
 sci-libs/Cgraph/metadata.xml                       |   5 +-
 sci-libs/bigdft-abi/ChangeLog                      |  29 ++
 sci-libs/bigdft-abi/Manifest                       |   1 +
 sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild        | 165 ++++++++++
 .../files/bigdft-abi-1.0.4-tests.tar.bz2           | Bin 0 -> 402968 bytes
 sci-libs/bigdft/metadata.xml                       |  19 +-
 sci-libs/cnsface-scripts/metadata.xml              |   3 -
 sci-libs/coinor-clp/ChangeLog                      |   6 +
 sci-libs/coinor-clp/Manifest                       |   2 +-
 ...-clp-1.15.0.ebuild => coinor-clp-1.15.1.ebuild} |   4 +-
 .../files/coinor-clp-1.15.1-mpi-header.patch       |  12 +
 sci-libs/driftwood/metadata.xml                    |   5 +-
 sci-libs/etsf_io/ChangeLog                         |  13 +-
 ..._io-1.0.3-r1.ebuild => etsf_io-1.0.3-r2.ebuild} |   6 +-
 sci-libs/etsf_io/metadata.xml                      |   5 +-
 sci-libs/fox/ChangeLog                             |  14 +-
 ...patch => 4.1.2-r2-install-customizations.patch} |   4 +-
 .../{fox-4.1.2-r1.ebuild => fox-4.1.2-r2.ebuild}   |  10 +-
 sci-libs/fox/metadata.xml                          |  19 +-
 sci-libs/libxc/ChangeLog                           |  11 +-
 sci-libs/libxc/Manifest                            |   2 +-
 .../{libxc-1.2.0.ebuild => libxc-1.2.0-r1.ebuild}  |  26 +-
 .../{libxc-1.1.0-r1.ebuild => libxc-2.0.1.ebuild}  |  27 +-
 sci-libs/libxc/libxc-9999.ebuild                   |  27 +-
 sci-libs/libxc/metadata.xml                        |   5 +-
 sci-libs/lwpr/ChangeLog                            |   9 +-
 sci-libs/lwpr/Manifest                             |   2 +-
 sci-libs/lwpr/files/lwpr-1.2.2-setup.py.patch      |  12 -
 sci-libs/lwpr/lwpr-1.2.2.ebuild                    |  83 -----
 sci-libs/lwpr/lwpr-1.2.5.ebuild                    |  51 +++
 sci-libs/lwpr/metadata.xml                         |  10 +-
 sci-libs/med/metadata.xml                          |   5 +-
 sci-libs/msms/metadata.xml                         |   5 +-
 sci-libs/mumps/ChangeLog                           |   5 +-
 sci-libs/mumps/mumps-4.10.0-r2.ebuild              |   5 +-
 sci-libs/pagmo/metadata.xml                        |  13 +-
 sci-libs/starparse/metadata.xml                    |   5 +-
 sci-libs/trilinos/ChangeLog                        |   7 +-
 sci-libs/trilinos/metadata.xml                     |  16 +
 sci-libs/trilinos/trilinos-11.2.3.ebuild           | 186 +++++++++++
 sci-libs/wannier90/ChangeLog                       |   7 +
 sci-libs/wannier90/metadata.xml                    |   5 +-
 ...annier90-1.2.ebuild => wannier90-1.2-r1.ebuild} |   0
 sci-mathematics/alt-ergo/metadata.xml              |  23 +-
 sci-mathematics/apron/metadata.xml                 |  31 +-
 sci-mathematics/flocq/metadata.xml                 |  17 +-
 sci-mathematics/frama-c/metadata.xml               |  28 +-
 sci-mathematics/gap-guava/metadata.xml             |   5 +-
 sci-mathematics/gappa/metadata.xml                 |  22 +-
 sci-mathematics/gappalib-coq/metadata.xml          |  15 +-
 sci-mathematics/giac/metadata.xml                  |  24 +-
 sci-mathematics/ltl2ba/metadata.xml                |   3 -
 sci-mathematics/pff/metadata.xml                   |  17 +-
 sci-mathematics/why/metadata.xml                   |  32 +-
 sci-physics/LoopTools/metadata.xml                 |   2 +-
 sci-physics/abinit/ChangeLog                       |  16 +
 sci-physics/abinit/Manifest                        |   3 +-
 sci-physics/abinit/abinit-7.0.5.ebuild             | 356 ---------------------
 .../{abinit-7.0.4.ebuild => abinit-7.2.2.ebuild}   |  75 +++--
 sci-physics/abinit/files/6.0.3-fftw.patch          |  14 -
 .../abinit/files/6.12.1-libabinit_options.patch    |  57 ----
 sci-physics/atompaw/ChangeLog                      |   7 +
 ...aw-3.0.1.9.ebuild => atompaw-3.0.1.9-r1.ebuild} |  11 +-
 sci-physics/atompaw/metadata.xml                   |  11 +-
 sci-physics/atompaw2abinit/metadata.xml            |   5 +-
 sci-physics/bigdft/ChangeLog                       | 160 +++++++++
 sci-physics/bigdft/Manifest                        |   1 +
 sci-physics/bigdft/bigdft-1.7_pre24.ebuild         | 142 ++++++++
 .../files/bigdft-1.7-dev.24-nolib_mods.patch       |  25 ++
 sci-physics/elk/ChangeLog                          |   4 +
 sci-physics/elk/elk-1.4.22.ebuild                  |   2 +-
 sci-physics/herwig++/metadata.xml                  |   2 +-
 sci-physics/lammps/ChangeLog                       |  10 +
 sci-physics/lammps/lammps-20130526.ebuild          |  56 +++-
 sci-physics/openmx/ChangeLog                       |   7 +
 sci-physics/openmx/Manifest                        |   2 +
 sci-physics/openmx/files/3.7-fortran_objects.patch |  15 +
 sci-physics/openmx/metadata.xml                    |   2 +-
 sci-physics/openmx/openmx-3.7.3.ebuild             | 161 ++++++++++
 sci-physics/thepeg/metadata.xml                    |   2 +-
 sci-visualization/gnuplot/ChangeLog                |   3 +
 sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild  |   2 +-
 sci-visualization/v_sim/metadata.xml               |   3 -
 sys-cluster/charm/ChangeLog                        |  17 +
 sys-cluster/charm/charm-6.5.0.ebuild               |  61 ++--
 sys-cluster/charm/metadata.xml                     |   2 +
 sys-cluster/charmdebug/ChangeLog                   |  12 +
 sys-cluster/charmdebug/Manifest                    |   1 +
 sys-cluster/charmdebug/charmdebug-6.2.0.ebuild     |  31 ++
 .../charmdebug}/metadata.xml                       |   0
 sys-cluster/modules/ChangeLog                      |  10 +
 sys-cluster/modules/files/createmodule.py          | 186 +++++++++++
 sys-cluster/modules/files/createmodule.sh          | 166 ++++++++++
 .../modules/files/modules-3.2.10-avail.patch       |  12 +
 .../modules/files/modules-3.2.10-bindir.patch      |  11 +
 .../modules/files/modules-3.2.10-clear.patch       |  11 +
 ...orline.patch => modules-3.2.10-errorline.patch} |   1 -
 .../modules/files/modules-3.2.10-versioning.patch  |  10 +
 .../modules/files/modules-3.2.9c-errorline.patch   |   1 -
 sys-cluster/modules/files/modules.sh.in            |   7 +
 sys-cluster/modules/metadata.xml                   |  20 +-
 sys-cluster/modules/modules-3.2.10-r1.ebuild       |  61 ++++
 sys-cluster/modules/modules-3.2.10.ebuild          |   6 +-
 sys-cluster/projections/ChangeLog                  |  13 +
 sys-cluster/projections/Manifest                   |   1 +
 .../projections}/metadata.xml                      |   0
 sys-cluster/projections/projections-6.2.1.ebuild   |  30 ++
 www-apps/py-swish-e/metadata.xml                   |   5 +-
 x11-libs/tr/metadata.xml                           |   3 -
 342 files changed, 4070 insertions(+), 2756 deletions(-)

[gentoo-commits] proj/sci:vtk commit in: /

[Justin Lecher]

commit:     ffbc434cc003a1d815b290608ba3e4e5e371d20c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 11 18:31:57 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jul 11 18:31:57 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ffbc434c

Merge branch 'jlec'

* jlec:
  sci-chemistry/coot: Update pc patch


 sci-chemistry/coot/ChangeLog           |   3 +
 sci-chemistry/coot/files/9999-pc.patch | 561 +++++++++++++++++----------------
 2 files changed, 284 insertions(+), 280 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ffbc434cc003a1d815b290608ba3e4e5e371d20c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 11 18:31:57 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jul 11 18:31:57 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ffbc434c

Merge branch 'jlec'

* jlec:
  sci-chemistry/coot: Update pc patch


 sci-chemistry/coot/ChangeLog           |   3 +
 sci-chemistry/coot/files/9999-pc.patch | 561 +++++++++++++++++----------------
 2 files changed, 284 insertions(+), 280 deletions(-)

[gentoo-commits] proj/sci:vtk commit in: /

[Justin Lecher]

commit:     68f704a5acc2a2db8dd7eae6fd683576af41e28c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jul  8 12:07:04 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jul  8 12:07:04 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=68f704a5

Merge branch 'jlec'

* jlec:
  Completly removed the directory check in the java source (we have everything under control in gentoo). Removed the .py extension from the -system.patch to make that part working again (it's installed without extensions to /usr/bin/!).
  Work in progress Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
  sci-chemistry/rosetta: Fix: Ebuild calls die in a subshell
  sci-chemistry/rosetta: Add patches from www.csrosetta.org
  update to new lange patches Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>


 sci-chemistry/shiftx2/ChangeLog                    |   8 +-
 ...xes.patch => shiftx2-1.07_p20120106-java.patch} |  45 +++-
 .../files/shiftx2-1.07_p20120106-system.patch      | 231 +++++++++++++++++++++
 .../shiftx2/shiftx2-1.07_p20120106.ebuild          |  30 ++-
 4 files changed, 299 insertions(+), 15 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     68f704a5acc2a2db8dd7eae6fd683576af41e28c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jul  8 12:07:04 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jul  8 12:07:04 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=68f704a5

Merge branch 'jlec'

* jlec:
  Completly removed the directory check in the java source (we have everything under control in gentoo). Removed the .py extension from the -system.patch to make that part working again (it's installed without extensions to /usr/bin/!).
  Work in progress Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
  sci-chemistry/rosetta: Fix: Ebuild calls die in a subshell
  sci-chemistry/rosetta: Add patches from www.csrosetta.org
  update to new lange patches Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>


 sci-chemistry/shiftx2/ChangeLog                    |   8 +-
 ...xes.patch => shiftx2-1.07_p20120106-java.patch} |  45 +++-
 .../files/shiftx2-1.07_p20120106-system.patch      | 231 +++++++++++++++++++++
 .../shiftx2/shiftx2-1.07_p20120106.ebuild          |  30 ++-
 4 files changed, 299 insertions(+), 15 deletions(-)

[gentoo-commits] proj/sci:vtk commit in: /

[Justin Lecher]

commit:     9fb3b01bb87df3f976ef259d9aa4a09012ac4988
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 26 14:54:49 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 26 14:54:49 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9fb3b01b

Merge branch 'master-broken'

* master-broken:
  sci-chemistry/ucsf-tools: Fix compilation with latest gcc
  sci-chemistry/modeller: Fix lib position, #474696
  sci-chemistry/pymol: Update repo uri
  sci-chemistry/pymol: Update repo uri

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     9fb3b01bb87df3f976ef259d9aa4a09012ac4988
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 26 14:54:49 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 26 14:54:49 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9fb3b01b

Merge branch 'master-broken'

* master-broken:
  sci-chemistry/ucsf-tools: Fix compilation with latest gcc
  sci-chemistry/modeller: Fix lib position, #474696
  sci-chemistry/pymol: Update repo uri
  sci-chemistry/pymol: Update repo uri

[gentoo-commits] proj/sci:vtk commit in: /

[Justin Lecher]

commit:     e2667d72a9cda457057fc4531574c2634dc92387
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 21 10:44:31 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 21 10:44:31 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e2667d72

Merge branch 'master' into jlec

* master: (29 commits)
  sci-chemistry/shiftx: Block shiftx2 at runtime
  sci-chemistry/shiftx: Fix patch and add patch for buffer overflow fix
  The announced, but forgotten, change in sci-libs/fox-4.1.2-r2 actually done.
  The announced, but forgotten, change in sci-libs/etsf_io-1.0.3-r2 actually done.
  sci-physics/abinit/files/6.12.3-gui-makefiles.tbz put back, its deletion was a mistake.
  sci-libs/trilinos: Version bump and rewrite
  sci-libs/coinor-clp: Version bump and patch for mpi
  For sci-libs/bigdft-abi and sci-physics/bigdft, filter LDFLAGS for cuda use not to break nvcc.
  To sci-libs/bigdft-abi and sci-physics/bigdft added dev-util/gdbus-codegen among dependencies.
  Spaces in the testing snippet of fortran code in sci-libs/bigdft-abi-1.0.4.ebuild protected from reformatting.
  fixed qt4 build
  fixing manifests
  big fixes of metadata and package sub-herd re-distribution
  sci-physics/openmx upgraded to 3.7.3 with some openMP and MPI C/F90 juggling, previous sci-physics/openmx-3.6 preserved for the time being.
  sci-chemistry/talosn: drop upstream path in favour of our
  sci-chemistry/modeller: Fix broken symlink, #473680
  sci-chemistry/mics: New package
  sci-chemistry/talosn: New package
  Abinit & friends upgraded to sci-physics/abinit-7.2.2. BigDFT moved from sci-libs to sci-physics, sci-physics/abinit uses sci-libs/bigdft-abi instead. Usage of LIBDIR/finclude abandoned in favour of /usr/include, as mostly used upstream. Old files cleaned up.
  Version of bigdft bumped to 1.7_pre24, moved from sci-libs to sci-physics. No longer used as a library by sci-physics/abinit. Usage of LIBDIR/finclude abandoned in favour of /usr/include, as used upstream.
  ...


 app-text/dgs/metadata.xml                          |   3 -
 app-text/jabref/ChangeLog                          |  10 +
 ...jabref-2.10b.ebuild => jabref-2.10_beta.ebuild} |   8 +-
 app-vim/freefem++-syntax/metadata.xml              |   7 +-
 app-vim/vim-gromacs/metadata.xml                   |   5 +-
 dev-db/cppdb/metadata.xml                          |  19 +-
 dev-libs/simclist/metadata.xml                     |  17 +-
 dev-ml/mlgmpidl/metadata.xml                       |  23 +-
 dev-ml/ocamlgraph/metadata.xml                     |  47 ++-
 dev-ml/zarith/metadata.xml                         |  20 +-
 dev-perl/opal-client/metadata.xml                  |   3 -
 dev-python/opal-client/metadata.xml                |   5 +-
 dev-tcltk/img_rotate/metadata.xml                  |   5 +-
 dev-tcltk/togl/metadata.xml                        |   3 -
 media-gfx/librecad/ChangeLog                       |   6 +
 media-gfx/librecad/Manifest                        |   4 +-
 media-gfx/librecad/files/1.0.0_rc2-gcc4.6.patch    |  38 ---
 .../files/librecad-1.0.0_rc2-version.patch         |  11 -
 media-gfx/librecad/librecad-1.0.2.ebuild           |  45 ---
 media-gfx/librecad/librecad-2.0.0_beta5.ebuild     |  48 ---
 media-gfx/librecad/librecad-2.0.0_rc1.ebuild       |  27 +-
 media-gfx/librecad/metadata.xml                    |  23 +-
 media-libs/OpenMOIV/metadata.xml                   |   3 -
 media-libs/libgfx/metadata.xml                     |   3 -
 profiles/package.mask                              |   6 +
 sci-biology/perlprimer/metadata.xml                |   3 -
 sci-chemistry/GromacsWrapper/metadata.xml          |   2 +-
 sci-chemistry/ball/metadata.xml                    |   2 +-
 sci-chemistry/burrow-owl/metadata.xml              |   5 +-
 sci-chemistry/camshift/metadata.xml                |   5 +-
 sci-chemistry/chemBuild/metadata.xml               |   2 +-
 sci-chemistry/chimera-bin/metadata.xml             |   2 +-
 sci-chemistry/chooch/metadata.xml                  |   5 +-
 sci-chemistry/cnsface/metadata.xml                 |   5 +-
 sci-chemistry/concoord/metadata.xml                |   2 +-
 sci-chemistry/coot/metadata.xml                    |   3 -
 sci-chemistry/cs-rosetta/metadata.xml              |   2 +-
 sci-chemistry/curvefit/metadata.xml                |   2 +-
 sci-chemistry/direx/metadata.xml                   |   3 -
 sci-chemistry/dssp2pdb/metadata.xml                |   3 -
 sci-chemistry/freeon/ChangeLog                     |   9 +
 ...ch => freeon-2012.05.03-no_internal_hdf5.patch} |  32 +-
 .../files/freeon-9999-no_internal_hdf5.patch       |  25 ++
 .../files/freeon-9999-no_internal_libs.patch       |  47 ---
 sci-chemistry/freeon/freeon-2012.05.03.ebuild      |   7 +-
 sci-chemistry/freeon/freeon-9999.ebuild            |   7 +-
 sci-chemistry/hydronmr/metadata.xml                |   2 +-
 sci-chemistry/jana2000/metadata.xml                |   3 -
 sci-chemistry/jligand/metadata.xml                 |   5 +-
 sci-chemistry/ligplot+/metadata.xml                |   2 +-
 sci-chemistry/mage/metadata.xml                    |   3 -
 sci-chemistry/mddnmr/metadata.xml                  |   5 +-
 sci-chemistry/mics/ChangeLog                       |  10 +
 sci-chemistry/mics/Manifest                        |   1 +
 .../{mgltools-autodocktools => mics}/metadata.xml  |   0
 sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild |  51 +++
 sci-chemistry/modelfree/metadata.xml               |   2 +-
 sci-chemistry/modeller/ChangeLog                   |   6 +
 ...odeller-9.12.ebuild => modeller-9.12-r1.ebuild} |   2 +-
 sci-chemistry/mtz2hkl/metadata.xml                 |   3 -
 sci-chemistry/mtz2sca/metadata.xml                 |   3 -
 sci-chemistry/nMOLDYN/ChangeLog                    |  12 +
 sci-chemistry/nMOLDYN/Manifest                     |   1 +
 sci-chemistry/{trajng => nMOLDYN}/metadata.xml     |   0
 sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild        |  24 ++
 sci-chemistry/phenix-bin/metadata.xml              |   2 +-
 sci-chemistry/polygon/metadata.xml                 |   5 +-
 sci-chemistry/pymol-apbs-plugin/metadata.xml       |   5 +-
 sci-chemistry/rosetta-tools/metadata.xml           |   3 -
 sci-chemistry/rosetta/metadata.xml                 |  23 +-
 sci-chemistry/shiftx/ChangeLog                     |   7 +
 sci-chemistry/shiftx/files/1.1-Makefile.patch      |  15 +-
 sci-chemistry/shiftx/files/1.1-bfr-overflow.patch  |  16 +
 sci-chemistry/shiftx/metadata.xml                  |   3 -
 sci-chemistry/shiftx/shiftx-1.1.ebuild             |   7 +-
 sci-chemistry/shiftx2/metadata.xml                 |   2 +-
 sci-chemistry/simpson/metadata.xml                 |   2 +-
 sci-chemistry/smmp/metadata.xml                    |   5 +-
 sci-chemistry/specView/metadata.xml                |   2 +-
 sci-chemistry/ssp/metadata.xml                     |   2 +-
 sci-chemistry/talosn/ChangeLog                     |  16 +
 sci-chemistry/talosn/Manifest                      |   1 +
 .../metadata.xml                                   |   0
 .../talosn/talosn-4.01.2013.148.15.55-r2.ebuild    |  68 ++++
 sci-chemistry/ucsf-tools/metadata.xml              |   2 +-
 sci-chemistry/unio/metadata.xml                    |   5 +-
 sci-libs/Cgraph/metadata.xml                       |   5 +-
 sci-libs/bigdft-abi/ChangeLog                      |  29 ++
 sci-libs/bigdft-abi/Manifest                       |   1 +
 .../bigdft-abi-1.0.4.ebuild}                       |  78 +++--
 .../files/bigdft-abi-1.0.4-tests.tar.bz2           | Bin 0 -> 402968 bytes
 sci-libs/bigdft/metadata.xml                       |  19 +-
 sci-libs/cnsface-scripts/metadata.xml              |   3 -
 sci-libs/coinor-clp/ChangeLog                      |   6 +
 sci-libs/coinor-clp/Manifest                       |   2 +-
 ...-clp-1.15.0.ebuild => coinor-clp-1.15.1.ebuild} |   4 +-
 .../files/coinor-clp-1.15.1-mpi-header.patch       |  12 +
 sci-libs/driftwood/metadata.xml                    |   5 +-
 sci-libs/etsf_io/ChangeLog                         |  13 +-
 ..._io-1.0.3-r1.ebuild => etsf_io-1.0.3-r2.ebuild} |   6 +-
 sci-libs/etsf_io/metadata.xml                      |   5 +-
 sci-libs/fox/ChangeLog                             |  14 +-
 ...patch => 4.1.2-r2-install-customizations.patch} |   4 +-
 .../{fox-4.1.2-r1.ebuild => fox-4.1.2-r2.ebuild}   |  10 +-
 sci-libs/fox/metadata.xml                          |  19 +-
 sci-libs/libxc/ChangeLog                           |  11 +-
 sci-libs/libxc/Manifest                            |   2 +-
 ...libxc-1.1.0-r1.ebuild => libxc-1.2.0-r1.ebuild} |  26 +-
 .../{libxc-1.2.0.ebuild => libxc-2.0.1.ebuild}     |  27 +-
 sci-libs/libxc/libxc-9999.ebuild                   |  27 +-
 sci-libs/libxc/metadata.xml                        |   5 +-
 sci-libs/med/metadata.xml                          |   5 +-
 sci-libs/msms/metadata.xml                         |   5 +-
 sci-libs/mumps/ChangeLog                           |   5 +-
 sci-libs/mumps/mumps-4.10.0-r2.ebuild              |   5 +-
 sci-libs/pagmo/metadata.xml                        |  13 +-
 sci-libs/starparse/metadata.xml                    |   5 +-
 sci-libs/trilinos/ChangeLog                        |   7 +-
 sci-libs/trilinos/metadata.xml                     |  16 +
 sci-libs/trilinos/trilinos-11.2.3.ebuild           | 186 +++++++++++
 sci-libs/wannier90/ChangeLog                       |   7 +
 sci-libs/wannier90/metadata.xml                    |   5 +-
 ...annier90-1.2.ebuild => wannier90-1.2-r1.ebuild} |   0
 sci-mathematics/alt-ergo/metadata.xml              |  23 +-
 sci-mathematics/apron/metadata.xml                 |  31 +-
 sci-mathematics/flocq/metadata.xml                 |  17 +-
 sci-mathematics/frama-c/metadata.xml               |  28 +-
 sci-mathematics/gap-guava/metadata.xml             |   5 +-
 sci-mathematics/gappa/metadata.xml                 |  22 +-
 sci-mathematics/gappalib-coq/metadata.xml          |  15 +-
 sci-mathematics/giac/metadata.xml                  |  24 +-
 sci-mathematics/ltl2ba/metadata.xml                |   3 -
 sci-mathematics/pff/metadata.xml                   |  17 +-
 sci-mathematics/why/metadata.xml                   |  32 +-
 sci-physics/LoopTools/metadata.xml                 |   2 +-
 sci-physics/abinit/ChangeLog                       |  16 +
 sci-physics/abinit/Manifest                        |   3 +-
 sci-physics/abinit/abinit-7.0.5.ebuild             | 356 ---------------------
 .../{abinit-7.0.4.ebuild => abinit-7.2.2.ebuild}   |  75 +++--
 sci-physics/abinit/files/6.0.3-fftw.patch          |  14 -
 .../abinit/files/6.12.1-libabinit_options.patch    |  57 ----
 sci-physics/atompaw/ChangeLog                      |   7 +
 ...aw-3.0.1.9.ebuild => atompaw-3.0.1.9-r1.ebuild} |  11 +-
 sci-physics/atompaw/metadata.xml                   |  11 +-
 sci-physics/atompaw2abinit/metadata.xml            |   5 +-
 {sci-libs => sci-physics}/bigdft/ChangeLog         |  23 +-
 sci-physics/bigdft/Manifest                        |   1 +
 .../bigdft/bigdft-1.7_pre24.ebuild                 |  37 +--
 .../files/bigdft-1.7-dev.24-nolib_mods.patch       |  14 +-
 sci-physics/elk/ChangeLog                          |   4 +
 sci-physics/elk/elk-1.4.22.ebuild                  |   2 +-
 sci-physics/herwig++/metadata.xml                  |   2 +-
 sci-physics/openmx/ChangeLog                       |   7 +
 sci-physics/openmx/Manifest                        |   2 +
 sci-physics/openmx/files/3.7-fortran_objects.patch |  15 +
 sci-physics/openmx/metadata.xml                    |   2 +-
 sci-physics/openmx/openmx-3.7.3.ebuild             | 161 ++++++++++
 sci-physics/thepeg/metadata.xml                    |   2 +-
 sci-visualization/gnuplot/ChangeLog                |   3 +
 sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild  |   2 +-
 sci-visualization/v_sim/metadata.xml               |   3 -
 www-apps/py-swish-e/metadata.xml                   |   5 +-
 x11-libs/tr/metadata.xml                           |   3 -
 163 files changed, 1278 insertions(+), 1264 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     e2667d72a9cda457057fc4531574c2634dc92387
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 21 10:44:31 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 21 10:44:31 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e2667d72

Merge branch 'master' into jlec

* master: (29 commits)
  sci-chemistry/shiftx: Block shiftx2 at runtime
  sci-chemistry/shiftx: Fix patch and add patch for buffer overflow fix
  The announced, but forgotten, change in sci-libs/fox-4.1.2-r2 actually done.
  The announced, but forgotten, change in sci-libs/etsf_io-1.0.3-r2 actually done.
  sci-physics/abinit/files/6.12.3-gui-makefiles.tbz put back, its deletion was a mistake.
  sci-libs/trilinos: Version bump and rewrite
  sci-libs/coinor-clp: Version bump and patch for mpi
  For sci-libs/bigdft-abi and sci-physics/bigdft, filter LDFLAGS for cuda use not to break nvcc.
  To sci-libs/bigdft-abi and sci-physics/bigdft added dev-util/gdbus-codegen among dependencies.
  Spaces in the testing snippet of fortran code in sci-libs/bigdft-abi-1.0.4.ebuild protected from reformatting.
  fixed qt4 build
  fixing manifests
  big fixes of metadata and package sub-herd re-distribution
  sci-physics/openmx upgraded to 3.7.3 with some openMP and MPI C/F90 juggling, previous sci-physics/openmx-3.6 preserved for the time being.
  sci-chemistry/talosn: drop upstream path in favour of our
  sci-chemistry/modeller: Fix broken symlink, #473680
  sci-chemistry/mics: New package
  sci-chemistry/talosn: New package
  Abinit & friends upgraded to sci-physics/abinit-7.2.2. BigDFT moved from sci-libs to sci-physics, sci-physics/abinit uses sci-libs/bigdft-abi instead. Usage of LIBDIR/finclude abandoned in favour of /usr/include, as mostly used upstream. Old files cleaned up.
  Version of bigdft bumped to 1.7_pre24, moved from sci-libs to sci-physics. No longer used as a library by sci-physics/abinit. Usage of LIBDIR/finclude abandoned in favour of /usr/include, as used upstream.
  ...


 app-text/dgs/metadata.xml                          |   3 -
 app-text/jabref/ChangeLog                          |  10 +
 ...jabref-2.10b.ebuild => jabref-2.10_beta.ebuild} |   8 +-
 app-vim/freefem++-syntax/metadata.xml              |   7 +-
 app-vim/vim-gromacs/metadata.xml                   |   5 +-
 dev-db/cppdb/metadata.xml                          |  19 +-
 dev-libs/simclist/metadata.xml                     |  17 +-
 dev-ml/mlgmpidl/metadata.xml                       |  23 +-
 dev-ml/ocamlgraph/metadata.xml                     |  47 ++-
 dev-ml/zarith/metadata.xml                         |  20 +-
 dev-perl/opal-client/metadata.xml                  |   3 -
 dev-python/opal-client/metadata.xml                |   5 +-
 dev-tcltk/img_rotate/metadata.xml                  |   5 +-
 dev-tcltk/togl/metadata.xml                        |   3 -
 media-gfx/librecad/ChangeLog                       |   6 +
 media-gfx/librecad/Manifest                        |   4 +-
 media-gfx/librecad/files/1.0.0_rc2-gcc4.6.patch    |  38 ---
 .../files/librecad-1.0.0_rc2-version.patch         |  11 -
 media-gfx/librecad/librecad-1.0.2.ebuild           |  45 ---
 media-gfx/librecad/librecad-2.0.0_beta5.ebuild     |  48 ---
 media-gfx/librecad/librecad-2.0.0_rc1.ebuild       |  27 +-
 media-gfx/librecad/metadata.xml                    |  23 +-
 media-libs/OpenMOIV/metadata.xml                   |   3 -
 media-libs/libgfx/metadata.xml                     |   3 -
 profiles/package.mask                              |   6 +
 sci-biology/perlprimer/metadata.xml                |   3 -
 sci-chemistry/GromacsWrapper/metadata.xml          |   2 +-
 sci-chemistry/ball/metadata.xml                    |   2 +-
 sci-chemistry/burrow-owl/metadata.xml              |   5 +-
 sci-chemistry/camshift/metadata.xml                |   5 +-
 sci-chemistry/chemBuild/metadata.xml               |   2 +-
 sci-chemistry/chimera-bin/metadata.xml             |   2 +-
 sci-chemistry/chooch/metadata.xml                  |   5 +-
 sci-chemistry/cnsface/metadata.xml                 |   5 +-
 sci-chemistry/concoord/metadata.xml                |   2 +-
 sci-chemistry/coot/metadata.xml                    |   3 -
 sci-chemistry/cs-rosetta/metadata.xml              |   2 +-
 sci-chemistry/curvefit/metadata.xml                |   2 +-
 sci-chemistry/direx/metadata.xml                   |   3 -
 sci-chemistry/dssp2pdb/metadata.xml                |   3 -
 sci-chemistry/freeon/ChangeLog                     |   9 +
 ...ch => freeon-2012.05.03-no_internal_hdf5.patch} |  32 +-
 .../files/freeon-9999-no_internal_hdf5.patch       |  25 ++
 .../files/freeon-9999-no_internal_libs.patch       |  47 ---
 sci-chemistry/freeon/freeon-2012.05.03.ebuild      |   7 +-
 sci-chemistry/freeon/freeon-9999.ebuild            |   7 +-
 sci-chemistry/hydronmr/metadata.xml                |   2 +-
 sci-chemistry/jana2000/metadata.xml                |   3 -
 sci-chemistry/jligand/metadata.xml                 |   5 +-
 sci-chemistry/ligplot+/metadata.xml                |   2 +-
 sci-chemistry/mage/metadata.xml                    |   3 -
 sci-chemistry/mddnmr/metadata.xml                  |   5 +-
 sci-chemistry/mics/ChangeLog                       |  10 +
 sci-chemistry/mics/Manifest                        |   1 +
 .../{mgltools-autodocktools => mics}/metadata.xml  |   0
 sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild |  51 +++
 sci-chemistry/modelfree/metadata.xml               |   2 +-
 sci-chemistry/modeller/ChangeLog                   |   6 +
 ...odeller-9.12.ebuild => modeller-9.12-r1.ebuild} |   2 +-
 sci-chemistry/mtz2hkl/metadata.xml                 |   3 -
 sci-chemistry/mtz2sca/metadata.xml                 |   3 -
 sci-chemistry/nMOLDYN/ChangeLog                    |  12 +
 sci-chemistry/nMOLDYN/Manifest                     |   1 +
 sci-chemistry/{trajng => nMOLDYN}/metadata.xml     |   0
 sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild        |  24 ++
 sci-chemistry/phenix-bin/metadata.xml              |   2 +-
 sci-chemistry/polygon/metadata.xml                 |   5 +-
 sci-chemistry/pymol-apbs-plugin/metadata.xml       |   5 +-
 sci-chemistry/rosetta-tools/metadata.xml           |   3 -
 sci-chemistry/rosetta/metadata.xml                 |  23 +-
 sci-chemistry/shiftx/ChangeLog                     |   7 +
 sci-chemistry/shiftx/files/1.1-Makefile.patch      |  15 +-
 sci-chemistry/shiftx/files/1.1-bfr-overflow.patch  |  16 +
 sci-chemistry/shiftx/metadata.xml                  |   3 -
 sci-chemistry/shiftx/shiftx-1.1.ebuild             |   7 +-
 sci-chemistry/shiftx2/metadata.xml                 |   2 +-
 sci-chemistry/simpson/metadata.xml                 |   2 +-
 sci-chemistry/smmp/metadata.xml                    |   5 +-
 sci-chemistry/specView/metadata.xml                |   2 +-
 sci-chemistry/ssp/metadata.xml                     |   2 +-
 sci-chemistry/talosn/ChangeLog                     |  16 +
 sci-chemistry/talosn/Manifest                      |   1 +
 .../metadata.xml                                   |   0
 .../talosn/talosn-4.01.2013.148.15.55-r2.ebuild    |  68 ++++
 sci-chemistry/ucsf-tools/metadata.xml              |   2 +-
 sci-chemistry/unio/metadata.xml                    |   5 +-
 sci-libs/Cgraph/metadata.xml                       |   5 +-
 sci-libs/bigdft-abi/ChangeLog                      |  29 ++
 sci-libs/bigdft-abi/Manifest                       |   1 +
 .../bigdft-abi-1.0.4.ebuild}                       |  78 +++--
 .../files/bigdft-abi-1.0.4-tests.tar.bz2           | Bin 0 -> 402968 bytes
 sci-libs/bigdft/metadata.xml                       |  19 +-
 sci-libs/cnsface-scripts/metadata.xml              |   3 -
 sci-libs/coinor-clp/ChangeLog                      |   6 +
 sci-libs/coinor-clp/Manifest                       |   2 +-
 ...-clp-1.15.0.ebuild => coinor-clp-1.15.1.ebuild} |   4 +-
 .../files/coinor-clp-1.15.1-mpi-header.patch       |  12 +
 sci-libs/driftwood/metadata.xml                    |   5 +-
 sci-libs/etsf_io/ChangeLog                         |  13 +-
 ..._io-1.0.3-r1.ebuild => etsf_io-1.0.3-r2.ebuild} |   6 +-
 sci-libs/etsf_io/metadata.xml                      |   5 +-
 sci-libs/fox/ChangeLog                             |  14 +-
 ...patch => 4.1.2-r2-install-customizations.patch} |   4 +-
 .../{fox-4.1.2-r1.ebuild => fox-4.1.2-r2.ebuild}   |  10 +-
 sci-libs/fox/metadata.xml                          |  19 +-
 sci-libs/libxc/ChangeLog                           |  11 +-
 sci-libs/libxc/Manifest                            |   2 +-
 ...libxc-1.1.0-r1.ebuild => libxc-1.2.0-r1.ebuild} |  26 +-
 .../{libxc-1.2.0.ebuild => libxc-2.0.1.ebuild}     |  27 +-
 sci-libs/libxc/libxc-9999.ebuild                   |  27 +-
 sci-libs/libxc/metadata.xml                        |   5 +-
 sci-libs/med/metadata.xml                          |   5 +-
 sci-libs/msms/metadata.xml                         |   5 +-
 sci-libs/mumps/ChangeLog                           |   5 +-
 sci-libs/mumps/mumps-4.10.0-r2.ebuild              |   5 +-
 sci-libs/pagmo/metadata.xml                        |  13 +-
 sci-libs/starparse/metadata.xml                    |   5 +-
 sci-libs/trilinos/ChangeLog                        |   7 +-
 sci-libs/trilinos/metadata.xml                     |  16 +
 sci-libs/trilinos/trilinos-11.2.3.ebuild           | 186 +++++++++++
 sci-libs/wannier90/ChangeLog                       |   7 +
 sci-libs/wannier90/metadata.xml                    |   5 +-
 ...annier90-1.2.ebuild => wannier90-1.2-r1.ebuild} |   0
 sci-mathematics/alt-ergo/metadata.xml              |  23 +-
 sci-mathematics/apron/metadata.xml                 |  31 +-
 sci-mathematics/flocq/metadata.xml                 |  17 +-
 sci-mathematics/frama-c/metadata.xml               |  28 +-
 sci-mathematics/gap-guava/metadata.xml             |   5 +-
 sci-mathematics/gappa/metadata.xml                 |  22 +-
 sci-mathematics/gappalib-coq/metadata.xml          |  15 +-
 sci-mathematics/giac/metadata.xml                  |  24 +-
 sci-mathematics/ltl2ba/metadata.xml                |   3 -
 sci-mathematics/pff/metadata.xml                   |  17 +-
 sci-mathematics/why/metadata.xml                   |  32 +-
 sci-physics/LoopTools/metadata.xml                 |   2 +-
 sci-physics/abinit/ChangeLog                       |  16 +
 sci-physics/abinit/Manifest                        |   3 +-
 sci-physics/abinit/abinit-7.0.5.ebuild             | 356 ---------------------
 .../{abinit-7.0.4.ebuild => abinit-7.2.2.ebuild}   |  75 +++--
 sci-physics/abinit/files/6.0.3-fftw.patch          |  14 -
 .../abinit/files/6.12.1-libabinit_options.patch    |  57 ----
 sci-physics/atompaw/ChangeLog                      |   7 +
 ...aw-3.0.1.9.ebuild => atompaw-3.0.1.9-r1.ebuild} |  11 +-
 sci-physics/atompaw/metadata.xml                   |  11 +-
 sci-physics/atompaw2abinit/metadata.xml            |   5 +-
 {sci-libs => sci-physics}/bigdft/ChangeLog         |  23 +-
 sci-physics/bigdft/Manifest                        |   1 +
 .../bigdft/bigdft-1.7_pre24.ebuild                 |  37 +--
 .../files/bigdft-1.7-dev.24-nolib_mods.patch       |  14 +-
 sci-physics/elk/ChangeLog                          |   4 +
 sci-physics/elk/elk-1.4.22.ebuild                  |   2 +-
 sci-physics/herwig++/metadata.xml                  |   2 +-
 sci-physics/openmx/ChangeLog                       |   7 +
 sci-physics/openmx/Manifest                        |   2 +
 sci-physics/openmx/files/3.7-fortran_objects.patch |  15 +
 sci-physics/openmx/metadata.xml                    |   2 +-
 sci-physics/openmx/openmx-3.7.3.ebuild             | 161 ++++++++++
 sci-physics/thepeg/metadata.xml                    |   2 +-
 sci-visualization/gnuplot/ChangeLog                |   3 +
 sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild  |   2 +-
 sci-visualization/v_sim/metadata.xml               |   3 -
 www-apps/py-swish-e/metadata.xml                   |   5 +-
 x11-libs/tr/metadata.xml                           |   3 -
 163 files changed, 1278 insertions(+), 1264 deletions(-)

[gentoo-commits] proj/sci:vtk commit in: /

[Justin Lecher]

commit:     f43609fc308239ce00e3b66ad121c43dbf15b1ed
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 17 05:55:15 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 17 05:55:15 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f43609fc

Merge branch 'master' into jlec

* master: (120 commits)
  add missing masks for live ebuilds
  dev-python/healpy: Initial import
  dev-java/jhealpix: Initial import
  sci-astronomy/healpix_idl: Initial import
  sci-astronomy/healpix_cxx: Initial import
  sci-astronomy/chealpix: Initial import
  sci-biology/twinscan: Bump to EAPI=5 and fix license
  sci-biology/ssaha2-bin: Version Bump; restrict license; add QA_PREBUILT for binaries
  sci-biology/smalt-bin: Version Bump; restrict license; add QA_PREBUILT for binaries
  sci-biology/sequin: Version BUmp; restrcit license; add QA_PREBUILT for binaries; install html files into sys path
  sci-biology/quicktree: Bump to EAPI=5 and fix license
  sci-biology/gap2caf: Bump to EAPI=5 and fix license; make it build with eautoreconf
  sci-biology/erpin: Bump to EAPI=5 and respect FLAGS / AR
  sci-biology/clover: Version BUmp; fixed license; respect LDFLAGS
  sci-chemistry/shiftx2: Respect FLAGS
  Enhanced the sci-chemistry/shiftx ebuild. Still needs some love for the emake part (portage complains about LDFLAGS not respected), but should work.
  sci-chemistry/pymol-plugins-psico: Bump to EAPI=5 and distutils-r1.eclass
  sci-chemistry/smmp: Bump to EAPI=5 and python-r1.eclass
  sci-chemistry/specView: Bump to EAPI=5 and python-single-r1.eclass
  sci-chemistry/pyquante: Bump to EAPI=5 and distutils-r1.eclass
  ...


 app-benchmarks/btl/ChangeLog                       |   5 +-
 app-benchmarks/btl/btl-9999.ebuild                 |  11 +-
 app-benchmarks/btl/metadata.xml                    |  14 +-
 app-benchmarks/numbench/ChangeLog                  |   8 +-
 app-benchmarks/numbench/metadata.xml               |  14 +-
 app-benchmarks/numbench/numbench-0.2.ebuild        |  28 +-
 app-benchmarks/numbench/numbench-9999.ebuild       |  28 +-
 app-doc/blacs-docs/Manifest                        |   2 +-
 app-doc/blas-docs/Manifest                         |   6 +-
 app-doc/lapack-docs/Manifest                       |   4 +-
 app-doc/root-docs/Manifest                         |   5 -
 app-text/dgs/Manifest                              |   2 +-
 app-vim/freefem++-syntax/Manifest                  |   2 +-
 dev-cpp/growler-arch/Manifest                      |   4 +-
 dev-cpp/growler-core/Manifest                      |   2 +-
 dev-cpp/growler-math/Manifest                      |   2 +-
 dev-cpp/growler-thread/Manifest                    |   2 +-
 dev-java/jeuclid-core/Manifest                     |   2 +-
 dev-java/jgraphx/ChangeLog                         |   7 +-
 dev-java/jgraphx/Manifest                          |   3 -
 dev-java/jgraphx/jgraphx-1.2.0.7.ebuild            |  44 --
 dev-java/jgraphx/jgraphx-1.3.0.2.ebuild            |  44 --
 dev-java/jgraphx/jgraphx-1.4.1.0.ebuild            |  18 +-
 dev-java/jgraphx/jgraphx-1.4.1.2.ebuild            |  44 --
 dev-java/jgraphx/jgraphx-1.8.0.6.ebuild            |  20 +-
 dev-java/jgraphx/metadata.xml                      |   4 +-
 dev-java/jhealpix/ChangeLog                        |   9 +
 dev-java/jhealpix/Manifest                         |   1 +
 dev-java/jhealpix/jhealpix-3.11.ebuild             |  43 ++
 dev-java/jhealpix/metadata.xml                     |  11 +
 dev-java/joda-convert/Manifest                     |   2 +-
 dev-java/vecmath/Manifest                          |   4 +-
 dev-lang/ispc/ChangeLog                            |   3 +
 dev-lang/ispc/ispc-9999.ebuild                     |   2 +-
 dev-lang/julia/ChangeLog                           |   5 +-
 dev-lang/julia/julia-9999.ebuild                   |   2 +-
 dev-lang/julia/metadata.xml                        |   4 +-
 dev-lang/path64/ChangeLog                          |   6 +-
 dev-lang/path64/metadata.xml                       |  22 +-
 dev-lang/path64/path64-9999.ebuild                 |   4 +-
 dev-libs/asmjit/ChangeLog                          |   8 +-
 dev-libs/asmjit/Manifest                           |   2 +-
 ...-1.0_beta_p2.ebuild => asmjit-1.0_beta4.ebuild} |   6 +-
 dev-libs/asmjit/metadata.xml                       |  12 +-
 dev-libs/libunzip/Manifest                         |   2 +-
 dev-libs/simclist/Manifest                         |   5 +-
 dev-ml/mlgmpidl/Manifest                           |   6 +-
 dev-ml/ocamlgraph/Manifest                         |   4 -
 dev-perl/BTLib/Manifest                            |   2 +-
 dev-perl/Lab-Instrument/Manifest                   |   2 +-
 dev-perl/Lab-Tools/Manifest                        |   2 +-
 dev-perl/Lab-VISA/Manifest                         |   2 +-
 dev-perl/go-db-perl/Manifest                       |   2 +-
 dev-perl/opal-client/Manifest                      |   2 +-
 dev-python/GOGrapher/ChangeLog                     |   3 +
 dev-python/GOGrapher/GOGrapher-9999.ebuild         |  21 +-
 dev-python/astropy/ChangeLog                       |   8 +
 dev-python/astropy/astropy-9999.ebuild             |  40 +-
 dev-python/astropy/metadata.xml                    |  10 +-
 dev-python/astropysics/ChangeLog                   |   6 +-
 dev-python/astropysics/astropysics-9999.ebuild     |  55 +-
 dev-python/astropysics/metadata.xml                |   4 +-
 dev-python/coards/ChangeLog                        |   8 +-
 dev-python/coards/Manifest                         |   2 +-
 dev-python/coards/coards-0.2.2.ebuild              |  22 -
 dev-python/coards/coards-1.0.5.ebuild              |  23 +
 dev-python/coards/metadata.xml                     |  10 +-
 dev-python/coords/ChangeLog                        |   6 +-
 dev-python/coords/Manifest                         |   2 +-
 dev-python/coords/coords-0.37.ebuild               |  22 +-
 dev-python/coords/metadata.xml                     |   4 +-
 dev-python/cosmocalc/ChangeLog                     |   6 +-
 dev-python/cosmocalc/Manifest                      |   2 +-
 dev-python/cosmocalc/cosmocalc-0.1.2-r1.ebuild     |  23 +-
 dev-python/cosmocalc/metadata.xml                  |   4 +-
 dev-python/dimensionful/ChangeLog                  |   6 +-
 dev-python/dimensionful/dimensionful-9999.ebuild   |  37 +-
 dev-python/dimensionful/metadata.xml               |   8 +-
 dev-python/emcee/ChangeLog                         |   8 +-
 dev-python/emcee/Manifest                          |   2 +-
 dev-python/emcee/emcee-1.0.1.ebuild                |  35 -
 dev-python/emcee/emcee-1.2.0.ebuild                |  27 +
 dev-python/emcee/metadata.xml                      |   4 +-
 dev-python/ffc/ChangeLog                           |   8 +-
 dev-python/ffc/Manifest                            |   2 +-
 dev-python/ffc/ffc-0.9.4.ebuild                    |  23 -
 dev-python/ffc/ffc-1.2.0.ebuild                    |  18 +
 dev-python/ffc/metadata.xml                        |   4 +-
 dev-python/fiat/ChangeLog                          |   8 +-
 dev-python/fiat/Manifest                           |   2 +-
 .../fiat/{fiat-0.9.2.ebuild => fiat-1.1.ebuild}    |  14 +-
 dev-python/fiat/metadata.xml                       |   4 +-
 dev-python/go-parser/ChangeLog                     |   6 +-
 dev-python/go-parser/Manifest                      |   2 +-
 dev-python/go-parser/go-parser-9999.ebuild         |  13 +-
 dev-python/go-parser/metadata.xml                  |  10 +-
 dev-python/healpy/ChangeLog                        |   9 +
 dev-python/healpy/Manifest                         |   1 +
 dev-python/healpy/healpy-1.6.2.ebuild              |  34 +
 dev-python/healpy/metadata.xml                     |  10 +
 dev-python/inference/ChangeLog                     |   7 +-
 dev-python/inference/inference-0.4.ebuild          |  31 +-
 dev-python/inference/metadata.xml                  |   4 +-
 dev-python/instant/ChangeLog                       |   8 +-
 dev-python/instant/Manifest                        |   2 +-
 dev-python/instant/instant-0.9.8.ebuild            |  23 -
 dev-python/instant/instant-1.2.0.ebuild            |  18 +
 dev-python/instant/metadata.xml                    |   4 +-
 dev-python/meshpy/ChangeLog                        |   8 +-
 dev-python/meshpy/Manifest                         |   2 +-
 ...meshpy-0.91.2.ebuild => meshpy-2013.1.2.ebuild} |  29 +-
 dev-python/meshpy/metadata.xml                     |   5 +-
 dev-python/numpydoc/ChangeLog                      |   6 +-
 dev-python/numpydoc/Manifest                       |   2 +-
 dev-python/numpydoc/metadata.xml                   |   4 +-
 dev-python/numpydoc/numpydoc-0.4.ebuild            |  22 +-
 dev-python/omniorbpy/ChangeLog                     |   6 +-
 dev-python/omniorbpy/Manifest                      |   2 +-
 dev-python/omniorbpy/metadata.xml                  |   2 +-
 dev-python/omniorbpy/omniorbpy-3.4.ebuild          |  90 +--
 dev-python/opal-client/ChangeLog                   |   8 +-
 dev-python/opal-client/Manifest                    |   2 +-
 dev-python/opal-client/metadata.xml                |   8 +-
 dev-python/opal-client/opal-client-2.2-r1.ebuild   |  55 --
 dev-python/opal-client/opal-client-2.4.1.ebuild    |  42 ++
 dev-python/pyhdf/ChangeLog                         |   8 +
 dev-python/pyhdf/Manifest                          |   2 +-
 dev-python/pyhdf/metadata.xml                      |  16 +-
 dev-python/pyhdf/pyhdf-0.8.3.ebuild                |  29 +-
 dev-python/pythoncgns/ChangeLog                    |   6 +-
 dev-python/pythoncgns/Manifest                     |   2 +-
 dev-python/pythoncgns/metadata.xml                 |   2 +-
 dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild |  10 +-
 dev-python/ufl/ChangeLog                           |   5 +-
 dev-python/ufl/Manifest                            |   2 +-
 dev-python/ufl/metadata.xml                        |   4 +-
 dev-python/ufl/ufl-0.5.4.ebuild                    |  17 +-
 dev-python/viper/ChangeLog                         |   8 +-
 dev-python/viper/Manifest                          |   2 +-
 dev-python/viper/metadata.xml                      |   4 +-
 dev-python/viper/viper-0.4.6.ebuild                |  23 -
 dev-python/viper/viper-1.0.1.ebuild                |  18 +
 dev-tcltk/img_rotate/ChangeLog                     |   6 +-
 dev-tcltk/img_rotate/Manifest                      |   2 +-
 dev-tcltk/img_rotate/img_rotate-1.1.ebuild         |  14 +-
 dev-tcltk/img_rotate/metadata.xml                  |   8 +-
 dev-tcltk/togl/Manifest                            |   2 +-
 dev-util/smartgit/Manifest                         |   2 +-
 licenses/GRL                                       |  15 +
 licenses/HSL                                       | 222 ++++++
 licenses/Tablet                                    |   8 +-
 media-gfx/brlcad/ChangeLog                         |   6 +-
 media-gfx/brlcad/brlcad-9999.ebuild                |   2 +-
 media-gfx/brlcad/metadata.xml                      |  26 +-
 media-gfx/librecad/ChangeLog                       |   6 +
 media-gfx/librecad/librecad-9999.ebuild            |  32 +-
 media-libs/OpenMOIV/Manifest                       |   2 +-
 media-libs/avbin-bin/Manifest                      |   4 +-
 media-libs/libgfx/Manifest                         |   2 +-
 net-firewall/gcb/Manifest                          |   2 +-
 net-ftp/bbftp-client/Manifest                      |   2 +-
 net-ftp/bbftp-server/Manifest                      |   2 +-
 net-misc/bbscp/Manifest                            |   2 +-
 net-misc/dhcp/ChangeLog                            |  61 --
 net-misc/dhcp/Manifest                             |   1 -
 net-misc/dhcp/dhcp-4.2.3_p2-r1.ebuild              | 245 -------
 net-misc/dhcp/files/dhcp-3.0-fix-perms.patch       |  15 -
 net-misc/dhcp/files/dhcp-3.0.3-dhclient-dbus.patch |  84 ---
 .../dhcp/files/dhcp-3.0.3-dhclient-no-down.patch   |  70 --
 net-misc/dhcp/files/dhcp-4.0-dhclient-ntp.patch    | 216 ------
 net-misc/dhcp/files/dhcp-4.2.0-PPP.patch           | 150 -----
 .../dhcp/files/dhcp-4.2.0-errwarn-message.patch    |  31 -
 .../dhcp/files/dhcp-4.2.2-bind-build-flags.patch   |  14 -
 net-misc/dhcp/files/dhcp-4.2.2-bind-disable.patch  |  13 -
 .../files/dhcp-4.2.2-bind-parallel-build.patch     |  14 -
 .../files/dhcp-4.2.2-dhclient-resolvconf.patch     | 409 ------------
 .../files/dhcp-4.2.2-dhclient-stdin-conf.patch     | 113 ----
 net-misc/dhcp/files/dhcp-4.2.2-gpxe-cid.patch      | 132 ----
 net-misc/dhcp/files/dhcp-4.2.2-improved-xid.patch  | 138 ----
 net-misc/dhcp/files/dhcp-4.2.2-lpf-ib.patch        | 538 ---------------
 net-misc/dhcp/files/dhcp-4.2.2-nogateway.patch     |  46 --
 net-misc/dhcp/files/dhcp-4.2.2-xen-checksum.patch  | 249 -------
 net-misc/dhcp/files/dhcp-4.2.3-options.patch       | 391 -----------
 net-misc/dhcp/files/dhcpd.conf2                    |  28 -
 net-misc/dhcp/files/dhcpd.init2                    |  94 ---
 net-misc/dhcp/files/dhcpd.init5                    | 114 ----
 net-misc/dhcp/files/dhcrelay.conf                  |  13 -
 net-misc/dhcp/files/dhcrelay.init2                 |  29 -
 net-misc/dhcp/metadata.xml                         |  10 -
 perl-core/encoding-warnings/Manifest               |   2 +-
 profiles/arch/amd64/no-multilib/package.mask       |  27 -
 profiles/arch/amd64/package.use.mask               |  23 -
 profiles/package.mask                              | 118 +---
 sci-astronomy/astrometry/ChangeLog                 |  23 +-
 sci-astronomy/astrometry/Manifest                  |   2 +-
 sci-astronomy/astrometry/astrometry-0.38.ebuild    |  57 --
 sci-astronomy/astrometry/astrometry-0.43.ebuild    |  87 +++
 .../astrometry/files/0.38-array-bounds.patch       |  11 -
 .../astrometry/files/0.38-as-needed.patch          | 694 -------------------
 .../astrometry/files/0.38-missing-headers.patch    |  11 -
 .../astrometry/files/0.38-strict-aliasing.patch    |  30 -
 .../astrometry/files/0.38-system-libs.patch        |  48 --
 .../astrometry/files/0.43-as-needed.patch          | 366 ++++++++++
 ...r-flags.patch => 0.43-respect-user-flags.patch} |   3 +
 .../astrometry/files/0.43-system-libs.patch        | 742 +++++++++++++++++++++
 sci-astronomy/astrometry/metadata.xml              |   7 +-
 sci-astronomy/bpz/ChangeLog                        |   5 +-
 sci-astronomy/bpz/bpz-1.99.3.ebuild                |  57 +-
 sci-astronomy/bpz/metadata.xml                     |   4 +-
 sci-astronomy/chealpix/ChangeLog                   |   9 +
 sci-astronomy/chealpix/Manifest                    |   1 +
 sci-astronomy/chealpix/chealpix-3.11.ebuild        |  30 +
 sci-astronomy/chealpix/metadata.xml                |  11 +
 sci-astronomy/eazy/ChangeLog                       |   5 +-
 sci-astronomy/eazy/eazy-1.00.ebuild                |  16 +-
 sci-astronomy/eazy/metadata.xml                    |   4 +-
 sci-astronomy/galfit-bin/ChangeLog                 |   3 +
 sci-astronomy/galfit-bin/galfit-bin-3.0.4.ebuild   |   6 +-
 sci-astronomy/healpix_cxx/ChangeLog                |   9 +
 sci-astronomy/healpix_cxx/Manifest                 |   1 +
 sci-astronomy/healpix_cxx/healpix_cxx-3.11.ebuild  |  54 ++
 sci-astronomy/healpix_cxx/metadata.xml             |  12 +
 sci-astronomy/healpix_idl/ChangeLog                |   9 +
 sci-astronomy/healpix_idl/Manifest                 |   1 +
 sci-astronomy/healpix_idl/healpix_idl-3.11.ebuild  |  37 +
 sci-astronomy/healpix_idl/metadata.xml             |  12 +
 sci-astronomy/psfex/ChangeLog                      |   5 +-
 sci-astronomy/psfex/metadata.xml                   |  10 +-
 sci-astronomy/psfex/psfex-9999.ebuild              |   3 +-
 sci-astronomy/scamp/ChangeLog                      |   5 +-
 sci-astronomy/scamp/metadata.xml                   |  10 +-
 sci-astronomy/scamp/scamp-9999.ebuild              |   3 +-
 sci-biology/ONTO-PERL/Manifest                     |   2 +-
 sci-biology/YASRA/ChangeLog                        |   4 +
 sci-biology/YASRA/Manifest                         |   2 +-
 .../YASRA/{YASRA-2.1.ebuild => YASRA-2.32.ebuild}  |  15 +-
 sci-biology/align_to_scf/Manifest                  |   2 +-
 sci-biology/amos-short/Manifest                    |   2 +-
 sci-biology/argo-bin/Manifest                      |   2 +-
 sci-biology/argo/Manifest                          |   2 +-
 sci-biology/autoeditor/Manifest                    |   4 +-
 sci-biology/bambus/Manifest                        |   2 +-
 sci-biology/brat/Manifest                          |   2 +-
 sci-biology/caftools/ChangeLog                     |   8 +
 sci-biology/caftools/Manifest                      |   4 +-
 sci-biology/caftools/caftools-2.0.2.ebuild         |  36 +-
 sci-biology/caftools/caftools-2.0.ebuild           |  38 --
 sci-biology/caftools/metadata.xml                  |  16 +-
 sci-biology/cap3-bin/Manifest                      |   4 +-
 sci-biology/cdbfasta/Manifest                      |   2 +-
 sci-biology/clover/ChangeLog                       |   6 +-
 sci-biology/clover/Manifest                        |   4 +-
 sci-biology/clover/clover-2010.02.19.ebuild        |  43 --
 sci-biology/clover/clover-2011.10.24.ebuild        |  40 ++
 sci-biology/clover/metadata.xml                    |   6 +-
 sci-biology/clview/Manifest                        |   4 +-
 sci-biology/codonw/Manifest                        |   2 +-
 sci-biology/cutadapt/ChangeLog                     |   6 +-
 sci-biology/cutadapt/Manifest                      |   2 +-
 .../{cutadapt-1.0.ebuild => cutadapt-1.2.1.ebuild} |  13 +-
 sci-biology/cutadapt/metadata.xml                  |  10 +-
 sci-biology/dawg/Manifest                          |   2 +-
 sci-biology/embassy-cbstools/Manifest              |   2 +-
 sci-biology/embassy-domainatrix/Manifest           |   2 +-
 sci-biology/embassy-domalign/Manifest              |   2 +-
 sci-biology/embassy-domsearch/Manifest             |   2 +-
 sci-biology/embassy-emnu/Manifest                  |   2 +-
 sci-biology/embassy-esim4/Manifest                 |   2 +-
 sci-biology/embassy-hmmer/Manifest                 |   2 +-
 sci-biology/embassy-iprscan/Manifest               |   2 +-
 sci-biology/embassy-mse/Manifest                   |   2 +-
 sci-biology/embassy-phylipnew/Manifest             |   2 +-
 sci-biology/embassy-signature/Manifest             |   2 +-
 sci-biology/embassy-structure/Manifest             |   2 +-
 sci-biology/embassy-topo/Manifest                  |   2 +-
 sci-biology/embassy-vienna/Manifest                |   2 +-
 sci-biology/erpin/ChangeLog                        |   5 +-
 sci-biology/erpin/Manifest                         |   4 +-
 sci-biology/erpin/erpin-5.5b.ebuild                |  23 +-
 sci-biology/erpin/metadata.xml                     |  10 +-
 sci-biology/est2uni/Manifest                       |  10 +-
 sci-biology/fastdnaml/Manifest                     |   4 +-
 sci-biology/gap2caf/ChangeLog                      |   8 +
 sci-biology/gap2caf/Manifest                       |   4 +-
 sci-biology/gap2caf/gap2caf-2.1.0.ebuild           |  45 +-
 sci-biology/gap2caf/metadata.xml                   |  10 +-
 sci-biology/gbench/Manifest                        |   2 +-
 sci-biology/genepop/Manifest                       |   2 +-
 sci-biology/generecon/Manifest                     |   2 +-
 sci-biology/genseed/Manifest                       |   2 +-
 sci-biology/grappa/Manifest                        |   2 +-
 sci-biology/jalview/Manifest                       |   2 +-
 sci-biology/lastz/ChangeLog                        |  12 +-
 sci-biology/lastz/Manifest                         |   3 +-
 sci-biology/lastz/files/lastz-1.03.34-build.patch  |  43 ++
 .../{lastz-1.02.00.ebuild => lastz-1.03.34.ebuild} |  28 +-
 sci-biology/lastz/metadata.xml                     |  10 +-
 sci-biology/lucy/Manifest                          |   2 +-
 sci-biology/mavid/Manifest                         |   2 +-
 sci-biology/merlin/Manifest                        |   2 +-
 sci-biology/miranda/Manifest                       |   2 +-
 sci-biology/mrbayes/Manifest                       |   2 +-
 sci-biology/mreps/Manifest                         |   2 +-
 sci-biology/mrfast/Manifest                        |   2 +-
 sci-biology/mrsfast/Manifest                       |   2 +-
 sci-biology/ncbi-tools++/ChangeLog                 |   6 +
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |   3 +-
 sci-biology/nrcl/Manifest                          |   4 +-
 sci-biology/perlprimer/Manifest                    |   2 +-
 sci-biology/phylobayes/ChangeLog                   |  10 -
 sci-biology/phylobayes/Manifest                    |   2 -
 sci-biology/phylobayes/metadata.xml                |   9 -
 sci-biology/phylobayes/phylobayes-3.3b.ebuild      |  37 -
 sci-biology/proda/Manifest                         |   2 +-
 sci-biology/psx/Manifest                           |   2 +-
 sci-biology/pybrain/ChangeLog                      |   6 +-
 sci-biology/pybrain/metadata.xml                   |   2 +-
 sci-biology/pybrain/pybrain-9999.ebuild            |  25 +-
 sci-biology/quicktree/ChangeLog                    |   6 +-
 sci-biology/quicktree/Manifest                     |   2 +-
 sci-biology/quicktree/metadata.xml                 |  10 +-
 sci-biology/quicktree/quicktree-1.1-r1.ebuild      |  17 +-
 sci-biology/rnaplex/Manifest                       |   2 +-
 sci-biology/roche454ace2caf/Manifest               |   2 +-
 sci-biology/sclust/Manifest                        |   4 +-
 sci-biology/sequin/ChangeLog                       |   9 +-
 sci-biology/sequin/Manifest                        |   4 +-
 sci-biology/sequin/sequin-20090722.ebuild          |  32 -
 sci-biology/sequin/sequin-20121202.ebuild          |  44 ++
 sci-biology/sff_dump/Manifest                      |   2 +-
 sci-biology/signalp/Manifest                       |   2 +-
 sci-biology/smalt-bin/ChangeLog                    |   8 +-
 sci-biology/smalt-bin/Manifest                     |   2 +-
 sci-biology/smalt-bin/metadata.xml                 |  10 +-
 sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild       |  25 -
 sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild       |  31 +
 sci-biology/ssaha2-bin/ChangeLog                   |   6 +-
 sci-biology/ssaha2-bin/Manifest                    |   9 +-
 sci-biology/ssaha2-bin/metadata.xml                |  10 +-
 ...a2-bin-2.5.3.ebuild => ssaha2-bin-2.5.5.ebuild} |  26 +-
 sci-biology/swissknife/Manifest                    |   2 +-
 sci-biology/tablet-bin/ChangeLog                   |   9 +-
 sci-biology/tablet-bin/Manifest                    |   3 +-
 sci-biology/tablet-bin/metadata.xml                |  10 +-
 .../tablet-bin/tablet-bin-1.11.11.01.ebuild        |  73 --
 ...1.05.03.ebuild => tablet-bin-1.13.05.17.ebuild} |  57 +-
 sci-biology/tclust/Manifest                        |   4 +-
 sci-biology/tgicl/Manifest                         |   2 +-
 sci-biology/tigr-assembler/Manifest                |   2 +-
 sci-biology/tigr-foundation-libs/Manifest          |   2 +-
 sci-biology/tmhmm/Manifest                         |   2 +-
 sci-biology/twinscan/ChangeLog                     |   6 +-
 sci-biology/twinscan/Manifest                      |   2 +-
 sci-biology/twinscan/metadata.xml                  |  10 +-
 sci-biology/twinscan/twinscan-4.1.2.ebuild         |  30 +-
 sci-biology/zmsort/Manifest                        |   4 +-
 sci-chemistry/almost/Manifest                      |   2 +-
 sci-chemistry/ball/ChangeLog                       |   3 +
 sci-chemistry/ball/ball-9999.ebuild                |  11 +-
 sci-chemistry/ball/metadata.xml                    |   2 +-
 sci-chemistry/bist/Manifest                        |   2 +-
 sci-chemistry/chemBuild/ChangeLog                  |   6 +-
 sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild     |  33 +-
 sci-chemistry/chemBuild/files/chemBuild            |   2 +-
 sci-chemistry/chemBuild/metadata.xml               |   2 +-
 sci-chemistry/cnsface/ChangeLog                    |   6 +-
 sci-chemistry/cnsface/Manifest                     |   2 +-
 sci-chemistry/cnsface/cnsface-0.0.12.ebuild        |  19 +-
 sci-chemistry/cnsface/metadata.xml                 |   8 +-
 sci-chemistry/direx/Manifest                       |   2 +-
 sci-chemistry/drawxtl/Manifest                     |   4 +-
 sci-chemistry/dssp2pdb/Manifest                    |   2 +-
 sci-chemistry/hydronmr/ChangeLog                   |   3 +
 sci-chemistry/hydronmr/hydronmr-7c.ebuild          |   1 -
 sci-chemistry/jana2000/Manifest                    |   2 +-
 sci-chemistry/jmol/Manifest                        |   2 +-
 sci-chemistry/mage/Manifest                        |   2 +-
 sci-chemistry/modeller/ChangeLog                   |   6 +-
 sci-chemistry/modeller/Manifest                    |   2 +-
 sci-chemistry/modeller/metadata.xml                |   2 +-
 .../{modeller-9.8.ebuild => modeller-9.12.ebuild}  |  96 ++-
 sci-chemistry/mtz2hkl/Manifest                     |   2 +-
 sci-chemistry/mtz2sca/Manifest                     |   2 +-
 sci-chemistry/nmrpipe/ChangeLog                    |   8 +
 .../nmrpipe/nmrpipe-7.9.2013.021.23.09-r2.ebuild   |   4 +-
 sci-chemistry/nmrview/ChangeLog                    |   6 +-
 sci-chemistry/nmrview/metadata.xml                 |  10 +-
 sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild      |  15 +-
 sci-chemistry/nwchem/ChangeLog                     |   4 +
 sci-chemistry/nwchem/Manifest                      |   1 -
 sci-chemistry/nwchem/nwchem-6.1.1.ebuild           | 126 ----
 sci-chemistry/nwchem/nwchem-6.3.ebuild             |  10 +-
 sci-chemistry/phaser/ChangeLog                     |  21 -
 sci-chemistry/phaser/Manifest                      |   1 -
 sci-chemistry/phaser/files/2.1.4-sadf.patch        |  64 --
 .../phaser/files/phaser-2.1.4-chmod.patch          |  11 -
 sci-chemistry/phaser/metadata.xml                  |  30 -
 sci-chemistry/phaser/phaser-2.1.4-r1.ebuild        | 138 ----
 sci-chemistry/phaser/phaser-2.1.4.ebuild           | 114 ----
 sci-chemistry/polygon/ChangeLog                    |   7 +-
 sci-chemistry/polygon/Manifest                     |   4 +-
 .../polygon/files/{0710-db.patch => 0612-db.patch} |  20 +-
 sci-chemistry/polygon/metadata.xml                 |   8 +-
 .../{polygon-0710.ebuild => polygon-0612.ebuild}   |  18 +-
 sci-chemistry/pymol-apbs-plugin/ChangeLog          |   9 +-
 sci-chemistry/pymol-apbs-plugin/metadata.xml       |   8 +-
 .../pymol-apbs-plugin-9999.ebuild                  |  53 +-
 sci-chemistry/pymol-plugins-ezviz/ChangeLog        |   4 +
 sci-chemistry/pymol-plugins-ezviz/Manifest         |   2 +-
 .../pymol-plugins-ezviz-1.0.2005.ebuild            |  56 +-
 sci-chemistry/pymol-plugins-psico/ChangeLog        |   3 +
 .../pymol-plugins-psico-9999.ebuild                |  15 +-
 sci-chemistry/pyquante/ChangeLog                   |   6 +-
 sci-chemistry/pyquante/Manifest                    |   2 +-
 sci-chemistry/pyquante/metadata.xml                |   2 +-
 sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild    |  11 +-
 sci-chemistry/rosetta-tools/Manifest               |   2 +-
 sci-chemistry/shiftx/ChangeLog                     |   5 +-
 sci-chemistry/shiftx/Manifest                      |   2 +-
 sci-chemistry/shiftx/metadata.xml                  |   8 +-
 sci-chemistry/shiftx/shiftx-1.1.ebuild             |  24 +-
 sci-chemistry/shiftx2/ChangeLog                    |   8 +
 sci-chemistry/shiftx2/Manifest                     |   1 +
 sci-chemistry/shiftx2/files/gentoo-fixes.patch     | 194 ++++++
 sci-chemistry/shiftx2/metadata.xml                 |  39 ++
 .../shiftx2/shiftx2-1.07_p20120106.ebuild          | 112 ++++
 sci-chemistry/smmp/ChangeLog                       |   5 +-
 sci-chemistry/smmp/Manifest                        |   2 +-
 sci-chemistry/smmp/metadata.xml                    |   8 +-
 sci-chemistry/smmp/smmp-3.0.5.ebuild               |  41 +-
 sci-chemistry/specView/ChangeLog                   |   3 +
 sci-chemistry/specView/specView-1.0.2.ebuild       |  52 +-
 sci-chemistry/ssp/ChangeLog                        |   5 +-
 sci-chemistry/ssp/metadata.xml                     |   8 +-
 sci-chemistry/ssp/ssp-09.11.ebuild                 |   6 +-
 sci-chemistry/unio/Manifest                        |   4 +-
 sci-electronics/player/Manifest                    |   2 +-
 sci-electronics/stage/Manifest                     |   2 +-
 sci-electronics/tnt/Manifest                       |   2 +-
 sci-geosciences/cdat-lite/Manifest                 |   4 +-
 sci-geosciences/congen/Manifest                    |   2 +-
 .../harmonics-dwf-free-noncomm/Manifest            |   2 +-
 sci-geosciences/harmonics-dwf-free/Manifest        |   4 +-
 sci-geosciences/libtcd/Manifest                    |   4 +-
 sci-geosciences/seawater/Manifest                  |   2 +-
 sci-geosciences/swmm/Manifest                      |   2 +-
 sci-geosciences/tappy/Manifest                     |   2 +-
 sci-geosciences/tcd-utils/Manifest                 |   4 +-
 sci-geosciences/xtide/Manifest                     |   4 +-
 sci-libs/blastdb/ChangeLog                         |   8 +
 sci-libs/blastdb/blastdb-9999.ebuild               |   8 +-
 sci-libs/blastdb/metadata.xml                      |  31 +-
 sci-libs/calculix-cgx/Manifest                     |   4 +-
 sci-libs/cgnsfoam/Manifest                         |   2 +-
 sci-libs/cgnslib/Manifest                          |   2 +-
 sci-libs/cnsface-scripts/Manifest                  |   2 +-
 sci-libs/coinhsl/ChangeLog                         |  12 +
 sci-libs/coinhsl/Manifest                          |   1 +
 sci-libs/coinhsl/coinhsl-2012.12.21.ebuild         |  36 +
 sci-libs/coinhsl/metadata.xml                      |  12 +
 sci-libs/dcmtk/Manifest                            |   6 +-
 sci-libs/driftwood/Manifest                        |   2 +-
 sci-libs/etsf_io/Manifest                          |   2 +-
 sci-libs/factory/Manifest                          |   2 +-
 sci-libs/fgsl/Manifest                             |   4 +-
 sci-libs/fox/Manifest                              |  12 +-
 sci-libs/fplll/Manifest                            |   2 +-
 sci-libs/framewave/Manifest                        |   2 +-
 sci-libs/geom/Manifest                             |   2 +-
 sci-libs/givaro/Manifest                           |   4 +-
 sci-libs/ipopt/ChangeLog                           |   9 +
 sci-libs/ipopt/Manifest                            |   2 +-
 .../{ipopt-3.10.3.ebuild => ipopt-3.11.0.ebuild}   |  19 +-
 sci-libs/ipopt/metadata.xml                        |  11 +-
 sci-libs/libcgnsoo/Manifest                        |   2 +-
 sci-libs/libfac/Manifest                           |   4 +-
 sci-libs/libxc/Manifest                            |   2 +-
 sci-libs/lwpr/Manifest                             |   2 +-
 sci-libs/m4ri/Manifest                             |   4 +-
 sci-libs/matio/Manifest                            |   2 +-
 sci-libs/mesquite/Manifest                         |   2 +-
 sci-libs/ni-visa/Manifest                          |   2 +-
 sci-libs/oasa/Manifest                             |   2 +-
 sci-libs/omalloc/Manifest                          |   2 +-
 sci-libs/symmetrica/Manifest                       |   2 +-
 sci-libs/trilinos/ChangeLog                        |   4 +
 sci-libs/trilinos/Manifest                         |   2 +-
 sci-libs/trilinos/metadata.xml                     |  56 +-
 sci-libs/trilinos/trilinos-10.10.1.ebuild          | 124 ----
 sci-libs/trilinos/trilinos-11.0.3.ebuild           |  12 +-
 sci-mathematics/Oid/Manifest                       |   4 +-
 sci-mathematics/acl2/Manifest                      |   2 +-
 sci-mathematics/algae/files/unbundle.patch         |  41 --
 sci-mathematics/apron/Manifest                     |   5 +-
 sci-mathematics/aribas/Manifest                    |   2 +-
 sci-mathematics/axiom/Manifest                     |   2 +-
 sci-mathematics/burrtools/Manifest                 |   4 +-
 sci-mathematics/cadabra/ChangeLog                  |   5 +
 sci-mathematics/cadabra/Manifest                   |   3 -
 sci-mathematics/cadabra/cadabra-1.25.ebuild        |  89 ---
 sci-mathematics/cadabra/cadabra-1.28.ebuild        |  87 ---
 sci-mathematics/cadabra/cadabra-1.29.ebuild        |  87 ---
 sci-mathematics/cadabra/cadabra-1.31.ebuild        |  14 +-
 sci-mathematics/cadabra/metadata.xml               |   4 +-
 sci-mathematics/dolfin/Manifest                    |   2 +-
 sci-mathematics/frama-c/Manifest                   |   3 -
 sci-mathematics/gap-guava/Manifest                 |   2 +-
 sci-mathematics/gap/Manifest                       |   4 +-
 sci-mathematics/gappa/Manifest                     |   3 -
 sci-mathematics/htk/Manifest                       |   4 +-
 sci-mathematics/kayali/Manifest                    |   2 +-
 sci-mathematics/libsfmt/Manifest                   |   2 +-
 sci-mathematics/lie/Manifest                       |   2 +-
 sci-mathematics/ltl2ba/Manifest                    |  25 +-
 sci-mathematics/netgen/Manifest                    |   2 +-
 sci-mathematics/open-axiom/Manifest                |   2 +-
 sci-mathematics/pest/Manifest                      |   6 +-
 sci-mathematics/ufc/Manifest                       |   2 +-
 sci-misc/finomaton/Manifest                        |   2 +-
 sci-misc/fitscut/Manifest                          |   2 +-
 sci-misc/jwnl/Manifest                             |   4 +-
 sci-misc/kotus-sanalista/Manifest                  |   2 +-
 sci-misc/nltk/Manifest                             |   2 +-
 sci-misc/omorfi/Manifest                           |   2 +-
 sci-misc/opennlp-maxent/Manifest                   |   2 +-
 sci-misc/opennlp-tools/Manifest                    |  88 +--
 sci-misc/pywordnet/Manifest                        |   2 +-
 sci-misc/salome-kernel/Manifest                    |   4 +-
 sci-misc/salome-pycalculator/Manifest              |   4 +-
 sci-misc/stanford-parser/Manifest                  |   2 +-
 sci-misc/stanford-tagger/Manifest                  |   2 +-
 sci-physics/espresso++/ChangeLog                   |   4 +
 sci-physics/espresso++/espresso++-9999.ebuild      |  22 +-
 sci-physics/espresso++/metadata.xml                |  16 +-
 sci-physics/espresso/ChangeLog                     |   4 +
 sci-physics/espresso/espresso-9999.ebuild          |  24 +-
 sci-physics/espresso/metadata.xml                  |  10 +-
 sci-physics/qcl/Manifest                           |   8 +-
 sci-visualization/gnuplot/ChangeLog                |   4 +
 sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild  |   2 +-
 sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild  |   2 +-
 sci-visualization/nodemon/Manifest                 |   2 +-
 sys-cluster/condor/ChangeLog                       |  40 --
 sys-cluster/condor/Manifest                        |   2 -
 sys-cluster/condor/condor-7.5.2.ebuild             | 160 -----
 sys-cluster/condor/condor-7.5.4.ebuild             | 160 -----
 sys-cluster/condor/files/condor.confd              |   2 -
 sys-cluster/condor/files/condor.initd              |  64 --
 sys-cluster/condor/files/condor_config.local       |  11 -
 sys-cluster/condor/metadata.xml                    |  26 -
 sys-cluster/ganglia_jobmonarch/Manifest            |   2 +-
 sys-cluster/lustre/ChangeLog                       |   4 +
 sys-cluster/lustre/lustre-9999.ebuild              |   6 +-
 sys-cluster/lustre/metadata.xml                    |  20 +-
 sys-cluster/modules/modules-3.2.9c-r1.ebuild       |   2 +-
 sys-cluster/mpe2/ChangeLog                         |  15 -
 sys-cluster/mpe2/Manifest                          |   1 -
 .../files/slog2sdk-trace_rlog-makefile-fixes.patch |  68 --
 .../slog2sdk-trace_sample-makefile-fixes.patch     |  68 --
 sys-cluster/mpe2/metadata.xml                      |  10 -
 sys-cluster/mpe2/mpe2-1.0.6_p1.ebuild              | 148 ----
 sys-cluster/nullmpi/ChangeLog                      |   6 +-
 sys-cluster/nullmpi/Manifest                       |   2 +-
 sys-cluster/nullmpi/metadata.xml                   |  10 +-
 sys-cluster/nullmpi/nullmpi-0.7.ebuild             |   4 +-
 sys-cluster/nullmpi/nullmpi-9999.ebuild            |  16 +-
 sys-cluster/pyslice/Manifest                       |   2 +-
 sys-devel/gdebugger/Manifest                       |   4 +-
 sys-infiniband/librxe/Manifest                     |   2 +-
 www-apps/py-swish-e/ChangeLog                      |   6 +-
 www-apps/py-swish-e/Manifest                       |   2 +-
 www-apps/py-swish-e/metadata.xml                   |   8 +-
 www-apps/py-swish-e/py-swish-e-0.5.ebuild          |  12 +-
 x11-libs/tr/Manifest                               |   2 +-
 x11-libs/xview-bin/ChangeLog                       |   3 +
 x11-libs/xview-bin/xview-bin-3.2_p1428.ebuild      |   2 +-
 x11-misc/envytools/ChangeLog                       |   6 +-
 x11-misc/envytools/envytools-9999.ebuild           |  18 +-
 x11-misc/envytools/metadata.xml                    |  10 +-
 579 files changed, 4325 insertions(+), 8161 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f43609fc308239ce00e3b66ad121c43dbf15b1ed
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 17 05:55:15 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 17 05:55:15 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f43609fc

Merge branch 'master' into jlec

* master: (120 commits)
  add missing masks for live ebuilds
  dev-python/healpy: Initial import
  dev-java/jhealpix: Initial import
  sci-astronomy/healpix_idl: Initial import
  sci-astronomy/healpix_cxx: Initial import
  sci-astronomy/chealpix: Initial import
  sci-biology/twinscan: Bump to EAPI=5 and fix license
  sci-biology/ssaha2-bin: Version Bump; restrict license; add QA_PREBUILT for binaries
  sci-biology/smalt-bin: Version Bump; restrict license; add QA_PREBUILT for binaries
  sci-biology/sequin: Version BUmp; restrcit license; add QA_PREBUILT for binaries; install html files into sys path
  sci-biology/quicktree: Bump to EAPI=5 and fix license
  sci-biology/gap2caf: Bump to EAPI=5 and fix license; make it build with eautoreconf
  sci-biology/erpin: Bump to EAPI=5 and respect FLAGS / AR
  sci-biology/clover: Version BUmp; fixed license; respect LDFLAGS
  sci-chemistry/shiftx2: Respect FLAGS
  Enhanced the sci-chemistry/shiftx ebuild. Still needs some love for the emake part (portage complains about LDFLAGS not respected), but should work.
  sci-chemistry/pymol-plugins-psico: Bump to EAPI=5 and distutils-r1.eclass
  sci-chemistry/smmp: Bump to EAPI=5 and python-r1.eclass
  sci-chemistry/specView: Bump to EAPI=5 and python-single-r1.eclass
  sci-chemistry/pyquante: Bump to EAPI=5 and distutils-r1.eclass
  ...


 app-benchmarks/btl/ChangeLog                       |   5 +-
 app-benchmarks/btl/btl-9999.ebuild                 |  11 +-
 app-benchmarks/btl/metadata.xml                    |  14 +-
 app-benchmarks/numbench/ChangeLog                  |   8 +-
 app-benchmarks/numbench/metadata.xml               |  14 +-
 app-benchmarks/numbench/numbench-0.2.ebuild        |  28 +-
 app-benchmarks/numbench/numbench-9999.ebuild       |  28 +-
 app-doc/blacs-docs/Manifest                        |   2 +-
 app-doc/blas-docs/Manifest                         |   6 +-
 app-doc/lapack-docs/Manifest                       |   4 +-
 app-doc/root-docs/Manifest                         |   5 -
 app-text/dgs/Manifest                              |   2 +-
 app-vim/freefem++-syntax/Manifest                  |   2 +-
 dev-cpp/growler-arch/Manifest                      |   4 +-
 dev-cpp/growler-core/Manifest                      |   2 +-
 dev-cpp/growler-math/Manifest                      |   2 +-
 dev-cpp/growler-thread/Manifest                    |   2 +-
 dev-java/jeuclid-core/Manifest                     |   2 +-
 dev-java/jgraphx/ChangeLog                         |   7 +-
 dev-java/jgraphx/Manifest                          |   3 -
 dev-java/jgraphx/jgraphx-1.2.0.7.ebuild            |  44 --
 dev-java/jgraphx/jgraphx-1.3.0.2.ebuild            |  44 --
 dev-java/jgraphx/jgraphx-1.4.1.0.ebuild            |  18 +-
 dev-java/jgraphx/jgraphx-1.4.1.2.ebuild            |  44 --
 dev-java/jgraphx/jgraphx-1.8.0.6.ebuild            |  20 +-
 dev-java/jgraphx/metadata.xml                      |   4 +-
 dev-java/jhealpix/ChangeLog                        |   9 +
 dev-java/jhealpix/Manifest                         |   1 +
 dev-java/jhealpix/jhealpix-3.11.ebuild             |  43 ++
 dev-java/jhealpix/metadata.xml                     |  11 +
 dev-java/joda-convert/Manifest                     |   2 +-
 dev-java/vecmath/Manifest                          |   4 +-
 dev-lang/ispc/ChangeLog                            |   3 +
 dev-lang/ispc/ispc-9999.ebuild                     |   2 +-
 dev-lang/julia/ChangeLog                           |   5 +-
 dev-lang/julia/julia-9999.ebuild                   |   2 +-
 dev-lang/julia/metadata.xml                        |   4 +-
 dev-lang/path64/ChangeLog                          |   6 +-
 dev-lang/path64/metadata.xml                       |  22 +-
 dev-lang/path64/path64-9999.ebuild                 |   4 +-
 dev-libs/asmjit/ChangeLog                          |   8 +-
 dev-libs/asmjit/Manifest                           |   2 +-
 ...-1.0_beta_p2.ebuild => asmjit-1.0_beta4.ebuild} |   6 +-
 dev-libs/asmjit/metadata.xml                       |  12 +-
 dev-libs/libunzip/Manifest                         |   2 +-
 dev-libs/simclist/Manifest                         |   5 +-
 dev-ml/mlgmpidl/Manifest                           |   6 +-
 dev-ml/ocamlgraph/Manifest                         |   4 -
 dev-perl/BTLib/Manifest                            |   2 +-
 dev-perl/Lab-Instrument/Manifest                   |   2 +-
 dev-perl/Lab-Tools/Manifest                        |   2 +-
 dev-perl/Lab-VISA/Manifest                         |   2 +-
 dev-perl/go-db-perl/Manifest                       |   2 +-
 dev-perl/opal-client/Manifest                      |   2 +-
 dev-python/GOGrapher/ChangeLog                     |   3 +
 dev-python/GOGrapher/GOGrapher-9999.ebuild         |  21 +-
 dev-python/astropy/ChangeLog                       |   8 +
 dev-python/astropy/astropy-9999.ebuild             |  40 +-
 dev-python/astropy/metadata.xml                    |  10 +-
 dev-python/astropysics/ChangeLog                   |   6 +-
 dev-python/astropysics/astropysics-9999.ebuild     |  55 +-
 dev-python/astropysics/metadata.xml                |   4 +-
 dev-python/coards/ChangeLog                        |   8 +-
 dev-python/coards/Manifest                         |   2 +-
 dev-python/coards/coards-0.2.2.ebuild              |  22 -
 dev-python/coards/coards-1.0.5.ebuild              |  23 +
 dev-python/coards/metadata.xml                     |  10 +-
 dev-python/coords/ChangeLog                        |   6 +-
 dev-python/coords/Manifest                         |   2 +-
 dev-python/coords/coords-0.37.ebuild               |  22 +-
 dev-python/coords/metadata.xml                     |   4 +-
 dev-python/cosmocalc/ChangeLog                     |   6 +-
 dev-python/cosmocalc/Manifest                      |   2 +-
 dev-python/cosmocalc/cosmocalc-0.1.2-r1.ebuild     |  23 +-
 dev-python/cosmocalc/metadata.xml                  |   4 +-
 dev-python/dimensionful/ChangeLog                  |   6 +-
 dev-python/dimensionful/dimensionful-9999.ebuild   |  37 +-
 dev-python/dimensionful/metadata.xml               |   8 +-
 dev-python/emcee/ChangeLog                         |   8 +-
 dev-python/emcee/Manifest                          |   2 +-
 dev-python/emcee/emcee-1.0.1.ebuild                |  35 -
 dev-python/emcee/emcee-1.2.0.ebuild                |  27 +
 dev-python/emcee/metadata.xml                      |   4 +-
 dev-python/ffc/ChangeLog                           |   8 +-
 dev-python/ffc/Manifest                            |   2 +-
 dev-python/ffc/ffc-0.9.4.ebuild                    |  23 -
 dev-python/ffc/ffc-1.2.0.ebuild                    |  18 +
 dev-python/ffc/metadata.xml                        |   4 +-
 dev-python/fiat/ChangeLog                          |   8 +-
 dev-python/fiat/Manifest                           |   2 +-
 .../fiat/{fiat-0.9.2.ebuild => fiat-1.1.ebuild}    |  14 +-
 dev-python/fiat/metadata.xml                       |   4 +-
 dev-python/go-parser/ChangeLog                     |   6 +-
 dev-python/go-parser/Manifest                      |   2 +-
 dev-python/go-parser/go-parser-9999.ebuild         |  13 +-
 dev-python/go-parser/metadata.xml                  |  10 +-
 dev-python/healpy/ChangeLog                        |   9 +
 dev-python/healpy/Manifest                         |   1 +
 dev-python/healpy/healpy-1.6.2.ebuild              |  34 +
 dev-python/healpy/metadata.xml                     |  10 +
 dev-python/inference/ChangeLog                     |   7 +-
 dev-python/inference/inference-0.4.ebuild          |  31 +-
 dev-python/inference/metadata.xml                  |   4 +-
 dev-python/instant/ChangeLog                       |   8 +-
 dev-python/instant/Manifest                        |   2 +-
 dev-python/instant/instant-0.9.8.ebuild            |  23 -
 dev-python/instant/instant-1.2.0.ebuild            |  18 +
 dev-python/instant/metadata.xml                    |   4 +-
 dev-python/meshpy/ChangeLog                        |   8 +-
 dev-python/meshpy/Manifest                         |   2 +-
 ...meshpy-0.91.2.ebuild => meshpy-2013.1.2.ebuild} |  29 +-
 dev-python/meshpy/metadata.xml                     |   5 +-
 dev-python/numpydoc/ChangeLog                      |   6 +-
 dev-python/numpydoc/Manifest                       |   2 +-
 dev-python/numpydoc/metadata.xml                   |   4 +-
 dev-python/numpydoc/numpydoc-0.4.ebuild            |  22 +-
 dev-python/omniorbpy/ChangeLog                     |   6 +-
 dev-python/omniorbpy/Manifest                      |   2 +-
 dev-python/omniorbpy/metadata.xml                  |   2 +-
 dev-python/omniorbpy/omniorbpy-3.4.ebuild          |  90 +--
 dev-python/opal-client/ChangeLog                   |   8 +-
 dev-python/opal-client/Manifest                    |   2 +-
 dev-python/opal-client/metadata.xml                |   8 +-
 dev-python/opal-client/opal-client-2.2-r1.ebuild   |  55 --
 dev-python/opal-client/opal-client-2.4.1.ebuild    |  42 ++
 dev-python/pyhdf/ChangeLog                         |   8 +
 dev-python/pyhdf/Manifest                          |   2 +-
 dev-python/pyhdf/metadata.xml                      |  16 +-
 dev-python/pyhdf/pyhdf-0.8.3.ebuild                |  29 +-
 dev-python/pythoncgns/ChangeLog                    |   6 +-
 dev-python/pythoncgns/Manifest                     |   2 +-
 dev-python/pythoncgns/metadata.xml                 |   2 +-
 dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild |  10 +-
 dev-python/ufl/ChangeLog                           |   5 +-
 dev-python/ufl/Manifest                            |   2 +-
 dev-python/ufl/metadata.xml                        |   4 +-
 dev-python/ufl/ufl-0.5.4.ebuild                    |  17 +-
 dev-python/viper/ChangeLog                         |   8 +-
 dev-python/viper/Manifest                          |   2 +-
 dev-python/viper/metadata.xml                      |   4 +-
 dev-python/viper/viper-0.4.6.ebuild                |  23 -
 dev-python/viper/viper-1.0.1.ebuild                |  18 +
 dev-tcltk/img_rotate/ChangeLog                     |   6 +-
 dev-tcltk/img_rotate/Manifest                      |   2 +-
 dev-tcltk/img_rotate/img_rotate-1.1.ebuild         |  14 +-
 dev-tcltk/img_rotate/metadata.xml                  |   8 +-
 dev-tcltk/togl/Manifest                            |   2 +-
 dev-util/smartgit/Manifest                         |   2 +-
 licenses/GRL                                       |  15 +
 licenses/HSL                                       | 222 ++++++
 licenses/Tablet                                    |   8 +-
 media-gfx/brlcad/ChangeLog                         |   6 +-
 media-gfx/brlcad/brlcad-9999.ebuild                |   2 +-
 media-gfx/brlcad/metadata.xml                      |  26 +-
 media-gfx/librecad/ChangeLog                       |   6 +
 media-gfx/librecad/librecad-9999.ebuild            |  32 +-
 media-libs/OpenMOIV/Manifest                       |   2 +-
 media-libs/avbin-bin/Manifest                      |   4 +-
 media-libs/libgfx/Manifest                         |   2 +-
 net-firewall/gcb/Manifest                          |   2 +-
 net-ftp/bbftp-client/Manifest                      |   2 +-
 net-ftp/bbftp-server/Manifest                      |   2 +-
 net-misc/bbscp/Manifest                            |   2 +-
 net-misc/dhcp/ChangeLog                            |  61 --
 net-misc/dhcp/Manifest                             |   1 -
 net-misc/dhcp/dhcp-4.2.3_p2-r1.ebuild              | 245 -------
 net-misc/dhcp/files/dhcp-3.0-fix-perms.patch       |  15 -
 net-misc/dhcp/files/dhcp-3.0.3-dhclient-dbus.patch |  84 ---
 .../dhcp/files/dhcp-3.0.3-dhclient-no-down.patch   |  70 --
 net-misc/dhcp/files/dhcp-4.0-dhclient-ntp.patch    | 216 ------
 net-misc/dhcp/files/dhcp-4.2.0-PPP.patch           | 150 -----
 .../dhcp/files/dhcp-4.2.0-errwarn-message.patch    |  31 -
 .../dhcp/files/dhcp-4.2.2-bind-build-flags.patch   |  14 -
 net-misc/dhcp/files/dhcp-4.2.2-bind-disable.patch  |  13 -
 .../files/dhcp-4.2.2-bind-parallel-build.patch     |  14 -
 .../files/dhcp-4.2.2-dhclient-resolvconf.patch     | 409 ------------
 .../files/dhcp-4.2.2-dhclient-stdin-conf.patch     | 113 ----
 net-misc/dhcp/files/dhcp-4.2.2-gpxe-cid.patch      | 132 ----
 net-misc/dhcp/files/dhcp-4.2.2-improved-xid.patch  | 138 ----
 net-misc/dhcp/files/dhcp-4.2.2-lpf-ib.patch        | 538 ---------------
 net-misc/dhcp/files/dhcp-4.2.2-nogateway.patch     |  46 --
 net-misc/dhcp/files/dhcp-4.2.2-xen-checksum.patch  | 249 -------
 net-misc/dhcp/files/dhcp-4.2.3-options.patch       | 391 -----------
 net-misc/dhcp/files/dhcpd.conf2                    |  28 -
 net-misc/dhcp/files/dhcpd.init2                    |  94 ---
 net-misc/dhcp/files/dhcpd.init5                    | 114 ----
 net-misc/dhcp/files/dhcrelay.conf                  |  13 -
 net-misc/dhcp/files/dhcrelay.init2                 |  29 -
 net-misc/dhcp/metadata.xml                         |  10 -
 perl-core/encoding-warnings/Manifest               |   2 +-
 profiles/arch/amd64/no-multilib/package.mask       |  27 -
 profiles/arch/amd64/package.use.mask               |  23 -
 profiles/package.mask                              | 118 +---
 sci-astronomy/astrometry/ChangeLog                 |  23 +-
 sci-astronomy/astrometry/Manifest                  |   2 +-
 sci-astronomy/astrometry/astrometry-0.38.ebuild    |  57 --
 sci-astronomy/astrometry/astrometry-0.43.ebuild    |  87 +++
 .../astrometry/files/0.38-array-bounds.patch       |  11 -
 .../astrometry/files/0.38-as-needed.patch          | 694 -------------------
 .../astrometry/files/0.38-missing-headers.patch    |  11 -
 .../astrometry/files/0.38-strict-aliasing.patch    |  30 -
 .../astrometry/files/0.38-system-libs.patch        |  48 --
 .../astrometry/files/0.43-as-needed.patch          | 366 ++++++++++
 ...r-flags.patch => 0.43-respect-user-flags.patch} |   3 +
 .../astrometry/files/0.43-system-libs.patch        | 742 +++++++++++++++++++++
 sci-astronomy/astrometry/metadata.xml              |   7 +-
 sci-astronomy/bpz/ChangeLog                        |   5 +-
 sci-astronomy/bpz/bpz-1.99.3.ebuild                |  57 +-
 sci-astronomy/bpz/metadata.xml                     |   4 +-
 sci-astronomy/chealpix/ChangeLog                   |   9 +
 sci-astronomy/chealpix/Manifest                    |   1 +
 sci-astronomy/chealpix/chealpix-3.11.ebuild        |  30 +
 sci-astronomy/chealpix/metadata.xml                |  11 +
 sci-astronomy/eazy/ChangeLog                       |   5 +-
 sci-astronomy/eazy/eazy-1.00.ebuild                |  16 +-
 sci-astronomy/eazy/metadata.xml                    |   4 +-
 sci-astronomy/galfit-bin/ChangeLog                 |   3 +
 sci-astronomy/galfit-bin/galfit-bin-3.0.4.ebuild   |   6 +-
 sci-astronomy/healpix_cxx/ChangeLog                |   9 +
 sci-astronomy/healpix_cxx/Manifest                 |   1 +
 sci-astronomy/healpix_cxx/healpix_cxx-3.11.ebuild  |  54 ++
 sci-astronomy/healpix_cxx/metadata.xml             |  12 +
 sci-astronomy/healpix_idl/ChangeLog                |   9 +
 sci-astronomy/healpix_idl/Manifest                 |   1 +
 sci-astronomy/healpix_idl/healpix_idl-3.11.ebuild  |  37 +
 sci-astronomy/healpix_idl/metadata.xml             |  12 +
 sci-astronomy/psfex/ChangeLog                      |   5 +-
 sci-astronomy/psfex/metadata.xml                   |  10 +-
 sci-astronomy/psfex/psfex-9999.ebuild              |   3 +-
 sci-astronomy/scamp/ChangeLog                      |   5 +-
 sci-astronomy/scamp/metadata.xml                   |  10 +-
 sci-astronomy/scamp/scamp-9999.ebuild              |   3 +-
 sci-biology/ONTO-PERL/Manifest                     |   2 +-
 sci-biology/YASRA/ChangeLog                        |   4 +
 sci-biology/YASRA/Manifest                         |   2 +-
 .../YASRA/{YASRA-2.1.ebuild => YASRA-2.32.ebuild}  |  15 +-
 sci-biology/align_to_scf/Manifest                  |   2 +-
 sci-biology/amos-short/Manifest                    |   2 +-
 sci-biology/argo-bin/Manifest                      |   2 +-
 sci-biology/argo/Manifest                          |   2 +-
 sci-biology/autoeditor/Manifest                    |   4 +-
 sci-biology/bambus/Manifest                        |   2 +-
 sci-biology/brat/Manifest                          |   2 +-
 sci-biology/caftools/ChangeLog                     |   8 +
 sci-biology/caftools/Manifest                      |   4 +-
 sci-biology/caftools/caftools-2.0.2.ebuild         |  36 +-
 sci-biology/caftools/caftools-2.0.ebuild           |  38 --
 sci-biology/caftools/metadata.xml                  |  16 +-
 sci-biology/cap3-bin/Manifest                      |   4 +-
 sci-biology/cdbfasta/Manifest                      |   2 +-
 sci-biology/clover/ChangeLog                       |   6 +-
 sci-biology/clover/Manifest                        |   4 +-
 sci-biology/clover/clover-2010.02.19.ebuild        |  43 --
 sci-biology/clover/clover-2011.10.24.ebuild        |  40 ++
 sci-biology/clover/metadata.xml                    |   6 +-
 sci-biology/clview/Manifest                        |   4 +-
 sci-biology/codonw/Manifest                        |   2 +-
 sci-biology/cutadapt/ChangeLog                     |   6 +-
 sci-biology/cutadapt/Manifest                      |   2 +-
 .../{cutadapt-1.0.ebuild => cutadapt-1.2.1.ebuild} |  13 +-
 sci-biology/cutadapt/metadata.xml                  |  10 +-
 sci-biology/dawg/Manifest                          |   2 +-
 sci-biology/embassy-cbstools/Manifest              |   2 +-
 sci-biology/embassy-domainatrix/Manifest           |   2 +-
 sci-biology/embassy-domalign/Manifest              |   2 +-
 sci-biology/embassy-domsearch/Manifest             |   2 +-
 sci-biology/embassy-emnu/Manifest                  |   2 +-
 sci-biology/embassy-esim4/Manifest                 |   2 +-
 sci-biology/embassy-hmmer/Manifest                 |   2 +-
 sci-biology/embassy-iprscan/Manifest               |   2 +-
 sci-biology/embassy-mse/Manifest                   |   2 +-
 sci-biology/embassy-phylipnew/Manifest             |   2 +-
 sci-biology/embassy-signature/Manifest             |   2 +-
 sci-biology/embassy-structure/Manifest             |   2 +-
 sci-biology/embassy-topo/Manifest                  |   2 +-
 sci-biology/embassy-vienna/Manifest                |   2 +-
 sci-biology/erpin/ChangeLog                        |   5 +-
 sci-biology/erpin/Manifest                         |   4 +-
 sci-biology/erpin/erpin-5.5b.ebuild                |  23 +-
 sci-biology/erpin/metadata.xml                     |  10 +-
 sci-biology/est2uni/Manifest                       |  10 +-
 sci-biology/fastdnaml/Manifest                     |   4 +-
 sci-biology/gap2caf/ChangeLog                      |   8 +
 sci-biology/gap2caf/Manifest                       |   4 +-
 sci-biology/gap2caf/gap2caf-2.1.0.ebuild           |  45 +-
 sci-biology/gap2caf/metadata.xml                   |  10 +-
 sci-biology/gbench/Manifest                        |   2 +-
 sci-biology/genepop/Manifest                       |   2 +-
 sci-biology/generecon/Manifest                     |   2 +-
 sci-biology/genseed/Manifest                       |   2 +-
 sci-biology/grappa/Manifest                        |   2 +-
 sci-biology/jalview/Manifest                       |   2 +-
 sci-biology/lastz/ChangeLog                        |  12 +-
 sci-biology/lastz/Manifest                         |   3 +-
 sci-biology/lastz/files/lastz-1.03.34-build.patch  |  43 ++
 .../{lastz-1.02.00.ebuild => lastz-1.03.34.ebuild} |  28 +-
 sci-biology/lastz/metadata.xml                     |  10 +-
 sci-biology/lucy/Manifest                          |   2 +-
 sci-biology/mavid/Manifest                         |   2 +-
 sci-biology/merlin/Manifest                        |   2 +-
 sci-biology/miranda/Manifest                       |   2 +-
 sci-biology/mrbayes/Manifest                       |   2 +-
 sci-biology/mreps/Manifest                         |   2 +-
 sci-biology/mrfast/Manifest                        |   2 +-
 sci-biology/mrsfast/Manifest                       |   2 +-
 sci-biology/ncbi-tools++/ChangeLog                 |   6 +
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |   3 +-
 sci-biology/nrcl/Manifest                          |   4 +-
 sci-biology/perlprimer/Manifest                    |   2 +-
 sci-biology/phylobayes/ChangeLog                   |  10 -
 sci-biology/phylobayes/Manifest                    |   2 -
 sci-biology/phylobayes/metadata.xml                |   9 -
 sci-biology/phylobayes/phylobayes-3.3b.ebuild      |  37 -
 sci-biology/proda/Manifest                         |   2 +-
 sci-biology/psx/Manifest                           |   2 +-
 sci-biology/pybrain/ChangeLog                      |   6 +-
 sci-biology/pybrain/metadata.xml                   |   2 +-
 sci-biology/pybrain/pybrain-9999.ebuild            |  25 +-
 sci-biology/quicktree/ChangeLog                    |   6 +-
 sci-biology/quicktree/Manifest                     |   2 +-
 sci-biology/quicktree/metadata.xml                 |  10 +-
 sci-biology/quicktree/quicktree-1.1-r1.ebuild      |  17 +-
 sci-biology/rnaplex/Manifest                       |   2 +-
 sci-biology/roche454ace2caf/Manifest               |   2 +-
 sci-biology/sclust/Manifest                        |   4 +-
 sci-biology/sequin/ChangeLog                       |   9 +-
 sci-biology/sequin/Manifest                        |   4 +-
 sci-biology/sequin/sequin-20090722.ebuild          |  32 -
 sci-biology/sequin/sequin-20121202.ebuild          |  44 ++
 sci-biology/sff_dump/Manifest                      |   2 +-
 sci-biology/signalp/Manifest                       |   2 +-
 sci-biology/smalt-bin/ChangeLog                    |   8 +-
 sci-biology/smalt-bin/Manifest                     |   2 +-
 sci-biology/smalt-bin/metadata.xml                 |  10 +-
 sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild       |  25 -
 sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild       |  31 +
 sci-biology/ssaha2-bin/ChangeLog                   |   6 +-
 sci-biology/ssaha2-bin/Manifest                    |   9 +-
 sci-biology/ssaha2-bin/metadata.xml                |  10 +-
 ...a2-bin-2.5.3.ebuild => ssaha2-bin-2.5.5.ebuild} |  26 +-
 sci-biology/swissknife/Manifest                    |   2 +-
 sci-biology/tablet-bin/ChangeLog                   |   9 +-
 sci-biology/tablet-bin/Manifest                    |   3 +-
 sci-biology/tablet-bin/metadata.xml                |  10 +-
 .../tablet-bin/tablet-bin-1.11.11.01.ebuild        |  73 --
 ...1.05.03.ebuild => tablet-bin-1.13.05.17.ebuild} |  57 +-
 sci-biology/tclust/Manifest                        |   4 +-
 sci-biology/tgicl/Manifest                         |   2 +-
 sci-biology/tigr-assembler/Manifest                |   2 +-
 sci-biology/tigr-foundation-libs/Manifest          |   2 +-
 sci-biology/tmhmm/Manifest                         |   2 +-
 sci-biology/twinscan/ChangeLog                     |   6 +-
 sci-biology/twinscan/Manifest                      |   2 +-
 sci-biology/twinscan/metadata.xml                  |  10 +-
 sci-biology/twinscan/twinscan-4.1.2.ebuild         |  30 +-
 sci-biology/zmsort/Manifest                        |   4 +-
 sci-chemistry/almost/Manifest                      |   2 +-
 sci-chemistry/ball/ChangeLog                       |   3 +
 sci-chemistry/ball/ball-9999.ebuild                |  11 +-
 sci-chemistry/ball/metadata.xml                    |   2 +-
 sci-chemistry/bist/Manifest                        |   2 +-
 sci-chemistry/chemBuild/ChangeLog                  |   6 +-
 sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild     |  33 +-
 sci-chemistry/chemBuild/files/chemBuild            |   2 +-
 sci-chemistry/chemBuild/metadata.xml               |   2 +-
 sci-chemistry/cnsface/ChangeLog                    |   6 +-
 sci-chemistry/cnsface/Manifest                     |   2 +-
 sci-chemistry/cnsface/cnsface-0.0.12.ebuild        |  19 +-
 sci-chemistry/cnsface/metadata.xml                 |   8 +-
 sci-chemistry/direx/Manifest                       |   2 +-
 sci-chemistry/drawxtl/Manifest                     |   4 +-
 sci-chemistry/dssp2pdb/Manifest                    |   2 +-
 sci-chemistry/hydronmr/ChangeLog                   |   3 +
 sci-chemistry/hydronmr/hydronmr-7c.ebuild          |   1 -
 sci-chemistry/jana2000/Manifest                    |   2 +-
 sci-chemistry/jmol/Manifest                        |   2 +-
 sci-chemistry/mage/Manifest                        |   2 +-
 sci-chemistry/modeller/ChangeLog                   |   6 +-
 sci-chemistry/modeller/Manifest                    |   2 +-
 sci-chemistry/modeller/metadata.xml                |   2 +-
 .../{modeller-9.8.ebuild => modeller-9.12.ebuild}  |  96 ++-
 sci-chemistry/mtz2hkl/Manifest                     |   2 +-
 sci-chemistry/mtz2sca/Manifest                     |   2 +-
 sci-chemistry/nmrpipe/ChangeLog                    |   8 +
 .../nmrpipe/nmrpipe-7.9.2013.021.23.09-r2.ebuild   |   4 +-
 sci-chemistry/nmrview/ChangeLog                    |   6 +-
 sci-chemistry/nmrview/metadata.xml                 |  10 +-
 sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild      |  15 +-
 sci-chemistry/nwchem/ChangeLog                     |   4 +
 sci-chemistry/nwchem/Manifest                      |   1 -
 sci-chemistry/nwchem/nwchem-6.1.1.ebuild           | 126 ----
 sci-chemistry/nwchem/nwchem-6.3.ebuild             |  10 +-
 sci-chemistry/phaser/ChangeLog                     |  21 -
 sci-chemistry/phaser/Manifest                      |   1 -
 sci-chemistry/phaser/files/2.1.4-sadf.patch        |  64 --
 .../phaser/files/phaser-2.1.4-chmod.patch          |  11 -
 sci-chemistry/phaser/metadata.xml                  |  30 -
 sci-chemistry/phaser/phaser-2.1.4-r1.ebuild        | 138 ----
 sci-chemistry/phaser/phaser-2.1.4.ebuild           | 114 ----
 sci-chemistry/polygon/ChangeLog                    |   7 +-
 sci-chemistry/polygon/Manifest                     |   4 +-
 .../polygon/files/{0710-db.patch => 0612-db.patch} |  20 +-
 sci-chemistry/polygon/metadata.xml                 |   8 +-
 .../{polygon-0710.ebuild => polygon-0612.ebuild}   |  18 +-
 sci-chemistry/pymol-apbs-plugin/ChangeLog          |   9 +-
 sci-chemistry/pymol-apbs-plugin/metadata.xml       |   8 +-
 .../pymol-apbs-plugin-9999.ebuild                  |  53 +-
 sci-chemistry/pymol-plugins-ezviz/ChangeLog        |   4 +
 sci-chemistry/pymol-plugins-ezviz/Manifest         |   2 +-
 .../pymol-plugins-ezviz-1.0.2005.ebuild            |  56 +-
 sci-chemistry/pymol-plugins-psico/ChangeLog        |   3 +
 .../pymol-plugins-psico-9999.ebuild                |  15 +-
 sci-chemistry/pyquante/ChangeLog                   |   6 +-
 sci-chemistry/pyquante/Manifest                    |   2 +-
 sci-chemistry/pyquante/metadata.xml                |   2 +-
 sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild    |  11 +-
 sci-chemistry/rosetta-tools/Manifest               |   2 +-
 sci-chemistry/shiftx/ChangeLog                     |   5 +-
 sci-chemistry/shiftx/Manifest                      |   2 +-
 sci-chemistry/shiftx/metadata.xml                  |   8 +-
 sci-chemistry/shiftx/shiftx-1.1.ebuild             |  24 +-
 sci-chemistry/shiftx2/ChangeLog                    |   8 +
 sci-chemistry/shiftx2/Manifest                     |   1 +
 sci-chemistry/shiftx2/files/gentoo-fixes.patch     | 194 ++++++
 sci-chemistry/shiftx2/metadata.xml                 |  39 ++
 .../shiftx2/shiftx2-1.07_p20120106.ebuild          | 112 ++++
 sci-chemistry/smmp/ChangeLog                       |   5 +-
 sci-chemistry/smmp/Manifest                        |   2 +-
 sci-chemistry/smmp/metadata.xml                    |   8 +-
 sci-chemistry/smmp/smmp-3.0.5.ebuild               |  41 +-
 sci-chemistry/specView/ChangeLog                   |   3 +
 sci-chemistry/specView/specView-1.0.2.ebuild       |  52 +-
 sci-chemistry/ssp/ChangeLog                        |   5 +-
 sci-chemistry/ssp/metadata.xml                     |   8 +-
 sci-chemistry/ssp/ssp-09.11.ebuild                 |   6 +-
 sci-chemistry/unio/Manifest                        |   4 +-
 sci-electronics/player/Manifest                    |   2 +-
 sci-electronics/stage/Manifest                     |   2 +-
 sci-electronics/tnt/Manifest                       |   2 +-
 sci-geosciences/cdat-lite/Manifest                 |   4 +-
 sci-geosciences/congen/Manifest                    |   2 +-
 .../harmonics-dwf-free-noncomm/Manifest            |   2 +-
 sci-geosciences/harmonics-dwf-free/Manifest        |   4 +-
 sci-geosciences/libtcd/Manifest                    |   4 +-
 sci-geosciences/seawater/Manifest                  |   2 +-
 sci-geosciences/swmm/Manifest                      |   2 +-
 sci-geosciences/tappy/Manifest                     |   2 +-
 sci-geosciences/tcd-utils/Manifest                 |   4 +-
 sci-geosciences/xtide/Manifest                     |   4 +-
 sci-libs/blastdb/ChangeLog                         |   8 +
 sci-libs/blastdb/blastdb-9999.ebuild               |   8 +-
 sci-libs/blastdb/metadata.xml                      |  31 +-
 sci-libs/calculix-cgx/Manifest                     |   4 +-
 sci-libs/cgnsfoam/Manifest                         |   2 +-
 sci-libs/cgnslib/Manifest                          |   2 +-
 sci-libs/cnsface-scripts/Manifest                  |   2 +-
 sci-libs/coinhsl/ChangeLog                         |  12 +
 sci-libs/coinhsl/Manifest                          |   1 +
 sci-libs/coinhsl/coinhsl-2012.12.21.ebuild         |  36 +
 sci-libs/coinhsl/metadata.xml                      |  12 +
 sci-libs/dcmtk/Manifest                            |   6 +-
 sci-libs/driftwood/Manifest                        |   2 +-
 sci-libs/etsf_io/Manifest                          |   2 +-
 sci-libs/factory/Manifest                          |   2 +-
 sci-libs/fgsl/Manifest                             |   4 +-
 sci-libs/fox/Manifest                              |  12 +-
 sci-libs/fplll/Manifest                            |   2 +-
 sci-libs/framewave/Manifest                        |   2 +-
 sci-libs/geom/Manifest                             |   2 +-
 sci-libs/givaro/Manifest                           |   4 +-
 sci-libs/ipopt/ChangeLog                           |   9 +
 sci-libs/ipopt/Manifest                            |   2 +-
 .../{ipopt-3.10.3.ebuild => ipopt-3.11.0.ebuild}   |  19 +-
 sci-libs/ipopt/metadata.xml                        |  11 +-
 sci-libs/libcgnsoo/Manifest                        |   2 +-
 sci-libs/libfac/Manifest                           |   4 +-
 sci-libs/libxc/Manifest                            |   2 +-
 sci-libs/lwpr/Manifest                             |   2 +-
 sci-libs/m4ri/Manifest                             |   4 +-
 sci-libs/matio/Manifest                            |   2 +-
 sci-libs/mesquite/Manifest                         |   2 +-
 sci-libs/ni-visa/Manifest                          |   2 +-
 sci-libs/oasa/Manifest                             |   2 +-
 sci-libs/omalloc/Manifest                          |   2 +-
 sci-libs/symmetrica/Manifest                       |   2 +-
 sci-libs/trilinos/ChangeLog                        |   4 +
 sci-libs/trilinos/Manifest                         |   2 +-
 sci-libs/trilinos/metadata.xml                     |  56 +-
 sci-libs/trilinos/trilinos-10.10.1.ebuild          | 124 ----
 sci-libs/trilinos/trilinos-11.0.3.ebuild           |  12 +-
 sci-mathematics/Oid/Manifest                       |   4 +-
 sci-mathematics/acl2/Manifest                      |   2 +-
 sci-mathematics/algae/files/unbundle.patch         |  41 --
 sci-mathematics/apron/Manifest                     |   5 +-
 sci-mathematics/aribas/Manifest                    |   2 +-
 sci-mathematics/axiom/Manifest                     |   2 +-
 sci-mathematics/burrtools/Manifest                 |   4 +-
 sci-mathematics/cadabra/ChangeLog                  |   5 +
 sci-mathematics/cadabra/Manifest                   |   3 -
 sci-mathematics/cadabra/cadabra-1.25.ebuild        |  89 ---
 sci-mathematics/cadabra/cadabra-1.28.ebuild        |  87 ---
 sci-mathematics/cadabra/cadabra-1.29.ebuild        |  87 ---
 sci-mathematics/cadabra/cadabra-1.31.ebuild        |  14 +-
 sci-mathematics/cadabra/metadata.xml               |   4 +-
 sci-mathematics/dolfin/Manifest                    |   2 +-
 sci-mathematics/frama-c/Manifest                   |   3 -
 sci-mathematics/gap-guava/Manifest                 |   2 +-
 sci-mathematics/gap/Manifest                       |   4 +-
 sci-mathematics/gappa/Manifest                     |   3 -
 sci-mathematics/htk/Manifest                       |   4 +-
 sci-mathematics/kayali/Manifest                    |   2 +-
 sci-mathematics/libsfmt/Manifest                   |   2 +-
 sci-mathematics/lie/Manifest                       |   2 +-
 sci-mathematics/ltl2ba/Manifest                    |  25 +-
 sci-mathematics/netgen/Manifest                    |   2 +-
 sci-mathematics/open-axiom/Manifest                |   2 +-
 sci-mathematics/pest/Manifest                      |   6 +-
 sci-mathematics/ufc/Manifest                       |   2 +-
 sci-misc/finomaton/Manifest                        |   2 +-
 sci-misc/fitscut/Manifest                          |   2 +-
 sci-misc/jwnl/Manifest                             |   4 +-
 sci-misc/kotus-sanalista/Manifest                  |   2 +-
 sci-misc/nltk/Manifest                             |   2 +-
 sci-misc/omorfi/Manifest                           |   2 +-
 sci-misc/opennlp-maxent/Manifest                   |   2 +-
 sci-misc/opennlp-tools/Manifest                    |  88 +--
 sci-misc/pywordnet/Manifest                        |   2 +-
 sci-misc/salome-kernel/Manifest                    |   4 +-
 sci-misc/salome-pycalculator/Manifest              |   4 +-
 sci-misc/stanford-parser/Manifest                  |   2 +-
 sci-misc/stanford-tagger/Manifest                  |   2 +-
 sci-physics/espresso++/ChangeLog                   |   4 +
 sci-physics/espresso++/espresso++-9999.ebuild      |  22 +-
 sci-physics/espresso++/metadata.xml                |  16 +-
 sci-physics/espresso/ChangeLog                     |   4 +
 sci-physics/espresso/espresso-9999.ebuild          |  24 +-
 sci-physics/espresso/metadata.xml                  |  10 +-
 sci-physics/qcl/Manifest                           |   8 +-
 sci-visualization/gnuplot/ChangeLog                |   4 +
 sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild  |   2 +-
 sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild  |   2 +-
 sci-visualization/nodemon/Manifest                 |   2 +-
 sys-cluster/condor/ChangeLog                       |  40 --
 sys-cluster/condor/Manifest                        |   2 -
 sys-cluster/condor/condor-7.5.2.ebuild             | 160 -----
 sys-cluster/condor/condor-7.5.4.ebuild             | 160 -----
 sys-cluster/condor/files/condor.confd              |   2 -
 sys-cluster/condor/files/condor.initd              |  64 --
 sys-cluster/condor/files/condor_config.local       |  11 -
 sys-cluster/condor/metadata.xml                    |  26 -
 sys-cluster/ganglia_jobmonarch/Manifest            |   2 +-
 sys-cluster/lustre/ChangeLog                       |   4 +
 sys-cluster/lustre/lustre-9999.ebuild              |   6 +-
 sys-cluster/lustre/metadata.xml                    |  20 +-
 sys-cluster/modules/modules-3.2.9c-r1.ebuild       |   2 +-
 sys-cluster/mpe2/ChangeLog                         |  15 -
 sys-cluster/mpe2/Manifest                          |   1 -
 .../files/slog2sdk-trace_rlog-makefile-fixes.patch |  68 --
 .../slog2sdk-trace_sample-makefile-fixes.patch     |  68 --
 sys-cluster/mpe2/metadata.xml                      |  10 -
 sys-cluster/mpe2/mpe2-1.0.6_p1.ebuild              | 148 ----
 sys-cluster/nullmpi/ChangeLog                      |   6 +-
 sys-cluster/nullmpi/Manifest                       |   2 +-
 sys-cluster/nullmpi/metadata.xml                   |  10 +-
 sys-cluster/nullmpi/nullmpi-0.7.ebuild             |   4 +-
 sys-cluster/nullmpi/nullmpi-9999.ebuild            |  16 +-
 sys-cluster/pyslice/Manifest                       |   2 +-
 sys-devel/gdebugger/Manifest                       |   4 +-
 sys-infiniband/librxe/Manifest                     |   2 +-
 www-apps/py-swish-e/ChangeLog                      |   6 +-
 www-apps/py-swish-e/Manifest                       |   2 +-
 www-apps/py-swish-e/metadata.xml                   |   8 +-
 www-apps/py-swish-e/py-swish-e-0.5.ebuild          |  12 +-
 x11-libs/tr/Manifest                               |   2 +-
 x11-libs/xview-bin/ChangeLog                       |   3 +
 x11-libs/xview-bin/xview-bin-3.2_p1428.ebuild      |   2 +-
 x11-misc/envytools/ChangeLog                       |   6 +-
 x11-misc/envytools/envytools-9999.ebuild           |  18 +-
 x11-misc/envytools/metadata.xml                    |  10 +-
 579 files changed, 4325 insertions(+), 8161 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     521c3879e88d373f4eb885af030528caa867d7e8
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Jul  9 23:48:53 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Jul  9 23:48:53 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=521c3879

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 licenses/mpich                                     | 39 ----------------------
 sci-physics/lammps/ChangeLog                       | 12 +++++++
 sci-physics/lammps/Manifest                        |  1 +
 ...mmps-20130701.ebuild => lammps-20130708.ebuild} | 16 +++++++--
 4 files changed, 26 insertions(+), 42 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     871dd6c9683391d6caedb0c82efac78e8befd55c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 30 15:31:13 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 30 15:31:13 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=871dd6c9

Merge branch 'master' into jlec

* master: (36 commits)
  sci-libs/msms: Version BUmp; Bump to new distutil-r1.eclass
  app-doc/root-docs: version bump
  sci-physics/root: version bump
  sys-cluster/hpl: version bump and fixes
  fixed deps
  In sci-libs/bigdft-abi-1.0.4-r1, CUDA support made compile.
  moved to gx86
  moved to gx86
  Beautify
  Beautify
  Beautify.
  Added new package: projections
  Added new package: projections
  Bashified package name mangling.
  sys-cluster/modules: Prefix keyworded. Added tests. FHS fixes. Add bunch of fedora patches
  Fixed missing use flag.
  sci-chemistry/ucsf-tools: Fix compilation with latest gcc
  sci-chemistry/modeller: Fix lib position, #474696
  sci-chemistry/pymol: Update repo uri
  sci-chemistry/pymol: Update repo uri
  ...


 app-admin/eselect/ChangeLog                        |   6 +
 app-admin/eselect/Manifest                         |   2 +-
 ...1.3.4-r100.ebuild => eselect-1.3.5-r100.ebuild} |   0
 app-doc/root-docs/ChangeLog                        |   6 +
 app-doc/root-docs/Manifest                         |   2 +-
 ...ocs-5.34.08.ebuild => root-docs-5.34.09.ebuild} |   2 +-
 dev-java/fits/ChangeLog                            |   9 +-
 dev-java/fits/Manifest                             |   2 +-
 .../{fits-1.08.1.ebuild => fits-1.11.0.ebuild}     |   6 +-
 dev-lang/ispc/ChangeLog                            |   3 +
 dev-lang/ispc/ispc-9999.ebuild                     |   3 +-
 sci-chemistry/ambertools/ChangeLog                 |   4 +-
 sci-chemistry/ambertools/ambertools-12.ebuild      |   2 +-
 sci-chemistry/gnome-chemistry-utils/ChangeLog      |   4 +
 .../gnome-chemistry-utils-0.14.2.ebuild            |   2 +-
 sci-chemistry/gnome-chemistry-utils/metadata.xml   |   8 +-
 sci-chemistry/modeller/ChangeLog                   |   4 +
 ...ller-9.12-r1.ebuild => modeller-9.12-r2.ebuild} |   3 +-
 sci-chemistry/pymol/ChangeLog                      |   3 +
 sci-chemistry/pymol/pymol-9999.ebuild              |   2 +-
 sci-chemistry/ucsf-tools/ChangeLog                 |   3 +
 sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild    |  13 +-
 sci-libs/bigdft-abi/ChangeLog                      |   8 +
 ...abi-1.0.4.ebuild => bigdft-abi-1.0.4-r1.ebuild} |   3 +
 .../files/bigdft-abi-1.0.4-CUDA_gethostname.patch  |  22 +++
 sci-libs/lwpr/ChangeLog                            |   9 +-
 sci-libs/lwpr/Manifest                             |   2 +-
 sci-libs/lwpr/files/lwpr-1.2.2-setup.py.patch      |  12 --
 sci-libs/lwpr/lwpr-1.2.2.ebuild                    |  83 ---------
 sci-libs/lwpr/lwpr-1.2.5.ebuild                    |  51 ++++++
 sci-libs/lwpr/metadata.xml                         |  10 +-
 sci-libs/msms/ChangeLog                            |  10 +-
 sci-libs/msms/Manifest                             |   3 +-
 sci-libs/msms/metadata.xml                         |   2 +-
 sci-libs/msms/msms-1.5.4-r1.ebuild                 |  54 ------
 .../{msms-1.5.6_rc2.ebuild => msms-1.5.6.ebuild}   |  19 +--
 sci-physics/lammps/ChangeLog                       |  55 ------
 sci-physics/lammps/Manifest                        |   3 -
 sci-physics/lammps/lammps-20130512.ebuild          |  72 --------
 sci-physics/lammps/lammps-20130514.ebuild          |  75 ---------
 sci-physics/lammps/lammps-20130526.ebuild          |  75 ---------
 sci-physics/lammps/metadata.xml                    |  30 ----
 sci-physics/root/ChangeLog                         |   6 +
 sci-physics/root/Manifest                          |   5 +-
 sci-physics/root/metadata.xml                      |   1 +
 .../{root-5.34.08.ebuild => root-5.34.09.ebuild}   |  15 +-
 sys-cluster/charm/ChangeLog                        |  26 ---
 sys-cluster/charm/Manifest                         |   1 -
 sys-cluster/charm/charm-6.5.0.ebuild               | 175 -------------------
 .../charm/files/charm-6.5.0-charmc-gentoo.patch    |  25 ---
 sys-cluster/charm/metadata.xml                     |  10 --
 sys-cluster/charmdebug/ChangeLog                   |  12 ++
 sys-cluster/charmdebug/Manifest                    |   1 +
 sys-cluster/charmdebug/charmdebug-6.2.0.ebuild     |  31 ++++
 .../charmdebug}/metadata.xml                       |   0
 sys-cluster/hpl/ChangeLog                          |   8 +
 sys-cluster/hpl/Manifest                           |   3 +-
 .../hpl/{hpl-2.0-r1.ebuild => hpl-2.1.ebuild}      |  33 ++--
 sys-cluster/modules/ChangeLog                      |  10 ++
 sys-cluster/modules/files/createmodule.py          | 186 +++++++++++++++++++++
 sys-cluster/modules/files/createmodule.sh          | 166 ++++++++++++++++++
 .../modules/files/modules-3.2.10-avail.patch       |  12 ++
 .../modules/files/modules-3.2.10-bindir.patch      |  11 ++
 .../modules/files/modules-3.2.10-clear.patch       |  11 ++
 ...orline.patch => modules-3.2.10-errorline.patch} |   1 -
 .../modules/files/modules-3.2.10-versioning.patch  |  10 ++
 .../modules/files/modules-3.2.9c-errorline.patch   |   1 -
 sys-cluster/modules/files/modules.sh.in            |   7 +
 sys-cluster/modules/metadata.xml                   |  20 ++-
 sys-cluster/modules/modules-3.2.10-r1.ebuild       |  61 +++++++
 sys-cluster/modules/modules-3.2.10.ebuild          |   6 +-
 sys-cluster/projections/ChangeLog                  |  13 ++
 sys-cluster/projections/Manifest                   |   1 +
 .../projections}/metadata.xml                      |   0
 sys-cluster/projections/projections-6.2.1.ebuild   |  30 ++++
 75 files changed, 811 insertions(+), 774 deletions(-)

[gentoo-commits] proj/sci:ccp4 commit in: /

[Justin Lecher]

commit:     d1167d3e9fbea263a965cb527c1ec46e27318474
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Wed Jun 26 07:24:32 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 26 07:24:32 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d1167d3e

Merge pull request #86 from gentryx/master

Added TCL patch to modules 3.2.10


 ...odules-3.2.9c-errorline.patch => modules-3.2.10-errorline.patch} | 1 -
 sys-cluster/modules/files/modules-3.2.9c-errorline.patch            | 1 -
 sys-cluster/modules/modules-3.2.10.ebuild                           | 6 +++---
 3 files changed, 3 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     d1167d3e9fbea263a965cb527c1ec46e27318474
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Wed Jun 26 07:24:32 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 26 07:24:32 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d1167d3e

Merge pull request #86 from gentryx/master

Added TCL patch to modules 3.2.10


 ...odules-3.2.9c-errorline.patch => modules-3.2.10-errorline.patch} | 1 -
 sys-cluster/modules/files/modules-3.2.9c-errorline.patch            | 1 -
 sys-cluster/modules/modules-3.2.10.ebuild                           | 6 +++---
 3 files changed, 3 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     f1dcaee3267c375546293c9210d39b80c00c4ca1
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Jul  7 23:30:15 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Jul  7 23:30:15 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f1dcaee3

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 sci-libs/libgeodecomp/Manifest                           |  1 +
 ...bgeodecomp-0.1.0.ebuild => libgeodecomp-0.2.0.ebuild} | 16 +++++++++++++---
 2 files changed, 14 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     bafcd12ba1034dd265fe4ac8d4f8497afdef8fe3
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Sun Jul  7 14:06:03 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sun Jul  7 14:06:03 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bafcd12b

Merge pull request #89 from gentryx/master

Added ebuild for LibGeoDecomp 0.2.0


 sci-libs/libgeodecomp/Manifest                           |  1 +
 ...bgeodecomp-0.1.0.ebuild => libgeodecomp-0.2.0.ebuild} | 16 +++++++++++++---
 2 files changed, 14 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     f8f8325388e6a8978ef271640515a144b53a8ed5
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Sat Jul  6 20:33:34 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Sat Jul  6 20:33:34 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f8f83253

Merge /usr/local/portage/andis_overlay


 sci-libs/libgeodecomp/Manifest                           |  1 +
 ...bgeodecomp-0.1.0.ebuild => libgeodecomp-0.2.0.ebuild} | 16 +++++++++++++---
 2 files changed, 14 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     9fbdb4ae6a0b9287dc4b9417e2ca7ced7b26c60b
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Thu Jul  4 19:10:29 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Jul  4 19:10:29 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9fbdb4ae

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 dev-util/amdapp/amdapp-2.8.ebuild                  | 19 ++++++-
 dev-util/intel-ocl-sdk/Manifest                    |  1 +
 .../intel-ocl-sdk/intel-ocl-sdk-3.0.67279.ebuild   | 65 ++++++++++++++++++++++
 dev-util/intel-ocl-sdk/metadata.xml                | 17 ++++++
 media-gfx/brlcad/ChangeLog                         |  3 +
 media-gfx/brlcad/Manifest                          |  1 +
 6 files changed, 103 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     7a1714a356cddb1aa2bb3ca5773328f973fe56b2
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Thu Jul  4 06:18:51 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Jul  4 06:18:51 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7a1714a3

Merge pull request #87 from gentryx/master

Fixed ebuild for AMDAPP and added updated ebuild for Intel OpenCL SDK


 dev-util/amdapp/amdapp-2.8.ebuild                  | 19 ++++++-
 dev-util/intel-ocl-sdk/Manifest                    |  1 +
 .../intel-ocl-sdk/intel-ocl-sdk-3.0.67279.ebuild   | 65 ++++++++++++++++++++++
 dev-util/intel-ocl-sdk/metadata.xml                | 17 ++++++
 4 files changed, 99 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     637e2d028af727c3d7c0ab09bb29bdd0f80beeb7
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed Jul  3 19:57:02 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Jul  3 19:57:02 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=637e2d02

Merge /usr/local/portage/andis_overlay


 dev-util/intel-ocl-sdk/metadata.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     f2d3e656f959b32f0c70626924c0dc06de747be5
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed Jul  3 19:53:51 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Jul  3 19:53:51 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f2d3e656

Merge /usr/local/portage/andis_overlay


 dev-util/amdapp/amdapp-2.8.ebuild                     |  6 ++++--
 dev-util/intel-ocl-sdk/intel-ocl-sdk-3.0.67279.ebuild | 10 +++++++---
 2 files changed, 11 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     70ee018686f6160008c53cc8e59ff3ce06612260
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed Jul  3 03:54:22 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Jul  3 03:54:22 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=70ee0186

Merge /usr/local/portage/andis_overlay


 dev-util/amdapp/amdapp-2.8.ebuild | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     0dbff7dea8ebc8bfc1b3708ba59cfcee34e0273c
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Tue Jul  2 20:03:06 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Jul  2 20:03:06 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0dbff7de

Merge https://github.com/gentoo-science/sci


 app-doc/root-docs/ChangeLog                        |   6 +
 app-doc/root-docs/Manifest                         |   2 +-
 ...ocs-5.34.08.ebuild => root-docs-5.34.09.ebuild} |   2 +-
 metadata/layout.conf                               |   6 +
 sci-chemistry/ambertools/ChangeLog                 |   4 +-
 sci-chemistry/ambertools/ambertools-12.ebuild      |   2 +-
 sci-chemistry/pymol-plugins-ezviz/ChangeLog        |   5 +
 ...uild => pymol-plugins-ezviz-1.0.2005-r1.ebuild} |   1 +
 sci-libs/bigdft-abi/ChangeLog                      |   8 +
 ...abi-1.0.4.ebuild => bigdft-abi-1.0.4-r1.ebuild} |   3 +
 .../files/bigdft-abi-1.0.4-CUDA_gethostname.patch  |  22 +++
 sci-libs/msms/ChangeLog                            |  10 +-
 sci-libs/msms/Manifest                             |   3 +-
 sci-libs/msms/metadata.xml                         |   2 +-
 sci-libs/msms/msms-1.5.4-r1.ebuild                 |  54 ------
 .../{msms-1.5.6_rc2.ebuild => msms-1.5.6.ebuild}   |  19 +--
 sci-mathematics/ufc/ChangeLog                      |   5 +-
 sci-mathematics/ufc/ufc-1.4.2.ebuild               |   4 +-
 sci-physics/root/ChangeLog                         |   6 +
 sci-physics/root/Manifest                          |   5 +-
 sci-physics/root/metadata.xml                      |   1 +
 .../{root-5.34.08.ebuild => root-5.34.09.ebuild}   |  15 +-
 sys-cluster/charm/ChangeLog                        |  13 ++
 sys-cluster/charm/Manifest                         |   1 +
 sys-cluster/charm/charm-6.5.1.ebuild               | 181 +++++++++++++++++++++
 .../charm/files/charm-6.5.0-charmc-gentoo.patch    |  25 +++
 sys-cluster/charm/metadata.xml                     |  15 ++
 sys-cluster/empi/ChangeLog                         |  14 ++
 .../empi/{empi-0.8.ebuild => empi-0.9.ebuild}      |  14 +-
 .../empi/files/{ChangeLog-0.8 => ChangeLog-0.9}    |   0
 sys-cluster/empi/files/{empi-0.8 => empi-0.9}      |   4 +-
 .../files/{eselect.mpi-0.8 => eselect.mpi-0.9}     |   0
 sys-cluster/empi/metadata.xml                      |   8 +-
 sys-cluster/hpl/ChangeLog                          |   8 +
 sys-cluster/hpl/Manifest                           |   3 +-
 .../hpl/{hpl-2.0-r1.ebuild => hpl-2.1.ebuild}      |  33 ++--
 sys-cluster/openmpi/ChangeLog                      |  11 +-
 ...le-malloc-override-inside-of-Gentoo-sandb.patch |  42 +++++
 ...penmpi-1.6.4.ebuild => openmpi-1.6.4-r1.ebuild} |   4 +-
 39 files changed, 451 insertions(+), 110 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     01912d585cd65e73ab596d080e2debe61de19930
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Tue Jul  2 20:02:52 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Jul  2 20:02:52 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=01912d58

Merge /usr/local/portage/andis_overlay


 dev-util/amdapp/amdapp-2.8.ebuild                     | 3 ++-
 dev-util/intel-ocl-sdk/intel-ocl-sdk-3.0.67279.ebuild | 6 ++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     fcddbe9646bf40e7743f3505b5cdca29d766ae4d
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Thu Jun 27 22:13:41 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Jun 27 22:13:41 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fcddbe96

Merge /usr/local/portage/andis_overlay


 dev-util/amdapp/amdapp-2.8.ebuild                  | 10 +++-
 dev-util/intel-ocl-sdk/Manifest                    |  1 +
 .../intel-ocl-sdk/intel-ocl-sdk-3.0.67279.ebuild   | 59 ++++++++++++++++++++++
 dev-util/intel-ocl-sdk/metadata.xml                | 14 +++++
 4 files changed, 83 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     76e58b23060b68622a22a9812e954a44a9c7037b
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Jul  3 19:57:29 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Jul  3 19:57:29 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=76e58b23

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-physics/lammps/ChangeLog              |   9 +++
 sci-physics/lammps/Manifest               |   1 +
 sci-physics/lammps/lammps-20130701.ebuild | 105 ++++++++++++++++++++++++++++++
 sci-physics/lammps/metadata.xml           |  31 +++++++++
 sys-cluster/charm/ChangeLog               |   7 ++
 sys-cluster/charm/charm-6.5.1.ebuild      |  46 ++++++++-----
 sys-cluster/charm/metadata.xml            |   3 +
 7 files changed, 184 insertions(+), 18 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     c5d9b66462d9cc0c9a17de7c4e95c85f12701a23
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Wed Jul  3 16:40:40 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Wed Jul  3 16:40:40 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c5d9b664

Merge branch 'master' of github.com:gentoo-science/sci


 sci-geosciences/pydap/ChangeLog                    |  8 ++++-
 sci-geosciences/pydap/Manifest                     |  2 +-
 sci-geosciences/pydap/metadata.xml                 | 12 +++----
 sci-geosciences/pydap/pydap-3.0.3.ebuild           | 34 -------------------
 sci-geosciences/pydap/pydap-3.1.ebuild             | 38 ++++++++++++++++++++++
 sci-libs/armadillo/ChangeLog                       |  6 ++++
 sci-libs/armadillo/Manifest                        |  2 +-
 ...llo-3.820.1.ebuild => armadillo-3.900.6.ebuild} |  2 +-
 sci-libs/mlpack/ChangeLog                          |  6 ++++
 sci-libs/mlpack/Manifest                           |  2 +-
 .../{mlpack-1.0.5.ebuild => mlpack-1.0.6.ebuild}   |  0
 11 files changed, 67 insertions(+), 45 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     e88605269a92bfb4a232752657f59519603709da
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Wed Jun 26 18:32:49 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Wed Jun 26 18:32:49 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e8860526

Merge branch 'master' of github.com:gentoo-science/sci


 dev-java/fits/ChangeLog                            |   9 +-
 dev-java/fits/Manifest                             |   2 +-
 .../{fits-1.08.1.ebuild => fits-1.11.0.ebuild}     |   6 +-
 sci-libs/lwpr/ChangeLog                            |   9 +-
 sci-libs/lwpr/Manifest                             |   2 +-
 sci-libs/lwpr/files/lwpr-1.2.2-setup.py.patch      |  12 --
 sci-libs/lwpr/lwpr-1.2.2.ebuild                    |  83 ---------
 sci-libs/lwpr/lwpr-1.2.5.ebuild                    |  51 ++++++
 sci-libs/lwpr/metadata.xml                         |  10 +-
 sys-cluster/modules/ChangeLog                      |  10 ++
 sys-cluster/modules/files/createmodule.py          | 186 +++++++++++++++++++++
 sys-cluster/modules/files/createmodule.sh          | 166 ++++++++++++++++++
 .../modules/files/modules-3.2.10-avail.patch       |  12 ++
 .../modules/files/modules-3.2.10-bindir.patch      |  11 ++
 .../modules/files/modules-3.2.10-clear.patch       |  11 ++
 .../modules/files/modules-3.2.10-versioning.patch  |  10 ++
 sys-cluster/modules/files/modules.sh.in            |   7 +
 sys-cluster/modules/metadata.xml                   |  20 ++-
 sys-cluster/modules/modules-3.2.10-r1.ebuild       |  61 +++++++
 19 files changed, 561 insertions(+), 117 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     f964406968cbe45f9268653af44c2dc6b52baadd
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 26 15:26:34 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Jun 26 15:26:34 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f9644069

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 dev-lang/ispc/ChangeLog                            |  3 ++
 dev-lang/ispc/ispc-9999.ebuild                     |  3 +-
 sci-chemistry/gnome-chemistry-utils/ChangeLog      |  4 ++
 .../gnome-chemistry-utils-0.14.2.ebuild            |  2 +-
 sci-chemistry/gnome-chemistry-utils/metadata.xml   |  8 ++--
 sci-chemistry/modeller/ChangeLog                   |  4 ++
 ...ller-9.12-r1.ebuild => modeller-9.12-r2.ebuild} |  3 +-
 sci-chemistry/pymol/ChangeLog                      |  3 ++
 sci-chemistry/pymol/pymol-9999.ebuild              |  2 +-
 sci-chemistry/ucsf-tools/ChangeLog                 |  3 ++
 sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild    | 13 +++++-
 sci-physics/lammps/ChangeLog                       |  3 ++
 sci-physics/lammps/lammps-20130526.ebuild          | 25 +++++------
 sys-cluster/charm/ChangeLog                        |  3 ++
 sys-cluster/charm/charm-6.5.0.ebuild               | 51 ++++++++--------------
 ...orline.patch => modules-3.2.10-errorline.patch} |  1 -
 .../modules/files/modules-3.2.9c-errorline.patch   |  1 -
 sys-cluster/modules/modules-3.2.10.ebuild          |  6 +--
 18 files changed, 79 insertions(+), 59 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     5bdbd20181a8d1c6e88a852b8c869804ebf450d1
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 26 16:53:22 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Jun 26 16:53:22 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5bdbd201

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-physics/lammps/ChangeLog              | 3 +++
 sci-physics/lammps/lammps-20130526.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

[gentoo-commits] proj/sci:jlec commit in: /

[Justin Lecher]

commit:     c40b625da6a65449986d4c2f7f1d90728531725c
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Fri Jun 21 13:50:53 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 21 13:50:53 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c40b625d

Merge pull request #85 from ercpe/jlec

Changes to the patch files to make the shiftx2 package working again.


 sci-chemistry/shiftx2/ChangeLog                    |  8 +++-
 .../files/shiftx2-1.07_p20120106-java.patch        | 45 +++++++++++++++++++---
 .../files/shiftx2-1.07_p20120106-system.patch      |  6 +--
 3 files changed, 49 insertions(+), 10 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c40b625da6a65449986d4c2f7f1d90728531725c
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Fri Jun 21 13:50:53 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 21 13:50:53 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c40b625d

Merge pull request #85 from ercpe/jlec

Changes to the patch files to make the shiftx2 package working again.


 sci-chemistry/shiftx2/ChangeLog                    |  8 +++-
 .../files/shiftx2-1.07_p20120106-java.patch        | 45 +++++++++++++++++++---
 .../files/shiftx2-1.07_p20120106-system.patch      |  6 +--
 3 files changed, 49 insertions(+), 10 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Honza Macháček]

commit:     43ae215b3409c36d8f51402580ead76fc6624763
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Tue Jun 18 13:55:47 2013 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Tue Jun 18 13:55:47 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=43ae215b

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

Looks like I have broken something. Conflicts are reported in sci-libs/libxc.
Trying desperately to recover.


 sci-chemistry/talosn/ChangeLog                              |  6 ++++++
 ...48.15.55.ebuild => talosn-4.01.2013.148.15.55-r2.ebuild} | 13 +++++++++++--
 2 files changed, 17 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Honza Macháček]

commit:     83a6f8e906f3701f214c034c05285f7106cc5413
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Tue Jun 18 13:54:29 2013 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Tue Jun 18 13:54:29 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=83a6f8e9

The dependency of several packages on sci-libs/libxc modified to reflect correctly the recent change in the upgrade of sci-physics/abinit & friends.


 profiles/package.mask                              |  6 +++
 sci-chemistry/freeon/freeon-2012.05.03.ebuild      |  7 +--
 sci-chemistry/freeon/freeon-9999.ebuild            |  7 +--
 sci-chemistry/mics/ChangeLog                       | 10 ++++
 sci-chemistry/mics/Manifest                        |  1 +
 .../{mgltools-autodocktools => mics}/metadata.xml  |  0
 sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild | 51 +++++++++++++++++++
 sci-chemistry/modeller/ChangeLog                   |  6 +++
 ...odeller-9.12.ebuild => modeller-9.12-r1.ebuild} |  2 +-
 sci-chemistry/talosn/ChangeLog                     | 10 ++++
 sci-chemistry/talosn/Manifest                      |  1 +
 .../metadata.xml                                   |  0
 .../talosn/talosn-4.01.2013.148.15.55.ebuild       | 59 ++++++++++++++++++++++
 sci-libs/bigdft-abi/ChangeLog                      |  4 ++
 sci-libs/bigdft-abi/Manifest                       |  2 -
 sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild        |  5 +-
 sci-libs/libxc/Manifest                            |  2 +-
 sci-libs/libxc/libxc-9999.ebuild                   | 27 ++++++----
 sci-libs/mumps/ChangeLog                           |  5 +-
 sci-libs/mumps/mumps-4.10.0-r2.ebuild              |  5 +-
 sci-physics/abinit/ChangeLog                       |  3 ++
 sci-physics/abinit/Manifest                        |  3 +-
 sci-physics/abinit/abinit-7.2.2.ebuild             |  2 +-
 sci-physics/bigdft/ChangeLog                       |  5 ++
 sci-physics/bigdft/bigdft-1.7_pre24.ebuild         |  2 +-
 sci-physics/elk/ChangeLog                          |  4 ++
 sci-physics/elk/elk-1.4.22.ebuild                  |  2 +-
 27 files changed, 196 insertions(+), 35 deletions(-)

diff --cc profiles/package.mask
index 0c270df,0c270df..f354cdf
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@@ -68,6 -68,6 +68,12 @@@
  >=sci-chemistry/coot-9999
  >=sci-chemistry/pymol-9999
  
++# Honza Macháček <Hloupy.Honza@centrum.cz> (17 June 2013)
++# bigdft moved from sci-libs to sci-physics
++# sci-physics/abinit now uses sci-libs/bigdft-abi instead
++# sci-libs/bigdft should be deleted in 30 days
++sci-libs/bigdft
++
  # Justin Lecher <jlec@gentoo.org> (03 March 2013)
  # Missing deps
  sci-biology/gbrowse
diff --cc sci-chemistry/freeon/freeon-2012.05.03.ebuild
index 99805e0,99805e0..5a9cc6a
--- a/sci-chemistry/freeon/freeon-2012.05.03.ebuild
+++ b/sci-chemistry/freeon/freeon-2012.05.03.ebuild
@@@ -33,11 -33,11 +33,8 @@@ DEPEND="${DEPEND
  S="${WORKDIR}/${REAL_PN}-${REAL_PV}"
  
  src_prepare() {
--	# Get rid of the obsolete internal hdf5
--	rm -r "${S}"/hdf5-1.8.3
--	# as well as of the internal lapack
--	rm -r "${S}"/lapack
--	epatch "${FILESDIR}"/"${P}"-no_internal_libs.patch
++	# Prevent the obsolete internal hdf5 breaking autoconf
++	epatch "${FILESDIR}"/"${P}"-no_internal_hdf5.patch
  	eautoreconf
  }
  
diff --cc sci-chemistry/freeon/freeon-9999.ebuild
index 369e063,369e063..6d02d93
--- a/sci-chemistry/freeon/freeon-9999.ebuild
+++ b/sci-chemistry/freeon/freeon-9999.ebuild
@@@ -31,11 -31,11 +31,8 @@@ DEPEND="${DEPEND
  	virtual/pkgconfig"
  
  src_prepare() {
--	# Get rid of the obsolete internal hdf5
--	rm -r "${S}"/Modules/hdf5-1.8.3
--	# as well as of the internal lapack
--	rm -r "${S}"/Modules/lapack
--	epatch "${FILESDIR}"/"${P}"-no_internal_libs.patch
++	# Prevent the obsolete internal hdf5 breaking autoconf
++	epatch "${FILESDIR}"/"${P}"-no_internal_hdf5.patch
  	eautoreconf
  }
  
diff --cc sci-libs/bigdft-abi/ChangeLog
index 4c48008,4c48008..10ecead
--- a/sci-libs/bigdft-abi/ChangeLog
+++ b/sci-libs/bigdft-abi/ChangeLog
@@@ -2,6 -2,6 +2,10 @@@
  # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
  # $Header: $
  
++  18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
++  bigdft-abi-1.0.4.ebuild:
++  The dependency on sci-libs/libxc modified to allow for 1.2.0-r1.
++
  *bigdft-abi-1.0.4 (17 Jun 2013)
  
    17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
diff --cc sci-libs/bigdft-abi/Manifest
index bd17fc5,bd17fc5..e8a8b97
--- a/sci-libs/bigdft-abi/Manifest
+++ b/sci-libs/bigdft-abi/Manifest
@@@ -1,3 -1,3 +1,1 @@@
--AUX bigdft-abi-1.0.4-tests.tar.bz2 402968 SHA256 11144208456b001f63b75cadce0e9b685054ef8bbc39a76cb08af61d5c86c4fb SHA512 3594d11a8d5834916f44bf6f049630ac9d092df6a7a3171701ef65e5ab56e9d039c2bb4603698cb4935a95189c65d7bf77f44b50617ea8c971a844a2757b3202 WHIRLPOOL 492b92805a4eecb5bb204dbf76acf9a40c790b39708a914e38628a2f4dadc3377eed79f8d986231c006bc8c5be0167af60c36f72212005156e8fe3a3c619281c
  DIST bigdft-abi-1.0.4.tar.gz 8982260 SHA256 345cf49da92275710252d50b4ac8364f2f3c33e8f28d84d7b13ccf6fd0c69310 SHA512 556001d1ffd08be70b97f07a8a150d5d033a4611957180a7a25b41963754e0e3d2bb2a4e9d5b6beb8ff6fb1eb6f4ae9b51633cfe3d7f5a8ed20a85be21031c35 WHIRLPOOL b7c58732b538306f2b9b89b1310d9212cc1bb038fded782e6707e54679013ebc8376d54b5bd1bd51464dc7878fa05102fcba8f70a5d38b4571720c8d57ee3af1
--EBUILD bigdft-abi-1.0.4.ebuild 4232 SHA256 006484b64a83d7971efc05670b77d26114eed87f0d062c39e9b9bf01a4a005ce SHA512 bc34310bf3b4b3999574be8f67db51072a53b2a14fbf340edb72d046989f088b3c12b65f98a781fb5791263ce4c947786ee250dcbe4c162dcd194711321db4b5 WHIRLPOOL 28a1b685e427500acda0e210c9d2e72bbcd24bfe2be1b09112a1aab829d1efe9a896e28b45b42ec7db29c4908bc7cb3b73c83d0ad77accf9269ee9774e310537
diff --cc sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild
index c285d63,c285d63..91e3bac
--- a/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild
+++ b/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild
@@@ -19,7 -19,7 +19,7 @@@ KEYWORDS="~amd64 ~x86 ~amd64-linux
  IUSE="cuda doc etsf_io mpi netcdf openmp opencl test"
  
  RDEPEND="
--	>=sci-libs/libxc-2.0.1[fortran]
++	>=sci-libs/libxc-1.2.0-r1[fortran]
  	virtual/blas
  	virtual/fortran
  	virtual/lapack
@@@ -75,9 -75,9 +75,6 @@@ pkg_setup() 
  }
  
  src_prepare() {
--# 	epatch \
--# 		"${FILESDIR}"/"${P}"-nolib_mods.patch
--#
  	tar -xjf "${FILESDIR}"/"${P}"-tests.tar.bz2 -C "${S}"/tests/DFT/
  	eautoreconf
  }
diff --cc sci-libs/libxc/Manifest
index fa863cf,fa863cf..a85ebc8
--- a/sci-libs/libxc/Manifest
+++ b/sci-libs/libxc/Manifest
@@@ -1,2 -1,2 +1,2 @@@
--DIST libxc-1.1.0.tar.gz 543168 SHA256 b75fb2a73a9e2d75e250cc77b71d5485c8e9b11c3b25c91899c366e217283c57 SHA512 a5ed3a4a7a7abaa11321fe877d01ff00132eab976205213e578cd57fbd2073eea00ce3a3afc188e30ebbd31deb32468c4472313df9992e8d9e3148e6f619936b WHIRLPOOL 8ff70acb2ee65b3373942b71e350fe146f1c205aa4c09dbb22adc04227ba6888482ce412b3e843a9402efd51f9cf6f478f9c65b97305b2035185e59b35484d9f
  DIST libxc-1.2.0.tar.gz 895527 SHA256 ee441c3cde2e2bd87828186aa17f6e4438d17b38634c5d29bb12d3b7554461fb SHA512 3ac0fd07e40db4feb0f0a4ebe1358fdd4de0fff21f6dd369895c658a14cd3bafedbbc374b89f68320401dfcfe16a6230e05403fdaccfcbebb98349ca06593125 WHIRLPOOL 66439bf65a656567c0e52a4ee20b206658a9185bdbd3e045daca00bf01ba0199ccbedea3e5034cf90fbc36dbc04d9666cde8bde46e2577ffd160800f1718bd2a
++DIST libxc-2.0.1.tar.gz 1062846 SHA256 c332f08648ec2bc7ccce83e45a84776215aa5dfebc64fae2a23f2ac546d41ea4 SHA512 c7d87134911fdfd91d985397a3fa990a63cc05d0752f0e2522e41dae0c2f39c43f9bd87ee6eb1972ab92b1aedeefad55a33ad84b1c66032e61ca03c87db02c5b WHIRLPOOL 16a5b999bb60177fde1371421f41f35736af4fcf8df123318ea438ffd34f487dcbadc95124ab9cf6ab2edeadd7983c56e0ca9d84bf528254de1f2a003addd402
diff --cc sci-libs/libxc/libxc-9999.ebuild
index baf29d4,baf29d4..2432915
--- a/sci-libs/libxc/libxc-9999.ebuild
+++ b/sci-libs/libxc/libxc-9999.ebuild
@@@ -1,8 -1,8 +1,8 @@@
--# Copyright 1999-2012 Gentoo Foundation
++# Copyright 1999-2013 Gentoo Foundation
  # Distributed under the terms of the GNU General Public License v2
  # $Header: $
  
--EAPI=4
++EAPI=5
  
  inherit autotools-utils fortran-2 multilib subversion
  
@@@ -14,7 -14,7 +14,7 @@@ ESVN_BOOTSTRAP="eautoreconf -i
  LICENSE="LGPL-3"
  SLOT="0"
  KEYWORDS=""
--IUSE="fortran static-libs"
++IUSE="fortran static-libs -test"
  
  MAKEOPTS+=" -j1"
  
@@@ -31,14 -31,14 +31,21 @@@ src_configure() 
  	autotools-utils_src_configure
  }
  
++## Upstream recommends not running the test suite because it requires
++## human expert interpretation to determine whether output is an error or
++## expected under certain circumstances. Nevertheless, experts might want the option.
++# The autotools src_test function modified not to die. Runs emake check in build directory.
++src_test() {
++	debug-print-function ${FUNCNAME} "$@"
++
++	_check_build_dir
++	pushd "${BUILD_DIR}" > /dev/null || die
++	make check || ewarn "Make check failed. See above for details."
++	einfo "emake check done"
++	popd > /dev/null || die
++}
++
  src_install() {
  	autotools-utils_src_install
  
--	if use fortran; then
--		insinto /usr/$(get_libdir)/finclude
--		pushd "${AUTOTOOLS_BUILD_DIR}"/src >/dev/null
--		doins *.mod || die
--		rm -f "${D}"/usr/include/*.mod || die
--		popd >/dev/null
--	fi
  }
diff --cc sci-physics/abinit/ChangeLog
index a4f623b,a4f623b..2f76ad0
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@@ -2,6 -2,6 +2,9 @@@
  # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
  # $Header: $
  
++  18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> abinit-7.2.2.ebuild:
++  The dependency on sci-libs/libxc modified to allow for 1.2.0-r1.
++
  *abinit-7.2.2 (17 Jun 2013)
  
    17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> -abinit-7.0.4.ebuild,
diff --cc sci-physics/abinit/Manifest
index dee0365,dee0365..f000cdc
--- a/sci-physics/abinit/Manifest
+++ b/sci-physics/abinit/Manifest
@@@ -1,2 -1,2 +1,1 @@@
--DIST abinit-7.0.4.tar.gz 61715030 SHA256 b3ad895b75b92b3ff05e873d42d0b26f6e6113b9de4579966f7b6d1b49d6004e SHA512 8edfe4019c968e6f912d0678fe331fc8a6ce2848f1b16973336d4181d010a776ed1ea2c5500499dac895d9d773d72165e20524705cf8928f91ede873272b0417 WHIRLPOOL 35da8681a68e435b460a11112e6cf6990fdf141d53d5849be45225d50e803e2bfc65cb05e5e576c704411be5734e47ed2e4ccca1fd1689311bd4febea937f0f8
--DIST abinit-7.0.5.tar.gz 61711550 SHA256 b16556aa05448781d872ab18f76ca6446a52be9eeed8d22015a0b63f4adf0f54 SHA512 007292cc7cdf459a5d62e907b29009d9496955952b5f491fa9183a5abb86dbf48020eb435b784d74037e381d65d2255a2b9a130322ee9bfecbff8ca075488ecd WHIRLPOOL 74d83a3a05817eaca402ace1b7ec3c3a6db3697a7ca0166549aee8155edfa2a7c8d516e2ae210a6f0e855f72617d704785bbb10e3a3ee262140964913608a307
++DIST abinit-7.2.2.tar.gz 63683267 SHA256 96f83e3af63e993cb886d9d6cd1c4fac04d50b5e460d5620330441050a909533 SHA512 fbc4898ae4625e12ea22d8f2da63e037eb947320fedf800bd40bd7e0015633ce54b7cb224cee3fc931d015774c51df5f8594ebe26a409cb0325e7a3ab0bf5e4a WHIRLPOOL a149d7ecea9b2b19b94b4e873f1924ce5fe221e037c642d6428727b552dc0c428b288551dda708286995da26080171c385a3ef3ad3766e065073139d4ef0f2e8
diff --cc sci-physics/abinit/abinit-7.2.2.ebuild
index 0a2b49b,0a2b49b..a420f51
--- a/sci-physics/abinit/abinit-7.2.2.ebuild
+++ b/sci-physics/abinit/abinit-7.2.2.ebuild
@@@ -16,7 -16,7 +16,7 @@@ KEYWORDS="~amd64 ~x86
  IUSE="cuda cuda-double -debug +etsf_io +fftw +fftw-threads +fox gsl gui +hdf5 libabinit mpi +netcdf openmp python -test +threads -vdwxc"
  
  RDEPEND="~sci-libs/bigdft-abi-1.0.4
--	>=sci-libs/libxc-2.0.1[fortran]
++	>=sci-libs/libxc-1.2.0-r1[fortran]
  	>=sci-physics/atompaw-3.0.1.9-r1[libxc]
  	etsf_io? ( >=sci-libs/etsf_io-1.0.3-r2 )
  	fox? ( >=sci-libs/fox-4.1.2-r2[sax] )
diff --cc sci-physics/bigdft/ChangeLog
index 0c32817,0c32817..3e78db9
--- a/sci-physics/bigdft/ChangeLog
+++ b/sci-physics/bigdft/ChangeLog
@@@ -2,6 -2,6 +2,11 @@@
  # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
  # $Header: $
  
++  18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
++  bigdft-1.7_pre24.ebuild:
++  The dependency on sci-libs/libxc corrected to reflect the recent change in
++  the upgrade of sci-physics/abinit & friends.
++
  *bigdft-1.7_pre24 (17 Jun 2013)
  
    17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
diff --cc sci-physics/bigdft/bigdft-1.7_pre24.ebuild
index d74906a,d74906a..4a354aa
--- a/sci-physics/bigdft/bigdft-1.7_pre24.ebuild
+++ b/sci-physics/bigdft/bigdft-1.7_pre24.ebuild
@@@ -20,7 -20,7 +20,7 @@@ KEYWORDS="~amd64 ~x86 ~amd64-linux
  IUSE="cuda doc etsf_io mpi netcdf openmp opencl test"
  
  RDEPEND="
--	>=sci-libs/libxc-1.0[fortran]
++	>=sci-libs/libxc-1.2.0-r1[fortran]
  	virtual/blas
  	virtual/fortran
  	virtual/lapack
diff --cc sci-physics/elk/ChangeLog
index 28ac97d,28ac97d..2a837bc
--- a/sci-physics/elk/ChangeLog
+++ b/sci-physics/elk/ChangeLog
@@@ -2,6 -2,6 +2,10 @@@
  # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
  # $Header: $
  
++  18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> elk-1.4.22.ebuild:
++  The dependency on sci-libs/libxc adapted to its recent change in the upgrade
++  of sci-physics/abinit & friends.
++
    21 Feb 2013; Justin Lecher <jlec@gentoo.org> elk-1.4.22.ebuild:
    Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config;
    add missing dep on virtual/pkgconfig; cleaning of ebuild
diff --cc sci-physics/elk/elk-1.4.22.ebuild
index ab7cd8d,ab7cd8d..5e99d05
--- a/sci-physics/elk/elk-1.4.22.ebuild
+++ b/sci-physics/elk/elk-1.4.22.ebuild
@@@ -19,7 -19,7 +19,7 @@@ RDEPEND=
  	lapack? (
  		virtual/blas
  		virtual/lapack )
--	libxc? ( =sci-libs/libxc-1*[fortran] )
++	libxc? ( >=sci-libs/libxc-1.2.0-r1[fortran] )
  	mpi? ( virtual/mpi )"
  DEPEND="${RDEPEND}
  	perl? ( dev-lang/perl )

[gentoo-commits] proj/sci:master commit in: /

[Honza Macháček]

commit:     4c8b2b623e9305166c334d9c5d3d219cb6b78129
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Mon Jun 17 18:58:38 2013 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Mon Jun 17 18:58:38 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4c8b2b62

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

Trying to commit a complex change of sci-physics/abinit and its libraries, I took some
time to put everything in pace so I have to pull some updates before puhing my work. Something
I do not fully understand is happening. If it breaks things I will try to clean up, as soon as
I understand the situation.


 app-text/jabref/ChangeLog                          | 10 +++++
 ...jabref-2.10b.ebuild => jabref-2.10_beta.ebuild} |  8 +++-
 media-gfx/librecad/ChangeLog                       |  6 +++
 media-gfx/librecad/Manifest                        |  4 +-
 media-gfx/librecad/files/1.0.0_rc2-gcc4.6.patch    | 38 -----------------
 .../files/librecad-1.0.0_rc2-version.patch         | 11 -----
 media-gfx/librecad/librecad-1.0.2.ebuild           | 45 --------------------
 media-gfx/librecad/librecad-2.0.0_beta5.ebuild     | 48 ----------------------
 media-gfx/librecad/librecad-2.0.0_rc1.ebuild       | 27 ++++++------
 media-gfx/librecad/metadata.xml                    | 23 ++++++-----
 10 files changed, 48 insertions(+), 172 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Honza Macháček]

commit:     4c8b2b623e9305166c334d9c5d3d219cb6b78129
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Mon Jun 17 18:58:38 2013 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Mon Jun 17 18:58:38 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4c8b2b62

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

Trying to commit a complex change of sci-physics/abinit and its libraries, I took some
time to put everything in pace so I have to pull some updates before puhing my work. Something
I do not fully understand is happening. If it breaks things I will try to clean up, as soon as
I understand the situation.


 app-text/jabref/ChangeLog                          | 10 +++++
 ...jabref-2.10b.ebuild => jabref-2.10_beta.ebuild} |  8 +++-
 media-gfx/librecad/ChangeLog                       |  6 +++
 media-gfx/librecad/Manifest                        |  4 +-
 media-gfx/librecad/files/1.0.0_rc2-gcc4.6.patch    | 38 -----------------
 .../files/librecad-1.0.0_rc2-version.patch         | 11 -----
 media-gfx/librecad/librecad-1.0.2.ebuild           | 45 --------------------
 media-gfx/librecad/librecad-2.0.0_beta5.ebuild     | 48 ----------------------
 media-gfx/librecad/librecad-2.0.0_rc1.ebuild       | 27 ++++++------
 media-gfx/librecad/metadata.xml                    | 23 ++++++-----
 10 files changed, 48 insertions(+), 172 deletions(-)

[gentoo-commits] proj/sci:jlec commit in: /

[Justin Lecher]

commit:     bccb9ee1e70dc0b9fba0b94cf87184fb0eb94d86
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Tue Jun 11 12:03:08 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 11 12:03:08 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bccb9ee1

Merge pull request #79 from gentryx/master

Fixed compilation of sys-cluster/modules with tcl 8.5.14 and older


 sys-cluster/modules/modules-3.2.9c-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     bccb9ee1e70dc0b9fba0b94cf87184fb0eb94d86
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Tue Jun 11 12:03:08 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 11 12:03:08 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bccb9ee1

Merge pull request #79 from gentryx/master

Fixed compilation of sys-cluster/modules with tcl 8.5.14 and older


 sys-cluster/modules/modules-3.2.9c-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:jlec commit in: /

[Justin Lecher]

commit:     c644db6fdedd51e557ca30e22152029d327eaf68
Author:     layman <layman <AT> localhost>
AuthorDate: Wed Jun 12 10:43:12 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 12 10:43:12 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c644db6f

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 dev-java/jgraphx/ChangeLog                         |  7 +++-
 dev-java/jgraphx/Manifest                          |  3 --
 dev-java/jgraphx/jgraphx-1.2.0.7.ebuild            | 44 ----------------------
 dev-java/jgraphx/jgraphx-1.3.0.2.ebuild            | 44 ----------------------
 dev-java/jgraphx/jgraphx-1.4.1.0.ebuild            | 18 +++++----
 dev-java/jgraphx/jgraphx-1.4.1.2.ebuild            | 44 ----------------------
 dev-java/jgraphx/jgraphx-1.8.0.6.ebuild            | 20 ++++++----
 dev-java/jgraphx/metadata.xml                      |  4 +-
 dev-libs/asmjit/ChangeLog                          |  8 +++-
 dev-libs/asmjit/Manifest                           |  2 +-
 ...-1.0_beta_p2.ebuild => asmjit-1.0_beta4.ebuild} |  6 +--
 dev-libs/asmjit/metadata.xml                       | 12 +++---
 media-gfx/librecad/ChangeLog                       |  3 ++
 media-gfx/librecad/librecad-9999.ebuild            | 21 +++++------
 profiles/arch/amd64/no-multilib/package.mask       | 27 -------------
 profiles/arch/amd64/package.use.mask               | 23 -----------
 sci-biology/lastz/ChangeLog                        | 12 +++++-
 sci-biology/lastz/Manifest                         |  3 +-
 sci-biology/lastz/files/lastz-1.03.34-build.patch  | 43 +++++++++++++++++++++
 .../{lastz-1.02.00.ebuild => lastz-1.03.34.ebuild} | 28 ++++++++------
 sci-biology/lastz/metadata.xml                     | 10 ++---
 sci-biology/phylobayes/ChangeLog                   | 10 -----
 sci-biology/phylobayes/Manifest                    |  2 -
 sci-biology/phylobayes/metadata.xml                |  9 -----
 sci-biology/phylobayes/phylobayes-3.3b.ebuild      | 37 ------------------
 sci-chemistry/rosetta/ChangeLog                    |  7 ++++
 sci-chemistry/rosetta/Manifest                     |  1 +
 ...-3.4-gcc4.7.patch => rosetta-3.4-gcc4.78.patch} |  2 +-
 .../rosetta/files/rosetta-3.4-lange-fix.patch      | 22 +++++++++++
 sci-chemistry/rosetta/metadata.xml                 |  1 +
 sci-chemistry/rosetta/rosetta-3.4.ebuild           | 21 ++++++++---
 sys-cluster/modules/modules-3.2.9c-r1.ebuild       |  2 +-
 32 files changed, 185 insertions(+), 311 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c644db6fdedd51e557ca30e22152029d327eaf68
Author:     layman <layman <AT> localhost>
AuthorDate: Wed Jun 12 10:43:12 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 12 10:43:12 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c644db6f

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 dev-java/jgraphx/ChangeLog                         |  7 +++-
 dev-java/jgraphx/Manifest                          |  3 --
 dev-java/jgraphx/jgraphx-1.2.0.7.ebuild            | 44 ----------------------
 dev-java/jgraphx/jgraphx-1.3.0.2.ebuild            | 44 ----------------------
 dev-java/jgraphx/jgraphx-1.4.1.0.ebuild            | 18 +++++----
 dev-java/jgraphx/jgraphx-1.4.1.2.ebuild            | 44 ----------------------
 dev-java/jgraphx/jgraphx-1.8.0.6.ebuild            | 20 ++++++----
 dev-java/jgraphx/metadata.xml                      |  4 +-
 dev-libs/asmjit/ChangeLog                          |  8 +++-
 dev-libs/asmjit/Manifest                           |  2 +-
 ...-1.0_beta_p2.ebuild => asmjit-1.0_beta4.ebuild} |  6 +--
 dev-libs/asmjit/metadata.xml                       | 12 +++---
 media-gfx/librecad/ChangeLog                       |  3 ++
 media-gfx/librecad/librecad-9999.ebuild            | 21 +++++------
 profiles/arch/amd64/no-multilib/package.mask       | 27 -------------
 profiles/arch/amd64/package.use.mask               | 23 -----------
 sci-biology/lastz/ChangeLog                        | 12 +++++-
 sci-biology/lastz/Manifest                         |  3 +-
 sci-biology/lastz/files/lastz-1.03.34-build.patch  | 43 +++++++++++++++++++++
 .../{lastz-1.02.00.ebuild => lastz-1.03.34.ebuild} | 28 ++++++++------
 sci-biology/lastz/metadata.xml                     | 10 ++---
 sci-biology/phylobayes/ChangeLog                   | 10 -----
 sci-biology/phylobayes/Manifest                    |  2 -
 sci-biology/phylobayes/metadata.xml                |  9 -----
 sci-biology/phylobayes/phylobayes-3.3b.ebuild      | 37 ------------------
 sci-chemistry/rosetta/ChangeLog                    |  7 ++++
 sci-chemistry/rosetta/Manifest                     |  1 +
 ...-3.4-gcc4.7.patch => rosetta-3.4-gcc4.78.patch} |  2 +-
 .../rosetta/files/rosetta-3.4-lange-fix.patch      | 22 +++++++++++
 sci-chemistry/rosetta/metadata.xml                 |  1 +
 sci-chemistry/rosetta/rosetta-3.4.ebuild           | 21 ++++++++---
 sys-cluster/modules/modules-3.2.9c-r1.ebuild       |  2 +-
 32 files changed, 185 insertions(+), 311 deletions(-)

[gentoo-commits] proj/sci:jlec commit in: /

[Justin Lecher]

commit:     9b700ba0279d32f705eeaf56d91164d18586254c
Author:     layman <layman <AT> localhost>
AuthorDate: Tue Jun 11 06:52:49 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 11 06:52:49 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9b700ba0

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 media-gfx/librecad/ChangeLog                       |  3 +
 media-gfx/librecad/Manifest                        |  1 +
 ....0.0_beta5.ebuild => librecad-2.0.0_rc1.ebuild} |  0
 sci-biology/psychopy/ChangeLog                     |  8 +++
 sci-biology/psychopy/metadata.xml                  |  8 +--
 sci-biology/psychopy/psychopy-1.75.01.ebuild       | 24 ++++---
 sci-biology/psychopy/psychopy-9999.ebuild          | 18 ++---
 sci-chemistry/mgltools-autodocktools/ChangeLog     |  8 +++
 sci-chemistry/mgltools-autodocktools/Manifest      |  1 -
 .../mgltools-autodocktools-1.5.4-r2.ebuild         | 77 ----------------------
 .../mgltools-autodocktools-1.5.6.ebuild            |  6 +-
 sci-chemistry/mgltools-bhtree/ChangeLog            |  4 ++
 sci-chemistry/mgltools-bhtree/Manifest             |  1 -
 .../mgltools-bhtree-1.5.4-r1.ebuild                | 54 ---------------
 .../mgltools-bhtree/mgltools-bhtree-1.5.6.ebuild   |  2 +-
 sci-chemistry/mgltools-cmolkit/ChangeLog           |  4 ++
 sci-chemistry/mgltools-cmolkit/Manifest            |  1 -
 .../mgltools-cmolkit-1.5.4-r1.ebuild               | 55 ----------------
 .../mgltools-cmolkit/mgltools-cmolkit-1.5.6.ebuild |  2 +-
 sci-chemistry/mgltools-dejavu/ChangeLog            |  4 ++
 sci-chemistry/mgltools-dejavu/Manifest             |  1 -
 .../mgltools-dejavu-1.5.4-r1.ebuild                | 55 ----------------
 .../mgltools-dejavu/mgltools-dejavu-1.5.6.ebuild   |  2 +-
 sci-chemistry/mgltools-geomutils/ChangeLog         |  4 ++
 sci-chemistry/mgltools-geomutils/Manifest          |  1 -
 .../mgltools-geomutils-1.5.4-r1.ebuild             | 57 ----------------
 .../mgltools-geomutils-1.5.6.ebuild                |  2 +-
 sci-chemistry/mgltools-gle/ChangeLog               |  4 ++
 sci-chemistry/mgltools-gle/Manifest                |  1 -
 .../mgltools-gle/mgltools-gle-1.5.4-r1.ebuild      | 53 ---------------
 .../mgltools-gle/mgltools-gle-1.5.6.ebuild         |  2 +-
 sci-chemistry/mgltools-mglutil/ChangeLog           |  4 ++
 sci-chemistry/mgltools-mglutil/Manifest            |  1 -
 .../mgltools-mglutil-1.5.4-r1.ebuild               | 57 ----------------
 .../mgltools-mglutil/mgltools-mglutil-1.5.6.ebuild |  2 +-
 sci-chemistry/mgltools-molkit/ChangeLog            |  4 ++
 sci-chemistry/mgltools-molkit/Manifest             |  1 -
 .../mgltools-molkit-1.5.4-r1.ebuild                | 56 ----------------
 .../mgltools-molkit/mgltools-molkit-1.5.6.ebuild   |  2 +-
 sci-chemistry/mgltools-networkeditor/ChangeLog     |  4 ++
 sci-chemistry/mgltools-networkeditor/Manifest      |  1 -
 .../mgltools-networkeditor-1.5.4-r1.ebuild         | 56 ----------------
 .../mgltools-networkeditor-1.5.6.ebuild            |  2 +-
 sci-chemistry/mgltools-opengltk/ChangeLog          |  4 ++
 sci-chemistry/mgltools-opengltk/Manifest           |  1 -
 .../mgltools-opengltk-1.5.4-r2.ebuild              | 63 ------------------
 .../mgltools-opengltk-1.5.6.ebuild                 |  2 +-
 sci-chemistry/mgltools-pmv/ChangeLog               |  4 ++
 sci-chemistry/mgltools-pmv/Manifest                |  1 -
 .../mgltools-pmv/mgltools-pmv-1.5.4-r1.ebuild      | 63 ------------------
 .../mgltools-pmv/mgltools-pmv-1.5.6.ebuild         |  2 +-
 sci-chemistry/mgltools-pyautodock/ChangeLog        |  4 ++
 sci-chemistry/mgltools-pyautodock/Manifest         |  1 -
 .../mgltools-pyautodock-1.5.4-r1.ebuild            | 54 ---------------
 .../mgltools-pyautodock-1.5.6.ebuild               |  2 +-
 sci-chemistry/mgltools-pybabel/ChangeLog           |  4 ++
 sci-chemistry/mgltools-pybabel/Manifest            |  1 -
 .../mgltools-pybabel-1.5.4-r1.ebuild               | 56 ----------------
 .../mgltools-pybabel/mgltools-pybabel-1.5.6.ebuild |  2 +-
 sci-chemistry/mgltools-pyglf/ChangeLog             |  4 ++
 sci-chemistry/mgltools-pyglf/Manifest              |  1 -
 .../mgltools-pyglf/mgltools-pyglf-1.5.4-r1.ebuild  | 54 ---------------
 .../mgltools-pyglf/mgltools-pyglf-1.5.6.ebuild     |  2 +-
 sci-chemistry/mgltools-qslimlib/ChangeLog          |  4 ++
 sci-chemistry/mgltools-qslimlib/Manifest           |  1 -
 .../mgltools-qslimlib-1.5.4-r1.ebuild              | 56 ----------------
 .../mgltools-qslimlib-1.5.6.ebuild                 |  2 +-
 sci-chemistry/mgltools-scenario/ChangeLog          | 34 ----------
 sci-chemistry/mgltools-scenario/Manifest           |  1 -
 sci-chemistry/mgltools-scenario/metadata.xml       |  5 --
 .../mgltools-scenario-1.5.4-r1.ebuild              | 58 ----------------
 sci-chemistry/mgltools-sff/ChangeLog               |  4 ++
 sci-chemistry/mgltools-sff/Manifest                |  1 -
 .../mgltools-sff/mgltools-sff-1.5.4-r1.ebuild      | 55 ----------------
 .../mgltools-sff/mgltools-sff-1.5.6.ebuild         |  2 +-
 sci-chemistry/mgltools-stride/ChangeLog            | 35 ----------
 sci-chemistry/mgltools-stride/Manifest             |  1 -
 sci-chemistry/mgltools-stride/metadata.xml         |  5 --
 .../mgltools-stride-1.5.4-r1.ebuild                | 54 ---------------
 sci-chemistry/mgltools-support/ChangeLog           |  4 ++
 sci-chemistry/mgltools-support/Manifest            |  1 -
 .../mgltools-support-1.5.4-r1.ebuild               | 56 ----------------
 .../mgltools-support/mgltools-support-1.5.6.ebuild |  2 +-
 sci-chemistry/mgltools-symserv/ChangeLog           |  4 ++
 sci-chemistry/mgltools-symserv/Manifest            |  1 -
 .../mgltools-symserv-1.5.4-r1.ebuild               | 54 ---------------
 .../mgltools-symserv/mgltools-symserv-1.5.6.ebuild |  2 +-
 sci-chemistry/mgltools-utpackages/ChangeLog        |  4 ++
 sci-chemistry/mgltools-utpackages/Manifest         |  1 -
 .../mgltools-utpackages-1.5.4-r1.ebuild            | 56 ----------------
 .../mgltools-utpackages-1.5.6.ebuild               |  2 +-
 sci-chemistry/mgltools-viewer-framework/ChangeLog  |  5 ++
 sci-chemistry/mgltools-viewer-framework/Manifest   |  1 -
 .../mgltools-viewer-framework-1.5.4-r2.ebuild      | 58 ----------------
 .../mgltools-viewer-framework-1.5.6.ebuild         |  2 +-
 sci-chemistry/mgltools-vision/ChangeLog            |  4 ++
 sci-chemistry/mgltools-vision/Manifest             |  1 -
 .../mgltools-vision-1.5.4-r1.ebuild                | 64 ------------------
 .../mgltools-vision/mgltools-vision-1.5.6.ebuild   |  2 +-
 sci-chemistry/mgltools-visionlib/ChangeLog         |  4 ++
 sci-chemistry/mgltools-visionlib/Manifest          |  1 -
 .../mgltools-visionlib-1.5.4-r1.ebuild             | 53 ---------------
 .../mgltools-visionlib-1.5.6.ebuild                |  2 +-
 sci-chemistry/mgltools-volume/ChangeLog            |  4 ++
 sci-chemistry/mgltools-volume/Manifest             |  1 -
 .../mgltools-volume-1.5.4-r1.ebuild                | 55 ----------------
 .../mgltools-volume/mgltools-volume-1.5.6.ebuild   |  2 +-
 sci-chemistry/mgltools-webservices/ChangeLog       |  4 ++
 sci-chemistry/mgltools-webservices/Manifest        |  1 -
 .../mgltools-webservices-1.5.4-r2.ebuild           | 50 --------------
 .../mgltools-webservices-1.5.6.ebuild              |  2 +-
 sci-chemistry/mgltools/ChangeLog                   |  7 ++
 sci-chemistry/mgltools/Manifest                    |  1 -
 sci-chemistry/mgltools/mgltools-1.5.4.ebuild       | 42 ------------
 sci-chemistry/mgltools/mgltools-1.5.6.ebuild       |  4 +-
 115 files changed, 173 insertions(+), 1680 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     9b700ba0279d32f705eeaf56d91164d18586254c
Author:     layman <layman <AT> localhost>
AuthorDate: Tue Jun 11 06:52:49 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 11 06:52:49 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9b700ba0

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 media-gfx/librecad/ChangeLog                       |  3 +
 media-gfx/librecad/Manifest                        |  1 +
 ....0.0_beta5.ebuild => librecad-2.0.0_rc1.ebuild} |  0
 sci-biology/psychopy/ChangeLog                     |  8 +++
 sci-biology/psychopy/metadata.xml                  |  8 +--
 sci-biology/psychopy/psychopy-1.75.01.ebuild       | 24 ++++---
 sci-biology/psychopy/psychopy-9999.ebuild          | 18 ++---
 sci-chemistry/mgltools-autodocktools/ChangeLog     |  8 +++
 sci-chemistry/mgltools-autodocktools/Manifest      |  1 -
 .../mgltools-autodocktools-1.5.4-r2.ebuild         | 77 ----------------------
 .../mgltools-autodocktools-1.5.6.ebuild            |  6 +-
 sci-chemistry/mgltools-bhtree/ChangeLog            |  4 ++
 sci-chemistry/mgltools-bhtree/Manifest             |  1 -
 .../mgltools-bhtree-1.5.4-r1.ebuild                | 54 ---------------
 .../mgltools-bhtree/mgltools-bhtree-1.5.6.ebuild   |  2 +-
 sci-chemistry/mgltools-cmolkit/ChangeLog           |  4 ++
 sci-chemistry/mgltools-cmolkit/Manifest            |  1 -
 .../mgltools-cmolkit-1.5.4-r1.ebuild               | 55 ----------------
 .../mgltools-cmolkit/mgltools-cmolkit-1.5.6.ebuild |  2 +-
 sci-chemistry/mgltools-dejavu/ChangeLog            |  4 ++
 sci-chemistry/mgltools-dejavu/Manifest             |  1 -
 .../mgltools-dejavu-1.5.4-r1.ebuild                | 55 ----------------
 .../mgltools-dejavu/mgltools-dejavu-1.5.6.ebuild   |  2 +-
 sci-chemistry/mgltools-geomutils/ChangeLog         |  4 ++
 sci-chemistry/mgltools-geomutils/Manifest          |  1 -
 .../mgltools-geomutils-1.5.4-r1.ebuild             | 57 ----------------
 .../mgltools-geomutils-1.5.6.ebuild                |  2 +-
 sci-chemistry/mgltools-gle/ChangeLog               |  4 ++
 sci-chemistry/mgltools-gle/Manifest                |  1 -
 .../mgltools-gle/mgltools-gle-1.5.4-r1.ebuild      | 53 ---------------
 .../mgltools-gle/mgltools-gle-1.5.6.ebuild         |  2 +-
 sci-chemistry/mgltools-mglutil/ChangeLog           |  4 ++
 sci-chemistry/mgltools-mglutil/Manifest            |  1 -
 .../mgltools-mglutil-1.5.4-r1.ebuild               | 57 ----------------
 .../mgltools-mglutil/mgltools-mglutil-1.5.6.ebuild |  2 +-
 sci-chemistry/mgltools-molkit/ChangeLog            |  4 ++
 sci-chemistry/mgltools-molkit/Manifest             |  1 -
 .../mgltools-molkit-1.5.4-r1.ebuild                | 56 ----------------
 .../mgltools-molkit/mgltools-molkit-1.5.6.ebuild   |  2 +-
 sci-chemistry/mgltools-networkeditor/ChangeLog     |  4 ++
 sci-chemistry/mgltools-networkeditor/Manifest      |  1 -
 .../mgltools-networkeditor-1.5.4-r1.ebuild         | 56 ----------------
 .../mgltools-networkeditor-1.5.6.ebuild            |  2 +-
 sci-chemistry/mgltools-opengltk/ChangeLog          |  4 ++
 sci-chemistry/mgltools-opengltk/Manifest           |  1 -
 .../mgltools-opengltk-1.5.4-r2.ebuild              | 63 ------------------
 .../mgltools-opengltk-1.5.6.ebuild                 |  2 +-
 sci-chemistry/mgltools-pmv/ChangeLog               |  4 ++
 sci-chemistry/mgltools-pmv/Manifest                |  1 -
 .../mgltools-pmv/mgltools-pmv-1.5.4-r1.ebuild      | 63 ------------------
 .../mgltools-pmv/mgltools-pmv-1.5.6.ebuild         |  2 +-
 sci-chemistry/mgltools-pyautodock/ChangeLog        |  4 ++
 sci-chemistry/mgltools-pyautodock/Manifest         |  1 -
 .../mgltools-pyautodock-1.5.4-r1.ebuild            | 54 ---------------
 .../mgltools-pyautodock-1.5.6.ebuild               |  2 +-
 sci-chemistry/mgltools-pybabel/ChangeLog           |  4 ++
 sci-chemistry/mgltools-pybabel/Manifest            |  1 -
 .../mgltools-pybabel-1.5.4-r1.ebuild               | 56 ----------------
 .../mgltools-pybabel/mgltools-pybabel-1.5.6.ebuild |  2 +-
 sci-chemistry/mgltools-pyglf/ChangeLog             |  4 ++
 sci-chemistry/mgltools-pyglf/Manifest              |  1 -
 .../mgltools-pyglf/mgltools-pyglf-1.5.4-r1.ebuild  | 54 ---------------
 .../mgltools-pyglf/mgltools-pyglf-1.5.6.ebuild     |  2 +-
 sci-chemistry/mgltools-qslimlib/ChangeLog          |  4 ++
 sci-chemistry/mgltools-qslimlib/Manifest           |  1 -
 .../mgltools-qslimlib-1.5.4-r1.ebuild              | 56 ----------------
 .../mgltools-qslimlib-1.5.6.ebuild                 |  2 +-
 sci-chemistry/mgltools-scenario/ChangeLog          | 34 ----------
 sci-chemistry/mgltools-scenario/Manifest           |  1 -
 sci-chemistry/mgltools-scenario/metadata.xml       |  5 --
 .../mgltools-scenario-1.5.4-r1.ebuild              | 58 ----------------
 sci-chemistry/mgltools-sff/ChangeLog               |  4 ++
 sci-chemistry/mgltools-sff/Manifest                |  1 -
 .../mgltools-sff/mgltools-sff-1.5.4-r1.ebuild      | 55 ----------------
 .../mgltools-sff/mgltools-sff-1.5.6.ebuild         |  2 +-
 sci-chemistry/mgltools-stride/ChangeLog            | 35 ----------
 sci-chemistry/mgltools-stride/Manifest             |  1 -
 sci-chemistry/mgltools-stride/metadata.xml         |  5 --
 .../mgltools-stride-1.5.4-r1.ebuild                | 54 ---------------
 sci-chemistry/mgltools-support/ChangeLog           |  4 ++
 sci-chemistry/mgltools-support/Manifest            |  1 -
 .../mgltools-support-1.5.4-r1.ebuild               | 56 ----------------
 .../mgltools-support/mgltools-support-1.5.6.ebuild |  2 +-
 sci-chemistry/mgltools-symserv/ChangeLog           |  4 ++
 sci-chemistry/mgltools-symserv/Manifest            |  1 -
 .../mgltools-symserv-1.5.4-r1.ebuild               | 54 ---------------
 .../mgltools-symserv/mgltools-symserv-1.5.6.ebuild |  2 +-
 sci-chemistry/mgltools-utpackages/ChangeLog        |  4 ++
 sci-chemistry/mgltools-utpackages/Manifest         |  1 -
 .../mgltools-utpackages-1.5.4-r1.ebuild            | 56 ----------------
 .../mgltools-utpackages-1.5.6.ebuild               |  2 +-
 sci-chemistry/mgltools-viewer-framework/ChangeLog  |  5 ++
 sci-chemistry/mgltools-viewer-framework/Manifest   |  1 -
 .../mgltools-viewer-framework-1.5.4-r2.ebuild      | 58 ----------------
 .../mgltools-viewer-framework-1.5.6.ebuild         |  2 +-
 sci-chemistry/mgltools-vision/ChangeLog            |  4 ++
 sci-chemistry/mgltools-vision/Manifest             |  1 -
 .../mgltools-vision-1.5.4-r1.ebuild                | 64 ------------------
 .../mgltools-vision/mgltools-vision-1.5.6.ebuild   |  2 +-
 sci-chemistry/mgltools-visionlib/ChangeLog         |  4 ++
 sci-chemistry/mgltools-visionlib/Manifest          |  1 -
 .../mgltools-visionlib-1.5.4-r1.ebuild             | 53 ---------------
 .../mgltools-visionlib-1.5.6.ebuild                |  2 +-
 sci-chemistry/mgltools-volume/ChangeLog            |  4 ++
 sci-chemistry/mgltools-volume/Manifest             |  1 -
 .../mgltools-volume-1.5.4-r1.ebuild                | 55 ----------------
 .../mgltools-volume/mgltools-volume-1.5.6.ebuild   |  2 +-
 sci-chemistry/mgltools-webservices/ChangeLog       |  4 ++
 sci-chemistry/mgltools-webservices/Manifest        |  1 -
 .../mgltools-webservices-1.5.4-r2.ebuild           | 50 --------------
 .../mgltools-webservices-1.5.6.ebuild              |  2 +-
 sci-chemistry/mgltools/ChangeLog                   |  7 ++
 sci-chemistry/mgltools/Manifest                    |  1 -
 sci-chemistry/mgltools/mgltools-1.5.4.ebuild       | 42 ------------
 sci-chemistry/mgltools/mgltools-1.5.6.ebuild       |  4 +-
 115 files changed, 173 insertions(+), 1680 deletions(-)

[gentoo-commits] proj/sci:fixing commit in: /

[Justin Lecher]

commit:     e1e48799c623338fedab433347c64dfce9b9aebe
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 16 20:18:52 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 16 20:18:52 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e1e48799

Merge branch 'fixing'

* fixing:
  sci-biology/twinscan: Bump to EAPI=5 and fix license
  sci-biology/ssaha2-bin: Version Bump; restrict license; add QA_PREBUILT for binaries
  sci-biology/smalt-bin: Version Bump; restrict license; add QA_PREBUILT for binaries
  sci-biology/sequin: Version BUmp; restrcit license; add QA_PREBUILT for binaries; install html files into sys path
  sci-biology/quicktree: Bump to EAPI=5 and fix license
  sci-biology/gap2caf: Bump to EAPI=5 and fix license; make it build with eautoreconf
  sci-biology/erpin: Bump to EAPI=5 and respect FLAGS / AR
  sci-biology/clover: Version BUmp; fixed license; respect LDFLAGS


 sci-biology/clover/ChangeLog                       |  6 ++-
 sci-biology/clover/Manifest                        |  4 +-
 sci-biology/clover/clover-2010.02.19.ebuild        | 43 ---------------------
 sci-biology/clover/clover-2011.10.24.ebuild        | 40 +++++++++++++++++++
 sci-biology/clover/metadata.xml                    |  6 ++-
 sci-biology/erpin/ChangeLog                        |  5 ++-
 sci-biology/erpin/Manifest                         |  4 +-
 sci-biology/erpin/erpin-5.5b.ebuild                | 23 ++++++-----
 sci-biology/erpin/metadata.xml                     | 10 ++---
 sci-biology/gap2caf/ChangeLog                      |  8 ++++
 sci-biology/gap2caf/Manifest                       |  4 +-
 sci-biology/gap2caf/gap2caf-2.1.0.ebuild           | 45 +++++++++++-----------
 sci-biology/gap2caf/metadata.xml                   | 10 ++---
 sci-biology/quicktree/ChangeLog                    |  6 ++-
 sci-biology/quicktree/Manifest                     |  2 +-
 sci-biology/quicktree/metadata.xml                 | 10 ++---
 sci-biology/quicktree/quicktree-1.1-r1.ebuild      | 17 ++++----
 sci-biology/sequin/ChangeLog                       |  9 ++++-
 sci-biology/sequin/Manifest                        |  4 +-
 sci-biology/sequin/sequin-20090722.ebuild          | 32 ---------------
 sci-biology/sequin/sequin-20121202.ebuild          | 44 +++++++++++++++++++++
 sci-biology/smalt-bin/ChangeLog                    |  8 +++-
 sci-biology/smalt-bin/Manifest                     |  2 +-
 sci-biology/smalt-bin/metadata.xml                 | 10 ++---
 sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild       | 25 ------------
 sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild       | 31 +++++++++++++++
 sci-biology/ssaha2-bin/ChangeLog                   |  6 ++-
 sci-biology/ssaha2-bin/Manifest                    |  9 ++---
 sci-biology/ssaha2-bin/metadata.xml                | 10 ++---
 ...a2-bin-2.5.3.ebuild => ssaha2-bin-2.5.5.ebuild} | 26 ++++++++-----
 sci-biology/twinscan/ChangeLog                     |  6 ++-
 sci-biology/twinscan/Manifest                      |  2 +-
 sci-biology/twinscan/metadata.xml                  | 10 ++---
 sci-biology/twinscan/twinscan-4.1.2.ebuild         | 30 ++++++++++-----
 34 files changed, 292 insertions(+), 215 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     e1e48799c623338fedab433347c64dfce9b9aebe
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 16 20:18:52 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 16 20:18:52 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e1e48799

Merge branch 'fixing'

* fixing:
  sci-biology/twinscan: Bump to EAPI=5 and fix license
  sci-biology/ssaha2-bin: Version Bump; restrict license; add QA_PREBUILT for binaries
  sci-biology/smalt-bin: Version Bump; restrict license; add QA_PREBUILT for binaries
  sci-biology/sequin: Version BUmp; restrcit license; add QA_PREBUILT for binaries; install html files into sys path
  sci-biology/quicktree: Bump to EAPI=5 and fix license
  sci-biology/gap2caf: Bump to EAPI=5 and fix license; make it build with eautoreconf
  sci-biology/erpin: Bump to EAPI=5 and respect FLAGS / AR
  sci-biology/clover: Version BUmp; fixed license; respect LDFLAGS


 sci-biology/clover/ChangeLog                       |  6 ++-
 sci-biology/clover/Manifest                        |  4 +-
 sci-biology/clover/clover-2010.02.19.ebuild        | 43 ---------------------
 sci-biology/clover/clover-2011.10.24.ebuild        | 40 +++++++++++++++++++
 sci-biology/clover/metadata.xml                    |  6 ++-
 sci-biology/erpin/ChangeLog                        |  5 ++-
 sci-biology/erpin/Manifest                         |  4 +-
 sci-biology/erpin/erpin-5.5b.ebuild                | 23 ++++++-----
 sci-biology/erpin/metadata.xml                     | 10 ++---
 sci-biology/gap2caf/ChangeLog                      |  8 ++++
 sci-biology/gap2caf/Manifest                       |  4 +-
 sci-biology/gap2caf/gap2caf-2.1.0.ebuild           | 45 +++++++++++-----------
 sci-biology/gap2caf/metadata.xml                   | 10 ++---
 sci-biology/quicktree/ChangeLog                    |  6 ++-
 sci-biology/quicktree/Manifest                     |  2 +-
 sci-biology/quicktree/metadata.xml                 | 10 ++---
 sci-biology/quicktree/quicktree-1.1-r1.ebuild      | 17 ++++----
 sci-biology/sequin/ChangeLog                       |  9 ++++-
 sci-biology/sequin/Manifest                        |  4 +-
 sci-biology/sequin/sequin-20090722.ebuild          | 32 ---------------
 sci-biology/sequin/sequin-20121202.ebuild          | 44 +++++++++++++++++++++
 sci-biology/smalt-bin/ChangeLog                    |  8 +++-
 sci-biology/smalt-bin/Manifest                     |  2 +-
 sci-biology/smalt-bin/metadata.xml                 | 10 ++---
 sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild       | 25 ------------
 sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild       | 31 +++++++++++++++
 sci-biology/ssaha2-bin/ChangeLog                   |  6 ++-
 sci-biology/ssaha2-bin/Manifest                    |  9 ++---
 sci-biology/ssaha2-bin/metadata.xml                | 10 ++---
 ...a2-bin-2.5.3.ebuild => ssaha2-bin-2.5.5.ebuild} | 26 ++++++++-----
 sci-biology/twinscan/ChangeLog                     |  6 ++-
 sci-biology/twinscan/Manifest                      |  2 +-
 sci-biology/twinscan/metadata.xml                  | 10 ++---
 sci-biology/twinscan/twinscan-4.1.2.ebuild         | 30 ++++++++++-----
 34 files changed, 292 insertions(+), 215 deletions(-)

[gentoo-commits] proj/sci:ccp4 commit in: /

[Justin Lecher]

commit:     1e83a4dec123f72a098067d9b7fc003f45aeabbe
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 16 17:22:53 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 16 17:22:53 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1e83a4de

Merge branch 'ercpe'

* ercpe:
  sci-chemistry/shiftx2: Respect FLAGS
  Enhanced the sci-chemistry/shiftx ebuild. Still needs some love for the emake part (portage complains about LDFLAGS not respected), but should work.
  broken ebuild for java fixing Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>


 sci-chemistry/shiftx2/ChangeLog                    |   8 +
 sci-chemistry/shiftx2/Manifest                     |   1 +
 sci-chemistry/shiftx2/files/gentoo-fixes.patch     | 194 +++++++++++++++++++++
 sci-chemistry/shiftx2/metadata.xml                 |  39 +++++
 .../shiftx2/shiftx2-1.07_p20120106.ebuild          | 112 ++++++++++++
 5 files changed, 354 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     1e83a4dec123f72a098067d9b7fc003f45aeabbe
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 16 17:22:53 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 16 17:22:53 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1e83a4de

Merge branch 'ercpe'

* ercpe:
  sci-chemistry/shiftx2: Respect FLAGS
  Enhanced the sci-chemistry/shiftx ebuild. Still needs some love for the emake part (portage complains about LDFLAGS not respected), but should work.
  broken ebuild for java fixing Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>


 sci-chemistry/shiftx2/ChangeLog                    |   8 +
 sci-chemistry/shiftx2/Manifest                     |   1 +
 sci-chemistry/shiftx2/files/gentoo-fixes.patch     | 194 +++++++++++++++++++++
 sci-chemistry/shiftx2/metadata.xml                 |  39 +++++
 .../shiftx2/shiftx2-1.07_p20120106.ebuild          | 112 ++++++++++++
 5 files changed, 354 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     945c34bebc2ff7e4d3c1769c0c4320ee9a0a13dd
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 16 20:57:33 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Sun Jun 16 20:57:33 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=945c34be

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-biology/clover/ChangeLog                       |   6 +-
 sci-biology/clover/Manifest                        |   4 +-
 sci-biology/clover/clover-2010.02.19.ebuild        |  43 -----
 sci-biology/clover/clover-2011.10.24.ebuild        |  40 +++++
 sci-biology/clover/metadata.xml                    |   6 +-
 sci-biology/erpin/ChangeLog                        |   5 +-
 sci-biology/erpin/Manifest                         |   4 +-
 sci-biology/erpin/erpin-5.5b.ebuild                |  23 +--
 sci-biology/erpin/metadata.xml                     |  10 +-
 sci-biology/gap2caf/ChangeLog                      |   8 +
 sci-biology/gap2caf/Manifest                       |   4 +-
 sci-biology/gap2caf/gap2caf-2.1.0.ebuild           |  45 ++---
 sci-biology/gap2caf/metadata.xml                   |  10 +-
 sci-biology/quicktree/ChangeLog                    |   6 +-
 sci-biology/quicktree/Manifest                     |   2 +-
 sci-biology/quicktree/metadata.xml                 |  10 +-
 sci-biology/quicktree/quicktree-1.1-r1.ebuild      |  17 +-
 sci-biology/sequin/ChangeLog                       |   9 +-
 sci-biology/sequin/Manifest                        |   4 +-
 sci-biology/sequin/sequin-20090722.ebuild          |  32 ----
 sci-biology/sequin/sequin-20121202.ebuild          |  44 +++++
 sci-biology/smalt-bin/ChangeLog                    |   8 +-
 sci-biology/smalt-bin/Manifest                     |   2 +-
 sci-biology/smalt-bin/metadata.xml                 |  10 +-
 sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild       |  25 ---
 sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild       |  31 ++++
 sci-biology/ssaha2-bin/ChangeLog                   |   6 +-
 sci-biology/ssaha2-bin/Manifest                    |   9 +-
 sci-biology/ssaha2-bin/metadata.xml                |  10 +-
 ...a2-bin-2.5.3.ebuild => ssaha2-bin-2.5.5.ebuild} |  26 +--
 sci-biology/twinscan/ChangeLog                     |   6 +-
 sci-biology/twinscan/Manifest                      |   2 +-
 sci-biology/twinscan/metadata.xml                  |  10 +-
 sci-biology/twinscan/twinscan-4.1.2.ebuild         |  30 ++--
 sci-chemistry/shiftx2/ChangeLog                    |   8 +
 sci-chemistry/shiftx2/Manifest                     |   1 +
 sci-chemistry/shiftx2/files/gentoo-fixes.patch     | 194 +++++++++++++++++++++
 sci-chemistry/shiftx2/metadata.xml                 |  39 +++++
 .../shiftx2/shiftx2-1.07_p20120106.ebuild          | 112 ++++++++++++
 39 files changed, 646 insertions(+), 215 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     574effd9590ac60471bebdc4225aaa87a727b8a5
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 16 16:03:40 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Sun Jun 16 16:03:40 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=574effd9

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 dev-python/opal-client/ChangeLog                   |   8 +-
 dev-python/opal-client/Manifest                    |   2 +-
 dev-python/opal-client/metadata.xml                |   8 +-
 dev-python/opal-client/opal-client-2.2-r1.ebuild   |  55 --------
 dev-python/opal-client/opal-client-2.4.1.ebuild    |  42 +++++++
 licenses/GRL                                       |  15 +++
 licenses/Tablet                                    |   8 +-
 sci-biology/YASRA/ChangeLog                        |   4 +
 sci-biology/YASRA/Manifest                         |   2 +-
 .../YASRA/{YASRA-2.1.ebuild => YASRA-2.32.ebuild}  |  15 +--
 sci-biology/caftools/ChangeLog                     |   8 ++
 sci-biology/caftools/Manifest                      |   4 +-
 sci-biology/caftools/caftools-2.0.2.ebuild         |  36 +++---
 sci-biology/caftools/caftools-2.0.ebuild           |  38 ------
 sci-biology/caftools/metadata.xml                  |  16 ++-
 sci-biology/cutadapt/ChangeLog                     |   6 +-
 sci-biology/cutadapt/Manifest                      |   2 +-
 .../{cutadapt-1.0.ebuild => cutadapt-1.2.1.ebuild} |  13 +-
 sci-biology/cutadapt/metadata.xml                  |  10 +-
 sci-biology/tablet-bin/ChangeLog                   |   9 +-
 sci-biology/tablet-bin/Manifest                    |   3 +-
 sci-biology/tablet-bin/metadata.xml                |  10 +-
 .../tablet-bin/tablet-bin-1.11.11.01.ebuild        |  73 -----------
 ...1.05.03.ebuild => tablet-bin-1.13.05.17.ebuild} |  57 ++++++---
 sci-chemistry/chemBuild/ChangeLog                  |   6 +-
 sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild     |  33 ++---
 sci-chemistry/chemBuild/files/chemBuild            |   2 +-
 sci-chemistry/chemBuild/metadata.xml               |   2 +-
 sci-chemistry/cnsface/ChangeLog                    |   6 +-
 sci-chemistry/cnsface/Manifest                     |   2 +-
 sci-chemistry/cnsface/cnsface-0.0.12.ebuild        |  19 ++-
 sci-chemistry/cnsface/metadata.xml                 |   8 +-
 sci-chemistry/modeller/ChangeLog                   |   6 +-
 sci-chemistry/modeller/Manifest                    |   2 +-
 sci-chemistry/modeller/metadata.xml                |   2 +-
 .../{modeller-9.8.ebuild => modeller-9.12.ebuild}  |  96 +++++++-------
 sci-chemistry/nmrpipe/ChangeLog                    |   8 ++
 .../nmrpipe/nmrpipe-7.9.2013.021.23.09-r2.ebuild   |   4 +-
 sci-chemistry/nmrview/ChangeLog                    |   6 +-
 sci-chemistry/nmrview/metadata.xml                 |  10 +-
 sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild      |  15 +--
 sci-chemistry/nwchem/ChangeLog                     |   4 +
 sci-chemistry/nwchem/Manifest                      |   1 -
 sci-chemistry/nwchem/nwchem-6.1.1.ebuild           | 126 -------------------
 sci-chemistry/nwchem/nwchem-6.3.ebuild             |  10 +-
 sci-chemistry/phaser/ChangeLog                     |  21 ----
 sci-chemistry/phaser/Manifest                      |   1 -
 sci-chemistry/phaser/files/2.1.4-sadf.patch        |  64 ----------
 .../phaser/files/phaser-2.1.4-chmod.patch          |  11 --
 sci-chemistry/phaser/metadata.xml                  |  30 -----
 sci-chemistry/phaser/phaser-2.1.4-r1.ebuild        | 138 ---------------------
 sci-chemistry/phaser/phaser-2.1.4.ebuild           | 114 -----------------
 sci-chemistry/polygon/ChangeLog                    |   7 +-
 sci-chemistry/polygon/Manifest                     |   4 +-
 .../polygon/files/{0710-db.patch => 0612-db.patch} |  20 +--
 sci-chemistry/polygon/metadata.xml                 |   8 +-
 .../{polygon-0710.ebuild => polygon-0612.ebuild}   |  18 ++-
 sci-chemistry/pymol-apbs-plugin/ChangeLog          |   9 +-
 sci-chemistry/pymol-apbs-plugin/metadata.xml       |   8 +-
 .../pymol-apbs-plugin-9999.ebuild                  |  53 +++-----
 sci-chemistry/pymol-plugins-ezviz/ChangeLog        |   4 +
 sci-chemistry/pymol-plugins-ezviz/Manifest         |   2 +-
 .../pymol-plugins-ezviz-1.0.2005.ebuild            |  56 ++++-----
 sci-chemistry/pymol-plugins-psico/ChangeLog        |   3 +
 .../pymol-plugins-psico-9999.ebuild                |  15 +--
 sci-chemistry/pyquante/ChangeLog                   |   6 +-
 sci-chemistry/pyquante/Manifest                    |   2 +-
 sci-chemistry/pyquante/metadata.xml                |   2 +-
 sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild    |  11 +-
 sci-chemistry/shiftx/ChangeLog                     |   5 +-
 sci-chemistry/shiftx/Manifest                      |   2 +-
 sci-chemistry/shiftx/metadata.xml                  |   8 +-
 sci-chemistry/shiftx/shiftx-1.1.ebuild             |  24 ++--
 sci-chemistry/smmp/ChangeLog                       |   5 +-
 sci-chemistry/smmp/Manifest                        |   2 +-
 sci-chemistry/smmp/metadata.xml                    |   8 +-
 sci-chemistry/smmp/smmp-3.0.5.ebuild               |  41 +++---
 sci-chemistry/specView/ChangeLog                   |   3 +
 sci-chemistry/specView/specView-1.0.2.ebuild       |  52 +++-----
 sci-chemistry/ssp/ChangeLog                        |   5 +-
 sci-chemistry/ssp/metadata.xml                     |   8 +-
 sci-chemistry/ssp/ssp-09.11.ebuild                 |   6 +-
 82 files changed, 499 insertions(+), 1089 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6fa652d6a78f49cc6734d72f07455cbc4fa215bd
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Sun Jun 16 17:01:33 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 16 17:01:33 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6fa652d6

Merge pull request #82 from ercpe/ercpe

Enhanced the sci-chemistry/shiftx ebuild. Still needs some love for the ...


 sci-chemistry/shiftx2/Manifest                     |   1 +
 sci-chemistry/shiftx2/files/gentoo-fixes.patch     | 194 +++++++++++++++++++++
 sci-chemistry/shiftx2/metadata.xml                 |  57 +++---
 .../shiftx2/shiftx2-1.07_p20120106.ebuild          |  56 ++++--
 4 files changed, 272 insertions(+), 36 deletions(-)

[gentoo-commits] proj/sci:fixing commit in: /

[Justin Lecher]

commit:     2e9cea16376950c1a30a2bb3a7096327d1070f1b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 16 11:31:24 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 16 11:31:24 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2e9cea16

Merge branch 'fixing'

* fixing:
  Update license Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
  sci-biology/caftools: Drop old; Bump to EAPI=5 and fix license
  New license Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
  sci-biology/YASRA: Version BUmp; add KEYWORDS
  sci-biology/tablet-bin: Version BUmp; BUmp to EAPI5 and python-r1.eclass; drop addpredict
  sci-chemistry/modeller: Version BUmp; BUmp to EAPI5 and distutils-r1.eclass
  sci-chemistry/cnsface: Bump to EAPI5 and distutils-r1.eclass
  sci-chemistry/chemBuild: Bump EAPI and python eclass
  sci-biology/tablet-bin: Version BUmp; BUmp to EAPI5 and python-r1.eclass
  Drop the license again Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
  tablet's modified for of BSD license Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
  sci-biology/cutadapt: Version BUmp; BUmp to EAPI5 and distutils-r1.eclass
  dev-python/opal-client: Version BUmp; BUmp to EAPI5 and python-r1.eclass


 dev-python/opal-client/ChangeLog                   |  8 +-
 dev-python/opal-client/Manifest                    |  2 +-
 dev-python/opal-client/metadata.xml                |  8 +-
 dev-python/opal-client/opal-client-2.2-r1.ebuild   | 55 -------------
 dev-python/opal-client/opal-client-2.4.1.ebuild    | 42 ++++++++++
 licenses/GRL                                       | 15 ++++
 licenses/Tablet                                    |  8 +-
 sci-biology/YASRA/ChangeLog                        |  4 +
 sci-biology/YASRA/Manifest                         |  2 +-
 .../YASRA/{YASRA-2.1.ebuild => YASRA-2.32.ebuild}  | 15 +---
 sci-biology/caftools/ChangeLog                     |  8 ++
 sci-biology/caftools/Manifest                      |  4 +-
 sci-biology/caftools/caftools-2.0.2.ebuild         | 36 ++++----
 sci-biology/caftools/caftools-2.0.ebuild           | 38 ---------
 sci-biology/caftools/metadata.xml                  | 16 ++--
 sci-biology/cutadapt/ChangeLog                     |  6 +-
 sci-biology/cutadapt/Manifest                      |  2 +-
 .../{cutadapt-1.0.ebuild => cutadapt-1.2.1.ebuild} | 13 ++-
 sci-biology/cutadapt/metadata.xml                  | 10 +--
 sci-biology/tablet-bin/ChangeLog                   |  9 +-
 sci-biology/tablet-bin/Manifest                    |  3 +-
 sci-biology/tablet-bin/metadata.xml                | 10 +--
 .../tablet-bin/tablet-bin-1.11.11.01.ebuild        | 73 ----------------
 ...1.05.03.ebuild => tablet-bin-1.13.05.17.ebuild} | 57 +++++++++----
 sci-chemistry/chemBuild/ChangeLog                  |  6 +-
 sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild     | 33 +++-----
 sci-chemistry/chemBuild/files/chemBuild            |  2 +-
 sci-chemistry/chemBuild/metadata.xml               |  2 +-
 sci-chemistry/cnsface/ChangeLog                    |  6 +-
 sci-chemistry/cnsface/Manifest                     |  2 +-
 sci-chemistry/cnsface/cnsface-0.0.12.ebuild        | 19 ++---
 sci-chemistry/cnsface/metadata.xml                 |  8 +-
 sci-chemistry/modeller/ChangeLog                   |  6 +-
 sci-chemistry/modeller/Manifest                    |  2 +-
 sci-chemistry/modeller/metadata.xml                |  2 +-
 .../{modeller-9.8.ebuild => modeller-9.12.ebuild}  | 96 ++++++++++------------
 36 files changed, 278 insertions(+), 350 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     2e9cea16376950c1a30a2bb3a7096327d1070f1b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 16 11:31:24 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 16 11:31:24 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2e9cea16

Merge branch 'fixing'

* fixing:
  Update license Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
  sci-biology/caftools: Drop old; Bump to EAPI=5 and fix license
  New license Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
  sci-biology/YASRA: Version BUmp; add KEYWORDS
  sci-biology/tablet-bin: Version BUmp; BUmp to EAPI5 and python-r1.eclass; drop addpredict
  sci-chemistry/modeller: Version BUmp; BUmp to EAPI5 and distutils-r1.eclass
  sci-chemistry/cnsface: Bump to EAPI5 and distutils-r1.eclass
  sci-chemistry/chemBuild: Bump EAPI and python eclass
  sci-biology/tablet-bin: Version BUmp; BUmp to EAPI5 and python-r1.eclass
  Drop the license again Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
  tablet's modified for of BSD license Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
  sci-biology/cutadapt: Version BUmp; BUmp to EAPI5 and distutils-r1.eclass
  dev-python/opal-client: Version BUmp; BUmp to EAPI5 and python-r1.eclass


 dev-python/opal-client/ChangeLog                   |  8 +-
 dev-python/opal-client/Manifest                    |  2 +-
 dev-python/opal-client/metadata.xml                |  8 +-
 dev-python/opal-client/opal-client-2.2-r1.ebuild   | 55 -------------
 dev-python/opal-client/opal-client-2.4.1.ebuild    | 42 ++++++++++
 licenses/GRL                                       | 15 ++++
 licenses/Tablet                                    |  8 +-
 sci-biology/YASRA/ChangeLog                        |  4 +
 sci-biology/YASRA/Manifest                         |  2 +-
 .../YASRA/{YASRA-2.1.ebuild => YASRA-2.32.ebuild}  | 15 +---
 sci-biology/caftools/ChangeLog                     |  8 ++
 sci-biology/caftools/Manifest                      |  4 +-
 sci-biology/caftools/caftools-2.0.2.ebuild         | 36 ++++----
 sci-biology/caftools/caftools-2.0.ebuild           | 38 ---------
 sci-biology/caftools/metadata.xml                  | 16 ++--
 sci-biology/cutadapt/ChangeLog                     |  6 +-
 sci-biology/cutadapt/Manifest                      |  2 +-
 .../{cutadapt-1.0.ebuild => cutadapt-1.2.1.ebuild} | 13 ++-
 sci-biology/cutadapt/metadata.xml                  | 10 +--
 sci-biology/tablet-bin/ChangeLog                   |  9 +-
 sci-biology/tablet-bin/Manifest                    |  3 +-
 sci-biology/tablet-bin/metadata.xml                | 10 +--
 .../tablet-bin/tablet-bin-1.11.11.01.ebuild        | 73 ----------------
 ...1.05.03.ebuild => tablet-bin-1.13.05.17.ebuild} | 57 +++++++++----
 sci-chemistry/chemBuild/ChangeLog                  |  6 +-
 sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild     | 33 +++-----
 sci-chemistry/chemBuild/files/chemBuild            |  2 +-
 sci-chemistry/chemBuild/metadata.xml               |  2 +-
 sci-chemistry/cnsface/ChangeLog                    |  6 +-
 sci-chemistry/cnsface/Manifest                     |  2 +-
 sci-chemistry/cnsface/cnsface-0.0.12.ebuild        | 19 ++---
 sci-chemistry/cnsface/metadata.xml                 |  8 +-
 sci-chemistry/modeller/ChangeLog                   |  6 +-
 sci-chemistry/modeller/Manifest                    |  2 +-
 sci-chemistry/modeller/metadata.xml                |  2 +-
 .../{modeller-9.8.ebuild => modeller-9.12.ebuild}  | 96 ++++++++++------------
 36 files changed, 278 insertions(+), 350 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     bf58457ca280114efa65882a39ba4b718c8f0523
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun 13 10:08:53 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun 13 11:21:33 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bf58457c

dev-python/GOGrapher: Bump to EAPI=5 and distutils-r1.eclass

Package-Manager: portage-2.2.0_alpha179

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f32a4a58229fe6970d343c12e75a471bc97cd42a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun 13 10:08:53 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun 13 11:21:45 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f32a4a58

dev-python/GOGrapher: Bump to EAPI=5 and distutils-r1.eclass

Package-Manager: portage-2.2.0_alpha179

[gentoo-commits] proj/sci:ccp4 commit in: /

[Justin Lecher]

commit:     683aa6f0fbbecfb35014a2366ed152166f942df9
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Fri Jun  7 12:33:24 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun  7 12:33:24 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=683aa6f0

Merge /usr/local/portage/andis_overlay


 sys-cluster/modules/modules-3.2.9c-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     683aa6f0fbbecfb35014a2366ed152166f942df9
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Fri Jun  7 12:33:24 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun  7 12:33:24 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=683aa6f0

Merge /usr/local/portage/andis_overlay


 sys-cluster/modules/modules-3.2.9c-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     26e27280f8681d111da0a0e75c5589ce427b0c31
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 12 22:01:16 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Jun 12 22:01:16 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=26e27280

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 profiles/package.mask                              | 113 ++++++-------------
 sci-biology/ncbi-tools++/ChangeLog                 |   6 +
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |   3 +-
 sci-chemistry/ball/ChangeLog                       |   3 +
 sci-chemistry/ball/ball-9999.ebuild                |  11 +-
 sci-chemistry/ball/metadata.xml                    |   2 +-
 sci-chemistry/hydronmr/ChangeLog                   |   3 +
 sci-chemistry/hydronmr/hydronmr-7c.ebuild          |   1 -
 sci-libs/trilinos/ChangeLog                        |   4 +
 sci-libs/trilinos/Manifest                         |   1 -
 sci-libs/trilinos/trilinos-10.10.1.ebuild          | 124 ---------------------
 sci-libs/trilinos/trilinos-11.0.3.ebuild           |  12 +-
 12 files changed, 62 insertions(+), 221 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     027da5d57b8f0fc38a8b0800aebf466b1fe9d1d0
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 10 11:57:07 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 10 11:57:07 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=027da5d5

Merge branch 'masterbroken'

* masterbroken: (33 commits)
  dropped old Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
  sci-biology/psychopy: Add missing python use dep, move to virtual/python-imaging
  sci-chemistry/mgltools: move to virtual/python-imaging
  sci-chemistry/mgltools-autodocktools: Add missing python use dep, move to virtual/python-imaging
  sci-chemistry/mgltools-webservices: Drop old
  sci-chemistry/mgltools-volume: Drop old
  sci-chemistry/mgltools-visionlib: Drop old
  sci-chemistry/mgltools-vision: Drop old
  sci-chemistry/mgltools-viewer-framework: Drop old
  sci-chemistry/mgltools-utpackages: Drop old
  sci-chemistry/mgltools-symserv: Drop old
  sci-chemistry/mgltools-support: Drop old
  sci-chemistry/mgltools-sff: Drop old
  sci-chemistry/mgltools-qslimlib: Drop old
  sci-chemistry/mgltools-pyglf: Drop old
  sci-chemistry/mgltools-pybabel: Drop old
  sci-chemistry/mgltools-pyautodock: Drop old
  sci-chemistry/mgltools-pmv: Drop old
  sci-chemistry/mgltools-opengltk: Drop old
  sci-chemistry/mgltools-networkeditor: Drop old
  ...


 dev-python/pysolar/ChangeLog                       |  8 ++-
 dev-python/pysolar/Manifest                        |  2 +-
 dev-python/pysolar/metadata.xml                    |  4 +-
 dev-python/pysolar/pysolar-0.4.3.ebuild            | 66 -------------------
 dev-python/pysolar/pysolar-0.4.4.ebuild            | 52 ++++++---------
 dev-python/pysolar/pysolar-0.5.ebuild              | 52 +++++++++++++++
 media-gfx/librecad/ChangeLog                       |  3 +
 media-gfx/librecad/Manifest                        |  1 +
 ....0.0_beta5.ebuild => librecad-2.0.0_rc1.ebuild} |  0
 sci-biology/psychopy/ChangeLog                     |  8 +++
 sci-biology/psychopy/metadata.xml                  |  8 +--
 sci-biology/psychopy/psychopy-1.75.01.ebuild       | 24 ++++---
 sci-biology/psychopy/psychopy-9999.ebuild          | 18 ++---
 sci-chemistry/mgltools-autodocktools/ChangeLog     |  8 +++
 sci-chemistry/mgltools-autodocktools/Manifest      |  1 -
 .../mgltools-autodocktools-1.5.4-r2.ebuild         | 77 ----------------------
 .../mgltools-autodocktools-1.5.6.ebuild            |  6 +-
 sci-chemistry/mgltools-bhtree/ChangeLog            |  4 ++
 sci-chemistry/mgltools-bhtree/Manifest             |  1 -
 .../mgltools-bhtree-1.5.4-r1.ebuild                | 54 ---------------
 .../mgltools-bhtree/mgltools-bhtree-1.5.6.ebuild   |  2 +-
 sci-chemistry/mgltools-cmolkit/ChangeLog           |  4 ++
 sci-chemistry/mgltools-cmolkit/Manifest            |  1 -
 .../mgltools-cmolkit-1.5.4-r1.ebuild               | 55 ----------------
 .../mgltools-cmolkit/mgltools-cmolkit-1.5.6.ebuild |  2 +-
 sci-chemistry/mgltools-dejavu/ChangeLog            |  4 ++
 sci-chemistry/mgltools-dejavu/Manifest             |  1 -
 .../mgltools-dejavu-1.5.4-r1.ebuild                | 55 ----------------
 .../mgltools-dejavu/mgltools-dejavu-1.5.6.ebuild   |  2 +-
 sci-chemistry/mgltools-geomutils/ChangeLog         |  4 ++
 sci-chemistry/mgltools-geomutils/Manifest          |  1 -
 .../mgltools-geomutils-1.5.4-r1.ebuild             | 57 ----------------
 .../mgltools-geomutils-1.5.6.ebuild                |  2 +-
 sci-chemistry/mgltools-gle/ChangeLog               |  4 ++
 sci-chemistry/mgltools-gle/Manifest                |  1 -
 .../mgltools-gle/mgltools-gle-1.5.4-r1.ebuild      | 53 ---------------
 .../mgltools-gle/mgltools-gle-1.5.6.ebuild         |  2 +-
 sci-chemistry/mgltools-mglutil/ChangeLog           |  4 ++
 sci-chemistry/mgltools-mglutil/Manifest            |  1 -
 .../mgltools-mglutil-1.5.4-r1.ebuild               | 57 ----------------
 .../mgltools-mglutil/mgltools-mglutil-1.5.6.ebuild |  2 +-
 sci-chemistry/mgltools-molkit/ChangeLog            |  4 ++
 sci-chemistry/mgltools-molkit/Manifest             |  1 -
 .../mgltools-molkit-1.5.4-r1.ebuild                | 56 ----------------
 .../mgltools-molkit/mgltools-molkit-1.5.6.ebuild   |  2 +-
 sci-chemistry/mgltools-networkeditor/ChangeLog     |  4 ++
 sci-chemistry/mgltools-networkeditor/Manifest      |  1 -
 .../mgltools-networkeditor-1.5.4-r1.ebuild         | 56 ----------------
 .../mgltools-networkeditor-1.5.6.ebuild            |  2 +-
 sci-chemistry/mgltools-opengltk/ChangeLog          |  4 ++
 sci-chemistry/mgltools-opengltk/Manifest           |  1 -
 .../mgltools-opengltk-1.5.4-r2.ebuild              | 63 ------------------
 .../mgltools-opengltk-1.5.6.ebuild                 |  2 +-
 sci-chemistry/mgltools-pmv/ChangeLog               |  4 ++
 sci-chemistry/mgltools-pmv/Manifest                |  1 -
 .../mgltools-pmv/mgltools-pmv-1.5.4-r1.ebuild      | 63 ------------------
 .../mgltools-pmv/mgltools-pmv-1.5.6.ebuild         |  2 +-
 sci-chemistry/mgltools-pyautodock/ChangeLog        |  4 ++
 sci-chemistry/mgltools-pyautodock/Manifest         |  1 -
 .../mgltools-pyautodock-1.5.4-r1.ebuild            | 54 ---------------
 .../mgltools-pyautodock-1.5.6.ebuild               |  2 +-
 sci-chemistry/mgltools-pybabel/ChangeLog           |  4 ++
 sci-chemistry/mgltools-pybabel/Manifest            |  1 -
 .../mgltools-pybabel-1.5.4-r1.ebuild               | 56 ----------------
 .../mgltools-pybabel/mgltools-pybabel-1.5.6.ebuild |  2 +-
 sci-chemistry/mgltools-pyglf/ChangeLog             |  4 ++
 sci-chemistry/mgltools-pyglf/Manifest              |  1 -
 .../mgltools-pyglf/mgltools-pyglf-1.5.4-r1.ebuild  | 54 ---------------
 .../mgltools-pyglf/mgltools-pyglf-1.5.6.ebuild     |  2 +-
 sci-chemistry/mgltools-qslimlib/ChangeLog          |  4 ++
 sci-chemistry/mgltools-qslimlib/Manifest           |  1 -
 .../mgltools-qslimlib-1.5.4-r1.ebuild              | 56 ----------------
 .../mgltools-qslimlib-1.5.6.ebuild                 |  2 +-
 sci-chemistry/mgltools-scenario/ChangeLog          | 34 ----------
 sci-chemistry/mgltools-scenario/Manifest           |  1 -
 sci-chemistry/mgltools-scenario/metadata.xml       |  5 --
 .../mgltools-scenario-1.5.4-r1.ebuild              | 58 ----------------
 sci-chemistry/mgltools-sff/ChangeLog               |  4 ++
 sci-chemistry/mgltools-sff/Manifest                |  1 -
 .../mgltools-sff/mgltools-sff-1.5.4-r1.ebuild      | 55 ----------------
 .../mgltools-sff/mgltools-sff-1.5.6.ebuild         |  2 +-
 sci-chemistry/mgltools-stride/ChangeLog            | 35 ----------
 sci-chemistry/mgltools-stride/Manifest             |  1 -
 sci-chemistry/mgltools-stride/metadata.xml         |  5 --
 .../mgltools-stride-1.5.4-r1.ebuild                | 54 ---------------
 sci-chemistry/mgltools-support/ChangeLog           |  4 ++
 sci-chemistry/mgltools-support/Manifest            |  1 -
 .../mgltools-support-1.5.4-r1.ebuild               | 56 ----------------
 .../mgltools-support/mgltools-support-1.5.6.ebuild |  2 +-
 sci-chemistry/mgltools-symserv/ChangeLog           |  4 ++
 sci-chemistry/mgltools-symserv/Manifest            |  1 -
 .../mgltools-symserv-1.5.4-r1.ebuild               | 54 ---------------
 .../mgltools-symserv/mgltools-symserv-1.5.6.ebuild |  2 +-
 sci-chemistry/mgltools-utpackages/ChangeLog        |  4 ++
 sci-chemistry/mgltools-utpackages/Manifest         |  1 -
 .../mgltools-utpackages-1.5.4-r1.ebuild            | 56 ----------------
 .../mgltools-utpackages-1.5.6.ebuild               |  2 +-
 sci-chemistry/mgltools-viewer-framework/ChangeLog  |  5 ++
 sci-chemistry/mgltools-viewer-framework/Manifest   |  1 -
 .../mgltools-viewer-framework-1.5.4-r2.ebuild      | 58 ----------------
 .../mgltools-viewer-framework-1.5.6.ebuild         |  2 +-
 sci-chemistry/mgltools-vision/ChangeLog            |  4 ++
 sci-chemistry/mgltools-vision/Manifest             |  1 -
 .../mgltools-vision-1.5.4-r1.ebuild                | 64 ------------------
 .../mgltools-vision/mgltools-vision-1.5.6.ebuild   |  2 +-
 sci-chemistry/mgltools-visionlib/ChangeLog         |  4 ++
 sci-chemistry/mgltools-visionlib/Manifest          |  1 -
 .../mgltools-visionlib-1.5.4-r1.ebuild             | 53 ---------------
 .../mgltools-visionlib-1.5.6.ebuild                |  2 +-
 sci-chemistry/mgltools-volume/ChangeLog            |  4 ++
 sci-chemistry/mgltools-volume/Manifest             |  1 -
 .../mgltools-volume-1.5.4-r1.ebuild                | 55 ----------------
 .../mgltools-volume/mgltools-volume-1.5.6.ebuild   |  2 +-
 sci-chemistry/mgltools-webservices/ChangeLog       |  4 ++
 sci-chemistry/mgltools-webservices/Manifest        |  1 -
 .../mgltools-webservices-1.5.4-r2.ebuild           | 50 --------------
 .../mgltools-webservices-1.5.6.ebuild              |  2 +-
 sci-chemistry/mgltools/ChangeLog                   |  7 ++
 sci-chemistry/mgltools/Manifest                    |  1 -
 sci-chemistry/mgltools/mgltools-1.5.4.ebuild       | 42 ------------
 sci-chemistry/mgltools/mgltools-1.5.6.ebuild       |  4 +-
 121 files changed, 254 insertions(+), 1783 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     2a5f132f1b7a8f4f184be72e97a0210042ff6048
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 10 11:35:34 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 10 11:35:34 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2a5f132f

Merge remote-tracking branch 'github/master'

* github/master:
  media-gfx/librecad: version bump, 2.0.0_rc1


 media-gfx/librecad/ChangeLog                                           | 3 +++
 media-gfx/librecad/Manifest                                            | 1 +
 .../{librecad-2.0.0_beta5.ebuild => librecad-2.0.0_rc1.ebuild}         | 0
 3 files changed, 4 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     2e117aae2ef793064afeb2676ca1e1f243d007e4
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Fri Jun  7 23:42:39 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Fri Jun  7 23:42:39 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2e117aae

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 sys-cluster/charm/charm-6.5.0.ebuild                     | 16 +++++++++++-----
 sys-cluster/charm/metadata.xml                           |  1 +
 sys-cluster/modules/ChangeLog                            |  9 +++++++--
 sys-cluster/modules/Manifest                             |  1 +
 .../{modules-3.2.9c-r1.ebuild => modules-3.2.10.ebuild}  |  8 ++++----
 5 files changed, 24 insertions(+), 11 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     ddc3495e1874a534526ab006232b9453d05a58d5
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Jun  3 23:33:21 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jun  3 23:33:21 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ddc3495e

Merge branch 'master' of ssh://github.com/gentoo-science/sci


 dev-lang/pgi/Manifest                              |   1 +
 dev-lang/pgi/files/pgi-13.5-glibc.patch            |  31 +++
 dev-lang/pgi/files/pgi-13.5-terminal.patch         |  39 +++
 {dev-util/amdapp => dev-lang/pgi}/metadata.xml     |   7 +-
 dev-lang/pgi/pgi-13.5.ebuild                       | 115 +++++++++
 licenses/PGI                                       | 262 +++++++++++++++++++++
 sci-mathematics/scilab/scilab-5.4.1.ebuild         |   6 +-
 sys-cluster/modules/Manifest                       |   2 +-
 .../modules/files/modules-3.2.9c-errorline.patch   |  15 ++
 sys-cluster/modules/modules-3.2.9c-r1.ebuild       |   6 +-
 10 files changed, 476 insertions(+), 8 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     37c670d2b2023da28771040ed39a12bcb8e2fb70
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Mon Jun  3 08:36:50 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jun  3 08:36:50 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=37c670d2

Merge pull request #75 from gentryx/master

Added ebuild for the PGI compiler suite


 dev-lang/pgi/Manifest                              |   1 +
 dev-lang/pgi/files/pgi-13.5-glibc.patch            |  31 +++
 dev-lang/pgi/files/pgi-13.5-terminal.patch         |  39 +++
 {dev-util/amdapp => dev-lang/pgi}/metadata.xml     |   7 +-
 dev-lang/pgi/pgi-13.5.ebuild                       | 115 +++++++++
 licenses/PGI                                       | 262 +++++++++++++++++++++
 sys-cluster/modules/Manifest                       |   2 +-
 .../modules/files/modules-3.2.9c-errorline.patch   |  15 ++
 sys-cluster/modules/modules-3.2.9c-r1.ebuild       |   6 +-
 9 files changed, 473 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     20d1eb3e5708da1f9ce3e9ea54df28962e4ac2e6
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Mon Jun  3 14:35:50 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Jun  3 14:35:50 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=20d1eb3e

Merge pull request #76 from ZeroPointEnergy/master

minimal versions update for scilab deps


 sci-mathematics/scilab/scilab-5.4.1.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     9c925b3b9c8753ba4f3cf41bb304c0870b4027fc
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Fri May 31 15:31:31 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Fri May 31 15:31:31 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9c925b3b

Merge branch 'master' of github.com:gentoo-science/sci


 dev-util/nvidia-cuda-toolkit/ChangeLog             | 186 +++++++++++++++++++++
 dev-util/nvidia-cuda-toolkit/Manifest              |   2 +
 dev-util/nvidia-cuda-toolkit/files/cuda-config.in  |  28 ++++
 .../files/nvidia-cuda-toolkit-2.2-enum_fix.patch   |  42 +++++
 .../files/nvidia-cuda-toolkit-3.0-enum_fix.patch   |  54 ++++++
 .../files/nvidia-cuda-toolkit-3.1-enum_fix.patch   |  24 +++
 dev-util/nvidia-cuda-toolkit/metadata.xml          |  19 +++
 .../nvidia-cuda-toolkit-5.5.11.ebuild              | 140 ++++++++++++++++
 8 files changed, 495 insertions(+)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     5829b50ce4ea2442bc66e5f5773ea393ad6c1217
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Fri May 31 13:10:20 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Fri May 31 13:10:20 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5829b50c

Merge pull request #74 from gentryx/master

Updated Nvidia CUDA Toolkit to version 5.5


 dev-util/nvidia-cuda-toolkit/ChangeLog             | 186 +++++++++++++++++++++
 dev-util/nvidia-cuda-toolkit/Manifest              |   2 +
 dev-util/nvidia-cuda-toolkit/files/cuda-config.in  |  28 ++++
 .../files/nvidia-cuda-toolkit-2.2-enum_fix.patch   |  42 +++++
 .../files/nvidia-cuda-toolkit-3.0-enum_fix.patch   |  54 ++++++
 .../files/nvidia-cuda-toolkit-3.1-enum_fix.patch   |  24 +++
 dev-util/nvidia-cuda-toolkit/metadata.xml          |  19 +++
 .../nvidia-cuda-toolkit-5.5.11.ebuild              | 140 ++++++++++++++++
 8 files changed, 495 insertions(+)

[gentoo-commits] proj/sci:ccp4 commit in: /

[Justin Lecher]

commit:     4eee2440583895501cb394c61ab68134729dace9
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue May  7 10:13:18 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue May  7 10:13:18 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4eee2440

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  Update lustre patches


 sys-cluster/lustre/ChangeLog                       |    29 +
 ...01-LU-1812-kernel-3.7-FC18-server-patches.patch |   380 +
 ...rnel-3.0-SuSE-and-3.6-FC18-server-patches.patch | 21302 -------------------
 ...el-sock_map_fd-replaced-by-sock_alloc_fi.patch} |     4 +-
 ...-kernel-Kernel-update-for-3.7.2-201.fc18.patch} |    10 +-
 ...at-posix_acl_-to-from-_xattr-take-user_n.patch} |    12 +-
 ...05-LU-2800-llite-introduce-local-getname.patch} |    16 +-
 ...tch => 0006-LU-2987-llite-rcu-free-inode.patch} |     8 +-
 ...0-kernel-3.8-upstream-removes-vmtruncate.patch} |     8 +-
 ...2850-kernel-3.8-upstream-kills-daemonize.patch} |   167 +-
 ...-build-zfs-0.6.1-kmod-dkms-compatibility.patch} |   175 +-
 ...d-make-AC-check-for-linux-arch-sandbox-f.patch} |     8 +-
 ...nel-3.9-hlist_for_each_entry-uses-3-args.patch} |     8 +-
 ...9-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch} |    10 +-
 ...fids-fix-compilation-error-with-gcc-4.7.2.patch |    29 -
 sys-cluster/lustre/lustre-9999.ebuild              |    25 +-
 16 files changed, 695 insertions(+), 21496 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     4eee2440583895501cb394c61ab68134729dace9
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue May  7 10:13:18 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue May  7 10:13:18 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4eee2440

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  Update lustre patches


 sys-cluster/lustre/ChangeLog                       |   29 +
 ...01-LU-1812-kernel-3.7-FC18-server-patches.patch |  380 +
 ...rnel-3.0-SuSE-and-3.6-FC18-server-patches.patch |21302 --------------------
 ...el-sock_map_fd-replaced-by-sock_alloc_fi.patch} |    4 +-
 ...-kernel-Kernel-update-for-3.7.2-201.fc18.patch} |   10 +-
 ...at-posix_acl_-to-from-_xattr-take-user_n.patch} |   12 +-
 ...05-LU-2800-llite-introduce-local-getname.patch} |   16 +-
 ...tch => 0006-LU-2987-llite-rcu-free-inode.patch} |    8 +-
 ...0-kernel-3.8-upstream-removes-vmtruncate.patch} |    8 +-
 ...2850-kernel-3.8-upstream-kills-daemonize.patch} |  167 +-
 ...-build-zfs-0.6.1-kmod-dkms-compatibility.patch} |  175 +-
 ...d-make-AC-check-for-linux-arch-sandbox-f.patch} |    8 +-
 ...nel-3.9-hlist_for_each_entry-uses-3-args.patch} |    8 +-
 ...9-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch} |   10 +-
 ...fids-fix-compilation-error-with-gcc-4.7.2.patch |   29 -
 sys-cluster/lustre/lustre-9999.ebuild              |   25 +-
 16 files changed, 695 insertions(+), 21496 deletions(-)

[gentoo-commits] proj/sci:ccp4 commit in: /

[Justin Lecher]

commit:     c211d024db7b25bcfa9f40787598e32f2e094ce3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon May  6 05:56:48 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon May  6 05:56:48 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c211d024

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  sync with gx86
  media-gfx/brlcad: version bumped to 7.22.0, bug#467456
  added recent 4.5.x version from gx86 (bug #468454)
  sci-libs/mkl: Version Bump
  selectively call cuda.eclass, depending on use flag
  reverting inheritance
  refactoring CUDA interaction
  conditional inheritance to fix compilation sans CUDA


 dev-util/VampirTrace/VampirTrace-5.14.3.ebuild     |  6 +-
 media-gfx/brlcad/ChangeLog                         |  5 +-
 media-gfx/brlcad/Manifest                          |  1 +
 .../{brlcad-7.20.4.ebuild => brlcad-7.22.0.ebuild} | 16 +++---
 media-gfx/brlcad/brlcad-9999.ebuild                |  8 +--
 sci-chemistry/gromacs/ChangeLog                    | 10 ++++
 sci-chemistry/gromacs/Manifest                     |  2 +
 .../files/gromacs-4.5.7-cmake-cpp-asm.patch        | 43 ++++++++++++++
 ...gromacs-9999.ebuild => gromacs-4.5.9999.ebuild} | 65 ++++++++++++++--------
 sci-chemistry/gromacs/metadata.xml                 |  1 +
 sci-libs/mkl/ChangeLog                             |  5 ++
 sci-libs/mkl/Manifest                              |  4 ++
 ...mkl-11.0.2.146.ebuild => mkl-11.0.3.163.ebuild} |  4 +-
 13 files changed, 130 insertions(+), 40 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     c211d024db7b25bcfa9f40787598e32f2e094ce3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon May  6 05:56:48 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon May  6 05:56:48 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c211d024

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  sync with gx86
  media-gfx/brlcad: version bumped to 7.22.0, bug#467456
  added recent 4.5.x version from gx86 (bug #468454)
  sci-libs/mkl: Version Bump
  selectively call cuda.eclass, depending on use flag
  reverting inheritance
  refactoring CUDA interaction
  conditional inheritance to fix compilation sans CUDA


 dev-util/VampirTrace/VampirTrace-5.14.3.ebuild     |    6 ++-
 media-gfx/brlcad/ChangeLog                         |    5 +-
 media-gfx/brlcad/Manifest                          |    1 +
 .../{brlcad-7.20.4.ebuild => brlcad-7.22.0.ebuild} |   16 +++---
 media-gfx/brlcad/brlcad-9999.ebuild                |    8 +--
 sci-chemistry/gromacs/ChangeLog                    |   10 +++
 sci-chemistry/gromacs/Manifest                     |    2 +
 .../files/gromacs-4.5.7-cmake-cpp-asm.patch        |   43 +++++++++++++
 ...gromacs-9999.ebuild => gromacs-4.5.9999.ebuild} |   65 +++++++++++++-------
 sci-chemistry/gromacs/metadata.xml                 |    1 +
 sci-libs/mkl/ChangeLog                             |    5 ++
 sci-libs/mkl/Manifest                              |    4 +
 ...mkl-11.0.2.146.ebuild => mkl-11.0.3.163.ebuild} |    4 +-
 13 files changed, 130 insertions(+), 40 deletions(-)

[gentoo-commits] proj/sci:ccp4 commit in: /

[Justin Lecher]

commit:     a95f26fa2fc4e7d22f146b6e233e6173236c3ac1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 30 09:44:29 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Apr 30 09:44:29 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a95f26fa

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  sci-biology/mira-3.9.15: bump to current besta version


 sci-biology/mira/ChangeLog                                 | 6 ++++++
 sci-biology/mira/Manifest                                  | 1 +
 sci-biology/mira/{mira-3.9.9.ebuild => mira-3.9.15.ebuild} | 9 ++++++---
 3 files changed, 13 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     a95f26fa2fc4e7d22f146b6e233e6173236c3ac1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 30 09:44:29 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Apr 30 09:44:29 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a95f26fa

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  sci-biology/mira-3.9.15: bump to current besta version


 sci-biology/mira/ChangeLog                         |    6 ++++++
 sci-biology/mira/Manifest                          |    1 +
 .../mira/{mira-3.9.9.ebuild => mira-3.9.15.ebuild} |    9 ++++++---
 3 files changed, 13 insertions(+), 3 deletions(-)

[gentoo-commits] proj/sci:ccp4 commit in: /

[Justin Lecher]

commit:     ee996859aa60cadce87685737ddbd62cae7a8652
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 30 07:17:21 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Apr 30 07:17:21 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ee996859

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  Update description
  Updated skel files
  sci-libs/armadillo: Version bump
  dev-python/astlib: Version bump
  dev-cpp/eigen: Version bump
  added missing metadata.xml
  removed superfluous dot
  corrected use flag-dependend configure switch
  pleasing repoman
  removed asciidata, replaced by astropy and asciitable
  added VampirTrace ebuild
  fixed conditional
  proper indentation
  added useflag to enable uncore events


 README.md                                          |   16 +-
 dev-cpp/eigen/ChangeLog                            |    8 +-
 dev-cpp/eigen/Manifest                             |    2 +-
 .../{eigen-3.1.2.ebuild => eigen-3.1.3-r1.ebuild}  |    0
 dev-cpp/eigen/eigen-9999.ebuild                    |   10 +-
 dev-python/asciidata/ChangeLog                     |   28 -
 dev-python/asciidata/Manifest                      |    1 -
 dev-python/asciidata/asciidata-1.1.1-r1.ebuild     |   41 -
 dev-python/asciidata/metadata.xml                  |   13 -
 dev-python/astlib/ChangeLog                        |    8 +-
 dev-python/astlib/Manifest                         |    2 +-
 .../{astlib-0.17.1.ebuild => astlib-0.7.0.ebuild}  |   31 +-
 .../astlib/files/astlib-0.17.1-wcstools.patch      |   75 -
 dev-python/astlib/metadata.xml                     |    3 +-
 dev-util/VampirTrace/Manifest                      |    1 +
 dev-util/VampirTrace/VampirTrace-5.14.3.ebuild     |   33 +
 dev-util/VampirTrace/metadata.xml                  |   13 +
 licenses/vampir                                    |   36 +
 sci-libs/armadillo/ChangeLog                       |    7 +
 sci-libs/armadillo/Manifest                        |    2 +-
 ...lo-3.6.3-r1.ebuild => armadillo-3.810.2.ebuild} |   35 +-
 .../files/armadillo-3.810.2-example-makefile.patch |   33 +
 .../armadillo/files/armadillo-3.810.2-hdf5.patch   |   19 +
 sci-libs/armadillo/metadata.xml                    |   20 +-
 skel.ChangeLog                                     | 8024 +-------------------
 skel.ebuild                                        |    2 +-
 skel.metadata.xml                                  |   38 +-
 sys-apps/likwid/files/use_uncore.patch             |   12 +
 sys-apps/likwid/likwid-3.0.ebuild                  |    5 +-
 sys-apps/likwid/metadata.xml                       |    7 +-
 30 files changed, 265 insertions(+), 8260 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     ee996859aa60cadce87685737ddbd62cae7a8652
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 30 07:17:21 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Apr 30 07:17:21 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ee996859

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  Update description
  Updated skel files
  sci-libs/armadillo: Version bump
  dev-python/astlib: Version bump
  dev-cpp/eigen: Version bump
  added missing metadata.xml
  removed superfluous dot
  corrected use flag-dependend configure switch
  pleasing repoman
  removed asciidata, replaced by astropy and asciitable
  added VampirTrace ebuild
  fixed conditional
  proper indentation
  added useflag to enable uncore events


 README.md                                          |   16 +-
 dev-cpp/eigen/ChangeLog                            |    8 +-
 dev-cpp/eigen/Manifest                             |    2 +-
 .../{eigen-3.1.2.ebuild => eigen-3.1.3-r1.ebuild}  |    0
 dev-cpp/eigen/eigen-9999.ebuild                    |   10 +-
 dev-python/asciidata/ChangeLog                     |   28 -
 dev-python/asciidata/Manifest                      |    1 -
 dev-python/asciidata/asciidata-1.1.1-r1.ebuild     |   41 -
 dev-python/asciidata/metadata.xml                  |   13 -
 dev-python/astlib/ChangeLog                        |    8 +-
 dev-python/astlib/Manifest                         |    2 +-
 .../{astlib-0.17.1.ebuild => astlib-0.7.0.ebuild}  |   31 +-
 .../astlib/files/astlib-0.17.1-wcstools.patch      |   75 -
 dev-python/astlib/metadata.xml                     |    3 +-
 dev-util/VampirTrace/Manifest                      |    1 +
 dev-util/VampirTrace/VampirTrace-5.14.3.ebuild     |   33 +
 dev-util/VampirTrace/metadata.xml                  |   13 +
 licenses/vampir                                    |   36 +
 sci-libs/armadillo/ChangeLog                       |    7 +
 sci-libs/armadillo/Manifest                        |    2 +-
 ...lo-3.6.3-r1.ebuild => armadillo-3.810.2.ebuild} |   35 +-
 .../files/armadillo-3.810.2-example-makefile.patch |   33 +
 .../armadillo/files/armadillo-3.810.2-hdf5.patch   |   19 +
 sci-libs/armadillo/metadata.xml                    |   20 +-
 skel.ChangeLog                                     | 8024 +-------------------
 skel.ebuild                                        |    2 +-
 skel.metadata.xml                                  |   38 +-
 sys-apps/likwid/files/use_uncore.patch             |   12 +
 sys-apps/likwid/likwid-3.0.ebuild                  |    5 +-
 sys-apps/likwid/metadata.xml                       |    7 +-
 30 files changed, 265 insertions(+), 8260 deletions(-)

[gentoo-commits] proj/sci:ccp4 commit in: /

[Justin Lecher]

commit:     5421e4619f5a5b5ff44341a896e4924ae7162470
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Apr 24 05:57:39 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Apr 24 05:57:39 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5421e461

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  dev-java/jlatexmath-fop version bump
  dev-java/jlatexmath version bump
  dev-java/xmlgraphics-commons import new version from bugzilla
  dev-java/flexdock version bump
  dev-java/scirenderer version bump
  Add rebased patches


 dev-java/flexdock/Manifest                         |  2 +-
 ....2-nodemo.patch => flexdock-1.2.3-nodemo.patch} |  0
 ...flexdock-1.2.2.ebuild => flexdock-1.2.3.ebuild} |  8 +--
 dev-java/jlatexmath-fop/Manifest                   |  3 +-
 .../files/jlatexmath-fop-1.0.2-fixpaths.patch      | 13 +++++
 dev-java/jlatexmath-fop/files/version.xml          |  5 ++
 .../jlatexmath-fop/jlatexmath-fop-0.9.7.ebuild     | 52 -------------------
 .../jlatexmath-fop/jlatexmath-fop-1.0.0.ebuild     | 52 -------------------
 .../jlatexmath-fop/jlatexmath-fop-1.0.2.ebuild     | 45 +++++++++++++++++
 dev-java/jlatexmath/Manifest                       |  3 +-
 dev-java/jlatexmath/jlatexmath-1.0.0.ebuild        | 32 ------------
 ...exmath-0.9.7.ebuild => jlatexmath-1.0.2.ebuild} | 22 ++++----
 dev-java/scirenderer/Manifest                      |  2 +-
 ...derer-1.0.5.ebuild => scirenderer-1.1.0.ebuild} |  4 +-
 dev-java/xmlgraphics-commons/Manifest              |  1 +
 .../files/disable-iccprofile-test.patch            | 38 ++++++++++++++
 .../{jrosetta => xmlgraphics-commons}/metadata.xml |  1 -
 .../xmlgraphics-commons-1.5.ebuild                 | 58 ++++++++++++++++++++++
 sys-cluster/lustre/ChangeLog                       | 19 +++++++
 ...ld-make-AC-check-for-linux-arch-sandbox-f.patch |  2 +-
 ...rnel-3.0-SuSE-and-3.6-FC18-server-patches.patch |  2 +-
 ...nel-sock_map_fd-replaced-by-sock_alloc_fi.patch |  2 +-
 ...6-kernel-Kernel-update-for-3.7.2-201.fc18.patch |  2 +-
 ...pat-posix_acl_-to-from-_xattr-take-user_n.patch |  6 +--
 ...006-LU-2800-llite-introduce-local-getname.patch |  2 +-
 .../files/0007-LU-2987-llite-rcu-free-inode.patch  |  2 +-
 ...50-kernel-3.8-upstream-removes-vmtruncate.patch |  2 +-
 ...-2850-kernel-3.8-upstream-kills-daemonize.patch | 55 ++++++++++----------
 ...rnel-3.9-hlist_for_each_entry-uses-3-args.patch |  2 +-
 ...79-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch |  2 +-
 ...ids-fix-compilation-error-with-gcc-4.7.2.patch} |  4 +-
 ...-build-zfs-0.6.1-kmod-dkms-compatibility.patch} |  4 +-
 sys-cluster/lustre/lustre-9999.ebuild              | 14 +-----
 33 files changed, 243 insertions(+), 218 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     5421e4619f5a5b5ff44341a896e4924ae7162470
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Apr 24 05:57:39 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Apr 24 05:57:39 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5421e461

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  dev-java/jlatexmath-fop version bump
  dev-java/jlatexmath version bump
  dev-java/xmlgraphics-commons import new version from bugzilla
  dev-java/flexdock version bump
  dev-java/scirenderer version bump
  Add rebased patches


 dev-java/flexdock/Manifest                         |    2 +-
 ....2-nodemo.patch => flexdock-1.2.3-nodemo.patch} |    0
 ...flexdock-1.2.2.ebuild => flexdock-1.2.3.ebuild} |    8 ++--
 dev-java/jlatexmath-fop/Manifest                   |    3 +-
 .../files/jlatexmath-fop-1.0.2-fixpaths.patch      |   13 +++++
 dev-java/jlatexmath-fop/files/version.xml          |    5 ++
 .../jlatexmath-fop/jlatexmath-fop-0.9.7.ebuild     |   52 ------------------
 .../jlatexmath-fop/jlatexmath-fop-1.0.0.ebuild     |   52 ------------------
 .../jlatexmath-fop/jlatexmath-fop-1.0.2.ebuild     |   45 +++++++++++++++
 dev-java/jlatexmath/Manifest                       |    3 +-
 dev-java/jlatexmath/jlatexmath-1.0.0.ebuild        |   32 -----------
 ...exmath-0.9.7.ebuild => jlatexmath-1.0.2.ebuild} |   22 ++++----
 dev-java/scirenderer/Manifest                      |    2 +-
 ...derer-1.0.5.ebuild => scirenderer-1.1.0.ebuild} |    4 +-
 dev-java/xmlgraphics-commons/Manifest              |    1 +
 .../files/disable-iccprofile-test.patch            |   38 +++++++++++++
 .../{jrosetta => xmlgraphics-commons}/metadata.xml |    1 -
 .../xmlgraphics-commons-1.5.ebuild                 |   58 ++++++++++++++++++++
 sys-cluster/lustre/ChangeLog                       |   19 +++++++
 ...ld-make-AC-check-for-linux-arch-sandbox-f.patch |    2 +-
 ...rnel-3.0-SuSE-and-3.6-FC18-server-patches.patch |    2 +-
 ...nel-sock_map_fd-replaced-by-sock_alloc_fi.patch |    2 +-
 ...6-kernel-Kernel-update-for-3.7.2-201.fc18.patch |    2 +-
 ...pat-posix_acl_-to-from-_xattr-take-user_n.patch |    6 +-
 ...006-LU-2800-llite-introduce-local-getname.patch |    2 +-
 .../files/0007-LU-2987-llite-rcu-free-inode.patch  |    2 +-
 ...50-kernel-3.8-upstream-removes-vmtruncate.patch |    2 +-
 ...-2850-kernel-3.8-upstream-kills-daemonize.patch |   55 +++++++++----------
 ...rnel-3.9-hlist_for_each_entry-uses-3-args.patch |    2 +-
 ...79-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch |    2 +-
 ...ids-fix-compilation-error-with-gcc-4.7.2.patch} |    4 +-
 ...-build-zfs-0.6.1-kmod-dkms-compatibility.patch} |    4 +-
 sys-cluster/lustre/lustre-9999.ebuild              |   14 +----
 33 files changed, 243 insertions(+), 218 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Andrew Savchenko]

commit:     09bde6b122936401cd0f27bafa2c565c1d29a9e1
Author:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
AuthorDate: Tue May 28 20:27:32 2013 +0000
Commit:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
CommitDate: Tue May 28 20:27:32 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=09bde6b1

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci


 sci-physics/lammps/ChangeLog                                  | 11 +++++++++++
 sci-physics/lammps/Manifest                                   |  1 +
 sci-physics/lammps/lammps-20130514.ebuild                     |  7 +++++--
 .../lammps/{lammps-20130514.ebuild => lammps-20130526.ebuild} |  9 ++++++---
 4 files changed, 23 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     d6c6e1c2e0344384f91edf1416824713ef207142
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Thu May 16 21:22:58 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Thu May 16 21:22:58 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d6c6e1c2

Merge branch 'master' of github.com:gentoo-science/sci


 dev-lang/berkeley_upc/berkeley_upc-2.16.2.ebuild |    3 +++
 1 files changed, 3 insertions(+), 0 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Nicolas Bock]

commit:     b81fff6dcf24a0ab91f631a42e9996b556a05439
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Thu May 16 06:33:04 2013 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Thu May 16 06:33:04 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b81fff6d

Merge pull request #72 from jauhien/berkeley_upc_2.16.2

dev-lang/berkeley_upc: dependency on virtual/mpi added


 dev-lang/berkeley_upc/berkeley_upc-2.16.2.ebuild |    3 +++
 1 files changed, 3 insertions(+), 0 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     622626fb55bac4fc611c9f41148e634d426efa20
Author:     Christoph Junghans <christoph.junghans <AT> googlemail <DOT> com>
AuthorDate: Wed May 15 19:48:11 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Wed May 15 19:48:11 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=622626fb

Merge pull request #69 from nicolasbock/master

Enable parallel (MPI) build of lammps


 sci-physics/lammps/ChangeLog                       |    5 +
 .../lammps/files/Makefile.gentoo-serial.patch      |  111 --------------------
 sci-physics/lammps/lammps-20130512.ebuild          |   73 +++++++------
 sci-physics/lammps/metadata.xml                    |    2 -
 4 files changed, 45 insertions(+), 146 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     d0e84807421952d08fa33651bca8034dd8d9ef66
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed May 15 10:59:54 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Wed May 15 10:59:54 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d0e84807

Merge /usr/local/portage/andis_overlay


 dev-util/amdapp/amdapp-2.8.ebuild |   20 +++++++++-----------
 1 files changed, 9 insertions(+), 11 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     00c58fa25bbf4f532f15d305b12b8cbb1a922fbb
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Wed May 15 11:30:37 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Wed May 15 11:30:37 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=00c58fa2

Merge pull request #71 from gentryx/master

Added ebuild for AMD APP


 dev-util/VampirTrace/metadata.xml  |    3 ++
 dev-util/amdapp/Manifest           |    2 +
 dev-util/amdapp/amdapp-2.8.ebuild  |   63 ++++++++++++++++++++++++++++++++++++
 dev-util/amdapp/metadata.xml       |   15 ++++++++
 sci-libs/libgeodecomp/metadata.xml |    3 ++
 sys-apps/likwid/metadata.xml       |    3 ++
 sys-cluster/hpx/metadata.xml       |    3 ++
 7 files changed, 92 insertions(+), 0 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     e2ebd47001ac3f20d9f10b3fea8091dacdfa757b
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed May 15 08:09:29 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Wed May 15 08:09:29 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e2ebd470

Merge https://github.com/gentoo-science/sci


 dev-lang/berkeley_upc/ChangeLog                    |    6 +
 dev-lang/berkeley_upc/Manifest                     |    2 +-
 ...pc-2.16.0.ebuild => berkeley_upc-2.16.2.ebuild} |    0
 dev-lang/berkeley_upc_translator/ChangeLog         |    8 +
 dev-lang/berkeley_upc_translator/Manifest          |    2 +-
 ...build => berkeley_upc_translator-2.16.2.ebuild} |    5 +-
 ...keley_upc_translator-2.16.0-stackoverflow.patch |   18 -
 dev-python/pysparse/ChangeLog                      |   11 +-
 dev-python/pysparse/Manifest                       |    3 +-
 dev-python/pysparse/metadata.xml                   |    4 +-
 dev-python/pysparse/pysparse-1.1.1-r1.ebuild       |   60 +
 dev-python/pysparse/pysparse-1.1.1.ebuild          |   53 -
 dev-python/pysparse/pysparse-1.1.ebuild            |   53 -
 media-gfx/brlcad/ChangeLog                         |    5 +-
 media-gfx/brlcad/Manifest                          |    1 +
 .../{brlcad-7.20.4.ebuild => brlcad-7.22.0.ebuild} |   16 +-
 media-gfx/brlcad/brlcad-9999.ebuild                |    8 +-
 sci-biology/mira/ChangeLog                         |    6 +
 sci-biology/mira/Manifest                          |    1 +
 .../mira/{mira-3.9.9.ebuild => mira-3.9.15.ebuild} |    9 +-
 sci-chemistry/curvefit/ChangeLog                   |    3 +
 sci-chemistry/curvefit/curvefit-1.40.ebuild        |    6 +-
 sci-chemistry/gromacs/ChangeLog                    |   10 +
 sci-chemistry/gromacs/Manifest                     |    2 +
 .../files/gromacs-4.5.7-cmake-cpp-asm.patch        |   43 +
 ...gromacs-9999.ebuild => gromacs-4.5.9999.ebuild} |   65 +-
 sci-chemistry/gromacs/metadata.xml                 |    1 +
 sci-chemistry/modelfree/ChangeLog                  |   12 +
 sci-chemistry/modelfree/modelfree-4.20.ebuild      |   33 +-
 sci-chemistry/ucsf-tools/ChangeLog                 |    8 +
 sci-chemistry/ucsf-tools/Manifest                  |    2 +
 sci-chemistry/ucsf-tools/metadata.xml              |   31 +-
 sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild    |    6 +-
 sci-libs/mkl/ChangeLog                             |    5 +
 sci-libs/mkl/Manifest                              |    4 +
 ...mkl-11.0.2.146.ebuild => mkl-11.0.3.163.ebuild} |    4 +-
 sci-libs/nfft/ChangeLog                            |   28 -
 sci-libs/nfft/Manifest                             |    1 -
 sci-libs/nfft/metadata.xml                         |    9 -
 sci-libs/nfft/nfft-3.2.2.ebuild                    |   32 -
 sci-mathematics/scilab/Manifest                    |    2 +-
 .../scilab/files/scilab-5.4.0-builddocs.patch      |  353 -
 .../scilab/files/scilab-5.4.0-fortran-link.patch   |   22 -
 .../scilab/files/scilab-5.4.0-java-heap.patch      |   12 -
 ... scilab-5.4.1-fix-random-runtime-failure.patch} |    0
 ...wlinks.patch => scilab-5.4.1-followlinks.patch} |    0
 ....0-gluegen.patch => scilab-5.4.1-gluegen.patch} |    0
 .../scilab/files/scilab-5.4.1-java-heap.patch      |   14 +
 .../{scilab-5.4.0.ebuild => scilab-5.4.1.ebuild}   |   45 +-
 sci-physics/lammps/ChangeLog                       |   31 +
 sci-physics/lammps/Manifest                        |    1 +
 .../lammps/files/Makefile.gentoo-serial.patch      |  111 +
 sci-physics/lammps/lammps-20130512.ebuild          |   65 +
 sci-physics/lammps/metadata.xml                    |   32 +
 sys-cluster/lustre/ChangeLog                       |   52 +
 ...01-LU-1812-kernel-3.7-FC18-server-patches.patch |  380 +
 ...rnel-3.0-SuSE-and-3.6-FC18-server-patches.patch |21302 --------------------
 ...el-sock_map_fd-replaced-by-sock_alloc_fi.patch} |    4 +-
 ...-kernel-Kernel-update-for-3.7.2-201.fc18.patch} |   22 +-
 ...at-posix_acl_-to-from-_xattr-take-user_n.patch} |   12 +-
 ...05-LU-2800-llite-introduce-local-getname.patch} |   16 +-
 ...tch => 0006-LU-2987-llite-rcu-free-inode.patch} |    8 +-
 ...0-kernel-3.8-upstream-removes-vmtruncate.patch} |    8 +-
 ...2850-kernel-3.8-upstream-kills-daemonize.patch} |  167 +-
 ...d-make-AC-check-for-linux-arch-sandbox-f.patch} |   10 +-
 ...rnel-3.9-hlist_for_each_entry-uses-3-args.patch |    8 +-
 ...79-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch |   10 +-
 ...uild-fix-compilation-error-with-gcc-4.7.2.patch |   43 +
 ...fids-fix-compilation-error-with-gcc-4.7.2.patch |   29 -
 ...7-build-zfs-0.6.1-kmod-dkms-compatibility.patch | 1038 -
 sys-cluster/lustre/lustre-9999.ebuild              |   29 +-
 71 files changed, 1196 insertions(+), 23206 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     dbf1d3a5ed02ce670672682a4bdc6fec652edd92
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed May 15 07:04:28 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Wed May 15 07:04:28 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=dbf1d3a5

merge


 README.md                                          |   16 +-
 app-doc/root-docs/ChangeLog                        |    9 +-
 app-doc/root-docs/Manifest                         |    3 +-
 app-doc/root-docs/root-docs-5.32.04.ebuild         |   96 -
 ...ocs-5.34.03.ebuild => root-docs-5.34.05.ebuild} |    5 +-
 app-doc/root-docs/root-docs-9999.ebuild            |    3 +-
 app-doc/scalapack-docs/ChangeLog                   |    7 +-
 app-doc/scalapack-docs/metadata.xml                |    3 +-
 app-doc/scalapack-docs/scalapack-docs-2.0.ebuild   |    6 +-
 app-forensics/vine/ChangeLog                       |   11 +
 app-forensics/vine/Manifest                        |    1 +
 app-forensics/vine/files/vine-1.0-binutils.patch   |   16 +
 app-forensics/vine/files/vine-1.0-gcc46.patch      |   37 +
 app-forensics/vine/files/vine-1.0-install.patch    |   89 +
 .../vine/files/vine-1.0-ocamlgraph182.patch        |   68 +
 {dev-lang/ispc => app-forensics/vine}/metadata.xml |    0
 app-forensics/vine/vine-1.0.ebuild                 |   40 +
 app-portage/g-octave/ChangeLog                     |    6 +-
 app-portage/g-octave/g-octave-9999.ebuild          |   44 +-
 app-portage/g-octave/metadata.xml                  |   10 +-
 app-text/jabref/ChangeLog                          |   12 +
 app-text/jabref/Manifest                           |    1 +
 ...{jabref-2.9.2-r1.ebuild => jabref-2.10b.ebuild} |   13 +-
 app-text/jabref/jabref-2.9.2-r1.ebuild             |    9 +-
 dev-cpp/eigen/ChangeLog                            |    8 +-
 dev-cpp/eigen/Manifest                             |    2 +-
 .../{eigen-3.1.2.ebuild => eigen-3.1.3-r1.ebuild}  |    0
 dev-cpp/eigen/eigen-9999.ebuild                    |   10 +-
 dev-db/cppdb/ChangeLog                             |   26 +
 dev-db/cppdb/Manifest                              |    1 +
 dev-db/cppdb/cppdb-0.3.1-r1.ebuild                 |   50 +
 dev-db/cppdb/metadata.xml                          |   13 +
 dev-java/flexdock/Manifest                         |    2 +-
 ....2-nodemo.patch => flexdock-1.2.3-nodemo.patch} |    0
 ...flexdock-1.2.2.ebuild => flexdock-1.2.3.ebuild} |    8 +-
 dev-java/gluegen/ChangeLog                         |    4 +
 dev-java/gluegen/gluegen-2.0_rc8.ebuild            |    2 +-
 dev-java/gluegen/metadata.xml                      |    4 +-
 dev-java/jcip-annotations/ChangeLog                |    6 +-
 dev-java/jcip-annotations/Manifest                 |    2 +-
 .../jcip-annotations-1.0-r1.ebuild                 |    7 +-
 dev-java/jcip-annotations/metadata.xml             |   13 +-
 dev-java/jlatexmath-fop/Manifest                   |    3 +-
 .../files/jlatexmath-fop-1.0.2-fixpaths.patch      |   13 +
 dev-java/jlatexmath-fop/files/version.xml          |    5 +
 .../jlatexmath-fop/jlatexmath-fop-0.9.7.ebuild     |   52 -
 .../jlatexmath-fop/jlatexmath-fop-1.0.0.ebuild     |   52 -
 .../jlatexmath-fop/jlatexmath-fop-1.0.2.ebuild     |   45 +
 dev-java/jlatexmath/Manifest                       |    3 +-
 dev-java/jlatexmath/jlatexmath-1.0.0.ebuild        |   32 -
 ...exmath-0.9.7.ebuild => jlatexmath-1.0.2.ebuild} |   22 +-
 dev-java/jogl/ChangeLog                            |    4 +
 dev-java/jogl/jogl-2.0_rc8-r1.ebuild               |    2 +-
 dev-java/jogl/metadata.xml                         |   10 +-
 dev-java/netcdf/Manifest                           |    2 +-
 dev-java/scirenderer/Manifest                      |    2 +-
 ...derer-1.0.5.ebuild => scirenderer-1.1.0.ebuild} |    4 +-
 dev-java/xmlgraphics-commons/Manifest              |    1 +
 .../files/disable-iccprofile-test.patch            |   38 +
 .../xmlgraphics-commons}/metadata.xml              |    2 +-
 .../xmlgraphics-commons-1.5.ebuild                 |   58 +
 dev-lang/berkeley_upc/ChangeLog                    |   10 +
 dev-lang/berkeley_upc/Manifest                     |    1 +
 dev-lang/berkeley_upc/berkeley_upc-2.16.0.ebuild   |   55 +
 dev-lang/berkeley_upc/metadata.xml                 |   25 +
 dev-lang/berkeley_upc_translator/ChangeLog         |   11 +
 dev-lang/berkeley_upc_translator/Manifest          |    1 +
 .../berkeley_upc_translator-2.16.0.ebuild          |   30 +
 ...keley_upc_translator-2.16.0-stackoverflow.patch |   18 +
 .../berkeley_upc_translator}/metadata.xml          |    4 +-
 dev-lang/julia/files/julia-nopatchelf.patch        |   14 +
 dev-lang/julia/julia-9999.ebuild                   |   28 +-
 dev-lang/julia/metadata.xml                        |    8 +-
 dev-lang/vtune/ChangeLog                           |    8 +-
 dev-lang/vtune/Manifest                            |    4 +-
 dev-lang/vtune/metadata.xml                        |    8 +-
 dev-lang/vtune/vtune-11.0.7.221625.ebuild          |   69 -
 dev-lang/vtune/vtune-13.1.4.270817.ebuild          |   38 +
 dev-libs/double-conversion/ChangeLog               |   10 +-
 dev-libs/double-conversion/Manifest                |    2 +-
 ...n-1.1.ebuild => double-conversion-1.1.1.ebuild} |    8 +-
 ...s.patch => double-conversion-1.1.1-scons.patch} |    0
 dev-libs/fortrancl/ChangeLog                       |    8 +
 dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild     |    5 +-
 dev-libs/fortrancl/metadata.xml                    |   12 +-
 dev-libs/libpfm/ChangeLog                          |   12 +
 dev-libs/libpfm/Manifest                           |    1 +
 dev-libs/libpfm/libpfm-4.3.0.ebuild                |   35 +
 .../envytools => dev-libs/libpfm}/metadata.xml     |    0
 dev-libs/mathjax/ChangeLog                         |   10 -
 dev-libs/mathjax/Manifest                          |    1 -
 dev-libs/mathjax/mathjax-2.0.ebuild                |   50 -
 dev-libs/mathjax/metadata.xml                      |   17 -
 dev-libs/papi/ChangeLog                            |    9 +
 dev-libs/papi/Manifest                             |    1 +
 {x11-misc/envytools => dev-libs/papi}/metadata.xml |    0
 dev-libs/papi/papi-5.1.0.2.ebuild                  |   30 +
 dev-ml/lacaml/ChangeLog                            |    6 +-
 dev-ml/lacaml/lacaml-7.0.3.ebuild                  |   12 +-
 dev-ml/lacaml/metadata.xml                         |    4 +-
 dev-ml/zarith/ChangeLog                            |    3 +
 dev-ml/zarith/Manifest                             |    3 -
 dev-ml/zarith/metadata.xml                         |   16 +-
 dev-ml/zarith/zarith-1.1.ebuild                    |   31 +-
 dev-perl/DBIx-DBStag/ChangeLog                     |    6 +-
 dev-perl/DBIx-DBStag/DBIx-DBStag-0.12.ebuild       |    9 +-
 dev-perl/DBIx-DBStag/Manifest                      |    2 +-
 dev-perl/DBIx-DBStag/metadata.xml                  |   10 +-
 dev-perl/Log-Cabin/ChangeLog                       |    9 +-
 dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild           |    9 +-
 dev-perl/Log-Cabin/Manifest                        |    2 +-
 dev-perl/Log-Cabin/metadata.xml                    |   10 +-
 dev-perl/Text-ParseWords/ChangeLog                 |    6 +-
 dev-perl/Text-ParseWords/Manifest                  |    2 +-
 .../Text-ParseWords/Text-ParseWords-3.27.ebuild    |    6 +-
 dev-perl/Text-ParseWords/metadata.xml              |   10 +-
 dev-perl/Time-Progress/ChangeLog                   |    6 +-
 dev-perl/Time-Progress/Manifest                    |    2 +-
 dev-perl/Time-Progress/Time-Progress-1.7.ebuild    |    6 +-
 dev-perl/Time-Progress/metadata.xml                |   10 +-
 dev-perl/go-perl/ChangeLog                         |    6 +-
 dev-perl/go-perl/Manifest                          |    2 +-
 dev-perl/go-perl/go-perl-0.13.ebuild               |   10 +-
 dev-perl/go-perl/metadata.xml                      |   10 +-
 dev-python/Forthon/ChangeLog                       |    8 +
 dev-python/Forthon/Forthon-0.8.11.ebuild           |   11 +-
 .../files/Forthon-0.8.11-fix_options_parser.patch  |   17 +
 dev-python/Forthon/metadata.xml                    |    8 +-
 dev-python/GOGrapher/ChangeLog                     |    6 +-
 dev-python/GOGrapher/GOGrapher-9999.ebuild         |   10 +-
 dev-python/GOGrapher/metadata.xml                  |   10 +-
 dev-python/RecSQL/ChangeLog                        |   18 +
 dev-python/RecSQL/RecSQL-9999.ebuild               |   33 +
 .../libcmatrix => dev-python/RecSQL}/metadata.xml  |    3 +-
 dev-python/asciidata/ChangeLog                     |   28 -
 dev-python/asciidata/Manifest                      |    1 -
 dev-python/asciidata/asciidata-1.1.1-r1.ebuild     |   41 -
 dev-python/asciidata/metadata.xml                  |   13 -
 dev-python/astlib/ChangeLog                        |    8 +-
 dev-python/astlib/Manifest                         |    2 +-
 .../{astlib-0.17.1.ebuild => astlib-0.7.0.ebuild}  |   31 +-
 .../astlib/files/astlib-0.17.1-wcstools.patch      |   75 -
 dev-python/astlib/metadata.xml                     |    3 +-
 dev-python/pymvpa/ChangeLog                        |    6 +-
 dev-python/pymvpa/metadata.xml                     |    4 +-
 dev-python/pymvpa/pymvpa-0.4.4.ebuild              |   30 +-
 dev-python/pythonocc/ChangeLog                     |   17 +-
 dev-python/pythonocc/Manifest                      |    2 +-
 dev-python/pythonocc/metadata.xml                  |    2 +-
 .../{pythonocc-0.4.ebuild => pythonocc-0.5.ebuild} |   19 +-
 dev-util/VampirTrace/Manifest                      |    1 +
 dev-util/VampirTrace/VampirTrace-5.14.3.ebuild     |   37 +
 dev-util/VampirTrace/metadata.xml                  |   13 +
 licenses/ECL-2.0                                   |   97 +
 licenses/blasr                                     |   65 +
 licenses/mgltools                                  |   42 +
 licenses/vampir                                    |   36 +
 media-gfx/PhiloGL/ChangeLog                        |    6 +-
 media-gfx/PhiloGL/PhiloGL-1.4.3.ebuild             |    6 +-
 media-gfx/PhiloGL/metadata.xml                     |    8 +-
 media-gfx/librecad/ChangeLog                       |   11 +-
 media-gfx/librecad/Manifest                        |    7 +-
 media-gfx/librecad/librecad-1.0.2.ebuild           |   10 +-
 ...librecad-1.0.1.ebuild => librecad-1.0.3.ebuild} |   15 +-
 media-gfx/librecad/librecad-2.0.0_alpha3.ebuild    |   48 -
 ...0_alpha4.ebuild => librecad-2.0.0_beta5.ebuild} |   10 +-
 media-gfx/librecad/librecad-9999.ebuild            |    8 +-
 media-gfx/librecad/metadata.xml                    |   18 +-
 profiles/arch.list                                 |   44 +
 profiles/hardened/package.mask                     |   27 -
 profiles/package.mask                              |   12 +
 sci-astronomy/astrometry/ChangeLog                 |    6 +-
 sci-astronomy/astrometry/astrometry-0.38.ebuild    |    9 +-
 sci-astronomy/astrometry/metadata.xml              |    4 +-
 sci-astronomy/eye/ChangeLog                        |    4 +-
 sci-astronomy/eye/eye-9999.ebuild                  |    3 +-
 sci-astronomy/eye/metadata.xml                     |    4 +-
 sci-astronomy/stiff/ChangeLog                      |    5 +-
 sci-astronomy/stiff/metadata.xml                   |    4 +-
 sci-astronomy/stiff/stiff-9999.ebuild              |   23 +-
 sci-astronomy/zebra/ChangeLog                      |    5 +-
 sci-astronomy/zebra/metadata.xml                   |    4 +-
 sci-astronomy/zebra/zebra-1.01.ebuild              |   16 +-
 sci-biology/Gambit/ChangeLog                       |    8 +
 sci-biology/Gambit/Gambit-0.4.145.ebuild           |    6 +-
 sci-biology/Gambit/Manifest                        |    4 +-
 sci-biology/Gambit/metadata.xml                    |   10 +-
 sci-biology/YASRA/ChangeLog                        |    5 +-
 sci-biology/YASRA/YASRA-2.1.ebuild                 |    4 +-
 sci-biology/YASRA/metadata.xml                     |   10 +-
 sci-biology/amos/ChangeLog                         |    8 +-
 sci-biology/amos/amos-9999.ebuild                  |   47 +-
 sci-biology/amos/metadata.xml                      |   17 +-
 sci-biology/artemis-bin/ChangeLog                  |    6 +-
 sci-biology/artemis-bin/Manifest                   |    2 +-
 sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild |    3 +-
 sci-biology/artemis-bin/metadata.xml               |   10 +-
 sci-biology/blasr/ChangeLog                        |    8 +-
 sci-biology/blasr/Manifest                         |    3 -
 sci-biology/blasr/blasr-9999.ebuild                |   13 +-
 sci-biology/blasr/metadata.xml                     |   10 +-
 sci-biology/cluster/ChangeLog                      |    6 +-
 sci-biology/cluster/cluster-1.50-r1.ebuild         |    4 +-
 sci-biology/cluster/cluster-1.50.ebuild            |    4 +-
 sci-biology/cluster/metadata.xml                   |   12 +-
 sci-biology/consed-bin/ChangeLog                   |    8 +
 sci-biology/consed-bin/Manifest                    |    4 +-
 sci-biology/consed-bin/consed-bin-20.ebuild        |    4 +-
 sci-biology/consed-bin/metadata.xml                |   10 +-
 sci-biology/estscan/ChangeLog                      |    5 +-
 sci-biology/estscan/Manifest                       |   18 +-
 sci-biology/estscan/metadata.xml                   |   16 +-
 sci-biology/hydra-sv/ChangeLog                     |    8 +
 sci-biology/hydra-sv/Manifest                      |    2 +-
 sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild         |   11 +-
 .../hydra-sv}/metadata.xml                         |    0
 sci-biology/manatee-igs/ChangeLog                  |    6 +-
 sci-biology/manatee-igs/Manifest                   |    4 +-
 sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild  |    4 +-
 sci-biology/manatee-igs/metadata.xml               |   10 +-
 sci-biology/mira/ChangeLog                         |   11 +-
 sci-biology/mira/Manifest                          |    7 +-
 .../mira/files/mira-3.4.0.2-boost-1.50.patch       |   24 +
 sci-biology/mira/mira-3.4.1.1.ebuild               |   61 +
 sci-biology/mira/mira-3.9.9.ebuild                 |   61 +
 sci-biology/ncbi-tools++/ChangeLog                 |   21 +
 .../files/ncbi-tools++-9.0.0-as-needed.patch       |  758 +-
 sci-biology/ncbi-tools++/metadata.xml              |   39 +
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |   95 +-
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild |    6 +-
 sci-biology/sra_sdk/ChangeLog                      |    6 +-
 sci-biology/sra_sdk/metadata.xml                   |   10 +-
 sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild           |    6 +-
 sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild          |    6 +-
 sci-biology/wcd/ChangeLog                          |    8 +-
 sci-biology/wcd/Manifest                           |    2 +-
 sci-biology/wcd/files/wcd-0.6.0-impl-decl.patch    |   15 +
 sci-biology/wcd/files/wcd-0.6.0-ldflags.patch      |   16 +
 sci-biology/wcd/metadata.xml                       |   10 +-
 sci-biology/wcd/wcd-0.6.0.ebuild                   |   41 +-
 sci-chemistry/GromacsWrapper/ChangeLog             |   25 +
 .../GromacsWrapper/GromacsWrapper-9999.ebuild      |   41 +
 .../files/0001-Drop-chmod-hack.patch               |   28 +
 .../GromacsWrapper}/metadata.xml                   |    3 +-
 sci-chemistry/ambertools/ChangeLog                 |   14 +-
 sci-chemistry/ambertools/ambertools-1.5-r2.ebuild  |  156 -
 sci-chemistry/ambertools/ambertools-1.5-r3.ebuild  |  158 -
 sci-chemistry/ambertools/ambertools-1.5-r4.ebuild  |   10 +-
 sci-chemistry/ambertools/ambertools-12.ebuild      |   16 +-
 sci-chemistry/ambertools/metadata.xml              |   10 +-
 sci-chemistry/ball/ChangeLog                       |    5 +-
 sci-chemistry/ball/ball-9999.ebuild                |   16 +-
 sci-chemistry/ball/metadata.xml                    |   20 +-
 sci-chemistry/burrow-owl/ChangeLog                 |    6 +-
 sci-chemistry/burrow-owl/burrow-owl-9999.ebuild    |    6 +-
 sci-chemistry/burrow-owl/metadata.xml              |    8 +-
 sci-chemistry/camshift/ChangeLog                   |    6 +-
 sci-chemistry/camshift/Manifest                    |    2 +-
 sci-chemistry/camshift/camshift-1.35.0.ebuild      |   45 +-
 sci-chemistry/camshift/files/1.35.0-gcc47.patch    |  148 +
 sci-chemistry/camshift/files/1.35.0-gentoo.patch   |   38 +
 sci-chemistry/camshift/metadata.xml                |    8 +-
 sci-chemistry/chooch/ChangeLog                     |    7 +-
 sci-chemistry/chooch/Manifest                      |    2 +-
 sci-chemistry/chooch/chooch-5.0.2-r1.ebuild        |   47 +-
 sci-chemistry/chooch/metadata.xml                  |    8 +-
 sci-chemistry/concoord/ChangeLog                   |    8 +-
 sci-chemistry/concoord/Manifest                    |    2 +
 .../{concoord-2.1.ebuild => concoord-2.1.2.ebuild} |   13 +-
 sci-chemistry/concoord/concoord-2.1.ebuild         |    4 +-
 sci-chemistry/concoord/metadata.xml                |    8 +-
 sci-chemistry/cs-rosetta/ChangeLog                 |   18 +
 sci-chemistry/cs-rosetta/Manifest                  |    3 +
 .../cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild |  104 +
 .../{phenix-bin => cs-rosetta}/metadata.xml        |    0
 sci-chemistry/curvefit/ChangeLog                   |    6 +-
 sci-chemistry/curvefit/curvefit-1.40.ebuild        |    6 +-
 sci-chemistry/curvefit/metadata.xml                |    2 +-
 sci-chemistry/freeon/ChangeLog                     |    7 +-
 sci-chemistry/freeon/freeon-9999.ebuild            |   21 +-
 sci-chemistry/freeon/metadata.xml                  |   12 +-
 sci-chemistry/gamess/ChangeLog                     |    6 +-
 .../gamess/files/gamess-20120501.1.gentoo.patch    |    4 +-
 sci-chemistry/gamess/gamess-20120501.1.ebuild      |    3 +-
 sci-chemistry/gamess/metadata.xml                  |   20 +-
 sci-chemistry/gnome-chemistry-utils/ChangeLog      |   20 +
 sci-chemistry/gnome-chemistry-utils/Manifest       |    1 +
 .../gnome-chemistry-utils-0.14.2.ebuild            |   44 +
 sci-chemistry/gnome-chemistry-utils/metadata.xml   |   11 +
 sci-chemistry/gromacs/ChangeLog                    |   18 +
 sci-chemistry/gromacs/Manifest                     |    2 -
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild      |  238 -
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild      |   47 +-
 sci-chemistry/gromacs/gromacs-9999.ebuild          |    1 -
 sci-chemistry/gromacs/metadata.xml                 |    1 -
 sci-chemistry/hydronmr/ChangeLog                   |   10 +
 sci-chemistry/hydronmr/Manifest                    |   13 +
 sci-chemistry/hydronmr/hydronmr-7c.ebuild          |   57 +
 .../{phenix-bin => hydronmr}/metadata.xml          |    0
 sci-chemistry/jligand/ChangeLog                    |    6 +-
 sci-chemistry/jligand/Manifest                     |    2 +-
 sci-chemistry/jligand/jligand-1.0.19.ebuild        |    4 +-
 sci-chemistry/jligand/metadata.xml                 |    8 +-
 sci-chemistry/mgltools-autodocktools/ChangeLog     |   16 +
 sci-chemistry/mgltools-autodocktools/Manifest      |    3 +-
 .../mgltools-autodocktools-1.5.4-r2.ebuild         |    4 +-
 ....ebuild => mgltools-autodocktools-1.5.6.ebuild} |    5 +-
 .../mgltools-autodocktools-1.5.6_rc2.ebuild        |   71 -
 sci-chemistry/mgltools-bhtree/ChangeLog            |   14 +
 sci-chemistry/mgltools-bhtree/Manifest             |    3 +-
 .../mgltools-bhtree-1.5.4-r1.ebuild                |    4 +-
 ...5.6_rc3.ebuild => mgltools-bhtree-1.5.6.ebuild} |    5 +-
 .../mgltools-bhtree-1.5.6_rc2.ebuild               |   48 -
 sci-chemistry/mgltools-cadd/ChangeLog              |   12 +
 sci-chemistry/mgltools-cadd/Manifest               |    3 +-
 ...1.5.6_rc3.ebuild => mgltools-cadd-1.5.6.ebuild} |    5 +-
 .../mgltools-cadd/mgltools-cadd-1.5.6_rc2.ebuild   |   48 -
 sci-chemistry/mgltools-cmolkit/ChangeLog           |   14 +
 sci-chemistry/mgltools-cmolkit/Manifest            |    3 +-
 .../mgltools-cmolkit-1.5.4-r1.ebuild               |    4 +-
 ....6_rc3.ebuild => mgltools-cmolkit-1.5.6.ebuild} |    5 +-
 .../mgltools-cmolkit-1.5.6_rc2.ebuild              |   48 -
 sci-chemistry/mgltools-dejavu/ChangeLog            |   14 +
 sci-chemistry/mgltools-dejavu/Manifest             |    3 +-
 .../mgltools-dejavu-1.5.4-r1.ebuild                |    4 +-
 ...5.6_rc3.ebuild => mgltools-dejavu-1.5.6.ebuild} |    5 +-
 .../mgltools-dejavu-1.5.6_rc2.ebuild               |   51 -
 sci-chemistry/mgltools-geomutils/ChangeLog         |   14 +
 sci-chemistry/mgltools-geomutils/Manifest          |    3 +-
 .../mgltools-geomutils-1.5.4-r1.ebuild             |    4 +-
 ..._rc3.ebuild => mgltools-geomutils-1.5.6.ebuild} |    5 +-
 .../mgltools-geomutils-1.5.6_rc2.ebuild            |   49 -
 sci-chemistry/mgltools-gle/ChangeLog               |   13 +
 sci-chemistry/mgltools-gle/Manifest                |    3 +-
 .../mgltools-gle/mgltools-gle-1.5.4-r1.ebuild      |    4 +-
 ...-1.5.6_rc3.ebuild => mgltools-gle-1.5.6.ebuild} |    5 +-
 .../mgltools-gle/mgltools-gle-1.5.6_rc2.ebuild     |   48 -
 sci-chemistry/mgltools-mglutil/ChangeLog           |   14 +
 sci-chemistry/mgltools-mglutil/Manifest            |    3 +-
 .../mgltools-mglutil-1.5.4-r1.ebuild               |    4 +-
 ....6_rc3.ebuild => mgltools-mglutil-1.5.6.ebuild} |    5 +-
 .../mgltools-mglutil-1.5.6_rc2.ebuild              |   51 -
 sci-chemistry/mgltools-molkit/ChangeLog            |   14 +
 sci-chemistry/mgltools-molkit/Manifest             |    3 +-
 .../mgltools-molkit-1.5.4-r1.ebuild                |    4 +-
 ...5.6_rc3.ebuild => mgltools-molkit-1.5.6.ebuild} |    5 +-
 .../mgltools-molkit-1.5.6_rc2.ebuild               |   50 -
 sci-chemistry/mgltools-networkeditor/ChangeLog     |   16 +
 sci-chemistry/mgltools-networkeditor/Manifest      |    3 +-
 .../mgltools-networkeditor-1.5.4-r1.ebuild         |    4 +-
 ....ebuild => mgltools-networkeditor-1.5.6.ebuild} |    5 +-
 .../mgltools-networkeditor-1.5.6_rc2.ebuild        |   50 -
 sci-chemistry/mgltools-opengltk/ChangeLog          |   14 +
 sci-chemistry/mgltools-opengltk/Manifest           |    3 +-
 .../mgltools-opengltk-1.5.4-r2.ebuild              |    4 +-
 ...6_rc3.ebuild => mgltools-opengltk-1.5.6.ebuild} |    5 +-
 .../mgltools-opengltk-1.5.6_rc2.ebuild             |   68 -
 sci-chemistry/mgltools-pmv/ChangeLog               |   13 +
 sci-chemistry/mgltools-pmv/Manifest                |    3 +-
 .../mgltools-pmv/mgltools-pmv-1.5.4-r1.ebuild      |    4 +-
 ...-1.5.6_rc3.ebuild => mgltools-pmv-1.5.6.ebuild} |    5 +-
 .../mgltools-pmv/mgltools-pmv-1.5.6_rc2.ebuild     |   52 -
 sci-chemistry/mgltools-pyautodock/ChangeLog        |   15 +
 sci-chemistry/mgltools-pyautodock/Manifest         |    3 +-
 .../mgltools-pyautodock-1.5.4-r1.ebuild            |    4 +-
 ...rc3.ebuild => mgltools-pyautodock-1.5.6.ebuild} |    5 +-
 .../mgltools-pyautodock-1.5.6_rc2.ebuild           |   48 -
 sci-chemistry/mgltools-pybabel/ChangeLog           |   14 +
 sci-chemistry/mgltools-pybabel/Manifest            |    3 +-
 .../mgltools-pybabel-1.5.4-r1.ebuild               |    4 +-
 ....6_rc3.ebuild => mgltools-pybabel-1.5.6.ebuild} |    5 +-
 .../mgltools-pybabel-1.5.6_rc2.ebuild              |   50 -
 sci-chemistry/mgltools-pyglf/ChangeLog             |   14 +
 sci-chemistry/mgltools-pyglf/Manifest              |    3 +-
 .../mgltools-pyglf/mgltools-pyglf-1.5.4-r1.ebuild  |    4 +-
 ....5.6_rc3.ebuild => mgltools-pyglf-1.5.6.ebuild} |    5 +-
 .../mgltools-pyglf/mgltools-pyglf-1.5.6_rc2.ebuild |   48 -
 sci-chemistry/mgltools-qslimlib/ChangeLog          |   14 +
 sci-chemistry/mgltools-qslimlib/Manifest           |    3 +-
 .../mgltools-qslimlib-1.5.4-r1.ebuild              |    4 +-
 ...6_rc3.ebuild => mgltools-qslimlib-1.5.6.ebuild} |    5 +-
 .../mgltools-qslimlib-1.5.6_rc2.ebuild             |   52 -
 sci-chemistry/mgltools-scenario/ChangeLog          |    4 +
 .../mgltools-scenario-1.5.4-r1.ebuild              |    4 +-
 sci-chemistry/mgltools-scenario2/ChangeLog         |   13 +
 sci-chemistry/mgltools-scenario2/Manifest          |    3 +-
 ..._rc3.ebuild => mgltools-scenario2-1.5.6.ebuild} |    5 +-
 .../mgltools-scenario2-1.5.6_rc2.ebuild            |   50 -
 sci-chemistry/mgltools-sff/ChangeLog               |   13 +
 sci-chemistry/mgltools-sff/Manifest                |    3 +-
 .../mgltools-sff/mgltools-sff-1.5.4-r1.ebuild      |    4 +-
 ...-1.5.6_rc3.ebuild => mgltools-sff-1.5.6.ebuild} |    5 +-
 .../mgltools-sff/mgltools-sff-1.5.6_rc2.ebuild     |   49 -
 sci-chemistry/mgltools-stride/ChangeLog            |    6 +
 .../mgltools-stride-1.5.4-r1.ebuild                |    4 +-
 sci-chemistry/mgltools-support/ChangeLog           |   14 +
 sci-chemistry/mgltools-support/Manifest            |    3 +-
 .../mgltools-support-1.5.4-r1.ebuild               |    4 +-
 ....6_rc3.ebuild => mgltools-support-1.5.6.ebuild} |    5 +-
 .../mgltools-support-1.5.6_rc2.ebuild              |   49 -
 sci-chemistry/mgltools-symserv/ChangeLog           |   12 +
 sci-chemistry/mgltools-symserv/Manifest            |    3 +-
 .../mgltools-symserv-1.5.4-r1.ebuild               |    4 +-
 ....6_rc3.ebuild => mgltools-symserv-1.5.6.ebuild} |    5 +-
 .../mgltools-symserv-1.5.6_rc2.ebuild              |   48 -
 sci-chemistry/mgltools-utpackages/ChangeLog        |   15 +
 sci-chemistry/mgltools-utpackages/Manifest         |    3 +-
 .../mgltools-utpackages-1.5.4-r1.ebuild            |    4 +-
 ...rc3.ebuild => mgltools-utpackages-1.5.6.ebuild} |    5 +-
 .../mgltools-utpackages-1.5.6_rc2.ebuild           |   49 -
 sci-chemistry/mgltools-viewer-framework/ChangeLog  |   17 +
 sci-chemistry/mgltools-viewer-framework/Manifest   |    3 +-
 .../mgltools-viewer-framework-1.5.4-r2.ebuild      |    4 +-
 ...uild => mgltools-viewer-framework-1.5.6.ebuild} |    5 +-
 .../mgltools-viewer-framework-1.5.6_rc2.ebuild     |   53 -
 sci-chemistry/mgltools-vision/ChangeLog            |   14 +
 sci-chemistry/mgltools-vision/Manifest             |    3 +-
 .../mgltools-vision-1.5.4-r1.ebuild                |    4 +-
 ...5.6_rc3.ebuild => mgltools-vision-1.5.6.ebuild} |    5 +-
 .../mgltools-vision-1.5.6_rc2.ebuild               |   59 -
 sci-chemistry/mgltools-visionlib/ChangeLog         |   14 +
 sci-chemistry/mgltools-visionlib/Manifest          |    3 +-
 .../mgltools-visionlib-1.5.4-r1.ebuild             |    4 +-
 ..._rc3.ebuild => mgltools-visionlib-1.5.6.ebuild} |    5 +-
 .../mgltools-visionlib-1.5.6_rc2.ebuild            |   48 -
 sci-chemistry/mgltools-volume/ChangeLog            |   14 +
 sci-chemistry/mgltools-volume/Manifest             |    3 +-
 .../mgltools-volume-1.5.4-r1.ebuild                |    4 +-
 ...5.6_rc3.ebuild => mgltools-volume-1.5.6.ebuild} |    5 +-
 .../mgltools-volume-1.5.6_rc2.ebuild               |   50 -
 sci-chemistry/mgltools-webservices/ChangeLog       |   11 +
 sci-chemistry/mgltools-webservices/Manifest        |    3 +-
 .../mgltools-webservices-1.5.4-r2.ebuild           |    4 +-
 ...c3.ebuild => mgltools-webservices-1.5.6.ebuild} |    5 +-
 .../mgltools-webservices-1.5.6_rc2.ebuild          |   49 -
 sci-chemistry/mgltools/ChangeLog                   |   10 +
 sci-chemistry/mgltools/Manifest                    |    3 +-
 sci-chemistry/mgltools/mgltools-1.5.4.ebuild       |    4 +-
 ...ools-1.5.6_rc3.ebuild => mgltools-1.5.6.ebuild} |    5 +-
 sci-chemistry/mgltools/mgltools-1.5.6_rc2.ebuild   |   39 -
 sci-chemistry/modelfree/ChangeLog                  |    6 +-
 sci-chemistry/modelfree/metadata.xml               |    8 +-
 sci-chemistry/modelfree/modelfree-4.20.ebuild      |    6 +-
 sci-chemistry/nmrpipe/ChangeLog                    |   10 +
 sci-chemistry/nmrpipe/Manifest                     |    4 +-
 ...ebuild => nmrpipe-7.9.2013.021.23.09-r2.ebuild} |    8 +-
 sci-chemistry/nwchem/ChangeLog                     |   10 +-
 sci-chemistry/nwchem/metadata.xml                  |   16 +-
 sci-chemistry/nwchem/nwchem-6.1.1.ebuild           |   91 +-
 sci-chemistry/phenix-bin/ChangeLog                 |    6 +
 sci-chemistry/phenix-bin/Manifest                  |    4 +-
 ....1.1168.ebuild => phenix-bin-1.8.2.1309.ebuild} |   28 +-
 sci-chemistry/pymol-plugins-ezviz/ChangeLog        |    5 +-
 sci-chemistry/pymol-plugins-ezviz/Manifest         |    2 +-
 sci-chemistry/pymol-plugins-ezviz/metadata.xml     |   11 +-
 sci-chemistry/pymol-plugins-psico/ChangeLog        |    6 +-
 sci-chemistry/pymol-plugins-psico/metadata.xml     |    8 +-
 .../pymol-plugins-psico-9999.ebuild                |    4 +-
 sci-chemistry/pymol/ChangeLog                      |   16 +
 sci-chemistry/pymol/files/pymol-9999-flags.patch   |   19 -
 sci-chemistry/pymol/files/pymol-9999-prefix.patch  |   41 -
 sci-chemistry/pymol/metadata.xml                   |    3 +-
 sci-chemistry/pymol/pymol-9999.ebuild              |   43 +-
 sci-chemistry/rosetta/ChangeLog                    |   25 +-
 sci-chemistry/rosetta/Manifest                     |    2 +-
 .../rosetta/files/3.0-user-settings.patch          |   26 -
 .../{3.0-boinc.patch => rosetta-3.4-boinc.patch}   |    0
 .../rosetta/files/rosetta-3.4-boost.patch          |   16 +
 ....patch => rosetta-3.4-fix-scons-warnings.patch} |    0
 ...lgrind.patch => rosetta-3.4-fix-valgrind.patch} |    0
 .../rosetta/files/rosetta-3.4-gcc4.7.patch         |   32 +
 ...0-platform.patch => rosetta-3.4-platform.patch} |    0
 .../rosetta/files/rosetta-3.4-unbundle.patch       |   47 +
 .../rosetta/files/rosetta-3.4-user-settings.patch  |   29 +
 .../{3.0-zlib.patch => rosetta-3.4-zlib.patch}     |    0
 sci-chemistry/rosetta/metadata.xml                 |   25 +-
 .../{rosetta-3.0-r1.ebuild => rosetta-3.4.ebuild}  |  102 +-
 sci-chemistry/simpson/ChangeLog                    |   11 +-
 sci-chemistry/simpson/files/3.0.1-gentoo.patch     |    2 +-
 sci-chemistry/simpson/files/3.1.0-gentoo.patch     |    2 +-
 sci-chemistry/simpson/files/3.1.2-gentoo.patch     |    2 +-
 sci-chemistry/simpson/metadata.xml                 |    2 +-
 sci-chemistry/simpson/simpson-3.0.1.ebuild         |    8 +-
 sci-chemistry/simpson/simpson-3.1.0.ebuild         |    8 +-
 sci-chemistry/simpson/simpson-3.1.2.ebuild         |    8 +-
 sci-chemistry/specView/ChangeLog                   |    6 +-
 sci-chemistry/specView/metadata.xml                |    2 +-
 sci-chemistry/specView/specView-1.0.2.ebuild       |   16 +-
 sci-chemistry/usf-tools/ChangeLog                  |    8 +-
 sci-chemistry/usf-tools/metadata.xml               |    5 +-
 sci-chemistry/usf-tools/usf-tools-9999.ebuild      |    4 +-
 sci-chemistry/votca-csg/ChangeLog                  |    3 +
 sci-chemistry/votca-csg/votca-csg-9999.ebuild      |    4 +-
 sci-geosciences/fullprof-bin/ChangeLog             |   10 +
 sci-geosciences/fullprof-bin/Manifest              |    1 +
 .../fullprof-bin/fullprof-bin-2012.11.ebuild       |   66 +
 sci-geosciences/fullprof-bin/metadata.xml          |   16 +
 sci-geosciences/qgis/ChangeLog                     |    5 +-
 sci-geosciences/qgis/Manifest                      |    2 +-
 sci-geosciences/qgis/metadata.xml                  |   11 +-
 sci-geosciences/qgis/qgis-9999.ebuild              |   12 +-
 sci-libs/Cgraph/Cgraph-2.04.ebuild                 |    5 +-
 sci-libs/Cgraph/ChangeLog                          |    6 +-
 sci-libs/Cgraph/Manifest                           |    2 +-
 sci-libs/Cgraph/metadata.xml                       |    8 +-
 sci-libs/acml/ChangeLog                            |    3 +
 sci-libs/acml/acml-5.3.0.ebuild                    |    1 +
 sci-libs/amdlibm/ChangeLog                         |    9 +-
 sci-libs/amdlibm/amdlibm-3.0.2.ebuild              |   23 +-
 sci-libs/amdlibm/metadata.xml                      |    4 +-
 sci-libs/armadillo/ChangeLog                       |   20 +
 sci-libs/armadillo/Manifest                        |    2 +-
 ...lo-3.6.2-r1.ebuild => armadillo-3.810.2.ebuild} |   44 +-
 .../files/armadillo-3.810.2-example-makefile.patch |   33 +
 .../armadillo/files/armadillo-3.810.2-hdf5.patch   |   19 +
 sci-libs/armadillo/metadata.xml                    |   12 +-
 sci-libs/atlas/ChangeLog                           |    8 +
 sci-libs/atlas/atlas-3.10.1-r1.ebuild              |  281 +
 sci-libs/bigdft/ChangeLog                          |   23 +-
 sci-libs/bigdft/Manifest                           |    1 -
 sci-libs/bigdft/bigdft-1.6.0-r2.ebuild             |   18 +-
 sci-libs/bigdft/bigdft-1.6_pre1-r4.ebuild          |  130 -
 sci-libs/bigdft/bigdft-1.7_pre12.ebuild            |   33 +-
 .../bigdft/files/bigdft-1.7-dev.12-GPUlink.patch   |   12 +
 sci-libs/bigdft/metadata.xml                       |   20 +-
 sci-libs/blas-reference/ChangeLog                  |    6 +-
 .../blas-reference/blas-reference-20120925.ebuild  |    5 +-
 .../blas-reference/blas-reference-99999999.ebuild  |    7 +-
 sci-libs/blas-reference/metadata.xml               |    4 +-
 sci-libs/blastdb/blastdb-9999.ebuild               |   27 +
 skel.metadata.xml => sci-libs/blastdb/metadata.xml |    0
 sci-libs/bliss/ChangeLog                           |   10 +
 sci-libs/bliss/Manifest                            |    1 +
 sci-libs/bliss/bliss-0.72.ebuild                   |   43 +
 sci-libs/bliss/files/bliss-0.72-autotools.patch    |  159 +
 sci-libs/bliss/files/bliss-0.72-fedora.patch       |  648 +
 .../concoord => sci-libs/bliss}/metadata.xml       |    3 +-
 sci-libs/calculix-ccx/ChangeLog                    |    8 +-
 sci-libs/calculix-ccx/Manifest                     |    6 +-
 sci-libs/calculix-ccx/calculix-ccx-2.2.ebuild      |   19 +-
 sci-libs/calculix-ccx/metadata.xml                 |    8 +-
 sci-libs/coinor-bonmin/ChangeLog                   |    5 +-
 sci-libs/coinor-bonmin/metadata.xml                |    7 +-
 sci-libs/coinor-cppad/ChangeLog                    |    4 +
 sci-libs/coinor-cppad/coinor-cppad-20130127.ebuild |    7 +-
 sci-libs/coinor-cppad/metadata.xml                 |    4 +-
 sci-libs/cs-rosetta-db/ChangeLog                   |   14 +
 sci-libs/cs-rosetta-db/Manifest                    |    7 +
 .../cs-rosetta-db-1.01.2009.1109.11.ebuild         |   61 +
 .../cs-rosetta-db}/metadata.xml                    |    0
 sci-libs/csrosetta-angless/ChangeLog               |   14 -
 sci-libs/csrosetta-angless/Manifest                |    1 -
 .../csrosetta-angless-2009.05.01.ebuild            |   24 -
 sci-libs/csrosetta-angless/metadata.xml            |    8 -
 sci-libs/csrosetta-cs/ChangeLog                    |   14 -
 sci-libs/csrosetta-cs/Manifest                     |    1 -
 .../csrosetta-cs/csrosetta-cs-2009.05.01.ebuild    |   24 -
 sci-libs/csrosetta-cs/metadata.xml                 |    8 -
 sci-libs/csrosetta-pdbh/ChangeLog                  |   14 -
 sci-libs/csrosetta-pdbh/Manifest                   |    1 -
 .../csrosetta-pdbh-2009.05.01.ebuild               |   24 -
 sci-libs/csrosetta-pdbh/metadata.xml               |    8 -
 sci-libs/gmsh/ChangeLog                            |    5 +-
 sci-libs/gmsh/gmsh-2.5.0.ebuild                    |    3 +-
 sci-libs/gmsh/metadata.xml                         |   24 +-
 sci-libs/gsl/ChangeLog                             |    6 +-
 sci-libs/gsl/gsl-1.15-r3.ebuild                    |    8 +-
 sci-libs/gsl/metadata.xml                          |   10 +-
 sci-libs/lapack-reference/ChangeLog                |    5 +-
 sci-libs/lapack-reference/metadata.xml             |   13 +-
 sci-libs/lemon/ChangeLog                           |    6 +-
 sci-libs/lemon/lemon-1.2.3.ebuild                  |   20 +-
 sci-libs/lemon/metadata.xml                        |   10 +-
 sci-libs/libcmatrix/ChangeLog                      |   69 -
 sci-libs/libcmatrix/Manifest                       |    1 -
 sci-libs/libcmatrix/files/3.11.0-shared.patch      |   80 -
 sci-libs/libcmatrix/files/3.2.1-atlas.patch        |   33 -
 sci-libs/libcmatrix/files/3.2.1-gcc4.4.patch       |   12 -
 sci-libs/libcmatrix/files/3.2.1-gcc4.6.patch       |   16 -
 sci-libs/libcmatrix/files/3.2.1-gcc4.7.patch       |  227 -
 sci-libs/libcmatrix/files/3.2.1-minuit2.patch      |   14 -
 sci-libs/libcmatrix/files/3.2.1-shared.patch       |   80 -
 sci-libs/libcmatrix/files/3.9.0-atlas.patch        |   24 -
 sci-libs/libcmatrix/libcmatrix-3.11.0.ebuild       |   55 -
 sci-libs/libspatialindex/ChangeLog                 |    6 +-
 sci-libs/libspatialindex/Manifest                  |    2 +-
 .../libspatialindex/libspatialindex-1.6.1.ebuild   |   17 +-
 sci-libs/libspatialindex/metadata.xml              |    2 +-
 sci-libs/magma/ChangeLog                           |    5 +
 sci-libs/magma/Manifest                            |    1 -
 .../files/magma-1.2.1-duplicate-symbols.patch      |  612 -
 sci-libs/magma/magma-1.2.1.ebuild                  |  139 -
 sci-libs/magma/magma-1.3.0.ebuild                  |   17 +-
 sci-libs/magma/metadata.xml                        |   12 +-
 sci-libs/mlpack/ChangeLog                          |   17 +
 sci-libs/mlpack/Manifest                           |    1 +
 sci-libs/mlpack/files/mlpack-1.0.4-libdir.patch    |   13 +
 sci-libs/mlpack/metadata.xml                       |   13 +
 sci-libs/mlpack/mlpack-1.0.4-r1.ebuild             |   49 +
 sci-libs/modglue/ChangeLog                         |    6 +-
 sci-libs/modglue/Manifest                          |    2 +-
 sci-libs/modglue/metadata.xml                      |   14 +-
 sci-libs/modglue/modglue-1.16.ebuild               |   15 +-
 sci-libs/o2scl/ChangeLog                           |    8 +-
 sci-libs/o2scl/Manifest                            |    2 +-
 .../{o2scl-0.911.ebuild => o2scl-0.912.ebuild}     |    7 +-
 sci-libs/openblas/ChangeLog                        |   11 +-
 sci-libs/openblas/Manifest                         |    2 +-
 ...openblas-0.2.5.ebuild => openblas-0.2.6.ebuild} |    0
 sci-libs/openblas/openblas-9999.ebuild             |   12 +-
 sci-libs/openlibm/ChangeLog                        |   10 +
 .../files/openlibm-respect-toolchain.patch         |   32 +
 sci-libs/openlibm/files/openlibm-soname.patch      |   11 +
 sci-libs/openlibm/metadata.xml                     |   18 +
 sci-libs/openlibm/openlibm-9999.ebuild             |   43 +
 sci-libs/optpp/ChangeLog                           |   11 +-
 sci-libs/optpp/metadata.xml                        |    2 +-
 sci-libs/optpp/optpp-2.4.ebuild                    |   15 +-
 sci-libs/parmetis/ChangeLog                        |    6 +-
 sci-libs/parmetis/metadata.xml                     |   12 +-
 sci-libs/parmetis/parmetis-4.0.2.ebuild            |    6 +-
 sci-libs/starparse/ChangeLog                       |    6 +-
 sci-libs/starparse/Manifest                        |    2 +-
 sci-libs/starparse/metadata.xml                    |    8 +-
 sci-libs/starparse/starparse-1.0.ebuild            |   25 +-
 sci-libs/starparse/starparse-9999.ebuild           |    8 +-
 sci-libs/starparse/starparse-9999_pre10.ebuild     |   22 +-
 sci-libs/tmglib/ChangeLog                          |    6 +-
 sci-libs/tmglib/metadata.xml                       |    4 +-
 sci-libs/tmglib/tmglib-3.4.2.ebuild                |    6 +-
 sci-libs/trilinos/ChangeLog                        |   12 +-
 sci-libs/trilinos/Manifest                         |    1 +
 .../files/trilinos-11.0.3-fix-install-paths.patch  |   76 +
 sci-libs/trilinos/metadata.xml                     |   37 +-
 sci-libs/trilinos/trilinos-10.10.1.ebuild          |   26 +-
 ...linos-10.10.1.ebuild => trilinos-11.0.3.ebuild} |   35 +-
 sci-libs/wannier90/ChangeLog                       |    7 +-
 sci-libs/wannier90/Manifest                        |    2 +-
 sci-libs/wannier90/metadata.xml                    |    8 +-
 sci-libs/wannier90/wannier90-1.2.ebuild            |   51 +-
 sci-libs/xblas/ChangeLog                           |    6 +-
 sci-libs/xblas/metadata.xml                        |    4 +-
 sci-libs/xblas/xblas-1.0.248.ebuild                |    8 +-
 sci-libs/zarja/ChangeLog                           |    7 +-
 sci-libs/zarja/Manifest                            |    2 +-
 sci-libs/zarja/metadata.xml                        |    4 +-
 sci-libs/zarja/zarja-1.1.1.ebuild                  |   22 +-
 sci-mathematics/Macaulay2/ChangeLog                |    8 +
 sci-mathematics/Macaulay2/Macaulay2-9999.ebuild    |   23 +-
 sci-mathematics/Macaulay2/Manifest                 |    4 +-
 sci-mathematics/Macaulay2/files/9999-lapack.patch  |    2 +-
 sci-mathematics/Macaulay2/metadata.xml             |   18 +-
 sci-mathematics/algae/ChangeLog                    |   18 -
 sci-mathematics/algae/Manifest                     |    1 -
 sci-mathematics/algae/algae-4.3.6.ebuild           |   55 -
 sci-mathematics/algae/files/Makefile.in-doc.patch  |    5 -
 sci-mathematics/algae/files/Makefile.in-src.patch  |    4 -
 sci-mathematics/algae/files/configure.in.patch     |   10 -
 sci-mathematics/algae/files/unbundle.patch         |   41 +
 sci-mathematics/algae/metadata.xml                 |   16 -
 sci-mathematics/alt-ergo/ChangeLog                 |    4 +
 sci-mathematics/alt-ergo/Manifest                  |    3 -
 sci-mathematics/alt-ergo/alt-ergo-0.95.ebuild      |   28 +-
 sci-mathematics/alt-ergo/metadata.xml              |   18 +-
 sci-mathematics/bertini/ChangeLog                  |    6 +-
 sci-mathematics/bertini/bertini-1.3.1.ebuild       |    3 +-
 sci-mathematics/bertini/metadata.xml               |   10 +-
 sci-mathematics/cadabra/ChangeLog                  |    8 +-
 sci-mathematics/cadabra/Manifest                   |    1 +
 sci-mathematics/cadabra/cadabra-1.31.ebuild        |   83 +
 sci-mathematics/cdfplayer/ChangeLog                |    7 +
 sci-mathematics/cdfplayer/Manifest                 |    2 +-
 ...fplayer-9.0.0.ebuild => cdfplayer-9.0.1.ebuild} |    2 +-
 ...aller.patch => cdfplayer-9.0.1-installer.patch} |    4 +-
 sci-mathematics/dsfmt/ChangeLog                    |    5 +-
 sci-mathematics/dsfmt/dsfmt-2.2.ebuild             |   11 +-
 sci-mathematics/dsfmt/metadata.xml                 |    4 +-
 sci-mathematics/flocq/ChangeLog                    |    4 +
 sci-mathematics/flocq/Manifest                     |    3 -
 sci-mathematics/flocq/flocq-2.1.0.ebuild           |   13 +-
 sci-mathematics/flocq/metadata.xml                 |   10 +-
 sci-mathematics/freefem++/ChangeLog                |    8 +-
 sci-mathematics/freefem++/Manifest                 |    3 +-
 .../files/freefem++-3.4.2-no-doc-autobuild.patch   |   30 -
 sci-mathematics/freefem++/freefem++-3.5.ebuild     |  156 -
 sci-mathematics/freefem++/freefem++-3.8.ebuild     |   18 +-
 sci-mathematics/freefem++/metadata.xml             |    4 +-
 sci-mathematics/gambit/ChangeLog                   |    6 +-
 sci-mathematics/gambit/Manifest                    |    2 +-
 sci-mathematics/gambit/gambit-0.2010.09.01.ebuild  |    4 +-
 sci-mathematics/gambit/metadata.xml                |   16 +-
 sci-mathematics/gappalib-coq/ChangeLog             |    4 +
 sci-mathematics/gappalib-coq/Manifest              |    4 -
 .../gappalib-coq/gappalib-coq-0.18.0.ebuild        |   28 +-
 sci-mathematics/gappalib-coq/metadata.xml          |   10 +-
 sci-mathematics/giac/ChangeLog                     |    3 +
 sci-mathematics/giac/Manifest                      |    3 -
 sci-mathematics/giac/giac-1.0.0.ebuild             |   33 +-
 sci-mathematics/giac/metadata.xml                  |   20 +-
 sci-mathematics/lattE-macchiato/ChangeLog          |    6 +-
 sci-mathematics/lattE-macchiato/Manifest           |    2 +-
 .../lattE-macchiato/lattE-macchiato-0.9.3.ebuild   |    5 +-
 sci-mathematics/lattE-macchiato/metadata.xml       |   12 +-
 sci-mathematics/mdp/ChangeLog                      |    5 +-
 sci-mathematics/mdp/mdp-9999.ebuild                |   12 +-
 sci-mathematics/mdp/metadata.xml                   |   12 +-
 sci-mathematics/petsc/ChangeLog                    |   14 +-
 sci-mathematics/petsc/Manifest                     |    2 -
 .../petsc/files/petsc-3.1_p8-configure-pic.patch   |   11 -
 .../petsc/files/petsc-3.1_p8-disable-rpath.patch   |   16 -
 .../petsc/files/petsc-3.2_p7-configure-pic.patch   |   11 -
 .../files/petsc-3.2_p7-disable-env-warnings.patch  |   13 -
 .../petsc/files/petsc-3.2_p7-disable-rpath.patch   |   16 -
 sci-mathematics/petsc/metadata.xml                 |   19 +-
 sci-mathematics/petsc/petsc-3.1_p8-r1.ebuild       |  202 -
 sci-mathematics/petsc/petsc-3.2_p7.ebuild          |  215 -
 sci-mathematics/petsc/petsc-3.3_p5.ebuild          |    6 +-
 sci-mathematics/pff/ChangeLog                      |    3 +
 sci-mathematics/pff/Manifest                       |    3 -
 sci-mathematics/pff/metadata.xml                   |   10 +-
 sci-mathematics/pff/pff-8.4.ebuild                 |   17 +-
 sci-mathematics/polymake/ChangeLog                 |    8 +
 sci-mathematics/polymake/metadata.xml              |   18 +-
 sci-mathematics/polymake/polymake-2.11-r1.ebuild   |    4 +-
 sci-mathematics/rstudio/ChangeLog                  |   19 -
 sci-mathematics/rstudio/Manifest                   |    7 -
 .../rstudio/files/rstudio-0.97.237-prefs.patch     |   20 -
 .../rstudio/files/rstudio-linker_flags.patch       |   13 -
 sci-mathematics/rstudio/files/rstudio-paths.patch  |  106 -
 sci-mathematics/rstudio/files/rstudio-prefs.patch  |   20 -
 .../rstudio/files/rstudio-rserver.initd            |   15 -
 .../rstudio/files/rstudio.desktop.patch            |   16 -
 sci-mathematics/rstudio/metadata.xml               |   13 -
 sci-mathematics/rstudio/rstudio-0.96.316.ebuild    |  141 -
 sci-mathematics/rstudio/rstudio-0.96.331.ebuild    |  141 -
 sci-mathematics/rstudio/rstudio-0.97.237.ebuild    |  139 -
 sci-mathematics/scilab/ChangeLog                   |    6 +-
 sci-mathematics/scilab/metadata.xml                |   16 +-
 sci-mathematics/scilab/scilab-5.3.3-r1.ebuild      |   26 +-
 sci-mathematics/scilab/scilab-5.4.0.ebuild         |   19 +-
 sci-mathematics/surfer/ChangeLog                   |    6 +-
 sci-mathematics/surfer/Manifest                    |    2 +-
 sci-mathematics/surfer/metadata.xml                |    2 +-
 sci-mathematics/surfer/surfer-0.0.197.ebuild       |   21 +-
 sci-mathematics/why/ChangeLog                      |    5 +-
 sci-mathematics/why/Manifest                       |    6 +-
 sci-mathematics/why/metadata.xml                   |   26 +-
 sci-mathematics/why/why-2.30.ebuild                |   74 +-
 sci-mathematics/yorick/ChangeLog                   |    6 +-
 sci-mathematics/yorick/Manifest                    |    2 +-
 sci-mathematics/yorick/metadata.xml                |   12 +-
 sci-mathematics/yorick/yorick-2.1.06.ebuild        |   29 +-
 sci-misc/foma/ChangeLog                            |    6 +-
 sci-misc/foma/foma-0.9.14_alpha.ebuild             |    4 +-
 sci-misc/foma/foma-0.9.16_alpha.ebuild             |    4 +-
 sci-misc/foma/metadata.xml                         |    6 +-
 sci-misc/hfst/ChangeLog                            |    6 +-
 sci-misc/hfst/hfst-3.0.2.ebuild                    |    4 +-
 sci-misc/hfst/hfst-3.3.12.ebuild                   |    6 +-
 sci-misc/hfst/metadata.xml                         |   16 +-
 sci-misc/openfst/ChangeLog                         |    6 +-
 sci-misc/openfst/metadata.xml                      |    6 +-
 sci-misc/openfst/openfst-1.2.7.ebuild              |    4 +-
 sci-misc/openfst/openfst-1.3.2.ebuild              |    4 +-
 sci-misc/praat/ChangeLog                           |    6 +-
 sci-misc/praat/Manifest                            |    4 +-
 sci-misc/praat/metadata.xml                        |    8 +-
 sci-misc/praat/praat-5.1.00.ebuild                 |   23 +-
 sci-misc/praat/praat-5.1.15.ebuild                 |   23 +-
 sci-misc/salome-component/ChangeLog                |    6 +-
 sci-misc/salome-component/Manifest                 |    4 +-
 sci-misc/salome-component/metadata.xml             |    2 +-
 .../salome-component/salome-component-5.1.3.ebuild |    8 +-
 .../salome-component/salome-component-5.1.4.ebuild |    8 +-
 sci-misc/salome-geom/ChangeLog                     |    6 +-
 sci-misc/salome-geom/Manifest                      |    4 +-
 sci-misc/salome-geom/metadata.xml                  |    2 +-
 sci-misc/salome-geom/salome-geom-5.1.3.ebuild      |   10 +-
 sci-misc/salome-geom/salome-geom-5.1.4.ebuild      |   10 +-
 sci-misc/salome-gui/ChangeLog                      |    6 +-
 sci-misc/salome-gui/Manifest                       |    4 +-
 sci-misc/salome-gui/metadata.xml                   |    2 +-
 sci-misc/salome-gui/salome-gui-5.1.3.ebuild        |   10 +-
 sci-misc/salome-gui/salome-gui-5.1.4.ebuild        |   10 +-
 sci-misc/salome-med/ChangeLog                      |    6 +-
 sci-misc/salome-med/Manifest                       |    4 +-
 sci-misc/salome-med/metadata.xml                   |   10 +-
 sci-misc/salome-med/salome-med-5.1.3.ebuild        |    8 +-
 sci-misc/salome-med/salome-med-5.1.4.ebuild        |    8 +-
 sci-misc/salome-smesh/ChangeLog                    |    6 +-
 sci-misc/salome-smesh/Manifest                     |    4 +-
 sci-misc/salome-smesh/metadata.xml                 |    2 +-
 sci-misc/salome-smesh/salome-smesh-5.1.3.ebuild    |    8 +-
 sci-misc/salome-smesh/salome-smesh-5.1.4.ebuild    |    8 +-
 sci-misc/salome-visu/ChangeLog                     |    6 +-
 sci-misc/salome-visu/Manifest                      |    4 +-
 sci-misc/salome-visu/metadata.xml                  |    2 +-
 sci-misc/salome-visu/salome-visu-5.1.3.ebuild      |    8 +-
 sci-misc/salome-visu/salome-visu-5.1.4.ebuild      |    8 +-
 sci-misc/salome-yacs/ChangeLog                     |    6 +-
 sci-misc/salome-yacs/Manifest                      |    4 +-
 sci-misc/salome-yacs/metadata.xml                  |    2 +-
 sci-misc/salome-yacs/salome-yacs-5.1.3.ebuild      |    8 +-
 sci-misc/salome-yacs/salome-yacs-5.1.4.ebuild      |    8 +-
 sci-misc/sfst/ChangeLog                            |    6 +-
 sci-misc/sfst/metadata.xml                         |   10 +-
 sci-misc/sfst/sfst-1.4.2.ebuild                    |    4 +-
 sci-misc/sfst/sfst-1.4.6g.ebuild                   |    4 +-
 sci-physics/abinit/ChangeLog                       |   13 +
 sci-physics/abinit/Manifest                        |    2 +-
 sci-physics/abinit/abinit-7.0.4.ebuild             |   27 +-
 ...abinit-6.12.3-r2.ebuild => abinit-7.0.5.ebuild} |   63 +-
 sci-physics/abinit/metadata.xml                    |   74 +-
 sci-physics/atompaw/ChangeLog                      |    5 +
 sci-physics/atompaw/atompaw-3.0.1.9.ebuild         |   14 +-
 sci-physics/atompaw/metadata.xml                   |   14 +-
 sci-physics/atompaw2abinit/ChangeLog               |    7 +-
 sci-physics/atompaw2abinit/Manifest                |    2 +-
 .../atompaw2abinit/atompaw2abinit-3.3.0-r1.ebuild  |   19 +-
 sci-physics/atompaw2abinit/metadata.xml            |    8 +-
 sci-physics/elk/ChangeLog                          |    6 +-
 sci-physics/elk/elk-1.4.22.ebuild                  |   92 +-
 sci-physics/elk/metadata.xml                       |   10 +-
 sci-physics/espresso/ChangeLog                     |    5 +-
 sci-physics/espresso/espresso-9999.ebuild          |   14 +-
 sci-physics/herwig++/ChangeLog                     |    7 +
 sci-physics/herwig++/Manifest                      |    2 +-
 ...ptools.patch => herwig++-2.6.3-looptools.patch} |    0
 ...herwig++-2.6.2.ebuild => herwig++-2.6.3.ebuild} |    2 +-
 sci-physics/openmx/ChangeLog                       |    8 +
 .../phenix-bin => sci-physics/openmx}/metadata.xml |    0
 sci-physics/openmx/openmx-3.6.ebuild               |   42 +-
 sci-physics/root/ChangeLog                         |   10 +
 sci-physics/root/Manifest                          |    4 +-
 .../root/files/root-5.34.05-nobyte-compile.patch   |  137 +
 sci-physics/root/metadata.xml                      |   38 +-
 .../{root-5.34.03.ebuild => root-5.34.05.ebuild}   |   19 +-
 sci-physics/root/root-9999.ebuild                  |   12 +-
 sci-physics/thepeg/ChangeLog                       |    7 +
 sci-physics/thepeg/Manifest                        |    6 +-
 ...eg-1.8.2-java.patch => thepeg-1.8.3-java.patch} |    0
 .../{thepeg-1.8.2.ebuild => thepeg-1.8.3.ebuild}   |    2 +-
 sci-visualization/ferret-bin/ChangeLog             |    7 +-
 sci-visualization/ferret-bin/Manifest              |   10 +-
 .../ferret-bin/ferret-bin-6.6.4.ebuild             |   52 +-
 sci-visualization/ferret-bin/metadata.xml          |   12 +-
 sci-visualization/gnuplot/ChangeLog                |   18 +-
 sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild  |  213 +-
 sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild  |  202 +-
 sci-visualization/gnuplot/metadata.xml             |   26 +-
 sci-visualization/paraview/ChangeLog               |    6 +-
 sci-visualization/paraview/metadata.xml            |   36 +-
 sci-visualization/paraview/paraview-3.10.1.ebuild  |   28 +-
 sci-visualization/paraview/paraview-3.12.0.ebuild  |   26 +-
 .../paraview/paraview-3.14.1-r4.ebuild             |   16 +-
 sci-visualization/v_sim/ChangeLog                  |    6 +-
 sci-visualization/v_sim/Manifest                   |    4 +-
 sci-visualization/v_sim/metadata.xml               |   26 +-
 sci-visualization/v_sim/v_sim-3.5.1.ebuild         |   80 -
 sci-visualization/v_sim/v_sim-3.5.2.ebuild         |   87 -
 sci-visualization/v_sim/v_sim-3.6.0.ebuild         |    4 +-
 sci-visualization/yt/yt-9999.ebuild                |    3 +-
 skel.ChangeLog                                     |    2 +-
 skel.ebuild                                        |    2 +-
 skel.metadata.xml                                  |   38 +-
 sys-apps/likwid/metadata.xml                       |    2 -
 sys-cluster/blcr/ChangeLog                         |    5 +-
 sys-cluster/blcr/blcr-0.8.4.ebuild                 |    3 +-
 sys-cluster/blcr/metadata.xml                      |    4 +-
 sys-cluster/empi/ChangeLog                         |   10 +-
 .../empi/{empi-0.7.ebuild => empi-0.8.ebuild}      |    2 +-
 sys-cluster/empi/files/ChangeLog-0.7               |  164 -
 sys-cluster/empi/files/ChangeLog-0.8               |   68 +
 sys-cluster/empi/files/empi-0.7                    |  408 -
 sys-cluster/empi/files/empi-0.8                    |  492 +
 .../files/{eselect.mpi-0.7 => eselect.mpi-0.8}     |    2 +-
 sys-cluster/hpl/ChangeLog                          |    9 +-
 sys-cluster/hpl/Manifest                           |    2 +-
 sys-cluster/hpl/hpl-2.0-r1.ebuild                  |   20 +-
 sys-cluster/hpl/metadata.xml                       |   12 +-
 sys-cluster/lustre/ChangeLog                       |  333 +
 ...ld-make-AC-check-for-linux-arch-sandbox-f.patch |   95 +
 ...rnel-3.0-SuSE-and-3.6-FC18-server-patches.patch |21302 ++++++++++++++++++++
 ...nel-sock_map_fd-replaced-by-sock_alloc_fi.patch |  137 +
 ...6-kernel-Kernel-update-for-3.7.2-201.fc18.patch |  184 +
 ...pat-posix_acl_-to-from-_xattr-take-user_n.patch |  159 +
 ...006-LU-2800-llite-introduce-local-getname.patch |   91 +
 .../files/0007-LU-2987-llite-rcu-free-inode.patch  |   89 +
 ...50-kernel-3.8-upstream-removes-vmtruncate.patch |   83 +
 ...-2850-kernel-3.8-upstream-kills-daemonize.patch | 2966 +++
 ...rnel-3.9-hlist_for_each_entry-uses-3-args.patch |  115 +
 ...79-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch |   82 +
 ...fids-fix-compilation-error-with-gcc-4.7.2.patch |   29 +
 ...7-build-zfs-0.6.1-kmod-dkms-compatibility.patch | 1038 +
 sys-cluster/lustre/lustre-9999.ebuild              |   94 +-
 sys-cluster/lustre/metadata.xml                    |    3 +
 sys-cluster/mvapich2/ChangeLog                     |    7 +
 sys-cluster/mvapich2/Manifest                      |    2 +-
 sys-cluster/mvapich2/mvapich2-1.6-r1.ebuild        |    4 +-
 sys-cluster/openmpi/ChangeLog                      |    6 +
 sys-cluster/openmpi/Manifest                       |    2 +-
 .../{openmpi-1.6.3.ebuild => openmpi-1.6.4.ebuild} |    7 +-
 sys-cluster/ovis/ChangeLog                         |    5 +-
 sys-cluster/ovis/metadata.xml                      |   10 +-
 sys-cluster/ovis/ovis-3.0.1.ebuild                 |    6 +-
 virtual/blas/ChangeLog                             |    2 +-
 virtual/lapack/ChangeLog                           |    8 +-
 virtual/lapack/lapack-3.3.ebuild                   |   23 -
 virtual/lapack/lapack-3.4.ebuild                   |   23 +
 virtual/lapack/metadata.xml                        |    3 +-
 virtual/scalapack/ChangeLog                        |    9 +-
 virtual/scalapack/metadata.xml                     |    4 +-
 .../{scalapack-1.8.ebuild => scalapack-2.0.ebuild} |    6 +-
 x11-libs/xview-bin/ChangeLog                       |    9 +-
 x11-libs/xview-bin/Manifest                        |    2 +-
 x11-libs/xview-bin/metadata.xml                    |   10 +-
 x11-libs/xview-bin/xview-bin-3.2_p1428.ebuild      |    6 +-
 x11-libs/xview/ChangeLog                           |   12 +-
 x11-libs/xview/Manifest                            |    1 +
 x11-libs/xview/metadata.xml                        |   10 +-
 x11-libs/xview/xview-3.2-r6.ebuild                 |    4 +-
 x11-libs/xview/xview-3.2-r7.ebuild                 |    4 +-
 .../{xview-3.2-r7.ebuild => xview-3.2-r8.ebuild}   |    8 +-
 923 files changed, 36037 insertions(+), 9438 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     93f7c9e6fb6b8cbb5a19a1ff93ef0218e5a3068a
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Wed May 15 06:07:41 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed May 15 06:07:41 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=93f7c9e6

Merge pull request #70 from jauhien/berkeley_upc_2.16.2

dev-lang/berkeley_upc and dev-lang/berkeley_upc_translator: version bump


 dev-lang/berkeley_upc/ChangeLog                    |    6 ++++++
 dev-lang/berkeley_upc/Manifest                     |    2 +-
 ...pc-2.16.0.ebuild => berkeley_upc-2.16.2.ebuild} |    0
 dev-lang/berkeley_upc_translator/ChangeLog         |    8 ++++++++
 dev-lang/berkeley_upc_translator/Manifest          |    2 +-
 ...build => berkeley_upc_translator-2.16.2.ebuild} |    5 +----
 ...keley_upc_translator-2.16.0-stackoverflow.patch |   18 ------------------
 7 files changed, 17 insertions(+), 24 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     f9333efdd2335abaa5be654ab21fbb55f9fe17a1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed May 15 06:19:29 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed May 15 06:19:29 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f9333efd

Merge remote-tracking branch 'github/master'

* github/master:
  dev-lang/berkeley_upc and dev-lang/berkeley_upc_translator: version bump


 dev-lang/berkeley_upc/ChangeLog                    |    6 ++++++
 dev-lang/berkeley_upc/Manifest                     |    2 +-
 ...pc-2.16.0.ebuild => berkeley_upc-2.16.2.ebuild} |    0
 dev-lang/berkeley_upc_translator/ChangeLog         |    8 ++++++++
 dev-lang/berkeley_upc_translator/Manifest          |    2 +-
 ...build => berkeley_upc_translator-2.16.2.ebuild} |    5 +----
 ...keley_upc_translator-2.16.0-stackoverflow.patch |   18 ------------------
 7 files changed, 17 insertions(+), 24 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     bed58ebacc7eae6a8064eb2ea3d0f3c28ebb833c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 29 06:17:22 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Apr 29 06:17:22 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bed58eba

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  remove la files, added static-libs use flag
  initial commit


 sci-libs/bliss/ChangeLog                        |   10 +
 sci-libs/bliss/Manifest                         |    1 +
 sci-libs/bliss/bliss-0.72.ebuild                |   43 ++
 sci-libs/bliss/files/bliss-0.72-autotools.patch |  159 ++++++
 sci-libs/bliss/files/bliss-0.72-fedora.patch    |  648 +++++++++++++++++++++++
 {dev-lang/ispc => sci-libs/bliss}/metadata.xml  |    1 +
 6 files changed, 862 insertions(+), 0 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     6ca1acbed7e02eeb48b39f436f2e22452c6d5e77
Author:     Kacper Kowalik (Xarthisius) <xarthisius <AT> gentoo <DOT> org>
AuthorDate: Wed May  1 20:09:09 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Wed May  1 20:09:09 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6ca1acbe

Merge branch 'master' of github.com:gentoo-science/sci


 dev-util/VampirTrace/VampirTrace-5.14.3.ebuild |    6 +++++-
 1 files changed, 5 insertions(+), 1 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     e334b4c9480ce3caa26dfe0f22d51d9fad528a5c
Author:     Kacper Kowalik <xarthisius.kk <AT> gmail <DOT> com>
AuthorDate: Wed May  1 20:07:14 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Wed May  1 20:07:14 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e334b4c9

Merge pull request #67 from gentryx/master

fix for bug #468034


 dev-util/VampirTrace/VampirTrace-5.14.3.ebuild |    6 +++++-
 1 files changed, 5 insertions(+), 1 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     d557b6f923a63df5cd78512561ec0f59ebf23369
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed May  1 18:29:34 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Wed May  1 18:29:34 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d557b6f9

Merge branch 'master' of https://github.com/gentoo-science/sci


 README.md                                          |   16 +-
 dev-cpp/eigen/ChangeLog                            |    8 +-
 dev-cpp/eigen/Manifest                             |    2 +-
 .../{eigen-3.1.2.ebuild => eigen-3.1.3-r1.ebuild}  |    0
 dev-cpp/eigen/eigen-9999.ebuild                    |   10 +-
 dev-python/asciidata/ChangeLog                     |   28 -
 dev-python/asciidata/Manifest                      |    1 -
 dev-python/asciidata/asciidata-1.1.1-r1.ebuild     |   41 -
 dev-python/asciidata/metadata.xml                  |   13 -
 dev-python/astlib/ChangeLog                        |    8 +-
 dev-python/astlib/Manifest                         |    2 +-
 .../{astlib-0.17.1.ebuild => astlib-0.7.0.ebuild}  |   31 +-
 .../astlib/files/astlib-0.17.1-wcstools.patch      |   75 -
 dev-python/astlib/metadata.xml                     |    3 +-
 sci-libs/armadillo/ChangeLog                       |    7 +
 sci-libs/armadillo/Manifest                        |    2 +-
 ...lo-3.6.3-r1.ebuild => armadillo-3.810.2.ebuild} |   35 +-
 .../files/armadillo-3.810.2-example-makefile.patch |   33 +
 .../armadillo/files/armadillo-3.810.2-hdf5.patch   |   19 +
 sci-libs/armadillo/metadata.xml                    |   20 +-
 sci-libs/bliss/ChangeLog                           |   10 +
 sci-libs/bliss/Manifest                            |    1 +
 sci-libs/bliss/bliss-0.72.ebuild                   |   43 +
 sci-libs/bliss/files/bliss-0.72-autotools.patch    |  159 +
 sci-libs/bliss/files/bliss-0.72-fedora.patch       |  648 ++
 {dev-lang/ispc => sci-libs/bliss}/metadata.xml     |    1 +
 skel.ChangeLog                                     | 8024 +-------------------
 skel.ebuild                                        |    2 +-
 skel.metadata.xml                                  |   38 +-
 29 files changed, 1024 insertions(+), 8256 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Kacper Kowalik]

commit:     0d7bd5b0a5573db70afe91a91985ea501de5990b
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed May  1 18:30:38 2013 +0000
Commit:     Kacper Kowalik <xarthisius <AT> gentoo <DOT> org>
CommitDate: Wed May  1 18:30:38 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0d7bd5b0

merge


 README.md                                          |   16 +-
 dev-cpp/eigen/ChangeLog                            |    8 +-
 dev-cpp/eigen/Manifest                             |    2 +-
 .../{eigen-3.1.2.ebuild => eigen-3.1.3-r1.ebuild}  |    0
 dev-cpp/eigen/eigen-9999.ebuild                    |   10 +-
 dev-python/asciidata/ChangeLog                     |   28 -
 dev-python/asciidata/Manifest                      |    1 -
 dev-python/asciidata/asciidata-1.1.1-r1.ebuild     |   41 -
 dev-python/asciidata/metadata.xml                  |   13 -
 dev-python/astlib/ChangeLog                        |    8 +-
 dev-python/astlib/Manifest                         |    2 +-
 .../{astlib-0.17.1.ebuild => astlib-0.7.0.ebuild}  |   31 +-
 .../astlib/files/astlib-0.17.1-wcstools.patch      |   75 -
 dev-python/astlib/metadata.xml                     |    3 +-
 sci-libs/armadillo/ChangeLog                       |    7 +
 sci-libs/armadillo/Manifest                        |    2 +-
 ...lo-3.6.3-r1.ebuild => armadillo-3.810.2.ebuild} |   35 +-
 .../files/armadillo-3.810.2-example-makefile.patch |   33 +
 .../armadillo/files/armadillo-3.810.2-hdf5.patch   |   19 +
 sci-libs/armadillo/metadata.xml                    |   20 +-
 sci-libs/bliss/ChangeLog                           |   10 +
 sci-libs/bliss/Manifest                            |    1 +
 sci-libs/bliss/bliss-0.72.ebuild                   |   43 +
 sci-libs/bliss/files/bliss-0.72-autotools.patch    |  159 +
 sci-libs/bliss/files/bliss-0.72-fedora.patch       |  648 ++
 {dev-lang/ispc => sci-libs/bliss}/metadata.xml     |    1 +
 skel.ChangeLog                                     | 8024 +-------------------
 skel.ebuild                                        |    2 +-
 skel.metadata.xml                                  |   38 +-
 29 files changed, 1024 insertions(+), 8256 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     9c4102d474c6084b66ca83821ab00ed776abb58b
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 29 16:32:15 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Apr 29 16:32:15 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9c4102d4

Update description

---
 README.md |   16 ++++++++++++----
 1 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index a4fa9e8..d4dc43f 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,12 @@
-Gentoo Science Overlay
-===
-
-Please fork! We will merge!
\ No newline at end of file
+Gentoo Science Overlay
+======================
+
+An overlay for Gentoo, geared towards scientific packages.
+
+Please fork! We will merge!
+
+Ask for help in #gentoo-science in irc freenode.
+
+Report issues on the github site:
+
+https://github.com/gentoo-science/sci/issues

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     92f5fe738767b83d6b5633fa9b2a1a14c4e68721
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 29 16:21:49 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Apr 29 16:21:49 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=92f5fe73

Merge github.com:gentoo-science/sci


 dev-util/VampirTrace/Manifest                   |    1 +
 dev-util/VampirTrace/VampirTrace-5.14.3.ebuild  |   33 ++
 dev-util/VampirTrace/metadata.xml               |   13 +
 licenses/vampir                                 |   36 ++
 sci-libs/bliss/ChangeLog                        |   10 +
 sci-libs/bliss/Manifest                         |    1 +
 sci-libs/bliss/bliss-0.72.ebuild                |   43 ++
 sci-libs/bliss/files/bliss-0.72-autotools.patch |  159 ++++++
 sci-libs/bliss/files/bliss-0.72-fedora.patch    |  648 +++++++++++++++++++++++
 {dev-lang/ispc => sci-libs/bliss}/metadata.xml  |    1 +
 sys-apps/likwid/files/use_uncore.patch          |   12 +
 sys-apps/likwid/likwid-3.0.ebuild               |    5 +-
 sys-apps/likwid/metadata.xml                    |    7 +-
 13 files changed, 965 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     e955c60cbd1e3f92222ea297a777fbd0f67b9d3c
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 29 16:29:23 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Apr 29 16:29:23 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e955c60c

Updated skel files

---
 skel.ChangeLog    | 8024 +----------------------------------------------------
 skel.ebuild       |    2 +-
 skel.metadata.xml |   38 +-
 3 files changed, 14 insertions(+), 8050 deletions(-)

diff --git a/skel.ChangeLog b/skel.ChangeLog
index 66ff00c..6a6f1d0 100644
--- a/skel.ChangeLog
+++ b/skel.ChangeLog
@@ -1,8027 +1,5 @@
-
-n.n.n / 2013-04-11 
-==================
-
-  * Bump, workaround #462602
-  * Jabref-2.10b does not build anymore with Java 6.
-  * Merge branch 'master' of github.com:gentoo-science/sci
-  * sci-chemistry/hydronmr: New addition
-  * Merge pull request #60 from lilrc/master
-  * sci-chemistry/gnome-chemistry-utils: Migrate to gnome2 eclass. Sort inherits. Add slots where suitable.
-  * Fix missing inherit.
-  * sci-chemistry/gnome-chemistry-utils: initial ebuild
-  * Adding jabref-2.10b (beta) ebuild.
-  * dev-lang/julia update dependency and remove useflag
-  * dev-libs/double-conversion version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/ncbi-tools++: Some Prefix love
-  * Add patches for gcc-4.8 and linux-3.9
-  * Enable more options
-  * Add patch to fix as-needed issue
-  * Fix autogen
-  * build was renamed to config
-  * Merge remote-tracking branch 'github/master'
-  * Update rebased patches
-  * Merge pull request #58 from jauhien/cadabra-1.31
-  * sci-mathematics/cadabra-1.31: new line fixes, thanks to jlec
-  * sci-mathemtics/cadabra-1.31: different fixes, thanks to jlec
-  * Update patches
-  * sci-chemistry/GromacsWrapper: Drop py 2.5 support
-  * sci-chemistry/GromacsWrapper: Enhance python r1 eclass usage
-  * dev-python/RecSQL: Enhance python r1 eclass usage
-  * sci-chemistry/GromacsWrapper: Drop in tree version
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Update deps
-  * sci-chemistry/pymol: Sync with tree
-  * Add patch to fix hack
-  * Add Gromacs Python wrapper
-  * Add RecSQL to tree
-  * sci-mathematics-cadabra-1.31: bump to EAPI-5
-  * Update patches for 3.9
-  * Merge remote-tracking branch 'github/master'
-  * Update patches for 3.8
-  * sci-chemistry/cs-rosetta: Missing exec bit for pdbrms
-  * sci-libs/cs-rosetta-db: Correct installation directory to mach the main package
-  * sci-mathematics/cadabra: version bump
-  * sci-chemistry/rosetta: Fix for mpi
-  * Merge pull request #57 from jauhien/thepeg-1.8.3_herwig++-2.6.3
-  * sci-physics/thepeg: manifest fix
-  * sci-chemistry/cs-rosetta: Use Fortran eclass
-  * sci-chemistry/rosetta: Use system path
-  * sci-chemistry/rosetta: Rename USE custom-flags -> custom-cflags
-  * sci-chemistry/cs-rosetta: New addition
-  * sci-libs/cs-rosetta-db: New addition
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * $PWD dont needed in automake invocation
-  * Fix escape sequence
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-chemistry/rosetta: Version Bump
-  * Merge pull request #56 from jauhien/berkeley_upc_translator-2.16.0
-  * dev-lang/berkeley_upc_translator: new ebuild for bug#462296, thanks to Paul H. Hargrove
-  * aggregated into sci-chemistry/cs-rosetta
-  * sci-biology/amos: Bump to latest git HEAD, fixes qt problems, #348031
-  * Update patches
-  * Merge remote-tracking branch 'github/master'
-  * Fix some install path
-  * Add gentoo style configure
-  * Fix error in mdt_handler.c
-  * Update metadata.xml
-  * Update berkeley_upc-2.16.0.ebuild
-  * Merge pull request #55 from jauhien/berkeley_upc-2.16.0
-  * dev-db/cppdb: Import from sunrise
-  * Update patch
-  * Update patch
-  * Add patch sended upstream
-  * Update patch
-  * Fix sandbox violation during configure
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Update lustre patches
-  * dev-lang/berkeley_upc: install into libexec
-  * dev-lang/berkeley_upc: New ebuild for bug#462026
-  * Merge ssh://github.com/gentoo-science/sci
-  * initial commit
-  * Update deps. thanks to Richard Yao
-  * Update media-gfx/librecad ebuilds.
-  * Make client and utils as default flags
-  * Update to reflect latest zfs changes
-  * nvcc flags dont needed anymore here
-  * Fix build with cuda enabled
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Drop Werror hack
-  * Now it builds and loads with 3.8
-  * More updates to lustre patches
-  * Update lustre patches. Now it builds against linux 3.8
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Improving mpi linking. It will now work with openmpi as well.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge ssh://github.com/gentoo-science/sci
-  * fix build without emacs
-  * sci-chemistry/usf-tools: Update license
-  * sci-chemistry/usf-tools: Drop myself as maintainer
-  * Merge pull request #53 from jauhien/cdfplayer-9.0.1
-  * Merge pull request #54 from jauhien/thepeg-1.8.3_herwig++-2.6.3
-  * sci-physics/herwig++: version bump
-  * sci-physics/thepeg: version bump
-  * sci-mathematics/cdfplayer: version bump
-  * sci-chemistry/phenix-bin: Version BUmp
-  * sci-chemistry/concoord: Version Bump; switch license to all-rights-reserved
-  * added cuda build fix from gx86
-  * sync with gx86
-  * fix doc build on darwin
-  * fixed deps + doc build on darwin
-  * Newer version in CVS
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sync wit gx86
-  * Fix typo
-  * Fix typo
-  * Realy add patches to ebuild
-  * Add patches for kernels 3.7 and 3.8
-  * sync with gx86 + clean up
-  * merge slew of jlec small fixes
-  * sci-libs/optpp: Removed uneeded python eclass, keyword for prefix
-  * sci-libs/o2scl: Version bump
-  * sci-libs/openblas: Version bump
-  * sci-libs/openlibm: Initial import
-  * Mask several package due to different QA issues
-  * sci-chemistry/ambertools: Add missing multilib.eclass
-  * sci-mathematics/yorick: Move to EAPI=5; add missing multilib.eclass
-  * sci-chemistry/jligand: Fix version of refmac dep
-  * sci-chemistry/pymol-plugins-psico: Rename sci-chemistry/mmtk to sci-libs/mmtk
-  * sci-geosciences/qgis: Update to new qt deps names
-  * sci-libs/lapack-reference: Add unocumented USE to metadata.xml
-  * sci-biology/estscan: Add local USE to metadata.xml
-  * sci-libs/coinor-bonmin: Add unocumented USE to metadata.xml
-  * sci-biology/ncbi-tools++: Document USE
-  * sci-chemistry/pymol-plugins-ezviz: Fix missing DOCTYPE
-  * sci-chemistry/pymol: Fix missing DOCTYPE
-  * dev-libs/fortrancl: Clean whitespace errors
-  * dev-ml/zarith: Clean wrong space and blank lines; move EAPI=5
-  * media-gfx/PhiloGL: Move to EAPI=5 and fix quoting
-  * sci-astronomy/astrometry: Clean wrong space and blank lines
-  * sci-libs/amdlibm: Updated download page and prefix'ed
-  * sci-astronomy/eye: Clean wrong space and blank lines
-  * sci-astronomy/stiff: Move to EAPI=5 and autotools-utils
-  * sci-chemistry/nmrpipe: Fix quoting
-  * sci-biology/artemis-bin: Clean whitespace errors
-  * sci-biology/ncbi-tools++: Clean whitespace errors
-  * sci-biology/sra_sdk: Drop useless blank line
-  * sci-chemistry/specView: Fix quoting
-  * sci-libs/amdlibm: Clean wrong space and blank lines
-  * sci-libs/coinor-cppad: Drop useless blank line
-  * sci-mathematics/alt-ergo: Move to EAPI=5; clean quoting and ebuild syntax and indention
-  * sci-libs/parmetis: Drop useless blank line
-  * sci-mathematics/giac: Drop useless blank line
-  * sci-mathematics/bertini: Clean wrong space and blank lines
-  * sci-mathematics/mdp: Clean wrong space and blank lines
-  * sys-cluster/blcr: Drop useless blank line
-  * sys-cluster/hpl: Sort *DEPEND correctly
-  * sci-libs/lemon: Move to EAPI=5; sort *DEPEND correctly
-  * sci-biology/ncbi-tools++: Add metadata.xml
-  * sci-biology/hydra-sv: Add metadata.xml; move to EAPI=5; cleaned ebuild syntax
-  * x11-libs/xview: Fix header
-  * x11-libs/xview-bin: Fix header
-  * sci-mathematics/gambit: Fix header and move to EAPI=5
-  * sci-libs/libspatialindex: Fix header and move to EAPI=5: cleaned ebuild syntax
-  * sci-mathematics/dsfmt: Fix header and move to EAPI=5; cleaned ebuild syntax
-  * dev-perl/go-perl: Fix header and move to EAPI=5
-  * dev-perl/Time-Progress: Fix header and move to EAPI=5
-  * dev-perl/Log-Cabin: Fix header and move to EAPI=5
-  * dev-perl/Text-ParseWords: Fix header and move to EAPI=5
-  * dev-perl/DBIx-DBStag: Fix header and move to EAPI=5
-  * sci-libs/zarja: Move to EAPI=5; fix slot for fftw dep; move to virtual/pkgconfig; clean ebuild syntax
-  * sci-libs/modglue: Move to EPAI=5 and virtual/pkgconfig; clean usage of autotools-utils.eclass
-  * sci-libs/blas-reference: Cleaned deps
-  * sci-chemistry/burrow-owl: Bump to EPAI=5 and move to virtual/pkgconfig
-  * sci-biology/manatee-igs: Shorten DESCRIPTION
-  * sci-physics/openmx: Move to EAPI=5 and shorten DESCRIPTION
-  * sci-chemistry/nwchem: Move to EAPI=5 and clean ebuild syntax style
-  * Add new license
-  * dev-python/Forthon: Correct license name
-  * dev-java/jcip-annotations: Correct license name
-  * sys-cluster/mvapich2: Add missing flag-o-matic.eclass
-  * sci-mathematics/polymake: Add missing multilib.eclass
-  * sci-libs/starparse: Add missing multilib.eclass; move to EAPI=5 and autotools-utils.eclass
-  * dev-lang/vtune: Version Bump; move to parallel studio tarball; add missing multilib.eclass
-  * sci-chemistry/modelfree: Add missing multilib.eclass; move to EAPI=5
-  * sci-chemistry/ambertools: Add missing multilib.eclass
-  * sci-biology/wcd: Add missing multilib.eclass; move to EAPI=5 and autotools-utils.eclass; simplify ebuild syntax; fix for ld.gold; fix implicid declarations
-  * correct license
-  * add new license
-  * sci-biology/blasr: Migrate to git2 eclass and EAPI=5
-  * app-portage/g-octave: Migrate to new python eclasses, git2 eclass and EAPI=5
-  * dev-python/GOGrapher: Set license to GPL-2
-  * sci-mathematics/flocq: Move to EAPI=5; assign RDEPEND explicitatly
-  * sys-cluster/ovis: Update to new qt deps names
-  * sci-visualization/paraview: Update to new qt deps names
-  * sci-visualization/gnuplot: Update to new qt deps names
-  * sci-chemistry/ball: Update to new qt deps names
-  * sci-biology/amos: Update to new qt deps names
-  * dev-python/pymvpa: Move to new python eclasses
-  * sci-misc/hfst: Add ~amd64 or ~x86 keywords for revdeps
-  * sci-misc/foma: Add ~amd64 or ~x86 keywords for revdeps
-  * sci-misc/sfst: Add ~amd64 or ~x86 keywords for revdeps
-  * sci-misc/openfst: Add ~amd64 or ~x86 keywords for revdeps
-  * sci-visualization/ferret-bin: Move to EAPI=5; clean ebuild style; add missing die; remove portage-internal (env-update)
-  * sci-mathematics/why: Drop ppc as deps are not keyworded; move to EAPI=5 and autotools-utils.eclass
-  * sci-mathematics/gappalib-coq: Drop pcc and sparc keywords as deps are not keyworded; move to EAPI=5
-  * sci-mathematics/lattE-macchiato: Fix rename of USE nocxx to cxx for dev-libs/gmp
-  * sci-mathematics/pff: Drop pcc and sparc keywords as deps are not keyworded; move to EAPI=5
-  * sci-mathematics/surfer: Move to autotools-utils.eclass; use virtual/pkgconfig
-  * sci-misc/praat: Update to new qt deps names; remove virtual/x11
-  * sci-misc/salome-geom: Update to new qt deps names
-  * sci-misc/salome-component: Update to new qt deps names
-  * sci-misc/salome-gui: Update to new qt deps names
-  * sci-misc/salome-med: Update to new qt deps names
-  * sci-misc/salome-smesh: Update to new qt deps names
-  * sci-misc/salome-visu: Update to new qt deps names
-  * sci-misc/salome-yacs: Update to new qt deps names
-  * sci-physics/abinit: Drop old
-  * sci-physics/root: Update to new qt deps names
-  * sci-libs/trilinos: Update to new qt deps names
-  * dev-perl/Log-Cabin: Add ~amd64 or ~x86 keywords for revdeps
-  * We can't do profile specific masks
-  * imported latest arch.list from gx86
-  * sci-chemistry/curvefit: Correct lib name of ref blas
-  * sci-biology/consed-bin: Correct motif dep naming
-  * sci-biology/cluster: Correct motif dep naming
-  * sci-biology/YASRA: Drop keywords as deps are unkeyworded
-  * sci-biology/Gambit: Update to new qt deps names
-  * dev-python/pythonocc: Version BUmp; change license; move to new python eclasses
-  * dev-python/pythonocc: Version BUmp; change license; move to new python eclasses
-  * media-gfx/librecad: Update to new qt deps names; drop old
-  * dev-java/jogl: Keyworded for ~x86
-  * dev-java/gluegen: Keyworded for ~x86
-  * sci-libs/bigdft: Fix issue 52
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * Initial import
-  * Add ~x86
-  * Initial import
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * sci-libs/mlpack: Added a patch to respect libdir, and debug flag for profiling and debugging (thanks Ryan Curtin)
-  * sci-libs/armadillo: Small prefix fix
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * sci-mathematics/Macaulay2: Use PKG_CONFIG instead of generic pkg-config
-  * sci-chemistry/simpson: Use PKG_CONFIG instead of generic pkg-config
-  * sci-chemistry/gamess: Use PKG_CONFIG instead of generic pkg-config
-  * sci-chemistry/nmrpipe: Fix broken Manifest, #458928
-  * sci-libs/acml: Add -lm -lrt for static linking on pc file
-  * sci-libs/openblas: Move threads to Libs.private in pc file
-  * x11-libs/xview: Version Bump
-  * x11-libs/xview-bin: Version Bump
-  * sci-libs/Cgraph: Add blocker
-  * sci-libs/mlpack: Initial import
-  * sci-libs/armadillo: Version bump. Respect libdir
-  * sci-libs/atlas: Switched threads libraries to Libs.private in pkg-config files
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * app-doc/root-docs: version bump
-  * sci-physics/root: version bump
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * sci-libs/tmglib: Add missing dep on virtual/blas
-  * sci-chemistry/freeon: Add missing dep on virtual/pkgconfig; bump to eapi=5; use pkg-config to detect blas
-  * sci-libs/gmsh: Add missing dep on virtual/pkgconfig
-  * sci-geosciences/fullprof-bin: Indent with tabs instead of spaces; use QA_PREBUILT for binary packages; restrict all arches but x86/amd64; bump EAPI to 5; clean DESCRIPTION; fix quoting
-  * Merge branch 'master' of github.com:gentoo-science/sci
-  * Merge pull request #28 from jamasi/master
-  * sci-visualization/v_sim: Drop old; add missing multilib.eclass
-  * Bundles all numeric libs, which are not easily unbundlable Various other QA issues
-  * sci-libs/trilinos: Correct USE dependency for virtual/pkgconfig; bump EAPI to 5
-  * sci-libs/armadillo: Correct USE dependency for virtual/pkgconfig
-  * sci-chemistry/simpson: Add missing dep on virtual/pkgconfig
-  * sci-chemistry/chooch: Bump to EAPI=5; add missing deps; drop additional virtual which aren't needed; move to autotools-utils
-  * sci-chemistry/camshift: Bump to EAPI=5; add missing deps; fix for gcc-4.7
-  * dev-ml/lacaml: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
-  * Revert "Merge branch 'jlec' of github.com:gentoo-science/sci"
-  * Revert "dev-ml/lacaml: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config"
-  * Merge branch 'master' of github.com:gentoo-science/sci
-  * Merge branch 'jlec' of github.com:gentoo-science/sci
-  * dev-ml/lacaml: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
-  * sci-astronomy/zebra: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
-  * sci-chemistry/ambertools: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
-  * sci-libs/bigdft: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; drop old
-  * sci-libs/calculix-ccx: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; bump to EAPI=5; add missing dep on virtual/pkgconfig; use pkgconfig to detect arpack
-  * sci-libs/gsl: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
-  * sci-libs/magma: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; drop old
-  * sci-libs/optpp: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; bump to EAPI=5; move to new python eclasses
-  * sci-libs/wannier90: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; bump to EAPI=5
-  * sci-libs/xblas: Bump EAPI to 5
-  * sci-mathematics/freefem++: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; drop old
-  * sci-mathematics/Macaulay2: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config#
-  * sci-mathematics/petsc: Drop unused local USE-description: 'metis'
-  * sci-mathematics/petsc: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; drop old
-  * sci-mathematics/scilab: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
-  * sci-physics/atompaw: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; correct dep for pkgconfig to virtual
-  * sci-physics/atompaw2abinit: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; correct dep for pkgconfig to virtual
-  * sci-physics/abinit: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; correct dep for pkgconfig to virtual; fix openmp compatibility detection
-  * empi:  bump 0.8
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * sci-biology/mira: current stable and development version bumps
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * First working patch
-  * sci-physics/elk: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; add missing dep on virtual/pkgconfig; cleaning of ebuild
-  * sci-physics/elk: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; add missing dep on virtual/pkgconfig; cleaning of ebuild
-  * sci-physics/openmx: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; add missing dep on virtual/pkgconfig
-  * sys-cluster/hpl: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; add missing dep on virtual/pkgconfig
-  * mathjax now in main tree
-  * app-doc/scalapack-docs: Cleaning and keywording for prefix
-  * virtual/scalapack: Bump to latest scalapack reference
-  * virtual/lapack: Bump to latest reference
-  * [dev-python/Forthon] Fix option parser to take into account that wrapper filename may have a suffix, use dodoc/docinto. Thanks to Michał Górny <mgorny@gentoo.org> for his help on this
-  * [sci-visualization/yt] update
-  * sci-libs/atlas: Move -lm -latlas to Libs.private in all pkg-config files
-  * app-text/jabref: Fixed doc generation, keyword amd64-linux and x86-linux
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * The setup of python for the compilation of the GPU support in sci-libs/bigdft-1.7_pre12 improved.
-  * Added sci-physics/abinit-7.0.5, compilation of GPU support in sci-libs/bigdft-1.7_pre12 improved.
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * rstudio now in main tree
-  * sci-chemistry/pymol: Fix sed syntax
-  * sci-chemistry/pymol: Fix sed syntax
-  * sci-chemistry/pymol: Adapt to current HEAD
-  * version bump
-  * Update live ebuild
-  * Update live ebuild
-  * newer version in the tree
-  * Added ~x86 KEYWORD and API/README do docs.
-  * Merge branch 'master' of github.com:gentoo-science/sci
-  * sci-chemistry/pymol: adopt to current HEAD
-  * Typo
-  * Added changes suggested by Christoph Junghans <ottxor@gentoo.org>.
-  * Adding first draft version of jabref-2.9.2 ebuild.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/mkl: Version Bump
-  * Fix probable trailing / in EROOT
-  * Prepare alternatives-2.eclass for the main tree
-  * sci-libs/mkl: Add KEYWORDS, #342185
-  * sse41 -> sse4_1 (bug #456886) + ninja has missing keywords
-  * added warning about petsc threads support
-  * Merge remote-tracking branch 'github/master'
-  * [sys-cluster/lustre] Update lustre ebuild
-  * Merge pull request #49 from gentryx/master
-  * Merge /usr/local/portage/andis_overlay
-  * moved fperms to correct ebuild phase
-  * Merge branch 'master' of https://github.com/gentoo-science/sci
-  * Merge /usr/local/portage/andis_overlay
-  * reverted to calling cutils eclass functions
-  * Merge /usr/local/portage/andis_overlay
-  * adapting to standard order of definitions, dropped some default-equivalent function definitions, re-added test build functions as tests wouldn't otherwise be run
-  * fixed petsc compile issue reported by disperato
-  * Merge /usr/local/portage/andis_overlay
-  * dropped superfluous vcs-snapshot eclass and functions equivalent to default
-  * minor improvements
-  * added linebreaks where necessary
-  * Merge ../sci.bitbucket
-  * Merge branch 'master' of https://github.com/gentoo-science/sci
-  * added proper quotes for variables, use fperms in favor of chmod
-  * updated Manifest
-  * fixed indenting, descriptions and updated to EAPI 5
-  * updated EAPI, dropped versionator eclass, added shortcut for package name
-  * added missing metadata.xml
-  * using new EAPI and skipping superfluous die
-  * adapted coding style to appease repoman
-  * resolved various warnings reported by repoman for LibGeoDecomp and HPX, also fixed shortcomings as requested by jlec in https://github.com/gentoo-science/sci/pull/49/files#r2931081
-  * Merge ../sci.bitbucket
-  * sci-libs/armadillo: Version bump
-  * Merge branch 'master' of https://github.com/gentoo-science/sci
-  * Merge branch 'master' of github.com:gentoo-science/sci
-  * virtual/blas: Rise eigen version in deps
-  * Merge pull request #48 from jauhien/thepeg_182_herwig_262
-  * sci-physics/herwig++: version bump
-  * sci-physics/thepeg: version bump
-  * Next couple of fixes
-  * Merge branch 'master' of https://github.com/gentoo-science/sci
-  * And another step forward
-  * dev-java/jogl import from the java-overlay
-  * dev-java/gluegen import from java-overlay
-  * Fixed name in ChangeLog and metadata.xml
-  * Removed CMAKE_VERBOSE=1 from libSUFR ebuilds
-  * clean up package.mask
-  * sci-chemistry/votca-csg-tutorials is part of sci-chemistry/votca-csg
-  * app-doc/votca-csg-manual is part of sci-chemistry/votca-csg
-  * Some more patching
-  * More work on as-needed problems
-  * fixed path
-  * set SUID bit for access daemon
-  * access-daemon needs a full path, thus we're hardcoding /usr to shut it up
-  * don't hardcode absolute patch for access daemon
-  * clean up + merge csg-{manual,tutorials}
-  * added subslot, removed gromacs-manual blocker
-  * gromacs-manual: got merged in gromacs ebuild
-  * clean up
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * sci-libs/coinor-csdp: use generic pkg-config
-  * sci-libs/coinor-blis: Add missing coinor-bcps dependency
-  * sci-libs/coinor-alps: Add missing coinor-cgl dependency for tests
-  * sci-libs/coinor-netlib: no more empty doc
-  * sci-libs/coinor-sample: no more empty doc
-  * my version
-  * fixed compilation with newer cmake, removed currently unused use flags
-  * sci-libs/ipopt: Version bump
-  * sci-libs/coinor-utils: Version bump
-  * sci-libs/coinor-symphony: Version bump
-  * sci-libs/coinor-sample: Version bump
-  * sci-libs/coinor-osi: Version bump
-  * sci-libs/coinor-netlib: Version bump
-  * sci-libs/coinor-cppad: Version bump
-  * sci-libs/coinor-couenne: Version bump
-  * sci-libs/coinor-clp: Version bump
-  * sci-libs/coinor-cgl: Version bump
-  * sci-libs/coinor-blis: Version bump
-  * added likwid ebuild
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-chemistry/pymol: Bump python eclass
-  * Merge pull request #45 from jhcloos/openmx
-  * Merge branch 'master' of https://github.com/gentoo-science/sci
-  * fixed copyright note
-  * unmask scilab-5.4
-  * sci-mathematics/scilab cleanup ebuild
-  * sci-libs/atlas: Version bump
-  * [sci-biology/psychopy] fix typo in inherit, add metadata, make repoman happy
-  * [dev-python/Forthon] version bump, add modified version of BSD license, port to distutils-r1
-  * Merge remote-tracking branch 'upstream/master'
-  * added app-doc/gromacs-manual in here
-  * Merge branch 'master' of github.com:gentoo-science/sci
-  * sci-chemistry/mgltools: Allow multiple py ABIs install
-  * sci-chemistry/mgltools: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-webservices: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-volume: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-visionlib: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-vision: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-viewer-framework: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-utpackages: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-symserv: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-support: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-stride: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-sff: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-scenario2: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-scenario: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-qslimlib: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-pyglf: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-pybabel: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-pyautodock: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-pmv: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-opengltk: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-networkeditor: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-molkit: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-mglutil: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-gle: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-geomutils: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-dejavu: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-cmolkit: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-cadd: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-bhtree: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-autodocktools: Version Bump; move to distutils-r1.eclass
-  * sci-chemistry/mgltools-autodocktools: Version Bump; move to distutils-r1.eclass
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge pull request #43 from TheChymera/master
-  * sync with gx86
-  * Inherited gnome2-utils and called cache update from pkg_postrm as well
-  * used gnome2-utils.eclass function instead of touch to update cache
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/libcmatrix: fixed
-  * merging github && overlays.g.o
-  * sci-libs/acml: Version bump, now fetch restricted.
-  * app-admin/eselect: Cleaned old
-  * alternatives-2: update eselect min version
-  * sci-libs/armadillo: Version bump
-  * sci-chemistry/nmrpipe: Upstream changed tarballs
-  * sci-mathematics/giac: it's supposed to be frozen...
-  * Already in the tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * sci-chemistry/nmrpipe: Version BUmp; drop fetch restriction as upstream provides and promotes direct access
-  * added missing manifest
-  * added ebuild for libgeodecomp 0.1.0
-  * added LibGeoDecomp ebuild which tracks the trunk on Bitbucket
-  * cosmetics
-  * Fix bug 452806
-  * cleaning ebuild
-  * added ebuild for HPX
-  * sci-chemistry/gromacs: use cuda.eclass
-  * replaced src_install with python_install_all
-  * fixed sci-chemistry/gromacs[test]
-  * sci-physics/geant-vmc: source geant4 shell script before compiling
-  * Updated minimum geant4 version
-  * [sci-chemistry/gromacs] Drop restrict test for 4.6
-  * [sci-chemistry/gromacs] Update 4.6 series ebuild
-  * Corrected source repository Had been changed for testing.
-  * Added pkg_postinst() in order  to refresh the timestamp and make the desktop environment regenerate the chace - otherwise the icon doesn't show up appropriately
-  * sci-physics/openmx:  Fix fftw dependency.
-  * dev-java/flexdock version bump
-  * dev-java/scirenderer version bump
-  * sci-mathematics/scilab update dependencies
-  * virtual/geant: Initial import
-  * Initial import
-  * virtual/geant:3 work
-  * sci-physics/geant-vmc: Initial import
-  * Added src_install() script to make a launcher and assign an icon to it.
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * In sci-physics/abinit-7.0.4 missing makefile sources for the gui added from the 6.12.3 version.
-  * yet another update for git
-  * Fperms instead of Chmod
-  * Merge ssh://github.com/gentoo-science/sci
-  * live ebuild update
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * sci-physics/openmx added, version 3.6. sci-physics/atompaw version bumped to 3.0.1.9. New versions of sci-physics/abinit and sci-libs/bigdft added, but sci-libs/bigdft-1.7_pre12 is a version from the Abinit site, and the bigdft support in sci-physics/abinit-7.0.4 segfaults; on the other hand abinit-7.0.4 supports openmp. GPU support in sci-libs/bigdft-1.7_pre12 and sci-physics/abinit-7.0.4 not yet tested.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-chemistry/phenix-bin: Add new dep on libtinfo.so
-  * sci-astronomy/galfit-bin: Since #452532 we have libtinfo.so in the tree
-  * Merge pull request #44 from jhcloos/cgns-tcltk
-  * sci-libs/cgnstools: Add patch for current tcl/tk.
-  * Added run permissions for the package's executable file Also upgraded to distutils-r1 and made other minor improvements to python-related metadata
-  * Executable priviledges for /app/psychopyApp.py Also generally improved 9999 build (many thanks to prometheanfire from #gentoo-dev-help!)
-  * dev-util/ndiff: updated DESCRIPTION and ebuild comments
-  * Merge pull request #41 from AstroFloyd/master
-  * Removed CMAKE_VERBOSE=1 in pg2plplot-0.2.0.ebuild
-  * Initial upload of sci-libs/libmatheval (bug 181417)
-  * moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/pff: version bump
-  * sci-mathematics/giac: version bump
-  * sci-mathematics/gappalib-coq: version bump
-  * sci-mathematics/gappa: version bump
-  * sci-mathematics/frama-c: version bump
-  * sci-mathematics/flocq: version bump
-  * sci-mathematics/alt-ergo: initial commit
-  * dev-ml/zarith: initial commit
-  * dev-ml/ocamlgraph: version bump
-  * moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * sci-libs/coinor-cbc: Version Bump
-  * sci-mathematics/pulp: Move to EAPI=5, distutils-r1.eclass and virtual/pyparsing, #449564; unbundle sci-libs/coinor-cbc
-  * inCvs Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-chemistry/nmrpipe: Version Bump
-  * Created first ebuild for PG2PLplot and added it to repo
-  * Upgraded to sci-libs/libsufr-0.4.1.ebuild; added ChangeLog to repo
-  * mpi.eclass:  fix whitespace
-  * moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * migrate to git-2 eclass, fix lapack support
-  * sync with gentoo-x86
-  * Merge pull request #40 from jauhien/LoopTools_manifest
-  * sci-physics/LoopTools: manifest fixed forever, thanks to jlec
-  * Merge pull request #39 from jauhien/cdfplayer_9_0_0
-  * sci-mathematics/cdfplayer: use domenu
-  * fixed python dep
-  * sci-mathematics/scilab-5.4.0 cleanup dependencies
-  * dev-java/scirenderer version bump
-  * dev-java/flexdock version bump
-  * dev-java/jrosetta fix ant build files
-  * reverting to --no-as-needed LDFLAG
-  * reverting to --no-as-needed LDFLAG
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * fixed repman issues
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * put back in the --as-needed LDFLAG to yield hopefully smaller executables; recreating the patch so that it applies automatically
-  * upated to latest petsc 3.3 release
-  * updated to latest petsc 3.2 release
-  * app-admin/eselect: Version Bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/ncbi-tools++-9.0.0: although masked a not passing repoman checks this ebuild works for me, finally. All patches from upstream.
-  * dev-lang/julia fix emacs filename
-  * dev-lang/julia fix version in previous update
-  * dev-lang/julia update dependencies
-  * sci-mathematics/cdfplayer: version bump
-  * sci-astronomy/lephare: Fixed manifest and removed patch, thanks James Cloos
-  * sci-libs/magma: Fixed URL, thanks James Cloos
-  * Merge pull request #37 from xhub/master
-  * update EHG_REPO_URI
-  * update EHG_REPO_URI
-  * update EHG_REPO_URI
-  * update EHG_REPO_URI
-  * update EHG_REPO_URI
-  * further clean up
-  * version bump
-  * Merge pull request #30 from jauhien/cdfplayer
-  * fixed build with newer mkl
-  * dev-util/ccache: fixed clang links
-  * sci-biology/ncbi-tools++-9.0.0: a sketch of an updated ebuild, bug #279606, does not pass repoman checks due to IUSE items
-  * sci-biology/sra_sdk-2.2.2a: a version bump, still requires MAKEOPTS=-j1 and copies softlinks to binaries and libraries as files, so everything is in 3 physical copies
-  * sci-libs/magma: Bump
-  * added for testing
-  * masked dev-util/ccache use flags
-  * sci-chemistry/gromacs: clean up
-  * ccache-{clang,icc} are part of ccache now
-  * fixed openmm suffix
-  * fixed another typo
-  * fixed typo
-  * Added mkl support
-  * added ~amd64
-  * updated profile
-  * added ~amd64
-  * version bump
-  * fix build with !cuda and python=3 + qa
-  * sync with gx86
-  * reworked emacs issue (bug #444526#c3) + move to git
-  * sync with gx86
-  * [sys-cluster/lustre] Add missing patch
-  * [sys-cluster/lustre] Fix disabling
-  * [sys-cluster/lustre] Disable Werror
-  * [sys-cluster/lustre] All patches for 3.6 was merge into mainline
-  * fortran is gone
-  * Remove last instances of vtkNetCDF from paraview-3.14
-  * Add cblas-external USE flag to sci-libs/gsl
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * dev-lang/julia add emacs config file
-  * dev-lang/julia new ebuild
-  * sci-libs/o2scl: Initial import
-  * Sort webkit dep in paraview 3.14
-  * Moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * sci-libs/scalapack: Use latest pkg-config, removed old
-  * sci-libs/lapackpp: Use latest pkg-config
-  * sci-libs/atlas: Update for lapack-3.4.2
-  * dev-cpp/eigen: Removed old
-  * sci-libs/acml: Removed old
-  * sci-libs/cblas-reference: Fixed pkg-config and fortran use
-  * sci-libs/blas-reference: Removed unused dependencies
-  * Removed unused dependencies
-  * sci-libs/levmar: Use virtual/pkgconfig and prefix keywords
-  * sci-libs/openblas: Version bump. Link latest version to live one
-  * sci-libs/armadillo: Version bump
-  * in Cvs, this was just a test Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Include suggestions from g-dev review
-  * Renamed eclass Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * sci-libs/mumps: Install libpord, force -j1 on makefile because of random parallel build failures, separate dummy sequential mpi library from the common mumps library
-  * sci-mathematics/rstudio: version bump
-  * InCvs Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * Drop nasty MAC crap Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * Update skel files Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * In Cvs Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * In Cvs Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * In Cvs Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * In Cvs Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * inCvs Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * sci-libs/mkl: Version BUmp
-  * sci-libs/ipp: Version BUmp
-  * sci-biology/pybrain: Drop comments from metadata.xml; drop keywords from live ebuild
-  * Merge branch 'master' of github.com:gentoo-science/sci
-  * Merge pull request #36 from TheChymera/master
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * updated + fix for bug #444526
-  * CMAKE_BUILD_DIR -> BUILD_DIR
-  * ran repoman -vdx fix as per jlec'S recommendation
-  * sci-chemistry/avogadro: Add patch to avoid textrels on i686, #439410
-  * sci-chemistry/avogadro: Restrict test phase https://sourceforge.net/p/avogadro/bugs/653/
-  * sci-chemistry/avogadro: Fix openbabel version, #442154
-  * Merge branch 'master' of github.com:gentoo-science/sci
-  * Moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * Moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * Moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * sci-chemistry/openbabel: Add missing dep for USE=doc
-  * Update README.md
-  * Create README.md
-  * Added live ebuild for pybrain
-  * updated deps
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * dev-lang/idb: Version bump
-  * [sci-chemistry/nwchem] Initial import from bug #393139. Mpi still doesnt work
-  * moved to gx86
-  * moved to gx86 profile
-  * sync with gx86
-  * use T for temp file
-  * remove graphical tools when -X
-  * version bump + improved ebuild for fullprof
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * dev-java/hdf-java: cleaned for old version, buggy
-  * fix typo in intel-sdp_pkg_pretend
-  * updated deps
-  * sci-chemistry/mddnmr: Version BUmp
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Drop stupid static-libs idea again Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * Last remaning underscored removed Signed-off-by: Justin Lecher <jlec@gentoo.org>
-  * sci-chemistry/vmd: Drop dep on old tk
-  * random files
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci into pkg-config
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/tmglib: Initial import
-  * removed mac files from jlec
-  * sci-astronomy/starlink-bin: Version bump
-  * sci-libs/plasma: Version bump. Introduce testing
-  * sci-libs/lapacke-reference: added tmg for testing, cleaning up ebuild
-  * sci-libs/lapack-reference: removed tmg flag, now separate ebuild
-  * sci-libs/lapack-reference: tmg flag description
-  * sci-libs/lapack-reference: Added tmg use flag, fix a failing post command test
-  * sci-libs/mmdb: Test version for new eclass
-  * Keep order in pc file
-  * full featured
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-chemistry/mddnmr: Version Bump
-  * Work in progress
-  * Implemented comments from g-dev review
-  * Be bin package friendly
-  * Fix typo in Copyright year
-  * Implemented comments from g-dev review
-  * Only handle documentation if present
-  * intel-sdp.eclass: fix install on x86 + qa
-  * updated license
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * * intel:   Drop USE=doc and add static-libs support   Speed up unpacking #431614   Drop additional blank lines.   Drop old testing functions   Resort general functions and variables at the beginning   Add descriptions to standard phase functions.   declare local variables at once   Use clear += insteat of repeating variables   Drop version restriction of rpm2targz   Drop Sebastien as maintainer   Enhancement of intel-sdp.eclass   dev-lang/icc: Version Bump   dev-lang/ifc: Version Bump   imported from tree   dev-libs/intel-common: Version Bump; drop creation of license dir   Imported from tree   import from tree
-  * dev-python/pytools: fix test related stuff and license
-  * Drop USE=doc and add static-libs support
-  * Speed up unpacking #431614
-  * Drop additional blank lines.
-  * Drop old testing functions
-  * Resort general functions and variables at the beginning
-  * Add descriptions to standard phase functions.
-  * declare local variables at once
-  * Use clear += insteat of repeating variables
-  * Drop version restriction of rpm2targz
-  * Drop Sebastien as maintainer
-  * Enhancement of intel-sdp.eclass
-  * dev-lang/icc: Version Bump
-  * dev-lang/ifc: Version Bump
-  * imported from tree
-  * dev-libs/intel-common: Version Bump; drop creation of license dir
-  * Imported from tree
-  * import from tree
-  * Merge pull request #33 from xhub/master
-  * dev-python/pytools: fix test related stuff and license
-  * added openmm support
-  * mask sci-chemistry/gromacs[openmm]
-  * re-added for gromacs
-  * sci-mathematics/scilab various fixes
-  * dev-python/pycuda: Bump EAPI to 5; add missing dep on dev-python/mako; use cuda.eclass and make use of cuda_gccbindir
-  * dev-python/pytools: Bump EAPI to 5; add missing dep for tests
-  * dev-python/pycuda: bump and add tests
-  * dev-python/pytools: bump and add tests
-  * # By Justin Lecher (20) and Olivier Huber (1) * cuda: (21 commits)   dev-util/nvidia-cuda-sdk: Version Bump, inclusive cuda.eclass usage   sci-chemistry/vmd: Using new cuda.eclass   Imported from tree   Preparing Version Bump   dev-util/nvidia-cuda-toolkit: Merge change in both versions; fix whitespace error   Correcting whitespace problem   Minor fixes   Be a little more informative.   do not call pkg_setup from cuda.eclass   Move pkg_postinst to dev-util/nvidia-cuda-toolkit   Adding ignores for Mac   Add comments and streamline   dev-util/nvidia-cuda-sdk: Preparing Version Bump   Add pkg_setup and gcc bindir detection   dev-util/nvidia-cuda-toolkit: Enhancing cuda-config   dev-util/nvidia-cuda-sdk: Reverted changes to bicatalis commit; Moving to cuda.eclass   dev-util/nvidia-cuda-toolkit: Version Bump   preliminary cuda.eclass   Work in progress towards cuda eclass usage   dev-util/nvidia-cuda-toolkit: Use cuda.eclass; install cuda-config; install doc and html into system path
  to support portages file filter   ...
-  * Merge github.com:gentoo-science/sci
-  * dev-util/nvidia-cuda-sdk: Version Bump, inclusive cuda.eclass usage
-  * sci-chemistry/vmd: Using new cuda.eclass
-  * Imported from tree
-  * Preparing Version Bump
-  * dev-util/nvidia-cuda-toolkit: Merge change in both versions; fix whitespace error
-  * Correcting whitespace problem
-  * Minor fixes
-  * Be a little more informative.
-  * do not call pkg_setup from cuda.eclass
-  * Move pkg_postinst to dev-util/nvidia-cuda-toolkit
-  * Adding ignores for Mac
-  * Add comments and streamline
-  * dev-util/nvidia-cuda-sdk: Preparing Version Bump
-  * Add pkg_setup and gcc bindir detection
-  * dev-util/nvidia-cuda-toolkit: Enhancing cuda-config
-  * dev-util/nvidia-cuda-sdk: Reverted changes to bicatalis commit; Moving to cuda.eclass
-  * dev-util/nvidia-cuda-toolkit: Version Bump
-  * preliminary cuda.eclass
-  * Work in progress towards cuda eclass usage
-  * dev-util/nvidia-cuda-toolkit: Use cuda.eclass; install cuda-config; install doc and html into system path to support portages file filter
-  * Misc fixes for sci-libs/magma
-  * * cuda:   dev-util/nvidia-cuda-sdk: Version Bump, inclusive cuda.eclass usage   sci-chemistry/vmd: Using new cuda.eclass   Imported from tree   Preparing Version Bump   dev-util/nvidia-cuda-toolkit: Merge change in both versions; fix whitespace error   Correcting whitespace problem   Minor fixes   Be a little more informative.   do not call pkg_setup from cuda.eclass   Move pkg_postinst to dev-util/nvidia-cuda-toolkit   Adding ignores for Mac   Add comments and streamline   dev-util/nvidia-cuda-sdk: Preparing Version Bump   Add pkg_setup and gcc bindir detection   dev-util/nvidia-cuda-toolkit: Enhancing cuda-config   dev-util/nvidia-cuda-sdk: Reverted changes to bicatalis commit; Moving to cuda.eclass   dev-util/nvidia-cuda-toolkit: Version Bump   preliminary cuda.eclass   Work in progress towards cuda eclass usage   dev-util/nvidia-cuda-toolkit: Use cuda.eclass; install cuda-config; install doc and html into system path to support portages file filter
-  * sci-chemistry/openbabel: Add test phase, check openmp correctly
-  * sci-biology/staden: Version Bump, move to sane portage like building
-  * sci-chemistry/nmrpipe: Version BUmp
-  * Misc fixes for sci-libs/magma
-  * dev-util/nvidia-cuda-sdk: Version Bump, inclusive cuda.eclass usage
-  * sci-chemistry/vmd: Using new cuda.eclass
-  * Imported from tree
-  * Preparing Version Bump
-  * hdf-java: version bump
-  * flexdock: fix outdated SRC_URI and broken Manifest
-  * Merge pull request #31 from xhub/master
-  * dev-util/nvidia-cuda-toolkit: Merge change in both versions; fix whitespace error
-  * Merge branch 'master' into cuda
-  * Correcting whitespace problem
-  * Merge branch 'cuda' of github.com:gentoo-science/sci into cuda
-  * Minor fixes
-  * Misc fixes for sci-libs/magma
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * Ignore .DS_Store
-  * Merge branch 'master' into cuda
-  * Merge branch 'master' into pkg-config
-  * First scratch of new pkgconfig.eclass
-  * sci-mathematics/cdfplayer: installation of desktop file/other fixes
-  * Be a little more informative.
-  * do not call pkg_setup from cuda.eclass
-  * Move pkg_postinst to dev-util/nvidia-cuda-toolkit
-  * Adding ignores for Mac
-  * Add comments and streamline
-  * sci-mathematics/cdfplayer: installation path fixed
-  * sci-mathematics/cdfplayer: new ebuild for bug #421019
-  * improved ebuild for fullprof, added docs + examples useflags
-  * Merge pull request #29 from jauhien/master
-  * sci-physics/LoopTools: Manifest fixed
-  * fixing manifest
-  * removed g-cran, broken
-  * Merge pull request #26 from TheChymera/master
-  * Re-manifesting
-  * dev-cpp/eigen: Version bump
-  * improved ebuild for fullprof
-  * improved ebuild for fullprof
-  * added an ebuild for fullprof
-  * Merge pull request #27 from wking/master
-  * live ebuild update
-  * updated build and deps
-  * dev-java/netcdf: Add the netCDF licence (which is *not* MIT)
-  * dev-util/nvidia-cuda-sdk: Preparing Version Bump
-  * Add pkg_setup and gcc bindir detection
-  * dev-util/nvidia-cuda-toolkit: Enhancing cuda-config
-  * dev-util/nvidia-cuda-sdk: Reverted changes to bicatalis commit; Moving to cuda.eclass
-  * dev-util/nvidia-cuda-toolkit: Version Bump
-  * preliminary cuda.eclass
-  * Work in progress towards cuda eclass usage
-  * dev-util/nvidia-cuda-toolkit: Use cuda.eclass; install cuda-config; install doc and html into system path to support portages file filter
-  * sci-chemistry/avogadro: Add test phase
-  * sci-chemistry/simpson: Fix underlinking
-  * Fix underlinking
-  * Move to dev-libs
-  * initial import of libcuda
-  * initial import of libgdev
-  * dev-lang/idb: in main tree
-  * Moved to Tree
-  * sci-chemistry/phenix-bin: Make no-fetch msg better understandable
-  * sci-chemistry/phenix-bin: Fix deps
-  * sci-chemistry/chimera-bin: Add dep on virtual/opengl
-  * sci-chemistry/chimera-bin: Fix deps
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Update live ebuild for latest Normaliz
-  * sci-libs/gmsh: Add another dep for opengl support
-  * sci-libs/gmsh: Addmissing dep on virtual/opengl
-  * Added live ebuild for MDP
-  * sci-libs/gmsh: Fix link problems with gold
-  * sci-libs/med: Fix SRC_URI; move to EAPI=5
-  * Fix dep on gmp[cxx] (Thanks Gerhard Bräunlich)
-  * x11-libs/xview-bin: Update to latest debian patches
-  * openbabel-python: Enter BUILD_DIR in src_install
-  * Merge pull request #24 from TheChymera/master
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * sci-biology/bamtools: Drop tree version, merge changes into live version
-  * Merge pull request #25 from jauhien/thepeg-herwig-version-bump
-  * sci-physics/herwig++: version bump
-  * sci-physics/thepeg: version bump
-  * sci-chemistry/ambertools: Add another fix for blas/lapack
-  * Revert "Update Copyright"
-  * Fix DEP on eselect
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * Update Copyright
-  * Merge pull request #21 from fredricj/master
-  * version bump
-  * Merge remote-tracking branch 'remotes/github/master'
-  * bump
-  * renamed dependency from openmotif to motif
-  * Fix linking against arbitrary lapack implementation
-  * net-fs/cvmfs: now in main tree
-  * Proper DEPEND list and eclass info
-  * Added MY_P key to SRC_URI path
-  * Defined general MY_P
-  * Removed redundant S= from git version, fixed faulty S= specification in 1.75.01
-  * New ebuild for stable psychopy version + manifest
-  * Ebuild improvements as per jauhien's instructions.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * New ebbuild for sci-biology/psychopy
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-physics/root: remove unused patch
-  * sci-chemistry/nmrpipe: Version Bump
-  * sci-chemistry/wxmacmolplt: Fix prefix awareness; correct desktop file creation
-  * sci-physics/root, app-doc/root-doc: update Manifest
-  * ambertools: export AMBERHOME in ebuild
-  * gamess: Version bump to 20120501.1
-  * sci-libs/mkl: Fix size of builddir
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/lapacke-reference: Version bump. Restore the reflapack library name instead of lapack
-  * sci-libs/lapack-reference: Version bump. Restore the reflapack library name instead of lapack
-  * Merge blas to master
-  * sci-physics/root: Drop virtual/fortran from DEP as it is provided by the fortran-2.eclass
-  * sys-cluster/mpich2: Move to EAPI=5, use fortran-2.eclass correctly
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * app-doc/root-docs: version bump
-  * sci-physics/root: version bump
-  * sci-astronomy/zpeg: Drop unnessecarry virtual/fortran dep
-  * dev-util/f90cache: Use fortran-2.eclass
-  * dev-python/inference: Move to EAPI=5; correct usage of fortran-2.eclass
-  * dev-python/ffnet: Move to EAPI=5; use distutils-r1.eclass; correct usage of fortran-2.eclass
-  * dev-cpp/growler-link: Fix for gcc-4.7; correct fortran-2.eclass usage; move to autotools-utils.eclass
-  * dev-cpp/eigen: Use vcs-snapshot.eclass, correct usage of fortran-2.eclass, some layout improvements
-  * Update M2 live ebuild
-  * inCvs
-  * sci-libs/inchi: Straighten out some minor things, respect AR and RANLIB
-  * app-admin/eselect: Bump to tree version
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * version bump
-  * vmd: Fix netcdf config, bug #406737
-  * wxmacmolplt: Version bump to 7.4.3
-  * sci-libs/blas-reference: Version bump, revert to change soname to refblas
-  * ambertools: Fix parallel tests
-  * ambertools: Version bump to 12
-  * avogadro: Version bump to 1.1.0
-  * app-doc/root-docs: version bump
-  * sci-physics/root: version bump
-  * openbabel-python: Fix typo
-  * openbabel-python: Add PYTHON_DEPS
-  * inchi: Add static-libs USE flag
-  * openbabel-python: Version bump to 2.3.2
-  * openbabel-perl: Version bump to 2.3.2
-  * openbabel: Version bump to 2.3.2
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-mathematics/scilab] revert part of commit 033255b367
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-mathematics/scilab] remove virtual/fortran
-  * [sci-mathematics/scilab] remove virtual/fortran
-  * Merge pull request #22 from jauhien/master
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-physics/LoopTools-2.8: Manifest fixed
-  * [sci-libs/openblas] Solved problem with fetching
-  * sci-chemistry/pymol: Add mime type definition
-  * Merge branch 'master' of github.com:gentoo-science/sci
-  * [sci-mathematics/scilab] fix slot dependencies
-  * Merge pull request #18 from jauhien/herwig
-  * bump boehm-gc, fix python
-  * Fix deps of live ebuild
-  * [x11-misc/envytools] There is no opcodes
-  * [x11-misc/envytools] Allow to build with recent bison
-  * [x11-misc/envytools] Add envytools
-  * improve live ebuild
-  * Removed the TODO item for the desktop file
-  * Added rstudio-0.96.331 and desktop file fix
-  * [sci-chemistry/trajng] Fix ebuild
-  * [sci-chemistry/trajng] Add keywords
-  * [sci-chemistry/xdrfile] Add keywords
-  * [sci-chemistry/trajng] Add to repo
-  * [sci-chemistry/xdrfile] actualy allow optional fortran
-  * [sci-chemistry/xdrfile] Add to repo
-  * inCVS
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * sci-chemistry/phenix-bin: Version Bump
-  * [app-vim/vim-gromacs] Fix typo
-  * [app-vim/vim-gromacs] Update vim syntax repo uri
-  * initial commit (thx to Torsten Stuehn)
-  * package.mask: added sci-physics/espresso++
-  * sync with gx86
-  * [sci-libs/openblas] Version bump
-  * [sys-cluster/lustre] Update patches
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * fix to build petsc in Gentoo Prefix (thanks to Matthias Maier)
-  * live ebuild update
-  * live ebuild update
-  * updated package.mask
-  * cmake-utils.eclass got merged in gx86
-  * hybrid stuff got merged
-  * [sci-mathematics/scilab] fix errors in previous commit
-  * [sci-mathematics/scilab] version bump
-  * [dev-java/scirenderer] version bump
-  * version bump
-  * app-benchmarks/numbench: Updated dependency for eselect alternatives
-  * sci-libs/mkl: Version bump
-  * sci-libs/acml: Version bump
-  * [sci-mathematics/scilab] update dependencies
-  * [dev-java/scirenderer] version bump
-  * [dev-java/jlatexmath-fop] version bump
-  * [dev-java/jlatexmath] version bump
-  * app-admin/eselect: rev-bumped to avoid conflict with tree
-  * sci-chemistry/specView: Needs webkit support in pyside
-  * sci-chemistry/chemBuild: Needs webkit support in pyside
-  * sci-chemistry/specView: Prefix offset for header dirs
-  * sci-chemistry/specView: Copile py code
-  * sci-chemistry/chemBuild: New addition
-  * import latest skel data from tree
-  * sci-chemistry/specView: New addition
-  * sci-chemistry/phenix-bin: Add missing dep
-  * sci-chemistry/chimera-bin: Don't strip
-  * sci-chemistry/chimera-bin: Set rpath on prefix
-  * sci-chemistry/phenix-bin: Don't double prefix
-  * sci-chemistry/phenix-bin: Not everyone installs on my box
-  * Version Bump
-  * [sys-cluster/lustre] call apply_user_patches
-  * [sys-cluster/lustre] Initial import
-  * in Cvs
-  * in Cvs
-  * in Cvs
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * new addition
-  * new addition
-  * new license
-  * new license
-  * change one useflag name in paraview 3.14.1
-  * in CVS
-  * in CVS
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * Enable postscript support in paraview 3.14.1 through gl2ps
-  * app-admin/eselect: Version BUmp
-  * sci-physics/herwig++: move sed stuff to pkg_preinst and change $D to $ED
-  * sci-chemistry/curvefit: Quote sed correctly
-  * sci-chemistry/curvefit: And it sits in EPREFIX
-  * sci-chemistry/curvefit: We have ls in usr/bin
-  * sci-chemistry/curvefit: Also include gcc-4.1 libdir in rpath
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * sci-chemistry/curvefit: New addition
-  * Merge pull request #19 from jauhien/looptools-2.8
-  * Bump iml to the same level as s-o-g overlay, make it work on prefix including OS X.
-  * sci-physics/LoopTools: version bump
-  * sci-physics/herwig++: RDEPEND fixed
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * dummy files added to make pcheck happy
-  * Merge pull request #17 from jauhien/thepeg
-  * New Ebuild for bug #433060
-  * sci-physics/thepeg: maintainer email fixed
-  * sci-physics/thepeg: DEPEND fixed
-  * New Ebuild for bug #424003 thanks to hasufell, mgorny and xarthisius.
-  * dev-python/astlib: Version bump
-  * sci-libs/exodusii: Version Bump
-  * Patches for sci-libs/bigdft to install GPU support corrected not to break linking against the compiled libraries
-  * unbundle netcdf from paraview
-  * update descriptions
-  * Bunch of fix and ubundling for paraview 3.14.1
-  * enabled commit signing
-  * add empty files for pcheck
-  * sci-chemistry/ligplot+: New addition
-  * a license is a license not an eclass
-  * add license
-  * sci-chemistry/ssp: Fix offset of reference CS DB
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * sci-chemistry/ssp: New addition
-  * Merge pull request #16 from jauhien/LoopTools_so_fortran
-  * ambertools: Add bugfix 28
-  * sci-physics/LoopTools: shared library generation and dependency on virtual/fortran added
-  * Merge branch 'master' of git+ssh://github.com/gentoo-science/sci
-  * [app-benchmarks/numbench] Version bump.
-  * paraview 3.14.1 initial import to greater masses
-  * sync with gx86
-  * better version in tree
-  * Merge pull request #15 from jauhien/master
-  * manifest fixed
-  * renamed -bin
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * Merge remote-tracking branch 'github/master'
-  * [sci-libs/openblas] Version bump
-  * update to EAPI=4, cosmetics, deps
-  * sci-chemistry/usf-tools: Bump to latest release
-  * Merge git+ssh://paul/local/overlays/sci
-  * ucsf-tools
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge pull request #14 from xhub/github-master
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * [dev-python/Forthon] version bump
-  * sci-chemistry/pymol: Correct Desktop entry
-  * Enable cross-compilation of {CBLAS,LAPACK}-reference
-  * [sci-mathematics/scilab] version bump
-  * [dev-java/scirenderer] version bump
-  * [dev-ml/zarith] fix license
-  * [dev-ml/gsl-ocaml] new package
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * sci-chemistry/nmrpipe: no function called from prefix.eclass; please drop
-  * sci-chemistry/nmrpipe: Enhancing prefix support
-  * x11-libs/xview-bin: Add stupid binary package
-  * use ninja if available
-  * cmake-utils.eclass: added ninja support
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * [sci-mathematics/scilab] live ebuild update
-  * [app-benchmarks/numbench] New revision, directory cleaned up.
-  * [app-benchmarks/numbench] Updated live ebuild.
-  * Update live dependencies
-  * [app-benchmarks/numbench] Version bump.
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * dev-java/scirenderer version bump
-  * dev-ml/lacaml version bump and cleanup old version
-  * dev-java/scirenderer version bump
-  * scotch in main tree
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * Version bump sfst to 1.4.6g
-  * Bump foma to version 0.9.16alpha.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Version bump hfst to 3.3.12
-  * x11-libs/xview: Add missing inherit of multilib
-  * x11-libs/xview: Use everything from debian; build only 32bit libs everywhere; be carefully this is very hacky approach
-  * sci-chemistry/nmrpipe: Version Bump, bring x11-libs/xview back into the game
-  * Version bump.
-  * sci-astronomy/galfit-bin: renamed to binary package
-  * Update live ebuild
-  * sci-astronomy/galfit: add links to ncurses/tinfo
-  * sci-astronomy/psfex: fixed for newer plplot
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * sci-astronomy/galfit: manifest/new tar file
-  * dev-java/scirenderer version bump
-  * dev-java/jgraphx version bump
-  * dev-java/flexdock version bump
-  * sci-mathematics/scilab live ebuild update
-  * updated min eselect version
-  * sci-libs/atlas: added a generic flag for more generic architectures, and possibility for user to pass configure options via standard EXTRA_ECONF flags
-  * sci-astronomy/zpeg: Initial import
-  * dev-cpp/eigen: Version bump. Changed license to MPL-2
-  * fix deps
-  * net-fs/cvmfs: fixed client init and setup, added config stage
-  * added ~x86-macos
-  * package.mask: removed obsolete entries
-  * sync with gx86
-  * sync with gx86
-  * sync with gx86
-  * sync with gx86
-  * sync with gx86
-  * net-fs/cvmfs: Initial import, need more work
-  * sci-chemistry/concoord: Use QA_PREBUILT for binary packages
-  * sci-physics/root: update User's Guide
-  * app-doc/root-docs: remove Manifest
-  * incvs
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * sci-physics/root-docs: version bump
-  * sci-physics/root: version bump
-  * sci-physics/root: improve cling support
-  * app-doc/root-docs: update live ebuild
-  * sci-physics/root: update live ebuild
-  * sci-physics/root: fix bug 426432
-  * sci-libs/armadillo: Adapted for new atlas
-  * sci-libs/coinor-dip: Initial import
-  * fixed license to CPL
-  * sci-libs/coinor-csdp: Initial import
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * [dev-util/nvidia-cuda-sdk] fix asneeded issues
-  * sci-libs/coinor-os: Initial import
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * added plcol patch with increased diff line count, bug #391669; same patch needs to go into offical emboss-6.3.1_p4
-  * sci-libs/coinor-cppad: Initial import
-  * sci-libs/coinor-couenne: Initial import
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * InCvs
-  * sci-libs/coinor-vol: Fixed for occasional parallel install breaks
-  * fixed description
-  * sci-libs/coinor-bonmin: Initial import
-  * sci-libs/coinor-bcp: Initial import
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * live ebuild update
-  * live ebuild update
-  * sci-chemistry/votca-{ctp,kmc,moo}: removed never realy used
-  * sci-astronomy/lephare: prefix keywording, version fix
-  * [dev-libs/fortrancl] fix patch
-  * sci-libs/coinor-symphony: Initial import
-  * sci-libs/coinor-mp: Initial import
-  * [sci-visualization/yt] update dependencies
-  * [dev-python/Forthon] version bump
-  * syntax error in passing lapack
-  * sci-libs/ipopt: Initial import
-  * sci-libs/coinor-blis: Initial import
-  * sci-libs/coinor-bcps: Initial import
-  * sci-libs/coinor-alps: Initial import
-  * sci-libs/coinor-cbc: Initial import
-  * sci-libs/coinor-cgl: Initial import
-  * sci-libs/coinor-clp: Initial import
-  * sci-libs/coinor-dylp: Initial import
-  * sci-libs/coinor-vol: Initial import
-  * sci-libs/coinor-osi: Initial import
-  * sci-libs/coinor-utils: Initial import
-  * sci-libs/coinor-netlib: Initial import
-  * sci-libs/coinor-sample: Initial import
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * Merge pull request #12 from xhub/0825f16ab3ec153827d9aadc60880028d81a9efe
-  * Add support for x32 ABI
-  * sci-libs/mumps: Merge dummy sequential mpi into sequential mumps
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * media-gfx/librecad: dependency fix, bug#426730
-  * clean up
-  * initial commit
-  * sci-libs/mumps: fix underlinking for sequential library
-  * sci-libs/magma: Shared library fixes, prefix love and ebuild cleanup
-  * sci-libs/xblas: Shared library fixes, prefix love and ebuild cleanup
-  * sci-libs/plasma: Shared library fixes and prefix love
-  * sci-libs/scotch: Shared library fixes and prefix love
-  * sci-libs/mumps: Shared library fixes and prefix love
-  * sci-libs/mpiblacs: Shared library fixes and prefix love
-  * sci-libs/fdlibm: Shared library fixes and prefix love
-  * sci-libs/cblas-reference: Shared library fixes and prefix love
-  * sci-libs/scalapack: dependencies fix, removed old
-  * sci-libs/mumps: prefix love
-  * remove duplicate
-  * dev-libs/double-conversion: Initial import
-  * sci-mathematics/dsfmt: Initial import
-  * sci-libs/fdlibm: Initial import
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * Made dev-util/nvidia-cuda-sdk-4.2.9 compile with USE=opencl
-  * [dev-java/scirenderer] version bump
-  * [sci-mathematics/scilab-5.3.999] test ebuild for 5.4 branch
-  * [dev-java/jrosetta] version bump
-  * sci-libs/atlas: Version bump, this is a stable release.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * The bigdft-1.6-tuto.1-GPUlibs.patch of sci-libs/bigdft-1.6_pre1-r3 updated not to forget the pkg-config file
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * remove old
-  * more sci-astronomy live ebuild masking
-  * sci-astronomy/stiff: live version, prefix keywording
-  * sci-astronomy/missfits: live version, prefix keywording
-  * sci-astronomy/weightwatcher: live version, prefix keywording
-  * sci-astronomy/eye: live version, prefix keywording
-  * prefix keywording
-  * prefix keywording
-  * sci-libs/openblas: version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * dev-cpp/eigen: version bump and more test fixes
-  * sci-libs/adolc: to main tree
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * sci-libs/dsdp: changes incorporated in main tree
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * pfft: removed - never used
-  * layout.conf: updated manifest-hashes
-  * version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * The version of sci-physics/elk bumped to 1.4.22, the old ones removed.
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * sync hash with new portage
-  * dev-java/jlatexmath-fop: remove old
-  * dev-java/jlatexmath: do not compile examples, bug #421743
-  * sci-libs/hdf5: in main tree
-  * Fixed typo.
-  * Moved prefix to /opt.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * Merge branch 'master' of github.com:gentoo-science/sci
-  * Updated DEPEND.
-  * Adding live build.
-  * Added package mask for live ebuild, sci-chemistry/freeon-9999.
-  * Merge pull request #9 from jauhien/master
-  * Added modules-3.2.9c-r1.ebuild.
-  * update metadata
-  * New ebuild sci-physics/LoopTools-2.7 for bug#424860
-  * root-docs: clean version moved to portage
-  * Mask live ebuilds from sci-astronomy
-  * sci-astronomy/stuff: Live version. Prefix love
-  * no blas
-  * Live version. Prefix love
-  * sci-astronomy/sextractor: cblas -> atlas
-  * sci-astronomy/scamp: cblas -> atlas
-  * sci-astronomy/psfex: live version
-  * sci-astronomy/swarp: added live version
-  * sci-astronomy/scamp: live version
-  * sci-astronomy/sextractor: Live version, introduced prefix love
-  * dev-util/nvidia-cuda-sdk: Adapted to newer nvidia-cuda-sdk
-  * dev-util/nvidia: rewrote ebuild
-  * a blind attempt to get from a pull-push confusion
-  * sci-libs/bigdft-1.6_pre1 from -r2 to -r3: patched to install necessary libraries for GPU support and to compile with gcc-4.6
-  * dev-util/nvidia-cuda-toolkit: This package is prebuilt so we are using QA_PREBUILT for everything
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/atlas: version bump. Adapt calls to compilers. Inherit multilib
-  * dev-util/nvidia-cuda-toolkit: fix for amd64-linux
-  * dev-util/nvidia-cuda-toolkit: fix for amd64-linux
-  * sci-libs/magma: Version bump. Updated patches
-  * dev-util/nvidia-cuda-toolkit: more prefix fixes
-  * dev-util/nvidia-cuda-sdk: import/clean/bump
-  * dev-util/nvidia-cuda-toolkit: import/clean/bump
-  * sci-chemistry/coot: Gcc-4.7 support included upstream
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-physics/root: backport fixes from the portage
-  * app-doc/root-docs: backport fixes from portage
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * more comments, .Rhistory
-  * sci-mathematics/rstudio: initial import
-  * dev-libs/mathjax: Initial import
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Moved to tree
-  * dev-python/bitarray: New package requested by jamasi on irc
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * dev-cpp/eigen: version bump
-  * keyword amd64-linux and x86-linux
-  * add pthread for as-needed
-  * fix license and add flag desc
-  * initial import
-  * sci-physics/root: Drop in tree versions
-  * [dev-python/pyhdf] whitespace
-  * [dev-python/pyhdf] initial import wrt #423953. Ebuild written by Paweł Rumian <gorkypl@gmail.com> with my modifications
-  * updated to petsc-3.3_p1
-  * sci-libs/openblas: fixed soname
-  * sci-libs/atlas: version bump
-  * sci-libs/atlas: version bump
-  * sci-libs/openblas: remove test flag
-  * sci-libs/openblas: version bump
-  * Merge github.com:gentoo-science/sci
-  * sci-libs/magma: Initial import
-  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci into overlay
-  * [sci-libs/libxc] add ~amd64-linux
-  * [sci-libs/libxc] add ~amd64-linux
-  * [sci-libs/bigdft] add ~amd64-linux
-  * [sci-libs/wannier90] add ~amd64-linux
-  * [sci-libs/fox] make it prefix aware
-  * Merge pull request #8 from nicolasbock/master
-  * Added libX11 dependency.
-  * [dev-java/joda-convert] add missing dependency on junit:4
-  * Merge branch 'master' of https://github.com/wking/science into wking-hdfview
-  * dev-java/hdf-java-2.8: fix hdfview script (quotes and sh-bang)
-  * dev-java/hdf-java-2.8: explicitly build packages for hdfview
-  * dev-java/hdf-java: fix HOMEPAGE in v2.8 ebuild.
-  * Fixed package description.
-  * First commit for modules package.
-  * app-doc/root-docs: backport htmldoc generation fixes
-  * sci-physics/root: backport htmldoc fixes to 5.32 branch
-  * sci-physics/root: remove redundant virtualx
-  * sci-physics/root: reuse htmldoc patch
-  * app-doc/root-docs: version bump for 5.34.00
-  * sci-physics/root: version bump for 5.34.00
-  * app-doc/root-docs: separate htmldoc from root package
-  * sci-physics/root: fix repoman warnings and update manifest
-  * sci-physics/root: separate htmldoc package
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Reflect the split of the fortran interface out of sci-libs/netcdf in sci-libs/bigdft and sci-libs/etsf_io. The version of sci-physics/elk bumped to 1.4.22, the old ones removed.
-  * [sci-chemistry/gromacs] Add new acceleration use flags for gromacs
-  * Reflect the split of the fortran interface out of sci-libs/netcdf in sci-physics/abinit-6.12.3-r2
-  * Merge github.com:gentoo-science/sci
-  * sci-libs/atlas: Version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * fixed redundant license (bug #421401)
-  * fixed redundant license (bug #421401)
-  * sci-geosciences/harmonics-dwf-20120302: Fixed problem where "S" directory wasn't found.
-  * Merge branch 'master' of github.com:gentoo-science/sci
-  * sci-geosciences/xtide: Version bump.  Removed "non-commercial" use since upstream received take-down notice and that dataset is no longer available.
-  * sci-geosciences/libtcd: Version bump.  Removed "non-commercial" use since upstream received a take-down notice and the "non-commercial" dataset is no longer available.
-  * sci-geosciences/harmonics-dwf-free: Version bump.
-  * dev-perl/Const-Fast, dev-perl/File-Map, dev-perl/OpenGL, dev-perl/PDL, dev-perl/PerlIO-Layers: now in main tree
-  * dev-perl/PerlIO-Layers: Initial import
-  * dev-perl/OpenGL: Initial import
-  * dev-perl/File-Map: Initial import
-  * dev-perl/Const-Fast: Initial import
-  * dev-perl/PDL: Version bump
-  * sci-astronomy/scamp: Fixed patch name
-  * sci-astronomy/lephare: Initial import
-  * sci-physics/root: update live ebuild
-  * initial commit
-  * masked dev-lang/ispc-9999
-  * sci-chemistry/coot: Fix for gcc-4.7
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-physics/root: sync with tree
-  * Masks moved to tree
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [dev-java/scirenderer] new ebuild
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * add support for new hybrid kernels
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/cluster: Correct masking, #419999
-  * added missing private headers
-  * added petsc-3.3-p0 ebuild
-  * sci-chemistry/mgltools-opengltk: Add missing dep on media-libs/glew and fix underlinking problem
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sys-devel/gdebugger: Fix Manifest
-  * sci-libs/atlas: Version bump
-  * Add missing hashes
-  * Drop unused licenses
-  * sci-biology/cluster: Rename cluster to cluster3, #419999
-  * Merge branch 'master' of github.com:gentoo-science/sci
-  * sci-chemistry/mgltools-qslimlib: Fix for gcc-4.7
-  * fixed info install
-  * sci-chemistry/mgltools-pmv: Fix for bytecompiling
-  * app-admin/eselect: Fix eaclocal call
-  * Mask old dssp and make sci overlay user to tester
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * improved die() message to inform user that gcc-4.5.3 does not work while gcc-4.3.6 does
-  * sci-chemistry/nmrview: Move to EAPI=4, specify QA_PREBUILT
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-physics/root: use virtualx eclass for Xvfb
-  * sci-chemistry/simpson: Correct blas to cblas for linking
-  * [sci-mathematics/scilab] force jgraphx version
-  * sci-physics/root: html documentation generation
-  * initial commit
-  * fixed EAPI bump
-  * initial commit
-  * sci-mathematics/scilab: fix bug #375769
-  * dev-java/jogl: adapted gluegen dependency
-  * sci-mathematics/scilab: fixed gui/xcos deps
-  * dev-java/gluegen: sync version with java-overlay
-  * sci-mathematics/scilab: complete ebuild revamp
-  * sci-physics/root: sync live ebuild with upstream
-  * [sys-cluster/hpl] add -Lflags from lapack and blas, fixes #400785 by Aleksandr Yakimov <yaleks@gentoo.ru>
-  * sci-biology/cluster: Version Bump, Move to EAPI=4
-  * dev-java/hdf-java: add hack for hdf5[mpi]
-  * dev-java/hdf-java: fixed missing use
-  * dev-java/flexdock: add missing jgoodies-looks dependency
-  * [dev-lang/path64] remove epause along with eutils.eclass since it does nothing for EAPI>2. Thanks to Jeremy Olexa <darkside@gentoo.org> for noticing
-  * [net-misc/dhcp] add user.eclass for enew{user,group}
-  * [sci-physics/root] add user.eclass for enew{user,group}
-  * [sys-cluster/condor] add user.eclass for enew{user,group}
-  * [dev-lang/path64] add eutils.eclass for epause
-  * [dev-util/smartgit] add eutils.eclass for make_desktop_entry
-  * [media-gfx/librecad] add eutils.eclass for make_desktop_entry
-  * [sci-mathematics/petsc] add eutils.eclass for epatch
-  * [sci-geosciences/qgis] add eutils.eclass for make_desktop_entry
-  * sci-physics/root: update User's Guide
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-astronomy/topcat: Initial import
-  * sci-libs/exodusii: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
-  * sci-libs/lapacke-reference: Add missing eutils.eclass
-  * sci-libs/scalapack: Add missing eutils.eclass
-  * sci-mathematics/dolfin: Add missing eutils.eclass, bump to EAPI=4
-  * sci-physics/abinit: Add missing eutils.eclass
-  * sci-physics/atompaw: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
-  * sys-cluster/ovis: Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; fix installation of envd file; correct leading spaces
-  * sci-astronomy/stilts: Initial import
-  * sys-cluster/ovis: Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; fix installation of envd file; correct leading spaces
-  * sys-cluster/ovis: Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; fix installation of envd file; correct leading spaces
-  * sci-physics/root: Add missing eutils.eclass
-  * sys-cluster/ovis: Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; fix installation of envd file; correct leading spaces
-  * sci-libs/cgnslib: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
-  * sci-libs/blas-reference: Add missing eutils.eclass
-  * sci-libs/bigdft: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
-  * sci-biology/mira: Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; drop old
-  * sci-biology/gbrowse: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
-  * sci-biology/est2uni: Bump to EAPI=4, remove unnecessary bits
-  * sci-biology/emboss: Add missing eutils.eclass
-  * sci-biology/amos: Bump to EAPI=4, remove unnecessary bits
-  * dev-perl/Bio-BigFile: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
-  * dev-java/jogl: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
-  * dev-java/flexdock: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
-  * Mask old version schema of ncbi-tools to make overlay user to be tester
-  * [dev-java/hdf-java] remove stray quotes
-  * media-gfx/librecad: added freetype to DEPS
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Mask >=sci-libs/arpack-96 to make overlay users to tester
-  * Fix repoman warning about position off EAPI
-  * sci-astronomy/starlink-bin: Initial import
-  * sci-astronomy/zebra: Initial import
-  * sci-libs/optpp: Initial import
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * dev-java/gluegen: Fix repoman warning about position off EAPI
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-physics/root: version bump
-  * sci-physics/abinit-6.12.3-r1 modified to accept revisions of sci-libs/bigdft-1.6_pre1
-  * The pkg-config file of sci-libs/bigdft corrected.
-  * masked scilab-5.4*
-  * dev-java/joda-time: import from wtk overlay
-  * dev-java/joda-convert: import from the java overlay
-  * dev-java/jrosetta: import from the java overlay
-  * dev-java/jogl: import from the java overlay
-  * dev-java/jcip-annotations: import from the java overlay
-  * dev-java/gluegen: import from the java overlay
-  * dev-java/jlatexmath-fop: Version bump
-  * dev-java/jlatexmath: Version bump
-  * dev-java/jeuclid-core: Version bump
-  * dev-java/hdf-java: Version bump. Added use flag hdfview. Adapted from the wtk overlay
-  * dev-java/netcdf: import to the science overlay and bump
-  * dev-java/fits: quotes
-  * dev-java/fits: updated herd and description
-  * dev-java/fits: Version bump and import to the science overlay
-  * sci-mathematics/flocq: QA fixe
-  * sci-mathematics/flocq: Various QA fixes
-  * [dev-python/cosmocalc] bump to eapi4, allow multiple python abis, call 2to3 for python3 support, reorder variables, add pypi to HOMEPAGE and SRC_URI, drop empty {R,}DEPEND
-  * [dev-python/asciidata] Reorder vars to comply with ebuild.skel, drop redundant PYTHON_DEPEND (already done via distutils.eclass) and src_test, add pyfits to RDEPEND, numpy is RDEPEND only, build docs instead of downloading them, bump to EAPI4
-  * [sci-mathematics/flocq] Fix ebuild eapi parsing and other minor issues
-  * [metadata] Enable md5-cache
-  * [dev-java/jgraphx] Fix ebuild eapi parsing and other minor issues
-  * [dev-lang/vtune] Fix ebuild eapi parsing and other minor issues
-  * sci-astronomy/galfit: Initial import
-  * sci-astronomy/eazy: Initial import
-  * sci-astronomy/bpz: Initial import
-  * sci-libs/scalapack: Version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-astronomy/astrometry: Initial import
-  * sci-mathematics/apron: fixes conflict of USE flags
-  * [sci-libs/atlas] Version bump.
-  * [sci-libs/openblas] Removed old alpha versions.
-  * [sci-libs/openblas] Version bump.
-  * sync with gx86
-  * [dev-python/astropy] fix depends, drop keywords from live ebuild to make repoman happy, whitespaces
-  * [dev-python/astropy] initial import, ebuild written by me
-  * [sys-devel/gdebugger] slight improvements, add proper depends
-  * Merge branch 'gdebugger' of https://github.com/nbigaouette/sci into nbigaouette-gdebugger
-  * Version bump, drop old, don't install unnecessary doc files
-  * sci-chemistry/pymol: Fix for latest HEAD
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Fix live ebuild
-  * sci-chemistry/nmrpipe: Version Bump, use QA_PREBUILT
-  * Bundled in nmrpipe
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Revert "Don't use "cp" for copying files/folders into ${D}, use insinto/doins -r instead."
-  * Assert sed execution with "die".
-  * Don't use "cp" for copying files/folders into ${D}, use insinto/doins -r instead. Note that an "mv" seems nessary to rename the installed folder (${My_PN} instead of ${My_PN}${PV}-${_arch}) and new variables ${_dest_folder} and ${_extracted_folder} are now used to prevent having ugly "basename" and "dirname" calls.
-  * Create directories just before installing files to them.
-  * Create destination directory just before first file copy.
-  * Go into WORKDIR instead of ".."
-  * Create .desktop file using "cat >> <<- EOF" instead of "echo".
-  * No need for a dot at end of description; not a sentence.
-  * Don't use html2text to create the license. Use the license from the overlay.
-  * Added license for sys-devel/gdebugger
-  * Add app-vim/vim-gromacs
-  * sci-chemistry/nmrpipe: Use QA_PREBUILT instead of QA_FLAGS_IGNORED
-  * sci-chemistry/nmrpipe: Version Bump, handle all binary files correctly for QA checks
-  * New ebuild: AMD gDEBugger version 6.2.438, an OpenCL and OpenGL debugger and memory analyzer.
-  * The dependence of sci-physics/abinit on sci-libs/fox corrected.
-  * mask =sci-libs/mmdb-1.24.20111208, no pkg-confiles installed
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-chemistry/gromacs] add more mirrors
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-chemistry/mgltools-webservices: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-volume: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-visionlib: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-vision: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-viewer-framework: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-utpackages: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-symserv: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-support: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-stride: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-sff: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-scenario2: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-scenario: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-qslimlib: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-pyglf: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-pybabel: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-pyautodock: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-pmv: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-opengltk: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-networkeditor: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-molkit: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-mglutil: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-gle: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-geomutils: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-dejavu: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-cmolkit: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-cadd: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-bhtree: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools-autodocktools: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-chemistry/mgltools: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
-  * sci-libs/msms: RESTRICT pypy
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * Merge pull request #2 from nbigaouette/vtune
-  * Put symbolic links in /usr/bin and create .desktop file.
-  * Added ebuild for vtune 11.0.7.221625 using the "intel-sdp" eclass.
-  * Don't hardcode "rpm" as being the archive subdirectory where RPMs are to be found. Instead, define "INTEL_RPMS_DIRS" in the ebuild and loop over searching for the RPM. If unset, defaults to "rpm".
-  * Matching the archive for ".tgz" specifically breaks VTune which has .tar.gz as archive. Instead, remove everything after the first dot (the .tar.gz or .tgz part).
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/blas-reference: applied lapack patch to not compile tmglib when not needed
-  * sci-libs/lapack-reference: fixed patch for testing
-  * fixed patch for testing
-  * sci-chemistry/coot: Drop libpng-1.5 patch, included upstream
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/blas-reference: Fix manifest
-  * sci-libs/lapack-reference: Fix manifest
-  * sci-libs/blas-reference: Clean checksums
-  * sci-libs/lapack-reference: Clean checksums
-  * sci-libs/lapacke-reference: Version bump
-  * sci-libs/lapack-reference: Version bump
-  * sci-libs/blas-reference: Version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/libxc version bumped to 1.2.0.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sys-cluster/ovis] Masked for testing.
-  * [sys-cluster/ovis] Initial ebuild.
-  * Fix docdir for prefix.  Thanks to Robert McGehee for reporting.
-  * in main tree
-  * dev-python/emcee: Initial import
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * dev-python/astlib: Version bump
-  * Minor improvements related to sci-libs/fox.
-  * sci-physics/abinit-6.12.* improved to find uudecode, a patch created for that by mistake removed once more. Several packages related to Abinit, including sci-physics/elk, version-bumped.
-  * [sci-chemistry/gromacs] Also add http mirror git uri
-  * Merge branch 'master' into overlay
-  * Merge branch 'master' of github.com:gentoo-science/sci
-  * media-gfx/librecad: version bumped 1.0.2 2.0.0_alpha3
-  * in main tree
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-physics/abinit bumped to 6.12.3, a patch file removed by mistake put back.
-  * sci-libs/levmar: Initial import
-  * Merge git+ssh://git.overlays.gentoo.org/proj/sci
-  * Fix test in dsdp
-  * Merge branch 'master' of github.com:gentoo-science/sci
-  * sci-geosciences/pydap and pydap plugins:
-  * [dev-java/hdf-java] updates SRC_URI
-  * [app-benchmarks/numbench] Version bump.
-  * [sci-libs/trilinos] Solved many issues.
-  * [sci-libs/trilinos] Masked for testing.
-  * [sci-libs/trilinos] Initial ebuild.
-  * Import dsdp to include a huge number of fixes and improvement
-  * sci-physics/root: Drop in tree version
-  * sci-physics/root: Fix EAPI=4 usage, don't mix CFLAGS/CXXFLAGS, respect LD
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-physics/root: fix bug 408987
-  * [dev-libs/fortrancl] version bump
-  * Merge branch 'master' of github.com:gentoo-science/sci
-  * [dev-python/Forthon] re-add as it is now released under BSD terms
-  * sci-physics/root: version bump
-  * [dev-python/Forthon] re-add as it is now released under BSD terms
-  * sci-physics/root: version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * media-gfx/librecad: version bumped 2.0.0_alpha2
-  * media-gfx/librecad: version bumped to 1.0.0_alpha2
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-libs/hdf5] snapshot bump
-  * [sci-libs/amdlibm] drop old, fix manifest
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/bigdft & sci-physics/abinit clean-up after sci-physics/abinit version bump to 6.12.2 and tests
-  * [dev-ml/zarith] version bump
-  * [dev-ml/lacaml] moved to new oasis eclass
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * correct URI for icons
-  * Add new icon files provided by Ramiro Téllez Sanz
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * Import tree changes
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * media-gfx/brlcad: file cleanup
-  * media-gfx/brlcad: added a missing patch
-  * media-gfx/brlcad: added missing patch
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * Fix patches to be in line with tree
-  * Correct usage of python.eclass
-  * New addition, written by me, #406401
-  * [dev-cpp/eigen] Added 3.1.0_alpha2 version. Uncomplete lapack implementation.
-  * [sci-libs/atlas] Version bump.
-  * Fixes bug #405455, again
-  * Fixes bug #405455, again
-  * Fixes bug #405455, again
-  * [sci-libs/openblas] Updated patch and removed useless and unclear ewarn.
-  * [sci-libs/openblas] First stable version.
-  * using PATCHES variable instead of epatch
-  * sci-physics/root: fix Manifest
-  * sci-physics/root: switch to virtual/shadow
-  * [sci-libs/hdf5] add developement snapshot
-  * sci-physics/abinit-6.12.1 fortran setup improvement corrected, gui preparation corrected
-  * sci-physics/abinit metadata updated (libabinit USE flag), sci-physics/abinit-6.12.1 fortran setup improved
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * Version Bump
-  * [sci-libs/amdlibm] version bump wrt #405803 by Matthias Dahl <ua_gentoo_bugzilla@binary-island.eu>
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * fix manifest
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Bump intel compiler suite
-  * New package, ebuild written by me
-  * sci-libs/bigdft-1.6.0 corrected, sci-physics/abinit-6.12.1 added and moved to autotools-utils, sci-libs/bigdft-1.6_pre1 it depends on added. Old versions of bigdft needed by old versions of abinit ressurected.
-  * version bump
-  * sci-physics/root: updave live ebuild
-  * sci-physics/root: bug fix for #406817
-  * New addition, written by me, #408995
-  * This version and newer is in the tree
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * pandas: bump to 0.7.2.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-libs/amdlibm] remove SRC_URI wrt #405803, add valid 'amdlibm' license (copied to txt from pdf)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/frama-c: fix install with doc USE flag
-  * dev-libs/simclist: version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/atlas: Version bump
-  * sci-libs/openblas: Version bump
-  * Drop gl and test patch -> included upstream
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/mosaik: masking mosaik-2.1.33 mosaik-9999
-  * Merge github.com:gentoo-science/sci
-  * Add a band aid to eselect's alternative2 framework for prefix
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/sra_sdk-2.1.9: added missing insinto
-  * Final fixes for OS X in gotoblas2
-  * correct small error
-  * switch to multilib in openblas, gotoblas2 will come later as it needs another fix
-  * [net-misc/dhcp] Import more patches to make also client work
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/sra_sdk-2.1.9: use EAPI=4 hoping it will handle symlinks in bin/ and lib/ directories properly (but it does not, bug #408199
-  * [net-misc/dhcp] Import patches from F17
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sys-cluster/blcr: added ' || die' calls
-  * [sci-mathematics/polymake] add missing metadata.xml
-  * [net-misc/dhcp] once again
-  * [net-misc/dhcp] once again
-  * [net-misc/dhcp] wrong one =D
-  * [net-misc/dhcp] Opps fix patch
-  * [net-misc/dhcp] Enable infiniband in new version
-  * sci-biology/mosaik: version bump for 2.1.33 and GIT HEAD, neither compiles so far; upstream re-contacted
-  * version bump, added the pdf documentation to SRC_URI, the compile process leaks through many 'Fastq.cpp:224: error: conditional expression between distinct pointer types 'gzFile_s*' and 'FILE*' lacks a cast' messages in Fastq.cpp:224, Fastq.cpp:226, Fasta.cpp:258, Fasta.cpp:260, Fasta.cpp:266, Fasta.cpp:268, but the package itself installs and executes at least
-  * Merge branch 'polymake' of https://github.com/burcin/sci
-  * add *-macos prefix support to gotblas2
-  * Add *-macos prefix support to openblas
-  * Remove old polybori ebuild from the tree. Get new stuff from sage-on-gentoo
-  * Make sci-mathematics/polymake work with gentoo-prefix.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-visualization/gnuplot: clean up
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/mumps: Fixed for sequential (non mpi) libraries
-  * sci-libs/scalapack: remove mpi from pc file
-  * sci-libs/mumps: only allow earlier metis versions
-  * sci-libs/scotch: added 64bits integer flag and described the tools flag
-  * sci-libs/parmetis: added 64bits integer and double precision flags
-  * masked parmetis-4
-  * imported mumps
-  * [sci-chemistry/simpson] fix metadata.xml wrt bug 407877 by Patrick Lauer <patrick@getnoo.org>
-  * sci-libs/parmetis: bump
-  * sci-libs/scotch bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-physics/root: add live ebuild
-  * sci-physics/root: fix llvm support
-  * sci-physics/root: version bump and bugfix
-  * sys-cluster/blcr: update SRC_HOME, SRC_URI and added a check for kernel version <2.6.30, resp. <2.6.38, a version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [dev-python/pysolar] version bump
-  * sci-libs/lemon: shortened DESCR line
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Removed maintainer, as herd is enough
-  * Enable all fortran with single USE flag, fix license.
-  * fixed petsc 3.1 ebuild (missing patch files)
-  * disabled imagemagick, fixed lib configuring
-  * moved comments out of the argument list
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * sci-mathematics/petsc: more cleaning
-  * fix missing linking if hypre and superlu enabled
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * added superlu on activated hypre flag
-  * got sparse flag working
-  * disabled non-working dependencies
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * Moved to tree
-  * moved to tree
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * fixed undefined reference when using afterimage
-  * Moved to tree
-  * Block pypy usage
-  * Added sci-libs/libsufr-0.3.2
-  * removed obsolete call to env-update
-  * reworked fortran and openmp support
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * sci-chemistry/ambertools: Add another buffer overflow patch
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * fixed disable X option and use deps
-  * sci-chemistry/ambertools: Add bugfixes 22-27
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * sci-libs/lemon: added a note how to eventually create a shared library
-  * added optional boost and afterimage dep
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * sci-libs/inchi: Version bump, new licence
-  * further simplification, added more optional deps
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * fixed banned dosed, added more comments
-  * reworked configure function
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * sci-biology/cutadapt: new package
-  * sci-biology/phylobayes: new package, no explicit LICENSE stated
-  * sci-biology/phylobayes: new package, no explicit LICENSE stated
-  * sci-biology/cufflinks: new package
-  * sci-libs/lemon: new package, required by sci-biology/cufflinks
-  * [media-gfx/PhiloGL] version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [dev-ml/zarith] new ebuild
-  * [dev-ml/lacaml] version bump
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * added new petsc 3.2-p6 ebuild
-  * Update deps in M2 live ebuild
-  * sci-physics/root: fix repoman warning
-  * sci-physics/root: version bump
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * [sci-libs/fgsl] add prefix love
-  * updated Manifest
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * [app-benchmarks/numbench] Updated live ebuild.
-  * [app-benchmarks/numbench] Version 0.2_beta1.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * sci-biology/sra_sdk-2.1.9: remove trailing whitespace
-  * sci-biology/sra_sdk-2.1.9: almost working ebuild
-  * sci-biology/gbrowse-2.48: added dependency on <=sci-biology/primer3-2, per http://generic-model-organism-system-database.450254.n5.nabble.com/PrimerDesigner-working-in-2-40-tp4724773p5479669.html
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * fixed hypre dependency
-  * sci-physics/root: fix build on non-english locales
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
-  * [dev-lang/path64] add use.flag description
-  * Commit package.mask as well, was missing in last commit
-  * Dropped eapi again, zmedico: you don't need EAPI 4-python, when the ::repo is implied rather than explicit; masked sci-bioligy/amboss as well
-  * Correct masking, thanks zmedico for help, bump EAPI to 4-python
-  * Cleaned old patches, added goocanvas config option
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * [dev-lang/path64] update metadata.xml
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * sci-libs/plasma: fixed some as-needed issues
-  * sci-libs/plasma: Initial import
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * making cblas-reference OS X aware
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * sci-libs/gsl: Fixed gsl-config/pkg-config issues
-  * sci-libs/atlas: Version bump
-  * app-doc/scalapack-docs: Bumping to match scalapack-2 which include blacs quick reference sheets
-  * sci-libs/mpiblacs: Removed old, blocking scalapack > 2
-  * sci-libs/scalapack: Version bump. CMake based building, BLACS is now included with ScaLAPACK
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * Correct usage of autotools-eclass, prevents double call of elibtoolize
-  * Keyworded for ~-linux prefix
-  * Keyworded for ~-linux prefix
-  * Keyworded for ~-linux prefix
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Keyworded for ~-linux prefix
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * Workaround file collision, #404257
-  * intermidiate commit
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-libs/mpiblacs] Install blacs headers.
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * sci-libs/atlas: Reverted to older lapack
-  * Correct masking syntax
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Mask all emboss and embassy packages from overlay
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [dev-python/dimensionful] initial import, ebuild written by me
-  * [sci-libs/atlas] correct Manifest
-  * Fix for current HEAD, correct desktop entry generation
-  * Drop Keywords from live version
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Move to EAPI=4 and autotools-util.eclass
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * fixed manifest
-  * sci-libs/lapacke-reference: Fixed pkg-config
-  * sci-libs/lapack-reference: Fixed pkg-config
-  * sci-libs/blas-reference: Fixed pkg-config
-  * [media-gfx/PhiloGL] don't mess with paths and follow upstream as close as possible
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * eapi4 goodness
-  * sci-libs/ipp: Bump
-  * add units
-  * sci-libs/mkl: Version bump
-  * dev-lang/idb: Version bump
-  * dev-lang/ifc: Version bump
-  * dev-lang/icc: Version bump
-  * dev-libs/intel-common: Version bump
-  * [media-gfx/PhiloGL] Initial import, ebuild written by me
-  * Remove Forthon until legal issues are cleared
-  * [dev-python/Forthon] initial import, ebuild written by me
-  * sci-libs/atlas: bump
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * sci-libs/lapacke-reference: bump, with home patches
-  * sci-libs/lapack-reference: bump, with home patches
-  * sci-libs/blas-reference: bump, with home patches
-  * Drop python herd from remaining packages
-  * Remove python herd from metadata per djc request
-  * Fix for HEAD
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * Update to latest head
-  * in main tree
-  * app-admin/eselect: sync with tree
-  * sci-libs/libsufr: added ebuild for new version 0.3.1
-  * sci-chemistry/gromacs: clean up
-  * media-gfx/brlcad: removed old version
-  * sci-chemistry/gromacs: fixed threads and mpi
-  * media-gfx/brlcad: fixed as-needed filtering
-  * [dev-cpp/eigen] version bump.
-  * [dev-python/coards] also fix this in similar way
-  * [sci-misc/salome*] Fix python depend
-  * [metadata] Enable git signed commits
-  * Moved to autotools-utils, some more sanity
-  * Remove double prefix
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Add this nasty binary package
-  * dev-perl/Bio-DB-Das-Chado-0.32: added the LICENSE line and require DBD-Pg to be installed before compiling this packge
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * dev-perl/Bio-BigFile: new package, initial ebuild, see bug #402835
-  * some clean up in paraview 3.12.0
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * EROOT fix
-  * fixing a missing EROOT
-  * Fix Jon's name
-  * Bertini-1.3.1 added
-  * [sci-libs/gmsh] bump to EAPI4 for required use, removed unused call to flag-o-matic.eclass, shorten description, fix dependencies on libpng and zlib, remove redundant dependency on cmake, use PATCHES instead of calling src_unpack, mycmakeargs is now bash array, remove obsolete dies, compile doc during src_compile
-  * Added gmsh-2.5.0-r1 to work with libpng-1.5. I also removed the 'png' and 'zlib' use flage as the two libraries are hard included in upstream code
-  * [sys-cluster/scalasca] removed
-  * Paraview 3.12.0 is in. ugly right now will shape it a bit better.
-  * sci-biology/artemis: adjust ebuild based on upstream providing a Makefile
-  * sci-biology/artemis: adjust ebuild based on upstream providing a Makefile
-  * sci-biology/apollo: new package
-  * sci-biology/tablet-bin: adjust PATH to point to the installation place
-  * adjust PATH to point to the installation place, few comment lines changes
-  * sci-biology/tablet-bin-1.11.11.01: make use of the TMPDIR variable
-  * added the addpredict() trick from tablet-bin*.ebuild to make the ACCESS DENIED messages quiet, bugs #402507 (learned from bug #387227)
-  * added the addpredict() trick from tablet-bin*.ebuild to make the ACCESS DENIED messages quiet, bugs #402507 (learned from bug #387227)
-  * sci-biology/OBO-Edit: more attempts to get rid of sandbox ACCESS VIOLATION SUMMARY errors
-  * sci-biology/OBO-Edit: more attempts to get rid of sandbox ACCESS VIOLATION SUMMARY errors
-  * sci-biology-sra_sdk-2.1.9: preserve libs written directly into  at the end of src_compile() and install them later on
-  * sci-biology/sra_sdk-2.1.6: dropping an old crap
-  * two more Makefiles needed a DESTDIR patch, in conjunction with an ugly symlink hack in  one can build the stuff; dobin does not transfer symliks so every binary appears installed 3 times; upstream bug http://jira.be-md.ncbi.nlm.nih.gov/browse/TR-10207
-  * sci-mathematics/why: version bump
-  * sci-mathematics/pff: version bump
-  * sci-mathematics/ltl2ba: QA fixe
-  * sci-mathematics/giac: QA fixes
-  * sci-mathematics/gappalib-coq: version bump
-  * sci-mathematics/gappa: version bump
-  * sci-mathematics/frama-c: version bump
-  * sci-mathematics/flocq: QA Fixes
-  * sci-mathematics/apron: QA fixes
-  * dev-ml/mlgmpidl: SRC_URI now uses HTTPS
-  * dev-ml/ocamlgraph: version bump
-  * sci-biology/sra_sdk-2.1.9: version bump and almost correct DESTDIR patch
-  * handle new vmd detection
-  * media-gfx/brlcad: version bumped 7.20.4
-  * media-gfx/librecad: version bumped to 1.0.1
-  * added openmp support
-  * Adding kash (binary version only)
-  * Add kash licence
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [zfs,spl] They are in tree already
-  * updated eselect dependency
-  * sci-biology/seaview: and the path to the helpfile was corrected in the Makefile to match intended location specified in ebuild
-  * sci-biology/seaview: version bump; add missing symlink so that the C++ header can be found; remove calll to xft-config and use pkg-config instead; set our Gentoo FLTK path (not include path) to /usr/include/fltk-1 so that svg.o gets included during linking, otherwise we get undefined reference to svg_tree_save(FD_nj_plot*)
-  * Added first ebuild for k3match, version 1.0
-  * Updated Manifest for ndiff-2.00
-  * Added an ebuild for ndiff-2.00
-  * sync with tree and bug #400999#c7
-  * sci-biology/wgs-assembler-7.0: version bump, would be nice if we could stop compilation of the kmer/ subdir (an r1916 snapshot) and DEPEND on the external http://kmer.sourceforge.net complete bundle instead
-  * updated package.mask
-  * version bump
-  * sci-libs/lapack-reference: Version bump
-  * sci-libs/blas-reference: Version bump
-  * [sci-visualization/yt] update deps, add pyx remove zlib
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/acml: Version bump
-  * sci-libs/lapackpp: Version bump
-  * Dropped DOCS as it is handled by default
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * CCP4 upstream took over the real maintance
-  * sci-libs/atlas: Version bump
-  * switched to main tree hypre
-  * now in main tree
-  * app-admin/eselect: merge with main tree
-  * [sci-visualization/labplot] Add live ebuild
-  * sci-physics/root: fix Manifest
-  * sci-physics/root: fix cfitsio linking
-  * cleanup xrootd removal
-  * [dev-java/flexdock] version bump
-  * [dev-python/astlib] Version bump, drop old
-  * version bump and some fixes so that it works with webappconfig again?
-  * [sci-visualization/yt] initial import, ebuild written by me
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * New addition
-  * sci-biology/lastz: A pairwise DNA sequence aligner (also chromosome to chromosome), a BLASTZ replacement
-  * sci-biology/YASRA: Yet Another Short Read Assembler to reference using LASTZ
-  * sci-biology/gbrowse: added dev-perl/TermReadKey to dependencies
-  * sci-biology/libgtextutils: Gordon text utils library
-  * [dev-libs/fortrancl] initial import, ebuild written by me
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Call python_pkg_setup always
-  * Convert to thin manifests (as suggested by alexxy and jlec)
-  * Removed because the sources cannot be fetched
-  * Removed because the file is non-fetchable
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * tweaks to mpich2
-  * mpich2:  add link to upstream report
-  * Now in main tree
-  * Move sci-misc/simpy -> dev-python/simpy
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Version Bump
-  * Remove patch, fixed upstream
-  * Drop failing tests for now, fix #393361
-  * Version bump
-  * Bumped EAPI to 4 and added new eautoreconf handling of autotools-utils.eclass
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Fix double installation of spectrum.h
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/artemis-bin: DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool
-  * sci-biology/artemis: DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * dev-python/GOGrapher: more robust version from same author is at https://github.com/ntamas/biopython/blob/gosupport which is a rewrite of https://github.com/gotgenes/biopython
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/manatee-igs: new package for prokaryotic genome annotation and editing using chado
-  * sci-biology/manatee-igs: new package for prokaryotic genome annotation and editing using chado
-  * dev-perl/Log-Cabin: new package, required by sci-biology/manatee-igs
-  * Bumped to new upstream repo uri
-  * Drop double call of emake in src_configure
-  * Bumped to new upstream repo uri
-  * New package, ebuild written by me
-  * in main tree
-  * now in main tree
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * moved to tree
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Version Bump, #373679
-  * Added DEP on dev-python/simpy
-  * CAT move for simpy package
-  * Add missing fortran support
-  * Initial commit
-  * blas svn
-  * switch sci herd to sci-* sub herds, full overlay re-manifest
-  * plplot-5.9.9 compatibility
-  * move dependency for xrootd from main tree
-  * move dependency for xrootd from main tree
-  * move dependency for xrootd from main tree
-  * nco in tree
-  * documented status of go-parser (as a very simple implementation) which should be dropped once its successor code get into biopython
-  * dev-python/go-parser: a Gene Ontology OBO file format parser
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Sync ebuild to use install4j as in sci-biology/tablet-bin. Awaiting a fix from upstream so that the installer really respects --destination or -dir options.
-  * sci-chemistry/nmrpipe: Remove dep on xview
-  * sci-chemistry/nmrpipe: Always use bundled xview
-  * sci-mathematics/scilab-5.3.3 fixes for jdk-1.7
-  * Fix digest
-  * [dev-java/flexdock] version bump to 1.1
-  * Version Bump
-  * eigen: version bump
-  * New package, ebuild written by me
-  * New package, ebuild written by me
-  * sci-physics/atompaw2abinit-3.3.0-r1.ebuild reflects the new structure of the abinit web
-  * media-gfx/brlcad: use system libraries for svn version
-  * media-gfx/brlcad: version bumped to 7.20.4
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/libxc-1.1.0-r1 forces compilation with -fPIC for sci-physics/atompaw-3.0.1.3 not to complain
-  * sci-physics/root: fix clarens dependency
-  * sci-phzsics/elk Manifest broken by mistake, now corrected
-  * media-gfx/librecad: version bumped to 1.0.0
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-physics/elk adapted to accept sci-libs/libxc-1.1.0 and upgraded to 1.4.5
-  * sci-physics/abinit updated to 6.10.3, sci-libs/bigdft to 1.2.0.5, and sci-libs/libxc to 1.1.0
-  * sci-geosciences/xtide: Moved the setting of the HFILE_PATH environment variable back to the xtide ebuild.  Made HFILE_PATH point to a standard directory /usr/share/harmonics.  Version bump to install xtide with new HFILE_PATH and all dependencies. sci-geosciences/libtcd: Version bump to reinstall dependencies. sci-geosciences/harmonics-dwf-free: Moved location of database file to /usr/share/harmonics sci-geosciences/harmonics-dwf-free-noncomm: Moved location of database file to /usr/share/harmonics
-  * media-gfx/librecad: version bump to 2.0.0_alpha1
-  * ebuild doc cleanup
-  * A seed-driven progressive assembly program
-  * sci-biology/estscan: added Manifest file
-  * added configuration.php.patch for VHOSTS setup
-  * sci-biology/est2uni: example of necessary config changes for vhosts setup
-  * removed arches for this -9999 ebuild for sanity
-  * fix determination of svn-based checkout number required for building
-  * remove offending double-quotes
-  * ebuild cleanup, works, releasing for testing
-  * fix sanbox violations on some systems
-  * added MYPV to the ebuild to make it more easily re-usable
-  * sci-physics/root: add ~x86-linux keyword
-  * sci-biology/tablet-bin: ebuild cleanup, version bump
-  * sci-biology/tablet-bin: ebuild cleanup, version bump
-  * sci-biology/tablet-bin: ebuild cleanup, version bump, #348029
-  * sci-biology/tablet-bin: ebuild cleanup, version bump
-  * sci-biology/mira: version bump
-  * sci-biology/biopython: 1.58 version bump
-  * Version Bump
-  * Fix pymol-9999-setup.py.patch for current HEAD
-  * sci-physics/root: fix afs patch
-  * sci-physics/root: new production release bump
-  * sci-physics/xrootd: unbundled package from ROOT
-  * app-doc/root-docs: version bump
-  * sci-mathematics/pulp: Initial ebuild.
-  * Another Version bump
-  * Version BUmp, added missing dep, found by louic and reported in irc
-  * New package, ebuild written by me
-  * fixed astromatic packages for recent ATLAS
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * dev-python/pandas: Version bump.
-  * [sci-physics/espresso] live ebuild update
-  * casacore now in main tree
-  * sci-physics/root: version bump
-  * + sci-geosciences/harmonics-dwf-free and + sci-geosciences/harmonics-dwf-free-noncomm: Now create /etc/env.d/50xtide_harm in both of these ebuilds which contains HFILE_PATH environment variable used by the xtide suite of programs to locate the tidal constituent databases.  Concluded that this was better suited here than in the xtide ebuild. + sci-geosciences/libtcd: Trivial change updating DEPEND to bring in the latest harmonics-dwf* versions. + sci-geosciences/xtide: Version bump.  Eliminated creation of /etc/xtide.conf by using HFILE_PATH environment variable created by the harmonics-dwf* ebuilds.
-  * Fix manifest for sci-geosciences/pydap_handlers_nca
-  * Changed my e-mail address...
-  * sci-mathematics/mdp: Version bump.
-  * sci-misc/simpy: Version bump.
-  * sci-geosciences/pydap_handlers_sqlite: Initial build.
-  * sci-geosciences/pydap_handlers_sql: Version bump.
-  * sci-geosciences/pydap_handlers_hdf5: Initial ebuild
-  * sci-geosciences/pydap_handlers_cdms: Version bump.
-  * [sci-libs/hdf5] drop old
-  * Fixed digest, #390723
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-geosciences/pydap: Version bump.
-  * Corrected Slotting of media-libs/libpng and media-libs/tiff
-  * [sci-mathematics/scilab] 5.3.3 version bump
-  * [dev-ml/lacaml] initial import
-  * openbabel-perl: Redigest
-  * Version Bump
-  * Masked sco-chemistry/nmrpipe where ever needed
-  * mask nmrpipe on multilib
-  * Fix blas + lapack for hpl
-  * openbabel-perl: Version bump to 2.3.1
-  * openbabel-python: Version bump to 2.3.1
-  * openbabel: Version bump to 2.3.1
-  * [sci-libs/libsufr] initial import
-  * sci-libs/bigdft Manifest broken by mistake, now corrected
-  * sci-physics/abinit bumped to 6.10.2, sci-physics/atompaw to 3.0.1.3
-  * lapack-docs: fix file clash with blas-docs
-  * initial commit
-  * fixed desc
-  * initial commit
-  * initial commit
-  * updated package.mask
-  * multilib support
-  * multilib support
-  * EAPI bump + multilib support
-  * live ebuild update
-  * live ebuild update
-  * live ebuild update
-  * live ebuild update
-  * Live ebuild updates
-  * Corrected email adress in ChangeLog entry
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * remanifest
-  * sci-chemistry/ambertools: Fix possible buffer overflow
-  * sci-chemistry/ambertools: Add bugfixes up to 21, other fixes
-  * Updated license
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Version Bump
-  * Removed no-herd from herd tag in metadata.xml
-  * Version Bump
-  * Removed no-herd from herd tag in metadata.xml
-  * Version Bump
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * fix usage of check-reqs.eclass Adopt changes in new intel tarball
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * Removed no-herd from herd tag in metadata.xml
-  * media-gfx/librecad: version bumped to 1.0.0_rc4
-  * fixed typo
-  * Fixed usage of check_reqs.eclass
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-physics/root: switch to EAPI 4
-  * sci-physics/root: remove old versions
-  * sci-physics/root: update to 5.30.03
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-geosciences/tappy: Version bump.
-  * Bump do fit with embassy-6.4.0
-  * [sci-libs/atlas] Version bump
-  * Fix undefined symbols because of missing gslcblas lib during linking
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * media-gfx/librecad: Cleaned up old versions
-  * In main tree
-  * sci-physics/root: 5.28.00g update
-  * [dev-cpp/eigen] Version bump
-  * Added dep on >=sys-devel/libtool-2.4-r2
-  * Moved to autotools-utils.eclass in order to have correct .a/la file handling, #385865; added png15 patch
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Add png15 support and don't build static libs
-  * media-gfx/librecad: added boost to DEPS
-  * Use virtualx.eclass
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-physics/root: version bump to 5.30.02
-  * [sci-chemistry/gromacs] added 4.6 live version
-  * updated package.mask
-  * [app-admin/eselect] Version bump
-  * sci-physics/abinit bumped to 6.8.2.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * dev-python/pandas: Initial ebuild. Pandas is a data analysis toolkit. Bug report page is https://bugs.gentoo.org/show_bug.cgi?id=384583
-  * media-gfx/brlcad: included patch for 7.20.2, bug#378273
-  * Fix live ebuild
-  * Fix tests better
-  * Use Fedora hosting because unpstream removed the patches
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/sra_sdk-2.1.6: adjust to altered source tree strcuture, add weird ncbi/ subdirs to be installed, more comments in the ebuild
-  * sci-biology/sra_sdk-2.1.6: version bump
-  * media-gfx/librecad: fixed a missing file
-  * media-gfx/librecad: fixed manifests
-  * [sci-mathematics/scilab] install scilab mimetype
-  * Updated to new revision scheme
-  * Download tarballs with package revision
-  * Silent upstream bump
-  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci
-  * media-gfx/librecad: version bump to 1.0.0_rc3
-  * [sci-libs/scilab] Various fixes
-  * [sci-libs/openmm] version 2.0 is not supported by upstream anymore
-  * [sci-libs/xdrfile] removed it was never really stable
-  * [sci-libs/nfft] updated metadata
-  * [dev-tex/picins] not needed by gnuplot anymore
-  * [sys-cluster/nullmpi] updated metadata
-  * Add $(use_enable debug) on request from mgorny
-  * [dev-python/astlib] bump
-  * update pest manifest (changelog wasn't matching)
-  * sci-mathematics/pest - Version bump to 12.2.
-  * [sci-libs/pfft] version bump
-  * media-gfx/librecad: fixed manifests
-  * removed unneeded entries to blas-reference
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Version bump with new buildsystem
-  * [sci-chemistry/votca-csg] remove obsolete bash-completion_pkg_postinst
-  * [sci-chemistry/votca-csg] Migrate to the bash-completion-r1 eclass
-  * [sci-chemistry/gromacs] Migrate to the bash-completion-r1 eclass
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * moved to new release download link and version bump, documented that included JsonCPP is a modified version
-  * media-gfx/librecad: remove qt3support dependency
-  * update pest manifest
-  * Point to current HOMEPAGE
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * updated dependencies
-  * upgrade version
-  * [app-admin/eselect] Fix manifest
-  * prefix fix and number update
-  * updated eselect dependency
-  * bump
-  * bump
-  * bump
-  * Version bump.
-  * [sci-chemistry/votca-csg] updates
-  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci
-  * media-gfx/librecad: qt3support not needed anymore
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Initial commit
-  * [sci-libs/wannier90] Fix blas stuff
-  * sci-mathematics/htk: metadata cleanup
-  * sci-mathematics/htk: fixed license filenames
-  * sci-mathematics/htk: new package, #245595
-  * media-gfx/librecad: more cleanup for metadata
-  * media-gfx/librecad: updated metadata
-  * [sys-infiniband/librxe] Add sw driver for roce
-  * [sci-libs/fftw] in tree
-  * Moved to tree
-  * In the tree
-  * Version Bump
-  * Latest changes on HEAD
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Corrected doc installation, thanks James Cloos for the fix
-  * Version bump.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-chemistry/votca-csgapps] use default instead of tip
-  * [sci-chemistry/votca-csg-tutorials] use default instead of tip
-  * [app-doc/votca-csg-manual] use default instead of tip
-  * Cleaned up ebuild
-  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci
-  * media-gfx/librecad: ebuild cleanup for 1.0.0_rc2
-  * [app-doc/votca-csg-manual] fixed deps
-  * >sci-libs/blas-reference-20
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-chemistry/votca-csgapps] fixed a typo
-  * [sci-chemistry/votca-csg] changes due to 1.2.1 release
-  * sci-chemistry/votca-csg-apps -> sci-chemistry/votca-csgapps
-  * sci-chemistry/votca-csg-apps -> sci-chemistry/votca-csgapps
-  * sci-chemistry/votca-csg-apps -> sci-chemistry/votca-csgapps
-  * [virtual] Add ~amd64-linux keywords
-  * sci-physics/root: version bump
-  * [sci-visualization/paraview] Drop old, fix building with gcc-4.6, add missing dependency on PyQt4
-  * adding old blas to properly mask
-  * mask blas-reference from tree
-  * fix manifest
-  * added num library docs
-  * added virtuals
-  * added gsl
-  * added mpiblacs
-  * added xblas
-  * added cblas-reference
-  * added mkl
-  * added lapacke
-  * added acml
-  * added gotoblas2
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * In main tree
-  * updated package.mask
-  * [sci-libs/fftw] version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Keywork-mask eigen-9999.
-  * Added svn version for lapack-reference.
-  * Fix Manifest.
-  * Added blas-reference form bicatali overlay.
-  * Added lapack-reference from bicatali overlay.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Added eigen-3.0.1-r2.
-  * Added eigen-9999.
-  * media-gfx/librecad: ebuild cleanup for 9999 version
-  * media-gfx/brlcad: fixed building issue for 9999 svn live build
-  * Fixed patches
-  * Fix manifest
-  * fixed pkgconfig cflags
-  * correct pkgconfig in openblas
-  * Updated manifest for numbench.
-  * numbench now uses distutils.
-  * media-gfx/brlcad: removed cmake version for 7.20.2
-  * media-gfx/brlcad: removed cmake ebuild for 7.20.2
-  * sci-mathematics/acl2: fixed broken git merge
-  * sci-mathematics/acl2: fixed manifest
-  * sci-mathematics/acl2: updated metadata
-  * [dev-python/numscons] obsolete
-  * [sys-cluster/openmpi] redundant cd ${S} statement on line
-  * [dev-java/vecmath] Useless blank line on last line
-  * [dev-java/hdf-java] Trailing whitespace
-  * Remove unused local USE-description: 'xblas'
-  * fix metadata
-  * fix metadata
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Cleaned ebuilds
-  * media-gfx/brlcad: allow using of system tcl/tk
-  * [dev-lang/path64] Apply fix for bug #377111, use direct path for crt1.o
-  * Added sample configuration files to numbench.
-  * [sci-chemistry/votca-csg] renamed boost useflag
-  * [sci-libs/votca-tools] renamed boost useflag
-  * Updated numbench.
-  * [sys-cluster/openmpi] Add slurm support by Nicolas Bigaouette <nbigaouette@gmail.com>
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Update use.local.desc
-  * Fix categories
-  * [sys-cluster/open-mx] Add different mtu support
-  * [sys-cluster/open-mx] Add new version of open-mx
-  * Masked live builds, librecad and brlcad
-  * media-gfx/brlcad: fixed libpng-1.5, added version 9999 back
-  * media-gfx/brlcad: No need to include cmake in deps
-  * manifest
-  * adjusting boehm-gc source file
-  * [sci-visualization/gri] newer version in tree
-  * round of manifest
-  * [app-admin/eselect] Add prefix ~amd64-linux
-  * [sci-libs/atlas] Add prefix ~amd64-linux
-  * numbench depends on btl
-  * Added BTL.
-  * Restored atlas-3.8.4 from bicatali.
-  * Version bump atlas
-  * updating skel files
-  * manifest
-  * cleaning
-  * [sci-astronomy/weightwatcher] switch herd
-  * [sci-astronomy/stuff] switch herd
-  * [sci-astronomy/skymaker] switch herd
-  * [sci-astronomy/psfex] switch herd
-  * [sci-astronomy/missfits] switch herd
-  * [sci-astronomy/eye] switch herd
-  * [sci-astronomy/casacore] switch herd
-  * [dev-python/pysolar] switch herd
-  * [dev-python/cosmocalc] switch herd
-  * [dev-python/coords] switch herd
-  * [dev-python/astropysics] switch herd
-  * [dev-python/astlib] switch herd
-  * [dev-python/asciidata] switch herd
-  * Dependency to eselect updated.
-  * Added versioned openblas. Import from the bicatali overlay.
-  * Version bump. atlas imported from the bicatali overlay.
-  * alternatives-2 imported from bicatali and intel-sdp corrected
-  * eselect-1.2.16-r1 imported from the bicatali overlay
-  * autobench renamed to numbench to avoid conflicts.
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * [media-libs/OpenMOIV] Initial import per bug #239321
-  * Use rpath if prefix is enabled.
-  * Version bump, see bug 374859.
-  * Fix commiter information in the ChangeLog
-  * Version bump based on bug 374709.
-  * New package
-  * Revert "New package"
-  * New package
-  * Make sure portage does not run gbrowse_metadb_config.pl otherwise sandbox violation occurs when modifying /var/www/gbrowse2/databases/users.sqlite* file, maybe we could copy these during src_install to the {}, fix there and copy back to live filesystem? Improve error handling in gbrowse_metadb_config.pl. Fix symlink creation during install procedure.
-  * sci-biology/gbrowse: add missing brackets cause a perl error while exporting a PNG image
-  * sci-biology/gbrowse: fix typo in an ewarn() message
-  * sci-biology/gbrowse: fix typo in an ewarn() message
-  * sci-biology/gbrowse: added support for --destdir, patch sent to upstream
-  * sci-biology/go-db-perl to dev-perl/go-db-perl move
-  * sci-biology/go-db-perl to dev-perl/go-db-perl move
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * backbone of a new package, should probably use a lot of stuff from ncbi-tools++ ebuild
-  * msms: build with 3.x kernels.
-  * update Manifest checksums
-  * backbone of a new package, should probably use a lot of stuff from ncbi-tools++ ebuild
-  * some ebuild cleanup
-  * sci-biology/est2uni: pushing out more patches albeit ugly
-  * version bump but still need to rewrite upstream's install procedure to prevent 'mkdir /var/lib/gbrowse2' from happening
-  * dev-perl/Bio-DB-Das-Chado: new package required by sci-biology/gbrowse
-  * [sci-physics/fastjet] general QA
-  * sci-physics/fastjet: No need to enable plugins individually
-  * sci-physics/fastjet: Added maintainer
-  * sci-physics/fastjet: new package, #375575
-  * [dev-lang/path64] move snapshot to g-x86
-  * Add script for generating path64 snapshots
-  * Mask live version of path64
-  * Moved to tree
-  * [sci-chemistry/acpype] Initial import
-  * [dev-lang/path64] Fix SRC_URI for snapshot
-  * [dev-lang/path64] Add snapshot
-  * Also moved to tree
-  * [sci-chemistry/ambertools] Moved to tree =D
-  * [sci-chemistry/ambertools] Update patch
-  * [sci-chemistry/ambertools] Fix typo
-  * [sci-chemistry/ambertools] Updates for ambertools and gcc-4.6
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Add missing LDPATH to env file
-  * now in main tree
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Removed lpsolve, better version is in tree.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Fixed Manifest
-  * [dev-lang/path64] Add valgrind IUSE for debugging
-  * Move dev-lang/ekopath-bin to dev-lang/ekopath
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [dev-lang/path64] Unset all env vars that may cause trouble, prevent stripping source when build with Release, clean up
-  * Migrating gap-guava from s-o-g to sci: an example of gap package.
-  * Addd package.use.mask. Mask dev-lang/path64[assembler]
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [dev-lang/path64] Change lib -> get_libdir
-  * [dev-lang/path64] gcc:4.2 is no longer a strict dep
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [dev-lang/path64] Unset all fortran vars
-  * [dev-lang/path64] Fix fortran specific env handling
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [dev-lang/path64] Add env file
-  * [dev-lang/path64] Promote native to prefereed, add assembler flag (not working at the moment), remove needless dep on gcc for native
-  * Grap some fedora stuff, fix shadrers patch for current head
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [dev-lang/path64] Add fortran,openmp,debugger to IUSE
-  * [dev-lang/path64] Add native use flag for release build
-  * [dev-lang/path64] Initial import, only debug version (compiled with gcc) is working now
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-chemistry/gromacs] sync with tree
-  * [eclass] Moved cmake-utils.eclass to main tree
-  * [dev-util/cmake] Moved to main tree
-  * Improve variables names
-  * Improve variable names
-  * cmake should of course install all modules
-  * Actually make it possible to disable the module removal
-  * Fix missing bracket
-  * Move module removal into configure phase (otherwise it might never be called), no src_prepare again
-  * Same magic for LAPACK
-  * Same magic for LAPACK
-  * Add CMAKE_REMOVE_MODULES feature
-  * Copied eclass from main tree
-  * Patch FindBLAS to prefer PkgConfig over all tests, for the sci guys
-  * [sci-chemistry/votca-csg] Added IUSE=extras
-  * [sci-chemistry/votca-csg-apps] initial commit
-  * added sci-chemistry/votca-csg-apps to package.mask
-  * [sci-chemistry/votca-csg] Added IUSE=examples
-  * [sci-chemistry/votca-csg-tutorials] initial commit
-  * added votca-csg-tutorial to package.mask
-  * Install demos through USE=examples, #374187
-  * Adopt to unbundled ssm
-  * inCvs
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * libssm bump
-  * sci-geosciences/cdat-lite: Version bump.
-  * Updated SRC_URI
-  * Clean up - old version that I renamed, but git didn't delete.
-  * sci-geosciences/swmm: Version bump.
-  * sci-mathematics/mdp: Version bump and added all supported Python versions.
-  * Mmdb fix
-  * media-gfx/brlcad: Fixed a config time error when building
-  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci
-  * media-gfx/brlcad: Added back virtual/jre deps
-  * [dev-python/astropysics] Update dependencies, move to git repo
-  * media-gfx/brlcad: folder cleanup
-  * media-gfx/brlcad: Switch to cmake as supported by upstream
-  * [sys-cluster/open-mx] Update init.d
-  * [sys-cluster/open-mx] Update init.d
-  * [sys-cluster/open-mx] Update init.d
-  * [sys-cluster/open-mx] Update init.d
-  * [sys-cluster/open-mx] Initial import
-  * Update ocfs2
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * Update ocfs2
-  * app-benchmarks/autobench imported from proj/auto-numerical-bench.
-  * Autobench imported from proj/auto-numerical-bench
-  * media-gfx/brlcad: version bump to 7.20.2
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Moved to tree
-  * [sci-chemistry/icm] Version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Restored the MPI support in sci-libs/bigdft-1.2.0.2, broken by the introduction of the fortran-2.eclass.
-  * sci-biology/gbrowse-2.38: added URL to Bio::DB::Sam
-  * sci-biology/staden: Documented that we have to install somehow /usr/share/doc/staden/manual/gap4.index which is looked up when user accesses built-in help menu item
-  * sci-biology/gbrowse-2.38: Documented dependency on >=perl-gcpan/Text-ParseWords-3.27, documented requirement of Bio::Root::Version >= 1.0069
-  * Removed old version and fixed deps of live version
-  * Removing long old version of normaliz
-  * sci-mathematics/acl2: updated ChangeLog
-  * sci-mathematics/acl2: version bump to 4.3
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Version Bump
-  * sci-biology/mira-3.2.1.20: version bump
-  * Moved to tree
-  * Update gentoo defconfig
-  * Fix permissions
-  * Enable maui support
-  * Add maui with slurm and pbs integration
-  * [slurm] one more update to init.d
-  * Fix typo
-  * Update init.d
-  * Fix order
-  * Add init.d and conf.d files
-  * Fix cgroup location
-  * Also install sample config files
-  * Fix collisions with mpi implentations
-  * Enable pbs compatibility
-  * More cleaning
-  * use eapi4 feature
-  * s/contrib/contribs/
-  * Enable pam module
-  * Another typo with hwloc
-  * Another typo with pam
-  * Fix typo =D
-  * [sys-cluster/slurm] Initial import
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * formated skel-metadata.xml
-  * Metadata for sci-physics/elk added to appease repoman.
-  * New ebuild sci-physics/elk-1.3.15 added (a GPL-3 all-electron FP-LAPW code, used for example by sci-physics/abinit developers for comparison).
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Fix manifest
-  * Drop old OFED
-  * [sys-cluster/mvapich2] Update to eapi4
-  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci
-  * Moved to tree
-  * Keep old stuff here for some time
-  * media-gfx/librecad: QA cleanup
-  * [sys-infiniband/srptools] Fix ofed suffix
-  * [sys-infiniband/openib] add srp tools use
-  * [sys-infiniband/srptools] Add x86 keyword for srptools
-  * [sys-infiniband/perftest] Some docs doesnt exist
-  * [sys-infiniband/libmlx4] Tarball doesnt have changelog
-  * [sys-infiniband] Fix unapck logic
-  * [eclass] Fix unpack logic
-  * [eclass] add missing inherit
-  * [eclass] Update OFED eclass
-  * [eclass,profiles] Updates to ib stuff
-  * [sys-infiniband] Updates to infiniband stuff
-  * [sys-cluster/mvapich2] Move and version bump for mvapich2
-  * [virtual/mpi] Update virtual mpi
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [scilab-5.3.2] fixed xcos dependency
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci into guillaume
-  * [media-gfx/librecad]: upgraded to EAPI=4
-  * test
-  * [sys-cluster/ganglia_jobmonarch] Dont need to compile
-  * [sys-cluster/ganglia_jobmonarch] Drop unneded patch
-  * [sys-cluster/ganglia_jobmonarch] Import per bug #297587
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Yet another quick version bump, no improvement to the ebuild. Compiles well for me but has problems testing. The fault may be just in my openmpi installation but use with caution.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Imported changes from tree
-  * Restored the support for threaded fftw. Works for me. NEVER DISABLE FEATURES FOR OTHERS.
-  * [sci-mathematics/scilab] fix patch name wrt bug 237572#c218
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Version Bump
-  * [sci-chemistry/jmol] Fix manifest
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Cleanup
-  * Manifest
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Latest version.
-  * Version Bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Cleaned ebuild
-  * Cleaned ebuild
-  * Cleaned ebuild
-  * Cleaned ebuild
-  * migrate from 'git' to 'git-2'
-  * Cleaned ebuild
-  * Cleaned ebuild
-  * Cleaned ebuild
-  * Cleaned ebuild
-  * Cleaned ebuild
-  * Cleaned ebuild
-  * Version Bump
-  * Version Bump
-  * removed .#Manifest.1.21
-  * Cleaned ebuild, unused local USE-description
-  * migrate from 'git' to 'git-2'
-  * Fixed Malformed CVS Header on line: 3
-  * Fixed dep on openfoam
-  * no non-qt3 build available
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * migrate from 'git' to 'git-2'
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * migrate from 'git' to 'git-2'
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * Cleaned ebuild
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
-  * Cleaned ebuild
-  * Cleaned ebuild
-  * Cleaned ebuild
-  * mv 0.1-build.patch 110625-build.patch
-  * Cleaned ebuild
-  * Cleaned ebuild
-  * Cleaned ebuild, 'http://search.cpan.org/CPAN' found in thirdpartymirrors
-  * Cleaned ebuild
-  * Cleaned ebuild, 'http://search.cpan.org/CPAN' found in thirdpartymirrors
-  * Cleaned ebuild
-  * Cleaned ebuild,  no eauto* function called
-  * Cleaned ebuild, unused local USE-description: 'plplot'
-  * empty dir
-  * 'http://pypi.python.org/packages/source' found in thirdpartymirrors
-  * 'http://pypi.python.org/packages/source' found in thirdpartymirrors
-  * 'http://pypi.python.org/packages/source' found in thirdpartymirrors
-  * Dropped keywords because deps are missing
-  * Fixed malformat CVS line in header
-  * migrate from 'git' to 'git-2'
-  * migrate from 'git' to 'git-2'
-  * RDEPEND is not explicitly assigned -> fixed
-  * migrate from 'git' to 'git-2'
-  * RDEPEND is not explicitly assigned -> fixed
-  * RDEPEND is not explicitly assigned -> fixed
-  * RDEPEND is not explicitly assigned -> fixed
-  * RDEPEND is not explicitly assigned -> fixed
-  * RDEPEND is not explicitly assigned -> fixed
-  * RDEPEND is not explicitly assigned -> fixed
-  * Version Bump, cleaned old
-  * Version Bump, cleaned old
-  * Cleaned ebuild
-  * Cleaned repoman issues, don't know if ebuild is still working
-  * Cleaned ebuild and fixed LICENSE
-  * Cleaned ebuild and fixed LICENSE
-  * [sys-cluster/nullmpi] migrate to git-2
-  * Cleaned ebuild and add USE description to metadata.xml
-  * Cleaned ebuild and add USE description to metadata.xml
-  * Added local USE description
-  * [sci-chemistry/gromacs] migrate to git-2
-  * [sci-physics/espresso] migrate to git-2
-  * [app-doc/gromacs-manual] migrate to git-2
-  * Define EAPI after inherit
-  * Fixed herd entry in metadata.xml
-  * Fixed herd entry in metadata.xml
-  * Fixed herd entry in metadata.xml
-  * Fixed herd entry in metadata.xml
-  * Fixed herd entry in metadata.xml
-  * Fixed herd entry in metadata.xml
-  * Fixed herd entry in metadata.xml
-  * Fixed herd entry in metadata.xml
-  * Fixed herd entry in metadata.xml
-  * Fixed herd entry in metadata.xml
-  * Cleaned ebuild
-  * Some ebuild cleaning
-  * Some ebuild cleaning
-  * Some ebuild cleaning
-  * Some ebuild cleaning
-  * Some ebuild cleaning
-  * Moved to EAPI=4
-  * Manifest fix
-  * SOme ebuild cleaning
-  * Moved from 'git' to 'git-2'
-  * Corrected ChangeLog
-  * Corrected ChangeLog
-  * Corrected ChangeLog
-  * Cleaned ebuild
-  * Fixed Manifest and cleaned ebuild
-  * Shorten Summary
-  * Manifest fix
-  * Manifest fix
-  * Manifest fix
-  * Manifest fix
-  * Manifest fix
-  * Manifest fix
-  * Manifest fix
-  * Manifest fix
-  * Fix repoman warnings
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Mask sci-visualization/vtkPOFFReader as paraview-3.8 is masked
-  * QA on package.mask
-  * sources are dead
-  * Sources not available anymore
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Dropped ~ppc as many deps aren't keyworded
-  * Dropped ~ppc as many deps aren't keyworded
-  * removed uneeded entry
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * broken old version
-  * QA on why
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * mask sci-libs/pfft as fftw-3.3 is masked
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Fix CVS Header , remove LICENSE from installation
-  * Sort inherit and/or USE
-  * metadata.xml added
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * EAPI bump
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Version Bump
-  * Streamlined fortran-2 eclass usage
-  * Sort inherit and/or USE
-  * Streamlined fortran-2 eclass usage
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Streamlined fortran-2 eclass usage
-  * Sort inherit and/or USE
-  * Streamlined fortran-2 eclass usage
-  * Sort inherit and/or USE
-  * Streamlined fortran-2 eclass usage
-  * Streamlined fortran-2 eclass usage
-  * Sort inherit and/or USE
-  * Streamlined fortran-2 eclass usage
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Streamlined fortran-2 eclass usage
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Streamlined fortran-2 eclass usage
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Sort inherit and/or USE
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/mira: libtool.m4 fix so we can safely run eautoreconf and a version bump
-  * Streamlined fortran-2 eclass usage
-  * Streamlined fortran-2 eclass usage
-  * Streamlined fortran-2 eclass usage
-  * Streamlined fortran-2 eclass usage
-  * Streamlined fortran-2 eclass usage
-  * Streamlined fortran-2 eclass usage
-  * Streamlined fortran-2 eclass usage
-  * Streamlined fortran-2 eclass usage
-  * And one more
-  * One more fix
-  * Fix typo
-  * Update cluster patches to support XRC on mlx4 devices
-  * Add new cluster sources
-  * Update init.d
-  * Make use of external locking optional
-  * Update deps
-  * Update patches
-  * Update ocfs2
-  * Update ocfs2
-  * [infiniband] Add ib support for dhcp
-  * [sci-chemistry/gromacs] only USE=fkernels needs fortran
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Added fortran-2.eclass support
-  * Tweak the ebuild
-  * commit
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Added fortran-2.eclass support
-  * Moved to tree
-  * commit
-  * commit
-  * Added fortran-2.eclass support
-  * Make cvxopt use pkg-config to set BLAS/LAPACK, add glpk useflag description in metadata.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Final changes before move to the main tree.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-chemistry/gromacs] switch to cmake
-  * media-gfx/librecad: version bump to 1.0.0rc1
-  * Mikes suggestions
-  * Version BUmp, added missing die
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/scilab-5.3.2.ebuild: ebuild fixes
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci into guillaume
-  * new version of paraview (3.10.1)
-  * Last changes before review.
-  * fortran-2.eclass nearly finished for review.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Updated to current HEAD
-  * fortan-2.eclass in progress
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * move to pkg_pretend for EAPI=4
-  * [fortran-2.eclass] remove unnecessary quotes
-  * fix typos
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Fix pkg-config files, #369263
-  * [fortran-2.eclass] FCOPENMP -> FC_NEED_OPENMP
-  * [fortran-2.eclass] add pathscale compiler to get_fcomp, fix tabs
-  * Also export F90=$FC
-  * fortran-2.eclass, added mpif* cpabilities and get_fcomp function
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * fortran-2 some cosmetic changes
-  * [fortran-2.eclass] tc-has-fortran -> have-valid-fortran, remove some quotes, add checks for openmp support for other compilers
-  * [fortran-2.eclass] Fix openmp check to be F77 compliant
-  * fortran-2.eclass added
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * media-gfx/librecad: fix manifest
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-mathematics/scilab] version bump to 5.3.2
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge remote-tracking branch 'origin/master'
-  * [sci-mathematics/scilab] version bump
-  * sci-biology/sra_sdk-2.0.1: quote properly
-  * sci-biology/sra_sdk-2.0.1: fix install for amd64
-  * sci-biology/sra_sdk-2.0.1: a new package to access NCBI Short Read Archive
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * media-gfx/librecad: clean up unused files folder
-  * media-gfx/librecad: added tagged version
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [dev-java/jlatexmath-fop] Fix broken manifest
-  * [dev-java/jlatexmath-fop] version bump
-  * [dev-java/jlatexmath] version bump
-  * [dev-java/jlatexmath] version bump
-  * sci-visualization/v_sim: added maintainer email
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-visualization/v_sim: version bump to 3.6.0
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [dev-java/hdf-java] version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-chemistry/ambertools: Version bump to 1.5
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-chemistry/votca-csg] use default instead of tip
-  * [sci-libs/votca-tools] use default instead of tip
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/cadabra: version bump to 1.29
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-libs/votca-tools] added sqlite3 support
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Fix collision with dev-python/webpy, #368947
-  * Fixes for latest HEAD
-  * idb bump
-  * [sci-misc/boinc-bin] Remove obsolete package version.
-  * ipp bump
-  * ipp bump
-  * [sci-visualization/gnuplot] sync with tree
-  * [sci-visualization/gnuplot] 4.4.3-r1 InCVS
-  * [sci-chemistry/votca-csg] added boost use flag
-  * Version Bump
-  * Version Bump
-  * Version Bump
-  * Cleaned for current HEAD
-  * Sandbox fix
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * media-gfx/librecad: switch from svn to git
-  * sci-biology/mira: revbump to force inclusion on dev-util/google-perftools deps
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * xdsstat-bin: bump to latest.
-  * Version Bump
-  * Correct for double prfix
-  * Fix license dir to  /opt/intel/composerxe-2011.2.137/licenses/
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Add missing path to LDPATH, #367959
-  * fix intel-sdp.eclass for prefix
-  * sci-biology/mira-3.2.1.17-r1: maks the devel. version until it can be compiled (due autoreconf issues)
-  * sci-biology/mira-3.2.1-r1: added an extra patch for traceinfo off-by-one error
-  * sci-biology/consed-20-r1: improve message on die()
-  * sci-biology/consed-20-r1: improve message on die()
-  * moved ipp from my overlay
-  * move icc,idb,ifc from my overlay
-  * added casacore
-  * sci-mathematics/giac: QA fixes
-  * sci-mathematics/giac: fix manifest
-  * [sys-fs/zfs] Patch merged upstream
-  * [sys-fs/zfs] Update patch
-  * [sys-fs/zfs] Fix typo
-  * [sys-fs/zfs] Fix gentoo detection
-  * [sys-fs/zfs] Update to recent version
-  * [sys-devel/spl] Update to recent version
-  * sci-mathematics/giac: fix when no fltk
-  * sci-mathematics/giac: new ebuild
-  * sci-mathematics/frama-c: manifest for typo
-  * sci-mathematics/frama-c: fix ebuild typo
-  * sci-mathematics/why: version bump
-  * sci-mathematics/frama-c: version bump
-  * sci-mathematics/flocq: version bump
-  * sci-mathematics/apron: fix doc building
-  * dev-ml/ocamlgraph: version bump
-  * sci-physics/abinit: fixed configure error for fftw3
-  * sci-biology/gbrowse-2.26: fixed sanbox violation but webap-config bug pops up afterwards (happens later during install)
-  * sci-mathematics/gambit: deleted from old category sci-misc
-  * Correct fix for #293665
-  * Another quick version bump. Minor cleanup, smp removed until usable. Bizzare 6.6.2 ebuild mostly ignored, but not deleted until discussed. In the list?
-  * Version bump.
-  * Version bump.
-  * Version bump.
-  * Version bu,p
-  * Remove file with missing download.
-  * Version bump
-  * Remove old ebuilds since the sources have disappeared
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * manifest fix
-  * Manifest fix
-  * tiff -> tiff-compat
-  * Moved from media-libs/tiff to media-libs/tiff-compat
-  * Moved from media-libs/tiff to media-libs/tiff-compat
-  * [sci-visualization/gnuplot] sync with tree and bug #366129#c11
-  * [media-libs/tiff] Undo the bump (see bug #364181)
-  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci
-  * media-gfx/librecad: fix for gcc-4.6
-  * Version bump to avoid conflict with tree
-  * sci-biology/Gambit: BAM file viewer
-  * Re-enable some tests
-  * Enable debugging as recommended by upstream (#362655)
-  * disable parallel install
-  * add hppa keyword, fix herd
-  * Sync with main tree.   Add ~hppa, fix comments, fix #293665 fix.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/tablet-bin: added missing die call
-  * [sci-physics/phun] removed: unsupported software
-  * sci-biology/tablet-bin: version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * merging
-  * sci-biology/tablet-bin: removed references to my /scratch filesystem
-  * [sci-libs/spr] moved to main tree
-  * [dev-python/idlsave] included in scipy-0.9.0
-  * [dev-python/cosmolopy] now in main tree
-  * Version Bump, notified by euscan
-  * Version Bump, notified by euscan
-  * Version Bump, notified by euscan
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * small fixes for spl
-  * Small fixes for zfs
-  * Fix x11-libs/goocanvas SLOT
-  * Version bump. Use system hwloc. Switch to hydra instead of mpd for pm. Disable more tests as suggested by upstream. #362655.
-  * add ppc and ppc64
-  * Fix hardened test failure (#360185) and cleanup.
-  * [sci-chemistry/gromacs] sync with tree
-  * More zfs updates
-  * more zfs stuff
-  * updates to zfs
-  * [sys-fs/zfs] Add init.d from bug #365435
-  * media-gfx/librecad: initial port, #344791
-  * sci-biology/tablet-bin-1.11.02.18: fixed ebuild for the package and version bump
-  * Version BUmp
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Fix include path  for zfs and spl
-  * Fixed underlinking problems
-  * Cleaned old patches
-  * Fixed patches for current HEAD
-  * Version Bump, Minor corrects to fullfil repoman QA
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/consed-20-r1: added nLine.h patch from upstream to fix negative line numbers in phd files wrapped in phd.ball.1
-  * Make zfs install to / not to /usr
-  * sci-physics/abinit: Removed old versions
-  * Fix broken manifest
-  * [sci-physics/espresso] live ebuild update
-  * sci-physics/abinit: version bump to 6.6.2
-  * [sci-physics/espresso] live ebuild update
-  * [sci-physics/espresso] added live ebuild
-  * updated package.mask
-  * update for petsc-3.1_p8 from bug 53386
-  * [media-gfx/brlcad] Moved to tree, updated metadata
-  * [sys-cluster/scalasca] accept flags
-  * sci-libs/vtk moved to tree and unmasked.
-  * sci-mathematics/gambit: new category, moved from sci-misc
-  * [sys-cluster/scalasca] updated homepage
-  * Moved to tree
-  * Made ebuild tree ready
-  * sci-misc/gambit: Initial port. #47670
-  * media-gfx/brlcad: Added dev-tcltk/tkpng to RDEPEND, #363251
-  * [sys-fs/zfs] Initial import from sping overlay
-  * [sys-devel/spl] Initial import
-  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/acl2: have to build books in place
-  * Fix ups
-  * Version Bump
-  * Fix for python ABI stuff
-  * Fix for python ABI stuff
-  * Fix for python ABI stuff
-  * Fix for python ABI stuff
-  * Fix for python ABI stuff
-  * media-gfx/brlcad: version bump to 7.18.4
-  * sci-mathematics/acl2: fixed certificate dir
-  * Slightly streamlined ebuild
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Make working with py-2.7
-  * Added missing RDEPEND
-  * Fixed for latest upstream release
-  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/acl2: industrial strength theorem prover, #49316
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * Updated to latest upstream tarball, #363283
-  * sci-mathematics/cadabra: version bump to 1.28. Fixed dev-cpp/pangomm slot to 1.4
-  * [app-doc/gromacs-manual] updated
-  * [sci-chemistry/gromacs] remove 4.0.* (EOM)
-  * v_sim: version bump to 3.5.2
-  * Fix FFTW3 lib path on amd64. Need more work to get C/Fortran bindings
-  * version bump; bug #248372. Restrict netcdf deps to current stable in tree
-  * sci-geosciences/seawater: Version bump
-  * sci-geosciences/swmm: Correcting 'Manifest'
-  * sci-geosciences/pydap: Version bump.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Corrected Slot of fltk to 1
-  * Corrected Slot of fltk to 1, thanks Jan M. Simons noticing this
-  * [sys-cluster/scalasca] version bump
-  * Fixed typo in emboss.eclass
-  * Useless blank line on line: 13
-  * Fix to latest head
-  * Missing script dirs included
-  * Adding keywords for testing by wider audience.
-  * Last fix for 64bitness
-  * Corrected slot of fltk, #360641
-  * Move sci-chemistry/stdinchi to sci-libs/inchi
-  * Add updates for sci-chemistry/inchi
-  * sci-libs/inchi moved to tree
-  * sci-chemistry/openbabel* moved to tree
-  * Install into vendor dir
-  * Moved swig to DEPEND
-  * Do not in gzipped libs, thanks rei4dan noticing me
-  * sci-chemistry/stdinchi removed. Duplication
-  * openbabel-perl: Fix install in sandbox
-  * openbabel-python: Add Python3 iterator and wrap OBInternalCoord patches
-  * Semi broken perl support for openbael
-  * Cleaned ebuild
-  * keyworded for ~x86
-  * moved inchi from sci-chemistry to sci-libs
-  * Removed python again
-  * Cleaned ebuild
-  * Cleaned ebuild, moved from sci-chemistry to sci-libs
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Fix compile correctly against postgresql, #359959
-  * Remove libtool if it was installed by USE=vt, bug #359917.
-  * Make the USE=vt blockers conditional on being an unclasssed merge.
-  * mpi.eclass:  Improve handling of unclassed dep strings
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Last cleanup to emboss.eclass
-  * Remove commented RESTRICT
-  * Bump #349076
-  * Implicit decs fix, thanks bicatali for help
-  * added nco for testing
-  * bumped to dev-python/pyamg-2.0.0
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Updates from review
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * Fixed for reviewed eclass
-  * added petsc-3.1_p8 ebuild
-  * added hypre-2.7.0b
-  * [sci-chemistry/gromacs] Update ebuild for using pkg-config and blas
-  * [sci-physics/root] now in main tree
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Straighten ENV
-  * Fixed doc installation path
-  * Fix malformated Header
-  * Remove fortran.eclass
-  * Ignore fatal patch size
-  * Manifest fixed
-  * New emboss_src_install used
-  * Fixed Manifest
-  * Last writing corrections
-  * Naming of eclass changed
-  * Naming of eclass changed
-  * Naming of eclass changed
-  * Naming of eclass changed
-  * Naming of eclass changed
-  * Naming of eclass changed
-  * Naming of eclass changed
-  * Naming of eclass changed
-  * Naming of eclass changed
-  * Naming of eclass changed
-  * Naming of eclass changed
-  * Naming of eclass changed
-  * Naming of eclass changed
-  * renamed embassy-ng -> emboss.eclass
-  * Naming of eclass changed
-  * Naming of eclass changed
-  * Naming of eclass changed
-  * Naming of eclass changed
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [dev-python/cosmolopy]: bump
-  * Version bump.  Use system sys-app/hwloc.
-  * Moved media-libs/jpeg -> virtual/jpeg
-  * Moved media-libs/jpeg -> virtual/jpeg
-  * Moved media-libs/jpeg -> virtual/jpeg
-  * Moved media-libs/jpeg -> virtual/jpeg
-  * Moved media-libs/jpeg -> virtual/jpeg
-  * Moved media-libs/jpeg -> virtual/jpeg
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * dev-python/pythonocc: Manifest commit
-  * dev-python/pythonocc: restrict to opencascade-6.3 dependency
-  * EOV not needed to be set anymore
-  * EOV not needed to be set anymore
-  * EOV not needed to be set anymore
-  * sci-visualization/vtkPOFFReader: changed SRC_URI top ESVN_REPO_URI due to problems with md5sum's
-  * EOV not needed to be set anymore
-  * EOV not needed to be set anymore
-  * EOV not needed to be set anymore
-  * EOV not needed to be set anymore
-  * EOV not needed to be set anymore
-  * EOV not needed to be set anymore
-  * EOV not needed to be set anymore
-  * EOV not needed to be set anymore
-  * EOV not needed to be set anymore
-  * EOV not needed to be set anymore
-  * EOV not needed to be set anymore
-  * EOV not needed to be set anymore
-  * EOV not needed to be set anymore
-  * Ebov not needed to be set anymore
-  * Last cleanings before review
-  * Version Bump
-  * Rev bump, to ahead of the tree ebuild
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sys-cluster/scalasca] cleanup + url updates
-  * [app-doc/gromacs-manual] updated
-  * updated package.mask
-  * [app-doc/votca-manual] moved to votca-csg-manual
-  * [app-doc/votca-csg-manual] move + update
-  * [sci-chemistry/votca-csg] updated deps
-  * [app-doc/votca-manual] renamed to votca-csg-manual
-  * Unset DOCS as we do not have any
-  * embassy-ng.eclass respects DOCS
-  * Correct naming of patch
-  * Move away from embass-ng_src_install
-  * Move away from embass-ng_src_install
-  * Move to new embassy-ng.eclass
-  * embassy-ng.eclass progressing
-  * Move to new embassy-ng.eclass
-  * Move to new embassy-ng.eclass
-  * Move to new embassy-ng.eclass
-  * Move to new embassy-ng.eclass
-  * Move to new embassy-ng.eclass
-  * Move to new embassy-ng.eclass
-  * Move to new embassy-ng.eclass
-  * Move to new embassy-ng.eclass
-  * Move to new embassy-ng.eclass
-  * Move to new embassy-ng.eclass
-  * Move to new embassy-ng.eclass
-  * Move to new embassy-ng.eclass
-  * Move to new embassy-ng.eclass
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Move to new embassy-ng.eclass
-  * Version Bump, Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * Version Bump, Move to new embassy-ng.eclass
-  * Move to new embassy-ng.eclass
-  * Move to new embassy-ng.eclass
-  * Move to new embassy-ng.eclass
-  * Version Bump, Move to new embassy-ng.eclass
-  * Removed largefile from local USE description
-  * Move to new embassy-ng.eclass
-  * Version Bump, Move to new embassy-ng.eclass
-  * defualt for largefile support
-  * Emboss-6.3.1 imported from tree
-  * [sci-mathematics/octave-epstk] in the main tree
-  * sci-visualization/paraview: removed OFF patch as this is now an external plugin
-  * sci-visualization/vtkPOFFReader: New ebuild for bug 358077
-  * sci-libs/geom: New ebuild from bug 358061
-  * sci-libs/gmsh: Added sci-mathematics/petsc support
-  * [sci-libs/votca-tools] 1.1.1 InCVS
-  * [sci-chemistry/votca-csg] 1.1.1 InCVS
-  * [sci-chemistry/gromacs] added fixes from 4.5.3-r4
-  * [ambertools] apply upstream bugfixes
-  * Fix another typo with symlinks
-  * Fix another typo with symlinks
-  * Fix another typo
-  * [sci-chemistry/ambertools] Fix typo
-  * [sci-chemistry/ambertools] Fix issues with path
-  * A quick bump to sci-physics/abinit-6.6.1. Some cleanup, some mess. Switched from fftw2 to fftw3. OpenMP still broken.
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * QA things
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * QA STUFF
-  * Correct Slots for gtk 3 introduction to tree
-  * QA STUFF
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * QA things
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * Correct Slots for gtk 3 introduction to tree
-  * Fix typo
-  * [sci-chemistry/ambertools] now it should work
-  * [sci-chemistry/ambertools] Now it compiles =D
-  * More updates and fixes
-  * Initial import =) may not work
-  * sci-biology/staden-2.0.0_beta8: provide LDPATH=/usr/lib/staden through /etc/env.d/99staden to /etc/ld.so.conf
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/gap2caf-2.1.0: ebuild cleanup
-  * [sci-libs/armadillo] move to the main tree
-  * healpix not yet ready
-  * [sci-libs/spooles] in main tree
-  * [media-gfx/freecad] Moved to main portage tree
-  * [media-gfx/freecad] Added comment about nature of parallel make failures
-  * sci-biology/amos-short: new package
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/smalt-bin-0.5.1: version bump
-  * [media-gfx/freecad] Add -DBOOST_FILESYSTEM_VERSION=2 workaround for boost-1.45
-  * [media-gfx/freecad] Circumvent parallel make issues :(
-  * [media-gfx/freecad] Version bump; added required RESTRICT with comments; many cleanups and enhancements
-  * [media-gfx/freecad] pkgmove from sci-misc to media-gfx category
-  * [dev-python/pivy] Moved to main tree
-  * [sci-chemistry/votca-csg] switched to cmake
-  * [sci-libs/votca-tools] switched to cmake
-  * [sci-chemistry/votca-csg] version bump
-  * [sci-libs/votca-tools] version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Adding noarch ebuild - work in progress.
-  * Adding noarch ebuild - work in progress.
-  * os-mpi moved to tree as native-mpi
-  * [os-mpi] update os-mpi for prefix
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [mpi] Add os-mpi for prefix support
-  * Coot live fixes
-  * sci-biology/smalt-bin: an alternative to ssaha2 for even shorter reads
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/bambus: added goBambus.pl script and perl/python dependencies
-  * [sci-libs/opencascade] Moved to main tree.
-  * sci-biology/ssaha2-bin: new package, the GRL license text extracted from the saha2-manual.pdf seems kind of ... not like a real License text
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/ssaha2: new package, the GRL license text extracted from the saha2-manual.pdf seems kind of ... not like a real License text
-  * Add epatch_user back for gromacs live ebuilds
-  * sci-mathematics/frama-c: fix install doc
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Cleaned ChangeLog
-  * Version Bump
-  * Version Bump
-  * Live ebuild updated
-  * [sci-physics] Fix manifests
-  * [sci-electronics/tnt] Assigned to sci-electronics herd
-  * [sci-electronics/tnt] New application
-  * A supporting utility of sci-physics/abinit to convert the data generated by sci-physics/atompaw for the use with abinit
-  * A program to generate atomic data for the Projector Augmented Wave method of DFT calculations. Added to support sci-physics/abinit
-  * sci-biology/est2uni: current Manifest file
-  * sci-biology/est2uni: working EST annotation package
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/est2uni: env.d/ file
-  * [sci-visualization/gnuplot] updated deps
-  * sci-mathematics/frama-c: temporary retro-compatibility patch
-  * sci-mathematics/frama-c: keep previous version for now
-  * [sci-visualization/gnuplot] removed pdf use flag + bump to EAPI=3
-  * moved to g-x86
-  * moved to g-x86
-  * sci-biology/tgicl: make sure we call perl and not perl-5.15.2 directly
-  * [sci-chemistry/votca-csg] fixed a typo
-  * [app-doc/votca-manual] fixed install location
-  * [app-doc/votca-manual] initial commit
-  * updated package.mask
-  * [sci-chemistry/votca-csg] version bump
-  * [sci-libs/votca-tools] version bump
-  * [sci-chemistry/gromacs] 4.5.3-r3 InCVS
-  * sci-biology/OBO-Edit: added license file
-  * sci-biology/OBO-Edit: added license file
-  * sci-biology/est2uni: EST assembly+annotation: a perl-based analysis pipeline including php-based web interface
-  * sci-biology/picard-tools: Java-based command-line utilities manipulating SAM/BAM files with Java API (SAM-JDK)
-  * sci-biology/OBO-Edit: Java-based editor optimized for the OBO biological ontology file format
-  * sci-biology/swissknife: fixed Gentoo Copyright text
-  * sci-biology/swissknife: Perl library of modules to manipulate SwissProt flatfiles
-  * sci-biology/go-db-perl: Gene Ontology Database perl API
-  * sci-biology/ONTO-PERL: tools to manipulate OWL- and OBO-formatted files
-  * [sci-chemistry/gromacs] version bump
-  * sci-biology/tgicl: metadata checksum fix in Manifest
-  * sci-biology/clview: metadata checksum fix in Manifest
-  * sci-biology/zmsort: metadata checksum fix in Manifest
-  * sci-biology/nrcl: metadata checksum fix in Manifest
-  * sci-biology/cdbfasta: metadata checksum fix in Manifest
-  * sci-biology/tclust: metadata checksum fix in Manifest
-  * sci-biology/psx: metadata checksum fix in Manifest
-  * sci-biology/sclust: metadata checksum fix in Manifest
-  * sci-biology/seqclean: description line cleanup
-  * sci-mathematics/gappalib-coq: sci-mathematics/flocq added as a dependency
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/gappa: bogus manifest fixed
-  * sci-biology/lucy: a sequencing masking tool
-  * sci-biology/staden-2.0.0_beta8: new release
-  * [sci-chemistry/gromacs] fixes bug #339837
-  * sci-biology/estscan: added missing EAPI line
-  * sci-biology/: fixing 3 of my Manifest files
-  * sci-biology/align_to_scf: fix sed trickery
-  * sci-biology/estscan: added the license text
-  * sci-biology/tablet-bin: version bump
-  * sci-biology/estscan: new package, something wrong with IUSE?
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/jalview: version bump
-  * sci-mathematics/why: version bump
-  * sci-biology/gbrowse: version bump, more DEPS added, tiny webappconfig improvement
-  * sci-mathematics/frama-c: previous beta compatible why
-  * sci-mathematics/frama-c: clean-up
-  * sci-mathematics/frama-c: version bump
-  * dev-libs/simclist: version bump
-  * dev-ml/ocamlgraph: version bump
-  * sci-mathematics/gappalib-coq: version bump
-  * sci-mathematics/flocq: new package
-  * [sci-chemistry/votca-csg] version bump
-  * [sci-libs/votca-tools] version bump
-  * [sci-chemistry/gromacs] qa fixes
-  * sci-mathematics/gappa: version bump
-  * sci-mathematics/apron: doc generation for cxx fixed using dev-tex/rubber
-  * [sci-chemistry/votca-csg] 1.0.1 moved to the main tree
-  * [sci-libs/votca-tools] 1.0.1 moved to the main tree
-  * [sci-chemistry/votca-csg] version bump
-  * [sci-libs/votca-tools] version bump
-  * Moved sci-math/jags to main tree per bug 317741
-  * moved to g-x86
-  * sys-cluster/heartbeat moved to main tree
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Version Bump
-  * sys-cluster/keepalived and pacemaker-gui bumps
-  * A simple version bump. An unsolved problem with fortran flags when USE="+netcdf -mpi" circumvented. Minor changes to reports and logs when testing
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [ocfs2] another small update to make it works
-  * Update deps for ocfs2
-  * [ocfs2] add new ebuild
-  * mpi.eclass:  support EAPI 3 and 4.
-  * Bump EAPI thanks to scarabeus.
-  * Fix SRC_URI and general cleanup
-  * Bump, #349076.  Re-enable tests with mpi-threads.  Add prefix stuff.
-  * solve file collision in paraview
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Changes in vtk's handling of python-2.7
-  * Improvements to paraview-3.8.1
-  * Fix up ebuild per bug #344721. Thanks to Joel Berendzen.
-  * [sys-block/tgt] Moved to tree
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * housekeeping in vtk
-  * New addition, written by me
-  * USE mask sse in sci-chemistry/almost, works only on 32bit
-  * [sci-chemistry/votca-csg] added doxygen docu
-  * [sci-libs/votca-tools] added doxygen docu
-  * sci-biology/tablet-bin: updated ebuild
-  * sys-block/tgt version bump
-  * [sci-physics/espresso] updated homepage
-  * [sys-cluster/nullmpi] added live ebuild
-  * updated package.mask
-  * [sys-cluster/nullmpi] added support for shared libs
-  * [virtual/mpi] initial version with sys-cluster/nullmpi support
-  * [sci-chemistry/votca-csg] fixes build with =gromacs-9999
-  * [sci-chemistry/gromacs] added back gsl/xml useflag
-  * [sci-chemistry/gromacs] fixed some typos
-  * Added missing env stuff
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Manifest fix
-  * [sci-chemistry/gromacs] add back live manual
-  * Just a forgotten update of Manifest
-  * The typo of getFC corrected to . By Jérôme Borme <jerome.borme@gmail.com>
-  * The typo of getFC corrected to . By Jérôme Borme <jerome.borme@gmail.com>
-  * [sys-cluster/ceph] Moved to tree
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Added missing variable installation in revbump
-  * Fix tests
-  * sys-cluster/ceph-0.24.1 version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * The conditional use of several configure options tweaked to actually work even if a USE flag is unset. Reported by Jérôme Borme <jerome.borme@gmail.com>
-  * Fixing categories, #351818
-  * Corrected the sources location. Thanks to jerome.borme@laposte.net from bug 329429.
-  * [sci-chemistry/gromacs] qa fixes
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * A libxc ebuild for sci-physics/abinit
-  * A FoX ebuild for sci-physics/abinit
-  * An ETSF IO ebuild for sci-physics/abinit
-  * A bigDFT ebuild for sci-physics/abinit; not the latest version but the abinit compatible one.
-  * An ebuild for abinit-6.4.2 using external dependencies as proper Gentoo packages. Based on bug 249493, still work in progress. With USE="smp" compiles, but crashes.
-  * A wannier90 ebuild for sci-physics/abinit
-  * An ebuild for abinit-6.4.2 using external dependencies as proper Gentoo packages. Based on bug 249493, still work in progress. With USE="smp" compiles, but crashes.
-  * [sys-cluster/pacemaker] cib needs to build before pengine
-  * [sys-cluster/pacemaker] further fixes
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Also get rid of valpha.tar during installation
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Update manifest
-  * [sys-cluster/pacemaker] add bits missed in previous commit
-  * [sys-cluster/pacemaker] fix lib ordering wrt #351329. Thanks to Rafał Mużyło <galtgendo@o2.pl> for suggestion.
-  * [sys-cluster/pacemaker] fix autotools issues, patch send upstream
-  * [dev-vcs/mercurial-server] InCVS
-  * Unmask icm-3.7
-  * Correctly manage openmp and otehr linking
-  * sys-cluster/pacemaker dependency bump and LIBADD patch
-  * sys-cluster/pacemaker-gui bump
-  * sys-cluster/pacemaker-gui upstream revision bump
-  * Fix repoman warnings and missing manifest
-  * synchronize polybori with s-o-g overlay
-  * Remove singular - now in tree
-  * sci-libs/cgnsfoam: Version bump
-  * sci-libs/libcgnsoo: Version bump
-  * sci-visualization/paraview: Added 2nd python path
-  * sci-libs/gmsh: delete old version, added some USE-flags
-  * sci-libs:/cgnslib: delete old version, made hdf5 really apply again
-  * moved to g-x86
-  * more cleaning
-  * more removing
-  * removed badly committed files
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-chemistry/gromacs] suffix fix
-  * [sci-chemistry/gromacs] 9999 version uses cmake-utils eclass
-  * [sci-chemistry/votca-csg] does not build with gromacs-9999 anymore
-  * [sci-chemistry/gromacs] 4.5.9999 now uses autotools-utils eclass
-  * [sci-libs/lpsolve] fixed manifest
-  * [dev-python/pymvpa] added manifest
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/consed-20: new ebuild, see bugs #346801 (fixed), #351133 (fixed), #351152 (still affects amd64)
-  * scikits now in in main tree
-  * sci-biology/staden: again dropping arches from live ebuild ;-)
-  * sci-biology/staden: fixed my email address in metadata.xml
-  * mask root svn
-  * condor bump
-  * root fixes
-  * masked root svn
-  * ÿorick bump
-  * maxima gone in tree
-  * sci-biology/consed-bin: fixing a typo and '' expansion, see bug #312893
-  * sci-biology/consed-bin: resurrecting an ebuild for binary package, was bug #253451
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Some QA on ebuild style
-  * Moving www-apps/SwishE to www-apps/py-swish-e
-  * Moving www-apps/SwishE to www-apps/py-swish-e part II
-  * Moving www-apps/SwishE to www-apps/py-swish-e
-  * Some QA on ebuild style
-  * moved to g-x86
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Version Bump
-  * sci-biology/tablet-bin: added licence file
-  * sci-biology/tablet-bin: some QA fixes, still broken ebuild
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * fixed my email in affected metadata.xml files
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/align_to_scf: QA fix, changed pkgdescr and created a README file
-  * updated to latest petsc patchset
-  * Fix manifest and ebuild syntax
-  * Mask sci-biology/tablet-bin #348029
-  * sci-biology/roche454ace2caf: improved description and polished deps
-  * sci-biology/roche454ace2caf: added ksh dependency
-  * sci-biology/align_to_scf: tools needed by roche454ace2caf
-  * license file for align_to_scf, roche454ace2caf, sff_dump
-  * sci-biology/roche454ace2caf: convert ace files to gap4 (part of staden v1)
-  * sci-biology/align_to_scf: new package
-  * sci-biology/sff_dump: convert sff files into fasta/qual formats
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Added missing env
-  * [sys-cluster/keepalived] version bump
-  * [sys-cluster/corosync] version bump
-  * Version Bump
-  * Moved to main tree.
-  * Moved to tree.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Fix typo in metadata.xml
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * synchronize cvxopt with the sage-on-gentoo overlay
-  * Patch vtk for python-2.7
-  * Several fix for paraview, drop old.
-  * [sys-cluster/heartbeat] version 3.0.4 bump
-  * fix bug #348783 about libnet dep on sys-cluster/cluster-glue and sys-cluster/resource-agents
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/bamtools: two current ebuilds
-  * bamtools/bamtools-0.7.47: removed old version
-  * To main tree
-  * [sci-physics/root] bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Fix for fortran detection, thanks Arfrever pointing on it
-  * [sci-libs/exodusii] build shared libs, added test USE flag
-  * Fixing for current HEAD
-  * [dev-vcs/mercurial-server] version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-mathematics/dolfin] Initial import.
-  * moved to main tree
-  * [sci-chemistry/votca-csg] now using autotools-utils eclass
-  * [sci-libs/votca-csg] removed link to live ebuild
-  * [sci-libs/votca-tools] using autotools-utils eclass
-  * [sci-libs/votca-tools] removed link to live ebuild
-  * Fortran detection fixes
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/bamtools: new package
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * fortran.eclass fixes
-  * fortran.eclass fixes
-  * fortran.eclass fixes
-  * Correct handling of OpenMp support
-  * sci-biology/apollo: added dep on java vm
-  * Fix for fortran.eclass removal
-  * Removal of fortran.eclass, #348851
-  * Removal of fortran.eclass, #348851
-  * Removal of fortran.eclass, #348851
-  * Removal of fortran.eclass, #348851
-  * Removal of fortran.eclass, #348851
-  * Removal of fortran.eclass, #348851
-  * again
-  * Update mask
-  * Mask new icm
-  * Update ebuild
-  * fix typo
-  * Add new icm
-  * Make tiff sloted for binary compatibility
-  * [sci-libs/exodusii] Initial import.
-  * Update openmm stuff
-  * [dev-python/viper] Initial import.
-  * [dev-python/instant] Initial import.
-  * [dev-python/ffc] Initial import.
-  * [dev-python/fiat] Initial import.
-  * [dev-python/ufl] Initial import.
-  * Fix maniifest
-  * Some QA, src_configure not needed
-  * [sci-mathematics/armadillo] update license, make BLAS, LAPACK, Boost hard dependencies
-  * [sci-libs/gmsh] Manifest update
-  * [dev-python/pyamg] added ChangeLog, QA fixes
-  * [dev-python/meshpy] added ChangeLog, QA fixes
-  * [sci-mathematics/ufc] added ChangeLog, QA fixes
-  * [sci-libs/armadillo] added ChangeLog
-  * QA fixes
-  * [sci-libs/gmsh] bump to 2.5.0
-  * [sci-mathematics/ufc] Initial commit for UFC 1.4.2
-  * [dev-python/cvxopt] Initial commit for CVXOPT 1.1.3
-  * [sci-libs/armadillo] Initial commit for Armadillo 1.0.0
-  * [dev-python/meshpy]: Initial commit for MeshPy 0.91.2
-  * added ebuild for PyAMG 1.0.0
-  * [sys-cluster/scalasca] version bump
-  * [sys-cluster/cluster-glue] moved to gx86
-  * [sys-cluster/cluster-glue] 1.0.7 version bump
-  * sci-biology/wcd: sequence clustering tool
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/apollo: added java classes to inherit
-  * sci-biology/argo-bin: new package, current 1.0.31 bin-only version
-  * sci-biology/argo: new package, an old 1.0.24 src version
-  * sci-biology/apollo: dropped keywords from live ebuild
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/apollo: dropped actually the whole keywords line from the live ebuild
-  * sci-biology/apollo: dropped actually the whole keywords line from the live ebuild
-  * sci-biology/apollo: dropped keywords from the live ebuild
-  * sci-biology/apollo: new package
-  * update digest
-  * Remove keywords for live ebuild
-  * sci-biology/tgicl: updated package description
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/amos: live ebuild
-  * Moved to tree
-  * [sci-chemistry/gamessq] Moved to tree
-  * Move changelog
-  * Import dev-java/vecmath with history and remanifest
-  * Remove old. (Portage version: 2.2_rc48/svn/Linux x86_64)
-  * Add ~x86.
-  * bump to vecmath-1.5.1
-  * Create repo_name in java-overlay and get rid of Manifest1 digest files.
-  * Changes to overlays according to http://overlays.gentoo.org/proj/java/wiki/March_2007_Summary#Changesinoverlays.
-  * sci-biology/tgicl: einfo additions
-  * sci-biology/tgi-tools: dropped altogether, use tgicl and its deps instead
-  * sci-biology/tgicl: add quotes
-  * sci-biology/tgicl: TIGR tgicl clustering tools
-  * sci-biology/zmsort: TIGR tgi-tools package
-  * sci-biology/seqclean: TIGR tgi-tools package
-  * sci-biology/tclust: TIGR tgi-tools package
-  * sci-biology/sclust: TIGR tgi-tools package
-  * sci-biology/psx: TIGR tgi-tools package
-  * sci-biology/nrcl: TIGR tgi-tools package
-  * sci-biology/clview: an assembly .ace file viewer from TIGR Gene Indices project tools
-  * sci-biology/cdbfasta: part of TIGR tgi-tools
-  * sci-biology/cap3-bin: EST assembler (no sources ever available)
-  * sci-biology/jalview: version bump
-  * sci-biology/staden: removed unused patches
-  * sci-biology/staden: removed unused patches
-  * sci-biology/staden: live SVN and one for upcoming 2.0.0b8
-  * sci-biology/caftools-2.0.2: newer version but lacking manpages and caf_find_misassemblies
-  * sci-biology/caftools: added einfo() line
-  * sci-biology/caftools: new package, bug #259842
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/autoeditor: automatiucally correct basecalling errors using multiple sequence alignments of the Sanger-based reads
-  * sci-biology/bambus: assembly scaffolder
-  * sci-biology/tigr-foundation-libs: TIGR C++ files used by bambus and autoEditor
-  * Bumped in Cvs
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-chemistry/votca-csg] version bump + clean up
-  * [sci-libs/votca-tools] version bump + clean up
-  * depends on scikits
-  * depends on scikits
-  * depends on scikits
-  * depends on scikits
-  * depends on scikits
-  * bump learn
-  * added a common scikits package
-  * added jags
-  * [sci-libs/votca-tools] version bump
-  * [sci-chemistry/gabedit] fix Manifest wrt bug 347697
-  * [sci-chemistry/gabedit] Version bump to 2.3.3
-  * sci-visualization/paraview: fixed python path
-  * Fixes for python stuff
-  * New addition
-  * New addition
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Added missing deps on media-fonts/font-sun-misc and x11-apps/xset.
-  * removed stale doc useflag. Fix by Guillaume Horel in bug 301048.
-  * sci-visualization/paraview: added new OpenFOAM patch
-  * sci-libs/mesquite: Initial commit
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-biology/tigr-assembler: fix quoting issues (QA)
-  * sci-biology/tigr-assembler: respect CC from environment, provide run_TA script as a bourne-shell script and not in csh syntax, provide src_test()
-  * added ~amd64
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * dropped erroneous description line
-  * initial and working ebuild
-  * dropped erroneous description line
-  * Version bump and lots of ebuild improvements, it works for me now
-  * Version bump per bug #311857, added description and longdescription to metadata
-  * Update manifest
-  * [sci-chemistry/gromacs] Moved to tree
-  * use original hypre download link
-  * disabled libpetsc.so RPATH
-  * fixed metadata
-  * added petsc parmetis and hdf5 support
-  * fixed petsc hypre support
-  * reworked hypre ebuild
-  * [sci-chemistry/gromacs] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * sci-geosciences:pydap_responses_xls: Version bump and change in numbering.
-  * sci-geosciences/pydap_responses_wms: Version bump.
-  * sci-geosciences/pydap_responses_matlab: Version bump and normalization of version numbering for download.
-  * sci-geosciences/pydap_responses_kml: Version bump.
-  * Version bump.
-  * sci-geosciences/pydap: Version bump.
-  * [sys-cluster/pacameker] 1.0.10 moved to g-x86
-  * [sys-cluster/glusterfs] moved to g-x86 wrt #345427
-  * sci-geosciences/xtide: Version bump.
-  * sci-geosciences/libtcd: Version bump.
-  * sci-geosciences/harmonics-dwf-free-noncomm: Version bump.
-  * sci-geosciences/harmonics-dwf-free: Version bump.
-  * Revert "Sip patch from bgo", fixed upstream
-  * inCvs
-  * QA on quoting
-  * fperms sucks, because it could not handle wildcards
-  * Better goocanvas detection
-  * Added x11-libs/goocanvas as DEPS
-  * Reomove more ifles
-  * Force removal of files
-  * Synchonized with tree ebuild
-  * Fix DEP on x11-libs/guile-gtk
-  * Missing files are executable now
-  * remove nmrproc.com as well
-  * added missfits
-  * sci-astronomy/psfex: Initial import
-  * sci-astronomy/weightwatcher: Initial import
-  * added eye
-  * License and web site changes
-  * License and web site changes
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/pest: Fixed compilation of some of the utilities.
-  * sci-mathematics/pest: Version bump and minor changes.
-  * sci-visualization/ferret-bin: Version bump.
-  * [sys-cluster/glusterfs] better glusterd init script
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sys-cluster/pacemaker] version bump
-  * sci-chemistry/openbabel: Fix testing
-  * sci-chemistry/openbabel: Use system libinchi, add gui USE
-  * New package sci-chemistry/inchi
-  * try to add hypre support to petsc
-  * added hypre version 2.4
-  * removed useless python use flag
-  * added hypre package
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-chemistry/openbabel-python: Version bump to 2.3.0
-  * sci-chemistry/openbabel: Version bump
-  * Bump and cleanup.  Drop keywords until #345231 is fixed.
-  * Macaulay2 back in the main tree. Cleanup
-  * lrslib in main tree
-  * sci-libs/cdd+ moved to main tree
-  * sci-math/gfan in main tree
-  * sci-libs/mpir is in the main tree
-  * [dev-libs/asmjit] Initial import wrt bug 345183
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/Macualay2 bump to 1.4
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-math/topcom -> main tree
-  * virtual/jpeg for paraview
-  * virtual/jpeg for vtk
-  * cleanup for sci-math/singular (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * moved to main tree
-  * [sci-biology/quicktree] Respect CC,CFLAGS,LDFLAGS. Drop empty deps, add missing die. Fix SRC_URI wrt bug 344715. Thanks to Joel Berendzen <joelb@lanl.gov> for the report.
-  * [sci-biology/codonw] Respect CC,CFLAGS,LDFLAGS. Add missing die. Drop empty deps.
-  * [sci-biology/miranda] Version bump wrt bug 144316. Thanks to Joel Berendzen <joelb@lanl.gov> for the report. Drop old.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-misc/flashdot moved to the main tree
-  * deps updated, ebuild QA (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * sci-mathematics/frobby moved to the main tree
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * removed octave-forge.eclass
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * revbump the news item
-  * fixed octave-forge news item
-  * Prefix fix
-  * Install wrapper correctly, bin QA hacks
-  * added news item for octave-forge removal
-  * removed octave-forge packages. please use g-octave instead
-  * I think I got all libsingular headers sorted now. Even so, sage still doesn't seem to build (compilation stall)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-chemistry/gabedit] ebuild for new version 2.3.2 added
-  * libsingular headers are completely broken so more fix
-  * Fix broken libsingular headers
-  * -r1 drops libsingular, -r0 small fixes. (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sys-cluster/ceph] adding reference for bug submitted upstream
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Fix typo in singular-3.1.2
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [dev-python/numpydoc] Add ~x86, restrict python-3.*. Thanks to W. Trevor King <wking@drexel.edu> for the report.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sys-cluster/ceph] Version bump. Thanks to Marcin Mirosław <bug@mejor.pl> for the report. Drop old.
-  * Fix build with as-needed, simplify deps, add new use flags for debug and libatomic-ops, remove logrotate flag, don't build static libs, general cleanup. Drop old
-  * sci-math/polymake added to main tree
-  * sci-math/normaliz in main tree, old versions remain for Macaulay2 (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * sci-math/singular: bump to 3.1.2 (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * InCvs
-  * sci-mathematics/unuran: bump
-  * [sci-chemistry/gromacs] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * sci-mathematics/frama-c: remove no-longer-needed patch
-  * sci-libs/calculix-cgx: Version bump
-  * sci-libs/calculix-ccx: Version bump
-  * Readd patch accidentally deleted.
-  * Restore paraview-3.8.0 while problems with 3.8.1 are sorted out.
-  * adding missing patch (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * Added missing patch (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * New Addition
-  * Version bump to sfst-1.4, add library installation
-  * sci-misc/salome-* bumped to 5.1.4 ebuild by Michael Riss in bug 330303
-  * Moved sci-math/nauty and its license to main tree
-  * Fix installation of internal copies of 3rd party libraries.
-  * bump to paraview 3.8.1
-  * Package.masking vtk-5.6.1
-  * Import new vtk-5.6.1 in the overlay. package asked a there are no stable version.
-  * [sys-cluster/pacemaker-gui] proposed ebuild
-  * [sys-cluster/pacemaker] proposed version bump
-  * glusterfs bump to better handle glusterd and gluster CLI
-  * [sci-chemistry/gromacs] added natural vmd support (bug #340651#c8) (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-libs/dcmtk] Version bump
-  * Keyworded for ~-linux prefix
-  * Merge branch 'master' of ssh://bes.ibi.kfa-juelich.de/opt/scisoft64/data/sci
-  * openmp fix
-  * Added missing Manifest
-  * Added all files
-  * Merge ssh://bes.ibi.kfa-juelich.de/opt/scisoft64/data/sci into HEAD
-  * Real OPENMP fix
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * Sip patch from bgo
-  * InCvs
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-chemistry/molsketch] tiny changes regarding style of metadata.xml and ebuild - thanks to Justin Lecher (jlec) for giving a hint
-  * reworked passing configure options to petsc config script
-  * [sci-chemistry/molsketch] initial import of version 0.2.0; thanks a lot to Kacper Kowalik (Xarthisius) for direction to a proper ebuild.
-  * [sci-chemistry/gromacs] multilib fix (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-chemistry/gromacs] added vmd use flag (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * sci-mathematics/normaliz QA (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * Version Bump
-  * Cleanup and gcc44 patch added, thanks Joel Berendzen
-  * [sci-mathematics/singular] Added symlink needed by prefixed Sage (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
-  * 4ti2 moved to the main tree
-  * bumped to 0.5.2, ebuild by Andrzej Krentosz in bug 266249 (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * sci-mathematics/netgen: Removed old version
-  * sci-mathematics/netgen: Version bump
-  * sci-mathematics/frama-c: various EAPI3 cleanups
-  * sci-chemistry/gabedit: Version bump. Thanks to maxb <max-braeu@gmx.de>. Drop old.
-  * [sci-chemistry/gromacs] renamed manual distfile (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * sci-mathematics/singular: backport fix for bug 341357
-  * sci-mathematics/lrslib: QA fixes (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
-  * Fixing dependencies of sci-mathematics/Macaulay2 (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Initial import
-  * Updated ebuild for ceph
-  * sci-mathematics/rngstreams: Initial import
-  * sci-mathematics/prng: Initial import
-  * sci-physics/root: backport upstream patch to fix build with gmake-3.82
-  * [sci-chemistry/votca-csg] deps update (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-chemistry/gromacs] live ebuild updates (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-chemistry/gromacs] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-libs/openmm] export OPENMM_PLUGIN_DIR (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * added changelog
-  * sci-libs/amdlibm: AMD libm replacement
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-physics/root: root experimental
-  * Remove non-working doins in kayali
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * mering Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-mathematics/singular] Added ~x86-linux keyword and Prefix patch (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
-  * now in main tree
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Fixing boost dependency and moved to qt4-r2 eclass in paraview
-  * sci-math/Macaulay2-1.4 fixed SRC_URI and small updates
-  * added a proposal of agenda for the first sci-electronics meeting
-  * [sys-cluster/ceph] Add initscripts from bug #338008
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Removing package.mask for sci-mathematics/axiom. Bug 336789 resolved by bump and unkeywording
-  * Bump: sci-mathematics/axiom-201009
-  * Macaulay2-1.4_pre SVN from 1.4 branch
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * Another prefix fix
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/frama-c: fixes Manifest
-  * sci-mathematics/frama-c/frama-c-20100401.ebuild: EAPI3 typos
-  * Prefix Fixes
-  * nmrpipe update
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [app-doc/gromacs-manual]: fixed install location (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * coot openmp
-  * Version Bump
-  * Openmp linking patch
-  * Bump jgraphx to 1.4.1.2
-  * petsc-3.1-p5: appending fortran configure flags dependent on fortran use-flag
-  * fixed digest
-  * added petsc ebuild of latest patchset
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/frama-c: EAPI3 cleanups
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Update ceph. init scripts will come soon
-  * [sci-libs/openmm] initial commit (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-libs/openmm] masked
-  * updated use.local.desc
-  * [sci-chemistry/votca-csg] fixed bootstrap for live ebuild (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * ucsf license added
-  * New addition
-  * unio license added
-  * [dev-tex/revtex] Moved to main tree
-  * [dev-tex/natbib] Moved to main tree
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [sci-chemistry/votca-csg] added live ebuild (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-chemistry/votca-csg] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-libs/votca-tools] added live ebuild (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-libs/votca-tools] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * dev-python/numpydoc: Bump
-  * Initial upload of dev-java/jlatexmat-fop Ebuild by Dmitry S. Kulyabov in bug 301048
-  * dev-java/jlatexmath bump due to Dmitry S. Kulyabov in bug #301048
-  * pyglet now in main tree
-  * masked fftw-3.3_alpha1
-  * sci-mathematics/Macaulay2-9999: Upstream fixed a bug
-  * [app-portage/g-octave] moved g-octave-0.4.ebuild to the main tree
-  * [sci-chemistry/gromacs] version 4.5.1 now in tree (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [dev-tex/revtex] Corrected texmf installation directory (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-tex/natbib] Corrected TEXMF installation directory (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [pmask] Mask axiom-201005 temporarily because of bug 338762
-  * Bump
-  * sci-math/axiom: Deps adjusted per bug 336789
-  * sci-mathematics/Macaulay2-9999 with split lrslib
-  * New package: sci-libs/lrslib Corresponding bug: 338685
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * [sci-electronics/gspiceui] Moved to main tree.
-  * coot: Fix build error and MTZ-opening crash.
-  * [sci-chemistry/gromacs] updated manifest (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-electronics/klayout] Moving to tree
-  * sci-math/Macaulay2-9999 fixed
-  * [sci-electronics/magic] Prepare moving this back to the tree.
-  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
-  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
-  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
-  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
-  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
-  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
-  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
-  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
-  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
-  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
-  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
-  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
-  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
-  * Better and more complete fix for parallel make in singular
-  * sci-math/Macaulay2 live ebuild
-  * One more parallel make fix for singular. Hopefully the last one.
-  * [sci-misc/gcam] In main tree now.
-  * New package: sci-mathematics/nauty Corresponding bug 337810
-  * new license: 'nauty' for sci-math/nauty
-  * Deps of Macaulay2 adjusted.
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * Minor prefix corrections
-  * [sci-libs/clapack] Was bumped to tree by bicatali.
-  * [sci-libs/pfft] added --disable-la-files option (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * Remove lam-mpi.
-  * [dev-tex/natbib] Fixed description, made myself maintainer, and removed RESTRICT. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-libs/clapack] Switch to cmake-based build system. Create install target and cmake export file. Build and run tests conditionally. Use f2c symbol prefix. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * fix repoman warnings
-  * Disable support for gforker as it breaks debug builds and is being abandonded upstream, see http://trac.mcs.anl.gov/projects/mpich2/ticket/898.
-  * Due to pvfs2 upstream continuously lagging behind the kernel the useflag is being dropped.
-  * Fix for petsc and adding license
-  * New package: sci-mathematics/petsc Ebuild due to J. M. Gottfried Corresponding Bug: 53386  (Meeh... that's from 2004!)
-  * Respect LDFLAGS, #335590.  Fix metadata.
-  * Respect LDFLAGS #336969.
-  * merge Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * Some scripts are in the wrong place
-  * [sci-libs/fftw] added static-libs useflag (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-libs/pfft] added static-libs useflag (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-libs/nfft] initial commit (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-libs/pfft]: initial commit (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-libs/fftw] Added alpha version to test mpi interface (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [dev-tex/revtex] Upstream bumped the patch level without renaming the file... (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
-  * mpir version bump
-  * Local bump of sci-mathematics/axiom-201005
-  * Version Bump
-  * Moved to the tree. See bug #79082.
-  * [dev-vcs/mercurial-server] updated elog messages (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * sci-mathematics/normaliz bump to 2.5
-  * Add missing factory headers for libsingular.
-  * Imort all my fixes to singular from the sage-on-gentoo overlay.
-  * Import Christopher's version of factory migrated to the autotools-utils eclass from the sage-on-gentoo overlay.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Version Bump
-  * Fixed patch
-  * sci-geosciences/swmm: Version bump.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Version bump.
-  * sci-geosciences/pydap: Version bump.
-  * [sci-chemistry/gromacs] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * moved to the main tree
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * New package: sci-mathematics/Oid Ebuild due to Johannes Rauh
-  * [sci-libs/mpir] Migrate to autotools-utils.eclass (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
-  * [sci-mathematics/4ti2] Use autotools-utils.eclass (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
-  * Fixed SRC_URI
-  * Cleaned ebuild (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Version Bump, removed old (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Keyworded for *-linux prefix (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Version bump, fixed umfpack version to <=0.5.4, reported by Philippe BAUCOUR (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Version Bump (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-chemistry/gromacs] switch to live manual (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [app-doc/gromacs-manual] initial commit (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * updated package.mask
-  * Moved to tree, see bug #135573
-  * [sci-biology/clover] Trivial version bump. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * Version bump, drop non-existent betas
-  * Fixed lib/lib64 troubles properly in modglue (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
-  * [sci-chemistry/bist] Moved from sunrise to sci overlay. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-misc/gcam] Version bump. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * Keyword factory ~ppc - I have the hardware.
-  * Keyword cadabra ~amd64 (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
-  * Keyword lie ~amd64 (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
-  * Fix parallel make in modglue. (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
-  * Keyword modglue ~amd64 and apply a patch for it. (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
-  * MAke xcadabra respect FLAGS in cadabra. (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
-  * Put lie's help system under /usr/share. (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
-  * [sci-libs/m4ri] Version bump (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
-  * sci-geosciences/pydap: Version bump.
-  * sci-geosciences/pydap_responses_matlab: Version bump.
-  * Version bump.
-  * Bump cadabra to 1.25, drop old.
-  * Bump modglue to 1.16, now respect LDFLAGS. (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
-  * [dev-python/pywcs] version bump
-  * update HOMEPAGE of astrolib pkgs
-  * [sci-geosciences/qgis] sync with portage ebuild
-  * [sci-libs/fgsl] Initial import
-  * Fix last QA issues - hopefully that solved parallel make for good. (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
-  * sci-geosciences/pydap_handlers_csv: Version bump.
-  * Migrated lie to EAPI 3 and fixed various QA. (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
-  * [sci-mathematics/normaliz] Fixed SRC_URI (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
-  * [sci-chemistry/avogadro] drop patch
-  * [sci-chemistry/avogadro] Add live ebuild for avogadro
-  * Add epatch_user =)
-  * bumped matio
-  * sci-geosciences/pydap_responses_xls: Initial ebuild.
-  * sci-geosciences/pydap_responses_netcdf: Version bump and changed SRC_URI to use mirror://pypi.
-  * sci-geosciences/pydap_responses_wms: Initial ebuild.
-  * sci-geosciences/pydap_responses_matlab: Initial ebuild.
-  * sci-geosciences/pydap_responses_kml: Version bump, changed SRC_URI to use mirror://pypi.
-  * sci-geosciences/pydap_handlers_sql: Initial ebuild.
-  * sci-geosciences/pydap_handlers_netcdf: Version bump.
-  * Deleted file that should have been included in much earlier commit.
-  * Initial ebuild.
-  * sci-geosciences/pydap_handlers_nca: Version bump and change to SRC_URI to use pypi mirror.
-  * sci-geosciences/pydap_handlers_csv: Initial ebuild to serve (handle) CSV files the pydap server.
-  * sci-geosciences/pydap_handlers_cdms: Changed SRC_URI to use pypi mirror.
-  * sci-geosciences/pydap: Version bump.  Minor edits to RDEPEND.
-  * [sci-geo/qgis] remove 1.5.0. Moved to main tree.
-  * scikits_learn bump
-  * Fix python handling, thanks to jlec for noticing. (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix #313045, add missing libs during linking (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * cleanup (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * [app-portage/g-octave] Updated the live ebuild. Added the USE flag 'doc' (Portage version: 2.2_rc67/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [app-portage/g-octave] Version bump (Portage version: 2.2_rc67/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [dev-python/cosmolopy] Version bump
-  * [dev-python/cosmolopy] Initial import
-  * [sci-chemistry/gromacs] Version bump + new manual (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [dev-python/atpy] Version bump
-  * [app-portage/g-octave] Removed the PySVN dependency from the live ebuild (Portage version: 2.2_rc67/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sci-chemistry/gromacs] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * masked gromacs-4.5.9999
-  * Correct SRC_URI in paraview-3.8.0 (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
-  * [sci-physics/espresso] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * Keyworded for *-linux (Portage version: 2.2.00.15842-prefix/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
-  * sci-mathematics/singular: Cloning libsingular fixes from sage-overlay, thanks to kiwifb.
-  * [sci-chemistry/gromacs] doc fixes (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-physics/espresso] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-chemistry/gromacs] ffamber now officialy shipped with gromacs =)
-  * [dev-python/pysolar]: Initial import
-  * sci-mathematics/singular: Install missing headers, upstream tarball change.
-  * sci-mathematics/frobby: QA
-  * vo bumped
-  * [sci-geosciences/qgis-1.5.0] keyword unstable
-  * New package: sci-mathematics/cipi Bug: 329169
-  * [sci-geosciences/qgis] add new qgis-1.5.0 version. fix inherit in 9999
-  * added inference
-  * removed doc and examples flags
-  * removed doc and examples flags
-  * added idlsave
-  * sci-mathematics/singular: Bump to 3.1.1.4 and cleanup
-  * [dev-python/numpydoc]: Initial import
-  * InCvs
-  * InCVS
-  * added cosmocalc
-  * [sci-electronics/gspiceui] Version bump. Fix for wrong doc path and missing lib files if USE=examples (Portage version: 2.1.8.3/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sys-cluster/scalasca] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * initial import of astlib
-  * asciitable added
-  * Keywording g-cran-9999.ebuild
-  * Fix manifest for g-cran
-  * [app-portage/g-octave] Live ebuild updated. Already works with py3k. (Portage version: 2.2_rc67/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-mathematics/gfan: Imported updated ebuild from sage overlay
-  * sci-mathematics/singular: libdir for amd64
-  * runtime text relocations preliminary fix, soname added to libsingular
-  * [package.mask] removed app-portage/g-octave-0.2.1
-  * [app-portage/g-octave] Version bump (Portage version: 2.2_rc67/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-mathematics/singular-3.1.1.3 revbump and QA
-  * [sci-astronomy/stuff]: Fixed typo in HOMEPAGE
-  * [sci-astronomy/kapteyn]: Moved to gentoo-x86
-  * [dev-java/jeuclid-core,sci-biology/jalview] Removed pmask for packages with dependencies in the java overlay. For now.
-  * Version bump. Fixes only bug wrt buffer overflow on long filenames. (Portage version: 2.1.8.3/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Merge branch 'singular'
-  * sci-math/singular: Experimental support for libsingular
-  * [sci-libs/omalloc]: Make shared libs, fix tests, fix install paths
-  * Macaulay2-1.3.1-r4: Various QA, static libfac/factory, respect CFLAGS, optimization USE-Flag
-  * [sci-libs/cgnslib] Made the hdf5 patches apply again. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * In tree
-  * Imported to tree
-  * [sci-visualization/nodemon] Silenced repoman. FIXME: it looks like the pbs switch is not implemented properly. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-visualization/paraview] Silenced repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-mathematics/gfan]: Respect CXX, LDFLAGS, fix build with GCC-4.5
-  * [sci-libs/factory]: fix as-needed issue and parallel build
-  * [sci-mathematics/why] Silenced repoman; dropped ~sparc since dependencies cannot be fulfilled. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-mathematics/frama-c] Dropped ~sparc since dependencies cannot be fulfilled. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-libs/cgnslib] Removed hdf5 functionality in ...3 since the required library versions are not available anymore. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-java/jeuclid-core] Masked for removal since dependencies cannot be fulfilled
-  * [package.mask] Mask sci-biology/jalview for removal
-  * [sci-biology/jalview] Masked for removal (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sys-infiniband/libnes] Silenced repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sys-infiniband/libmlx4] Silenced repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sys-infiniband/libibvpp] Silenced repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sys-infiniband/libibcm] Silenced repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sys-infiniband/openib-srptools] Silenced repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-chemistry/procheck] Silence repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-chemistry/phaser] Silence repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-chemistry/openbabel-ruby] Silence repoman. Drop openbabel-ruby-2.2.0 since dependencies cannot be fulfilled anymore. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-chemistry/openbabel-python] Silence repoman. Drop openbabel-python-2.2.0 since dependencies cannot be fulfilled anymore. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-chemistry/openbabel-perl] Silence repoman. Drop openbabel-perl-2.2.0 since dependencies cannot be fulfilled anymore. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-chemistry/jligand] Silence repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * Fixed handling of long path and filenames (Portage version: 2.1.8.3/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sci-libs/factory]: remove old
-  * [sci-libs/factory]: Make shared libs, fix install paths, QA
-  * [sys-infiniband/libibmad] Shortened description. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sys-cluster/ceph] Shortened description (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-mathematics/octave-forge-communications] Silence repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-mathematics/octave-forge-splines] Added metadata.xml (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-mathematics/octave-forge-octgpr] Added metadata.xml (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * Bump mpir to version 2.1.1.
-  * Import an enhanced vtk-5.6.0 with support for database and ffmpeg.
-  * Import gl2ps with automagic dependencies fix.
-  * [sci-chemistry/gromacs] fix for bug #301854 (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * sci-mathematics/why: Version bump
-  * sci-mathematics/frama-c: Version bump
-  * dev-ml/ocamlgraph: some RDEPEND clean-ups
-  * sci-mathematics/*: some ChangeLog clean-ups
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * trivial fixes, keyword x86
-  * sci-mathematics/singular: Even better readline support and QA
-  * sci-mathematics/singular: readline support fixed
-  * [sci-geosciences/qgis-9999] add live ebuild to test version 1.5 (to be released soon)
-  * Bump sci-libs/libfac-3.1.1
-  * Bump sci-libs/factory-3.1.1
-  * dev-ml/ocamlgraph: depend fixes
-  * [sys-infiniband/openib-drivers]: no /sbin/lsmod symlink for >sys-apps/module-init-tools-3.6
-  * [app-portage/g-octave] masked version 0.2.1, due to broken SRC_URI
-  * [app-portage/g-octave] live ebuild now using the git repository (Portage version: 2.2_rc67/git/Linux i686)  (Signed Manifest commit)
-  * [sci-libs/omalloc]: Cleanup
-  * new package: sci-libs/omalloc
-  * [sci-chemistry/gromacs]: fortran fix (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [dev-tex/revtex] Needs a newer natbib than in texlive 2009... (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-tex/natbib] Added RESTRICT=primaryuri (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-tex/natbib] New package, updated natbib version required by revtex-4.1 (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-chemistry/gromacs] Fixes for Bug #326331 (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [dev-tex/revtex] Version bump to enforce reinstallation (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-tex/revtex] Added installation of the required rtx files (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-misc/finomaton] ChangeLog update
-  * [sci-misc/finomaton] Silence repoman; fix metapost dependency (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-misc/nltk] Silence repoman; drop ~amd64 since dependencies cannot be fulfilled. No keywords left. :( (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-misc/stanford-tagger] Silence repoman (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-misc/stanford-parser] Silence repoman (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-mathematics/ltl2ba] Silence repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [licenses] Added CeCILL-2.0 as referenced by sci-mathematics/gappa
-  * [sci-mathematics/gappa] Silence repoman; improve license description; move doc generation dependencies to RDEPEND (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-mathematics/apron] Silence repoman; drop ~sparc since dependencies cannot be fulfilled; move doc generation dependencies to RDEPEND (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * dev-ml/ocamlgraph: version bump 1.5
-  * Local bump of sci-math/singular
-  * sci-mathematics/pff: QA fixes
-  * sci-mathematics/gappalib-coq: Version bump 0.13
-  * sci-mathematics/gappa: Version bump 0.13.0
-  * sci-mathematics/gappalib-coq: QA fixes
-  * sci-mathematics/gappa: QA fixes
-  * sci-mathematics/apron: building process fixed for the latest sources
-  * Added longdescription to metadata.xml (Portage version: 2.1.8.3/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Initial ebuild (see bug #316807) (Portage version: 2.1.8.3/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Dropped Lucas from maintainership on his request. Taking it over (Portage version: 2.1.8.3/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Dropped Lucas from maintainership on his request (Portage version: 2.1.8.3/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sci-chemistry/gamessq] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [licenses] Added missing license of sci-physics/phun
-  * [sci-electronics/gsmc] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-python/numexpr]: Moved to gentoo-x86
-  * [dev-python/pytables]: Moved to gentoo-x86
-  * [dev-python/numexpr]: Cleanup. Thanks to Arfrever
-  * [dev-python/pytables]: Cleanup. Thanks to Arfrever
-  * [dev-python/pytables]: Tests fail only with hdf5[debug]. Removing patch.
-  * sci-mathematics/apron: QA fixes
-  * dev-ml/mlgmpid: mpfr-3.0.0 compatibility
-  * Remove debug code (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Update python handling (#316937). Cleanup deps. Automatically turn on threads if mpi-threads are requested. (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * [app-portage/g-octave] Version bump with cleanup (Portage version: 2.2_rc67/git/Linux i686)  (Signed Manifest commit)
-  * [sci-electronics/magic] Make it use LDFLAGS, improve tutorial file location (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * dev-libs/simclist: simclist-1.4.4_rc3 version bump
-  * dev-libs/libanomaly dropped
-  * [dev-python/pytables]: Version bump
-  * [app-portage/g-octave] Version bump and cleanup. (Portage version: 2.2_rc67/git/Linux i686)  (Signed Manifest commit)
-  * Updated the app-portage/g-octave live ebuild (Portage version: 2.2_rc67/git/Linux i686)  (Signed Manifest commit)
-  * [sci-electronics/magic] Version bump with cleanups, also fixing bug 299476 (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-electronics/magic] Cleanup: removed versions without keywords. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-electronics/magic] Copied from main tree
-  * New ebuild for sci-electronics/xnec2c. Based on the work of Dominique Michel <dominique.michel@vtxnet.ch> in bug #138770
-  * [sci-visualization/v_sim] New application, see bug 109547. Ebuild submitted by Jérôme Borme.
-  * added myself to docs/proj/index.html
-  * Fix manifest
-  * Adding self to docs/proj/index.xml
-  * Adding myself to project page
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Version bump
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [docs/index.xml] Added myself.
-  * Added myself to docs/proj/index.xml
-  * added app-portage/g-octave-0.2_rc1. URL fixes (Portage version: 2.2_rc67/git/Linux i686)  (Signed Manifest commit)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * added app-portage/g-octave (Portage version: 2.2_rc67/git/Linux i686)  (Signed Manifest commit)
-  * octave-forge-image bump
-  * Version Bump, EAPI bump, drop patch included upstream (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * cleanup (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Moving g-cran from sys-apps to app-portage
-  * Remove empty lines (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Remove empty lines (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * removed old (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * removed old (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * removed old (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * removed old (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes, implicit declaration fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Borken with current stuff (numpy, etc)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Clean ancient version (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * gone
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Import a version of maxima-5.20.1 that solve bug #255673
-  * sci-libs/calculix-cgx: Version bump
-  * sci-libs/calculix-ccx: Version bump
-  * [sci-chemistry/gromacs]: added missing patch (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * removed gentoo_prefix again
-  * renamed patch (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Added prefix to masters
-  * Version BUmp (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes and fixes for implicit declarations (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes II (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * No support for current stuf like py >2.5 and numpy
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Removed old (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Respecting LDFLAGS (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Version Bump, Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * InCvs
-  * [licenses] Added tmhmm license as referenced in sci-biology/tmhmm
-  * [sci-biology/twinscan] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-biology/tmhmm] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-biology/tgi-tools] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-biology/signalp] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-biology/samtools] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [package.mask] Mask sci-biology/newbler for removal (no download source)
-  * [sci-biology/mrbayes] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * Update manifests
-  * Add prefix support and drop old versions
-  * Add development ebuild for G-CRAN
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix PYTHON ABI Stuff (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix PYTHON ABI Stuff (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix PYTHON ABI Stuff (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Another little fix (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix PYTHON ABI Stuff (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix PYTHON ABI Stuff (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * email changed
-  * Fixed octave dep, #285236 (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fixed my mail in metadata.xml (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fixed my mail in metadata.xml (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-libs/xdrfile] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-libs/symmetrica] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-libs/oasa] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-libs/msms] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-libs/med] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * Revert "[sci-libs/factory] QA fixes, removed useflag singular which had no effect" because of side effects
-  * [sci-libs/gmsh] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-libs/factory] QA fixes, removed useflag singular which had no effect (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-libs/csrosetta-pdbh] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-libs/csrosetta-cs] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-libs/csrosetta-angless] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-libs/cddlib] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-libs/calculix-cgx] QA fixes: ghostscript dependency, built_with_use replaced (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-libs/calculix-ccx] QA fixes: ghostscript dependency (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sys-cluster/ceph] Version bump
-  * [sci-chemistry/gromacs] fixed prefix (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * [sci-biology/cluster] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-biology/clover] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [net-misc/bbscp] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [net-ftp/bbftp-server] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [net-ftp/bbftp-client] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-tex/picins] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [licenses] Added AURA license as referenced in dev-python/pywcs
-  * [dev-python/omniorbpy] QA fixes: removed ~ia64 keyword, bad dependencies (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-python/ffnet] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-ml/mlgmpidl] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-libs/simclist] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-libs/libunzip] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [package.mask] Mask dev-lang/aldor for removal (no sources available anymore)
-  * [dev-cpp/growler-thread] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-cpp/growler-math] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-cpp/growler-link] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-cpp/growler-core] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-cpp/growler-arch] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [app-vim/freefem++-syntax] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [app-text/dgs] Added note: upstream is dead (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [app-text/dgs] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-chemistry/rosetta] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-cpp/growler] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-mathematics/frama-c] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-ml/ocamlgraph] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-libs/simclist] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [dev-libs/libanomaly] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-misc/jwnl] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-mathematics/lattE-macchiato] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/gromacs: added stable patch + prefix (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * condor: more config fixes
-  * fixed sed line
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * condor: more initd fixes, now local config will reside in /var/lib
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * [dev-perl] Imported packages Lab::VISA, Lab::Instrument, and Lab::Tools (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [perl-core/encoding-warnings] Imported package. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-libs/ni-visa] Added dummy ebuild...
-  * sys-infiniband/librdmacm: adding pc file
-  * sys-infiniband/libibverbs: adding pc file
-  * Imported changes from tree (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Upstream already included this patch (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fixed my mail in metadata.xml (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fixed my mail in metadata.xml (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fixed my mail in metadata.xml (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fixed my mail in metadata.xml (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fixed my mail in metadata.xml (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * changed my mail adress
-  * Fixed metadata (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * remanifesting
-  * condor version bump
-  * Trying a fix for paraview-3.8.0 with mpi.
-  * Undelete Jmol
-  * InCvs
-  * Added missing dep on dev-libs/popt (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fixing compilation with gcc4, repecting CXXFLAGS/LDFLAGS, reMANIFEST (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Rename 1.4.1 as 1.4.1-r1 so users can easily get stable version from main tree. (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * dev-python/pytables: Adding dropped ~x86 keyword
-  * dev-python/numexpr: add ~x86 and src_test
-  * Bump to EAPI=2, temporarily drop ~ppc, ~x86
-  * dev-python/pytables: adding last rc for testing
-  * Adding support for multiple python abis
-  * Need qt4 ruby bindings which aren't available
-  * [dev-tex/revtex] New package (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix for compilation with gcc4.4, #271017 (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * InCvs as sci-libs/punc
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * dev-java/jgrapx is not available
-  * InCvs
-  * InCvs
-  * InCvs
-  * removed masks
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * inCvs
-  * [sci-misc/gcam] Moved from sunrise to sci overlay. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
-  * inCvs
-  * Version Bump, Prefixify, keyworeded for ~-linux (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * modeller bump
-  * [sci-electronics/gspiceui] Imported from sunrise. (Portage version: 2.1.8.3/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sci-electronics/klayout] Fixed manifest. (See bug 321871...)
-  * [sci-electronics/klayout] Trivial version bump. Still needs proper rubyfication.
-  * [sci-electronics/klayout] Imported from sunrise.
-  * classads bump
-  * [sci-geosciences/grass] remove the grass version. better one available in portage now
-  * dev-tex/atexmk-416a now in portage
-  * Importing new version of paraview in the overlay for testing
-  * Fixes for envs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * added missing envs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fixed patch (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * nrpie patch fixed
-  * Version Bump (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-biology/foldingathome] move files (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-biology/foldingathome] Version bump (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * dev-ml/ocamlgsl now in portage
-  * Fixing SRC_URI wrt to bug 322383
-  * dev-tex/latexmk: version bump + bash completion (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
-  * removed gasgano, cpl, esorex, now in main tree
-  * remove old
-  * remove old
-  * octave-forge-optim bump
-  * qcl fixes for gcc and deps
-  * coot missing link lib patch
-  * sci-mathematics/mdp: fixed manifest
-  * sci-mathematics/mdp: Version bump to 2.6
-  * Fixed HOMEPAGE (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * mpir revbump and clean.
-  * sci-libs/cgnstools: Fixed gcc-4.4 compile problems
-  * InCvs
-  * coot updated to fit with current head (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * in tree
-  * libf2c removed agauibn
-  * HEAD fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Added pysparse
-  * libf2c added temporarly
-  * New Addition (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * New package, ebuild written by me
-  * [sys-cluster/ceph] Version bump (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * inherit prefix (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * keyword ~amd64-linux ~x86-linux (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Fixing procheck (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Version bump, now using a patch from the Fedora project to honor FHS.
-  * dev-python/astropysics: Adding proper
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * InCvs
-  * fixing ChangeLog
-  * dev-python/astropysics: initial import wrt bug 317655
-  * dev-python/vo: Skipping failing tests, fixing assertions.
-  * dev-python/vo: removing docs, updating deps and Python style
-  * dev-python/pywcs-1.8.1: updating dependencies and Python style
-  * New package, ebuild written by me
-  * sci-astronomy/kapteyn: vesion bump
-  * renamed patch (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * dev-python/coords: initial import wrt bug #317365
-  * dev-python/pywcs-1.8.1: version bump
-  * sci-geosciences/pydap*: Updated to latest python ebuild standards.
-  * sci-geosciences/cdat-lite: Updated to latest style for Python ebuilds.
-  * dev-python/coards: Updated to latest style for Python ebuilds.
-  * dev-python/numexpr: Updated to latest style for Python ebuilds.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * version Bump (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Corrected Manifest file
-  * Initial commit for bug 315801
-  * sci-mathematics/polymake bump
-  * [sys-cluster/ceph] Version bump (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Manifest fixed (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-visualization/ferret-bin: Version bump
-  * sci-libs/gmsh-9999: added sci-libs/taucs support
-  * Imported from tree (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-misc/salome-*: changed fetch URL + cleaning (thanks Oliver), new patch + modifs to (partially) solve med_int issues on amd64
-  * Importet tree changes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Changed DEPEND of media-libs/SoQt from 1.4.2_alpha4181 to 1.4.2_alpha1841 (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Update and clean cadabra.
-  * Added scikits_statsmodels
-  * Added scikits_image
-  * Added scikits_learn
-  * Added test suite
-  * Added scikits_optimization
-  * Now really installing docs
-  * Cleanup, added x86
-  * sys-cluster/nullmpi: initial commit (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * sys-cluster/scalasca: version bump (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * sci-physics/espresso: fixed a typo (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * Remanifesting
-  * sci-physics/espresso: version bump (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * bump
-  * new: dev-libs/simclist
-  * app-admin/syscall_anomaly dropped
-  * [sys-cluster] Add ceph - distributed petascale fs
-  * Corrected removing of valpha tarball (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * Corrected behaviour in EAPI>1 (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * removed old prefix support behaviour (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-misc/salome-*: make egencache work again
-  * sci-chemistry/votca-csg: added dev use flag (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/votca-tools: added dev use flag (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/votca-csg: update (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/votca-tools: update (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * sci-visualization/gnuplot: Sync with tree and clean up (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * [sci-chemistry/votca-csg] Fix small typo (Portage version: 2.2_rc65/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-chemistry/votca-csg: gcc-4.4 fix (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/votca-csg: added support for gromacs double-precision (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * New version with additional USE-flag source
-  * Fixing final QA issue on sci-mathematics/Macaulay2
-  * QA for sci-mathematics/Macaulay2
-  * sci-chemistry/votca-csg: version bump (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/votca-tools: version bump (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * New upstream version, cleanup new ebuild
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Added examples USE-flag; replaced all installation paths with variable
-  * sci-mathematics/topcom overhaul and ~amd64
-  * updated 6.3 to eapi=2 and make repoman happy; removed old
-  * libfac URI updated
-  * sci-misc/salome-* : Version bump (5.1.3) + removed broken 3.2.6
-  * Add hydra pm.  #309353 (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * Bump and fix #293665 (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * dev-vcs/mercurial-server: fixed bug #286695#c8 (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * Added doc generation to burrtools
-  * InCvs
-  * nmrview readded (Portage version: 2.2_rc65/git/Linux x86_64)  (Signed Manifest commit)
-  * Keyworded for ~amd64-linux ~x86-linux (Portage version: 2.2_rc65/git/Linux x86_64)  (Signed Manifest commit)
-  * Keyworded for ~amd64 ~x86 (Portage version: 2.2_rc65/git/Linux x86_64)  (Signed Manifest commit)
-  * rm valpha*.tar (Portage version: 2.2_rc65/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * app-admin/eselect-gnuplot: useless, dropped gnuplot mulitslot useflag
-  * dev-vcs/mercurial-server: dev-util -> dev-vcs (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * dev-vcs/mercurial-server: dev-util -> dev-vcs
-  * dev-util/mercurial-server: clean up (Portage version: 2.1.7.17/git/Linux i686, RepoMan options: --force)  (Signed Manifest commit)
-  * sci-visualization/gnuplot removed multislot use flag (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * sci-visualization/gnuplot-4.5.9999: checkout right branch (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
-  * sys-libs/libtermcap-compat not needed anymore (Portage version: 2.2_rc65/git/Linux x86_64)  (Signed Manifest commit)
-  * Added flexdock
-  * sci-mathematics/normaliz QA
-  * QA for sci-mathematics/gfan
-  * sci-mathematics/frobby QA/ebuild improvements
-  * sci-mathematics/4ti2: Ebuild improvements
-  * sci-mathematics/Macaulay2 ebuild improvements
-  * QA: respecting FLAGS, metadata.xml fixed (Portage version: 2.2_rc63/git/Linux x86_64)  (Signed Manifest commit)
-  * InCvs
-  * Update uri for ffamber (Portage version: 2.2_rc63/git/Linux x86_64)  (Signed Manifest commit)
-  * InCvs
-  * Remanifesting
-  * [sci-chemistry/gromacs] Fix typo (Portage version: 2.2_rc63/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sci-chemistry/gromacs] Fix typo (Portage version: 2.2_rc63/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sci-chemistry/gromacs] Fix typo (Portage version: 2.2_rc63/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sci-chemistry/gromacs] Add missing patch (Portage version: 2.2_rc63/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sci-chemistry/gromacs] Add ffamber port to gromacs (Portage version: 2.2_rc63/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-mathematics/Macaulay2-1.3.1-r3 since upstream changed source files
-  * Cleaning scilab
-  * Masked >=jgraphx1.3, unmasked scilab for wider exposure
-  * Version bumps for jgraphx
-  * More fixes introduced by Guillaume Horel. Disabling blind Debian patches until further recommandation
-  * [sci-mathematics/scilab] regenerate manifest (Portage version: 2.2_rc63/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * InCvs
-  * inCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * scilab version bump
-  * Removed brlcad, now in main tree
-  * Removed tnt and jama, now in main tree
-  * Moved to tree
-  * sci-visualization/gnuplot-4.4.9999 added stable cvs-gnuplot (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
-  * package.mask: added =sci-visualization/gnuplot-4.4.9999
-  * sci-visualization/gnuplot-4.5.9999 patch went upstream (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
-  * Fix minorsyn errors
-  * Version bump.
-  * touch mpir to enable testing on non-x86/amd64 archs. Remove old mpir.
-  * InCvs
-  * Removed old versions of Macaulay2 and updated deps
-  * move mpir in sci-libs and adjust Macaulay2-1.3.* dependencies accordingly.
-  * [sci-chemistry/gromacs] patch appliyed upstream (Portage version: 2.2_rc62/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sci-chemistry/gromacs] Update dirent.h patch (Portage version: 2.2_rc62/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sci-chemistry/gromacs] Dropped unneded patches. They all were applied to git master (Portage version: 2.2_rc62/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sci-chemistry/gromacs] Add dirent detection patch (Portage version: 2.2_rc62/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-mathmatics/topcom-0.16.2 added Kudos to Johannes Rauh
-  * [sci-chemistry/gromacs] threads now on by default and they works fine with mpi (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-visualization/gnuplot-4.5.9999: clean up (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
-  * condor bump
-  * InCvs
-  * more scilab love
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * more scilab love
-  * Bump
-  * Bump
-  * Bump
-  * Added comments in ChangeLog
-  * New patches for scilab
-  * mpi goodness to hdf-java
-  * scripts dir cleaned
-  * InCvs
-  * sci-chemistry/gromacs-9999: added as-needed fix (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
-  * InCvs
-  * sci-chemistry/votca-csg: fixed as-neeeded bug (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/votca-csg: Version bump (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/votca-tools: Version bump (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
-  * sci-visualization/gnuplot: app-default patch went upstream (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
-  * added missing RDEP (Portage version: 2.2_rc62/git/Linux i686)  (Signed Manifest commit)
-  * added RDEP sci-chemistry/mgltools-mglutil (Portage version: 2.2_rc62/git/Linux i686)  (Signed Manifest commit)
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * InCvs
-  * InCvs
-  * InCvs
-  * sci-chemistry/gromacs-4.0.7-r1: InCvs (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/gromacs: docdir patch went upstream (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
-  * [media-gfx/tachyon] Fix sed line sequence (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * revbumped mpir to 1.3.1, changed nocxx to +cxx
-  * Added lattE-macchiato Bug 303653
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs
-  * Remove Safe-World from DEPEND per bug 303589
-  * Remove Safe-World from DEPEND per bug 303589
-  * Version bump
-  * Fixed wrong description for cdd+
-  * added myself to index.xml
-  * Add myself to index.xml
-  * added myself in the doc
-  * mpi and libc fixes
-  * added mpi support for hdf-java
-  * Fixed conflict man dir for brlcad
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Remanifest
-  * add vina_license
-  * [sci-chemistry/autodock_vina] Initial import per bug #282682 (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccpn-2.1.2.1_p100204 -- Added todays python fixes (Portage version: 2.2_rc62/git/Linux i686)  (Signed Manifest commit)
-  * sci-visualization/gnuplot: some fixes went upstream (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
-  * Add upstream fix for wrapper flag ordering
-  * InCvs
-  * InCvs
-  * InCvs
-  * InCvs (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * brlcad version bump (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * Version bump (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * removed old versions Upstream proper tarball added (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * Initial commit of fitscut (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * [media-gfx/tachyon] Now tachyon compiles with gentoo cflags (Portage version: 2.2_rc62/git/Linux x86_64)  (Unsigned Manifest commit)
-  * apbs plugin support now depends on sci-chemistry/pymol-apbs-plugin (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * InCvs (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/gromacs: live ebuild update (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
-  * removed octave fixes, now in main tree
-  * some syntax fixes
-  * inCvs
-  * inCvs
-  * sci-geosciences/seawater: Removed the earlier setting for S which with the new upstream numbering isn'g needed.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-geosciences/seawater: Upstream change numbering conventions.
-  * sci-chemistry/oasis -- RDEPEND changed sci-chemistry/ccp4 -> sci-chemistry/ccp4-apps, thanks alexxy for reporting (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccp4-apps -- Fix for 301762, thanks Johan Hattne for the patch (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/oasis -- remove forced RDEPEND on arp-warp (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * littel update to tachyon ebuild (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * [media-gfx/tachyon] Initial import. thanks to Christopher Schwan (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-visualization/ferret-bin: Removed old ebuilds. Reformatted to removed duplicate blank lines.
-  * sci-mathematics/pest: Removed unnecesary line.
-  * sci-mathematics/mdp: Removed unnecessary blank lines and fixed copyright years.
-  * sci-libs/scikits_timeseries: Removed unnecessary blank line at end of ebuild.
-  * dev-python/numexpr: Removed ending blank line.
-  * dev-python/coards: Removed useless blank lines.
-  * sys-cluster/pyslice: Removed unnecessary ending blank line. (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sys-cluster/blcr: Repoman sweep (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-geosciences/tcd-utils: Removed useless blank lines (leaving the useful lines alone) and fixed copyright years. (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-geosciences/tcd-editor: Removed useless blank lines. (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-geosciences/tappy: Useless blank line at end and fixed copyright years. (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-geosciences/seawater: Useless ending line. (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-geosciences/swmm: Useless blank lines and copyright fix (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-geosciences/congen: Useless blank line. (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-geosciences/cdat-lite: Blank line fixes from repoman. (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-geosciences/pydap*: Minor repoman fixes (removed ending blank lines)
-  * sci-chemistry/imosflm -- Version Bump (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-chemistry/coot -- Version Bump (Portage version: 2.2_rc62/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/ccp4-apps -- Bad upstream, changed tarball w/o bumping (Portage version: 2.2_rc62/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/ccp4-apps -- Bad upstream, changed tarball w/o bumping (Portage version: 2.2_rc62/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/ccp4-apps -- Bad upstream, changed tarball w/o bumping (Portage version: 2.2_rc62/git/Linux i686)  (Signed Manifest commit)
-  * sci-geosciences/pydap*: Corrected the license.
-  * sci-libs/votca-tools: version bump (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/votca-csg: version bump (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/votca-csg: completion file was moved (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/monomer-db -- version bump (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/superlu -- fixed bug #302763 (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * bumped mpir to 1.3.0, remove old rc, adjust copyright in 1.2.2
-  * sci-chemistry/pymol-apbs-plugin -- fixes for some file locations (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-chemistry/ccpn-2.1.2.1_p100129 -- Added todays python fixes (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/pymol-apbs-plugin -- Initial addition by me (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/pymol-apbs-plugin masked
-  * sci-visualization/gnuplot: Added ~amd64 keyword (bug #232363) (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/refmac -- Version bump (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/refmac -- Version bump (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/refmac -- Version bump (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-geosciences/pydap*: Corrected license.
-  * sci-geosciences/seawater: Corrected license. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
-  * dev-python/numexpr: Initial ebuild. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-geosciences/seawater: Initial ebuild (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sci-geosciences/grass-6.4.0_rc5] sync with portage version and add a missing patch
-  * sci-visualization/ferret-bin: Changed ebuild to correctly install according to x86 and amd64 architectures. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-visualization/ferret-bin: Version bump. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Added ffnet
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * fixed superlu for newer tar ball
-  * sci-misc/simpy: Deleted old ebuild. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sys-cluster/pyslice: Removed old ebuild. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sys-cluster/blcr: Removed old ebuild and updated copyright years on 0.8.2. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-mathematics/pest: Version bump, plus new download file naming convention.  Removed old non-working ebuilds. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-geosciences/xtide: Included 'non-commercial' use flag in metadata.xml.  Fixed dependencies. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-geosciences/libtcd: Included use flag 'non-commercial' in metadata.xml. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-geosciences/tcd-editor: Updated copyright years. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-geosciences/tappy: Updated manifest and removed old ebuild. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Fixed copyright year. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sci-geosciences/qgis-9999] add gps useflag again and make QWT optional
-  * Removed qgis-1.4 now in main tree
-  * sci-geosciences/pydap_handlers_cdms: Initial ebuild.
-  * sci-geosciences/cdat-lite: Initial ebuild.
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-chemistry/votca-csg: dep fix (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/gromacs: Fixes bug #302048 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/ccpn -- updated patches and corrected versioning (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-geosciences/pydap_responses_kml: Initial ebuild.
-  * sci-geosciences/pydap_handlers_nca: Corrected RDEPEND.
-  * sci-geosciences/pydap_handlers_netcdf: Forgot the ChangeLog
-  * sci-geosciences/pydap_handlers_nca: Initial ebuild.
-  * sci-geosciences/pydap_handlers_netcdf: Initial ebuild.
-  * sci-geosciences/pydap_responses_netcdf: Updated Manifest
-  * sci-geosciences/pydap_responses_netcdf: Initial ebuild.
-  * sci-geosciences/pydap: Initial ebuild.
-  * dev-python/coards: Initial ebuild.  Converts from COARDS time (days since X) into python datetime.
-  * sci-visualization/gnuplot: some fixes went upstream (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/votca-csg: live ebuild added (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/votca-tools: live ebuild added (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * added masks for votca live ebuilds
-  * sci-chemistry/votca-csg: added ~amd64 keyword (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/votca-tools: added ~amd64 keyword (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/gromacs: fixed --as-needed confusion (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-biology/samtools: Fixed manifest (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * Version bump
-  * Added open-axiom
-  * Fixed octave dep to libX11
-  * Masked scilab
-  * Import of newer scilab
-  * Initial import of jlatexmath
-  * Import of jgraphx
-  * Import of jeuclid-core
-  * Initial import of hdf-java
-  * move EGIT stuff up before inherit
-  * sci-chemistry/scala -- Version bump (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/pointless -- Version bump -- thanks Johan Hattne for reporting (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci/sci-chemistry/gromacs: sync with tree and removed old versions (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * cleanup (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * Stable x86 and amd64 (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * Version bump with fixes to env.d files. (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * Cleanup (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * Remove older hdf5
-  * revbump to avoid conflicts with portage tree. (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/cyana added (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/scikits_timeseries: fixed Manifest (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/scikits_timeseries: Version bump, fixed licenses, and added pytables to RDEPEND.
-  * New Package sci-libs/cdd+
-  * Move include files into a subdirectory
-  * Remove paraview as it has been revbumped in the main tree by Markus Dittrich
-  * Only mask the paraview version in the science overlay
-  * sci-visualization/gnuplot: multislot fixes (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/ccpn -- todays patches added (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/refmac -- version bump (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-libs/monomer-db -- version bump (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * dev-util/smartgit -- version bump (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-libs/clipper -- Version Bump, nuking the as-needed patch (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ksdssp added (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/libpdb missed header wrong place (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/libpdb++ missed header wrong place (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/libpdb missed header installation (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/libpdb++ missed header installation (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/libpdb added (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/libpdb++ added (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/dssp2pdb added (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * dev-util/mercurial-server: Added ~am64 keyword (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * Bump sys-cluster/openmpi-1.4.1
-  * [sci-geosciences/qgis] version 1.4.0 released. remove live ebuild for this version
-  * [sci-chemistry/pyquante] Initial version bump (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * Initial import of burrtools
-  * Bump. Now based on Debian modifications
-  * There is now blast-db anymore, use ncbi-tools++ instead
-  * sci-biology/psipred -- Fixed dep another time (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-biology/blast-db -- missing perl DEPS added (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/mars --  RDEPEND on sci-biology/psipred (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-biology/psipred -- exprefixed (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-biology/psipred --  adopted to new blast-db (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/nmrpipe -- EPREFIXed (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-biology/blast-db --  We do not install the complete db anymore (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/nmrpipe -- EPREFIXed (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/nmrpipe -- missing patch moved (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/nmrpipe -- Version Bump 5.0.2010.008.16.00 (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/scala -- Version Bump 3.3.16 (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/mars -- EPREFIXed (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/mars -- final fixes part 2 (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/mars -- final fixes (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/mars -- more fixes part 2 (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/mars -- more fixes (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/mars -- fixed ebuild (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/mars -- New Ebuild Added (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/ccp4-apps-6.1.2* is blocking sci-chemistry/sfcheck (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
-  * sci-visualization/gnuplot added multislot support (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * app-admin/eselect-gnuplot: needed for gnuplot[multislot] (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * New package sci-misc/flashdot Bug 300384
-  * Adding ocamlgsl(Bug 280939) from sunrise to science.
-  * [sci-geosciences/qgis] added new 1.4 live version until the release happens, fixed deps of qgis-9999 (gps no longer optional)
-  * added patch to fix missing definitions
-  * added patch to fix missing definitions
-  * Add mpi.eclass enabled sci-libs/hdf5
-  * new ebuild: app-admin/syscall_anomaly and dev-libs/libanomaly
-  * sci-visualization/qtiplot is bumped in the tree
-  * cforms is in tree now
-  * sci-chemistry/refmac -- version bump (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * dev-util/mercurial-server: version bump (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * x11-libs/xforms -- version bump (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/rasmol PREFIX ready (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-libs/neartree -- PREFIX ready (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/cbflib -- PREFIX ready (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/cbflib -- PREFIX ready (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-libs/cbflib -- PREFIX ready (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-libs/cbflib prefix ready (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/talos+ -- depending on rasmol (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/talos+ PREFIX ready (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/mddnmr Initial commit (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  *  sci-chemistry/arp-warp-bin -- needs specific revision of ccp4 (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * update license
-  * mddnmr license added
-  *  sci-chemistry/ccpn -- fixed some python stuff (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/pymol-1.2.2 is in the tree (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/sparky -- Fixed usage of python.eclass (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * app-arch/lbzip2 -- added symlink USE, to link lbzip to /usr/bin/bzip2 (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/pointless -- Version Bump PREFIX whitelist ready (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/sparky -- Version bump 3.115 complete rewrite: multilib aware, not using crappy buildsystem for installation, fixing locations, as-needed respecting, no fixed python version (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/sparky imported from tree
-  * sci-chemistry/pymol -- QA work (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * dev-tex/qtexengine x11-libs/gl2ps are in the tree now
-  * sci-chemistry/pynmr -- imported to save (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * app-arch/lbzip2-0.20 -- Version bump and cleanup of old versions (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/xds-bin -- version bump (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/sfcheck -- nano sfcheck-7.03.16.ebuild <ccp4-apps-6.1.3 (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/sfcheck -- blocking <ccp4-apps-6.1.3 (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccp4-apps -- don't build sfchack, but depend on it (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/sfcheck -- Initial commit (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-libs/balbes-db -- Version bump (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccp4-apps -- Version bump (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccp4i -- Version bump (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-libs/ccp4-libs -- Version bump (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccp4 -- Version bump (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccpn -- inclusion of todays patchset (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccpn -- fixes for doc installation (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/poitnless -- version bug (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/xia2 -- version bug, fixes bug 297238 (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
-  * media-libs/soqt removed
-  * dev-util/smartgit --  version bump to 1.0.1 (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
-  * Update dev-libs/mpir-1.2 branch. Using portage yasm now.
-  * sci-mathematics/frobby QA: Respect users -O setting and no pre-stripping
-  * media-libs/SoQt -- little QA (Portage version: 2.2_rc59/git/Linux x86_64)  (Signed Manifest commit)
-  * media-libs/SoQt -- is maintainer-needed (Portage version: 2.2_rc59/git/Linux x86_64)  (Signed Manifest commit)
-  * media-libs/SoQt -- renamed correctly soqt -> SoQt (Portage version: 2.2_rc59/git/Linux x86_64)  (Signed Manifest commit)
-  * we don't need .svn
-  * sci-chemistry/votca-csg: Version bump (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/votca-tools: Version bump (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-mathematics/polymake revbump
-  * Repairing some depencies of freecad
-  * Initial import of Pivy
-  * Soqt back in science , because it's still not in main tree
-  * paraview ebuild improvements.
-  * [sci-geosciences/qgis-9999] adapt ebuild to portage changes plus some extras
-  * sci-chemistry/coot -- clean up (Portage version: 2.2_rc58/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-mathematics/octave-forge-meta -- dep of sci-mathematics/octave-forge-quaternion added, thanks by Emil Karlsson (Portage version: 2.2_rc58/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-mathematics/octave-forge-quaternion -- Initial commit, written by Emil Karlsson (Portage version: 2.2_rc58/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/votca-csg: added googlecode mirror (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/votca-tools: added googlecode mirror (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * >=sci-visualization/paraview-3.6.1-r2: HARDMASKED as this is an experimental ebuild
-  * Import "improved" paraview ebuild
-  * [sci-geosciences/swmm] Update manifest and remove stale ebuild
-  * Version bump.  Removed documentation since upstream changes without changing name so manifest could not be kept up to date.
-  * dev-util/mercurial-server: version bump to 1.0 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/votca-csg: corrected description (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-visualization/gnuplot: added version 4.4.0_rc1 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/votca-csg initial add - bug #296707 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/votca-tools initial add - bug #296707 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * Deleted because it's in the main tree
-  * sci-chemistry/coot -- some fixes towards the gtk-2 migration from upstream (Portage version: 2.2_rc58/git/Linux x86_64)  (Signed Manifest commit)
-  * Deleted coin because it's has reached main tree
-  * Version bump to version 4.1.2 revision 4181
-  * sci-libs/framewave: Add ~amd64 keyword and fix deps
-  * sci-mathematics/frama-c/files/frama-c-20090901-always_init.patch
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/frama-c/files/frama-c-20090901-always_init.patch
-  * Added patch to fix incorrectly declared variable (#293905).
-  * dev-scheme/guile-gnome-platform: Deleted since it's already in main tree
-  * Changed error in MY_P
-  * In main tree
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * dev-util/smartgit -- SRC_URI fixed (Portage version: 2.2_rc56/git/Linux i686)  (Signed Manifest commit)
-  * dev-util/smartgit -- version bump the release 1 (Portage version: 2.2_rc56/git/Linux i686)  (Signed Manifest commit)
-  * Added ~x86. Thanks to Derk W. te Bokkel
-  * Fully commit the openmpi-1.4 bump.
-  * Bump openmpi-1.4.
-  * sci-chemistry/openbabel-python: Block openbabel[python], #288199
-  * [sci-libs/coin] Fix b0rked manifest (Portage version: 2.2_rc55/git/Linux x86_64)  (Signed Manifest commit)
-  * Version bump of Coin to 3.1.2
-  * sci-chemistry/burrow-owl fixed starparse dpe to >=1.0 (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
-  * workaround for parallel installation added, fixes bug 288235 (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/nmrpipe fixed missing lip.patch (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
-  * dev-scheme/guile-gnome-platform correctly assigned contributer -- thanks Rafael G. Martins (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
-  * dev-scheme/guile-gnome-platform added to fix bug 293655 (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-libs/starparse unkeyworded te live ebuild again (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-libs/starparse release 1.0 added (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/mrbump don't use /usr/lib64/ccp4/ccp4i (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
-  * nmrpipe version bump (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * To main tree
-  * deleted freecad in wrong directory
-  * Change user from root to Roelof Wobben
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Change user from root to Roelof Wobben
-  * Add sci-libs/framewave-1.3.1
-  * x11-libs/guile-gtk: Removed because it was commited to main tree
-  *  Initial import of freecad
-  * add mpi_pkg_set_ld_library_path()
-  * Fix eselect-mpi config file.
-  * Fix eselect-mpi config file.
-  * Add MPI_PKG_USE_ROMIO to mpi.eclass.
-  * Note revisions of patches in upstream repo.
-  * sci-chemistry/coot -- version bump to 0.6 and cleanup of old versions (Portage version: 2.2_rc55/git/Linux i686)  (Signed Manifest commit)
-  * app-arch/lbzip2 -- version bump to 0.1.9 (Portage version: 2.2_rc55/git/Linux i686)  (Signed Manifest commit)
-  * pdb-extract-3.004 has been merged into portage tree.
-  * sci-chemistry/mage Everything fixed (Portage version: 2.2_rc54/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/mage Imported fron dberkholz overlay (Portage version: 2.2_rc54/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/probe Everything fixed (Portage version: 2.2_rc54/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/probe Imported fron dberkholz overlay (Portage version: 2.2_rc54/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/neartree -- version bump to 2.1.4 (Portage version: 2.2_rc54/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/gromacs docdir->htmldir (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/gromacs: htmldoc was installed in the wrong path (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/factory Manifest
-  * sci-visualization/gnuplot: fixed bug #294467 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-mathematics/frama-c20090901: always_init.patch -> fix ptr init
-  * Repomans QA issues in sci-libs
-  * Added use flag descriptions for 'singular' used in sci-libs/factory and sci-libs/libfac
-  * sci-mathematics/Macaulay2 updated dependencies
-  * Repomans QA fixes in my sci-mathematics packages
-  * drop dapl support, seems not needed if you use infiniband
-  * Re-manifest
-  * Added patches to octave
-  * sci-mathematics/octave-forge-meta -- sci-mathematics/octave-forge-video added as dep (Portage version: 2.2_rc52/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-mathematics/octave-forge-video -- Written by Emil Karlson (Portage version: 2.2_rc51/git/Linux i686)  (Signed Manifest commit)
-  * add infiniband and dapl support via extrenal libs to openmpi
-  * sci-chemistry/ccp4-apps -- nesseccary fix to work together with Arp/Warp (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-mathematics/frama-c-20090901: always_init.patch
-  * Added to tree
-  * sci-chemistry/drawxtl -- SRC_URI fix, thanks to Hannes Krueger (Portage version: 2.2_rc51/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/ccp4i -- Manifest fixed (Portage version: 2.2_rc51/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/arp-warp-bin -- Fixed instruction when python is bumped (Portage version: 2.2_rc51/git/Linux i686)  (Signed Manifest commit)
-  * Macaulay2-1.3.1-r2 completely split ebuild
-  * Frobby, now installing missing header
-  * New package sci-mathematics/frobby Final dep for Split Macaulay :) Bug #294503
-  * Update homepage at request of upstream. (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccp4-apps -- masked bad version (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/pointless-1.4.5 -- version bump (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccp4-apps -- missing $ and pisa/sbase installation fix (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccp4i -- typo corrected
-  * sci-libs/balbes-db -- set env BALBES_ROOT (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * ccp4-apps start to fix usage of ccp4.setup.*
-  * New package: sci-libs/factory Dependency of sci-libs/libfac
-  * New package sci-libs/libfac A dependency of sci-mathematics/Macaulay2 and sci-mathematics/Singular
-  * Remove older versions of sys-cluster/mpich2 (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * bump sys-cluster/mpich2-1.2.1 (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * qgis-9999: add sqlite use dep to python. needed for the OSG plugin to work.
-  * sci-mathematics/frama-c-20090901: always_define.patch
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * Added an experimental octave
-  * sci-mathematics/frama-c-20090901: init_locals_defined.patch
-  * New package, ebuild written by me
-  * sci-chemistry/ccpn -- Bad mistake in setting compile options --> leads to opengl crashes (Portage version: 2.2_rc51/git/Linux i686)  (Signed Manifest commit)
-  * Needs octave > 3.2, bug #293814
-  * Normaliz Manifest. Upstream did change that file!!!
-  * Filesize for mpir-1.2.2 Did upstream change that .tar.gz??
-  * Importing iml-1.0.3
-  * Fix openib.init.d and env.d (Portage version: 2.2_rc51/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * sci-chemistry/gromacs build mpi and non-mpi libs in 4.0.5-r1 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-visualization/qtiplot -- Fixed sip patch to work with <sip-4.9 (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix openib.conf for modprobe (Portage version: 2.2_rc51/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Import polybori
-  * Add a patch and a use flag to dev-libs/mpir
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * qgis-9999: fix the subdir paths so that extensions work again. Still getting QA reports from portage. maybe someone else can look at that?
-  * Fix manifest (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * missing dep (Portage version: 2.2_rc50/git/Linux i686)  (Unsigned Manifest commit)
-  * [sci-geosciences/qgis-9999]: remove unneeded patch
-  * qwt removed again
-  * sci-visualization/qtiplot version bump to 0.9.7.10 (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * x11-libs/gl2ps -- Version bump & ported to cmake buildsystem (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * x11-libs/gl2ps imported from tree
-  * media-libs/emfengine missing dep added (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * media-libs/emfengine added (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * dev-tex/qtexengine -- add missing deps and compile dynamic lib (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * dev-tex/qtexengine -- use it right (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * dev-tex/qtexengine -- use of PATCHES from qt4.eclass (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * x11-libs/qwt -- version bump to latest commit in svn, needed for qtiplot (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * dev-tex/qtexengine added (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
-  * qtiplot imported
-  * refetching qgis samples
-  * qgis now in main tree, adapted svn qgis
-  * mpir 1.2 branch updated. Sage people will care for 1.3
-  * Updated deps of Macaualay
-  * Revert "sci-geosciences/swmm: Version bump and upstream now includes version in"
-  * sci-geosciences/swmm: Version bump and upstream now includes version in download file.
-  * Manifest fix for mpir
-  * sci-mathematics/4ti2 good to go on amd64
-  * sci-mathematics/Macaulay2-1.3.1-r1 with doc fixes. Removed old versions
-  * gredata Manifest fix
-  * sci-chemistry/solve-resolve-bin -- Manifest fix (Portage version: 2.2_rc50/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/ccp4 -- oasis4 USE removed again (Portage version: 2.2_rc50/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/oasis4 -- oasis4 USE removed again (Portage version: 2.2_rc50/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccp4-apps -- oasis4 USE removed again (Portage version: 2.2_rc50/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccp4i -- oasis4 use removed again (Portage version: 2.2_rc50/git/Linux x86_64)  (Signed Manifest commit)
-  * BUGS is not in distribution
-  * add emake install and dodoc to src_install
-  * Initial ebuild of HFST package
-  * Manifest for gfan
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Initial condor ebuild
-  * sci-chemistry/oasis -- Initial commit Written by me fixes bug 290588 (Portage version: 2.2_rc50/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccp4i commiting all fixes for oasis support (Portage version: 2.2_rc50/git/Linux x86_64)  (Signed Manifest commit)
-  * last fix for oasis support in ccp4-apps (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
-  * mv SCIAPPS in ccp4-apps to PEDEPEND (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
-  * fixed oasis USE dep to ccp4-apps (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/solve-resolve-bin added to overlay (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
-  * add solve license
-  * oasis license added
-  * sci-mathematics/Macaulay2-1.3.1 revbump
-  * New Package: dev-libs/mpir (integer arithmetics, drop-in replacement for gmp) Bug #293383
-  * New package sci-mathematics/gfan (Computations in tropical and toric algebra) Bug #293381
-  * sci-chemistry/xia2 -- added missing fixes for bytecompiling (Portage version: 2.2_rc50/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/xia2 -- SRC_URI fix (Portage version: 2.2_rc50/git/Linux i686)  (Signed Manifest commit)
-  * dev-python/omniorbpy: copied last version from portage
-  * dev-util/mercurial-server version bump to 0.9 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/coot -- greg-data digest fixed (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/refmac -- Upstream did a change to the tarball (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/xia2 -- version bump (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
-  * app-text/txt2tags-2.5 added to fix bug #278317 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/gromacs fix for bug #284431 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/ccpn -- fixes for internal help and opengl usage (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/coot -- dev-scheme/goosh dep removed (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
-  * dev-util/smartgit version bump (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccpn version bump (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
-  * fixed inherit, stupid me (Portage version: 2.2_rc49/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/smmp ifrst checkin (Portage version: 2.2_rc49/git/Linux i686)  (Signed Manifest commit)
-  * removed ntl, in main tree
-  * fixes patching for sci-chemistry/ccpn (Portage version: 2.2_rc49/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/nmrpipe -- corrected patch name (Portage version: 2.2_rc49/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/ccpn -- version bump (Portage version: 2.2_rc49/git/Linux i686)  (Signed Manifest commit)
-  * version bump (Portage version: 2.2_rc49/git/Linux i686)  (Signed Manifest commit)
-  * fasta version bump and fix of chatastrophic ebuild, src_test is still broken (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
-  * [sys-block/tgt] Version bump (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
-  * Added acknowledgement (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-libs/clapack -- fixed SRC_URI to upstreams (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
-  * givaro bump
-  * sci-libs/cctbx version bump fixes boost <-> python-2.6.4 issues (Portage version: 2.2_rc48/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-chemistry/coot bumped to bills latest stable release (Portage version: 2.2_rc48/git/Linux x86_64)  (Unsigned Manifest commit)
-  * greg-data Manifest fix (Portage version: 2.2_rc48/git/Linux x86_64)  (Signed Manifest commit)
-  * Fixed sprintf bug (fixes #290373).
-  * Merged Justin's fix into portage.
-  * Moved to tree
-  * Add ICM License
-  * icm-browser version bump (Portage version: 2.2_rc46/git/Linux x86_64)  (Unsigned Manifest commit)
-  * icm version bump (Portage version: 2.2_rc46/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-chemistry/coot bumped to latested release from fink (Portage version: 2.2_rc48/git/Linux x86_64)  (Signed Manifest commit)
-  * m4ri version bump
-  * give some gcc-4.4 love to modglue
-  * more parallel make fixes for lie
-  * cadabra version bump
-  * sci-chemistry/ccp4i fix for f2mtz bug 289379
-  * sci-visualization/gnuplot: version bump to 4.5.9999 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * update package.mask for gnuplot-4.5.9999
-  * sci-libs/opencascade fix for java include, reported via IRC by roelof
-  * fix bug 291597
-  * small fix (Portage version: 2.2_rc48/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/libcmatrix version bump to 3.2.1 (Portage version: 2.2_rc48/git/Linux i686)  (Signed Manifest commit)
-  * Add GamessQ (Portage version: 2.2_rc48/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-chemistry/wxmacmolplt] Moved to tree
-  * ccp4-libs -- fixed the 64bit fix (Portage version: 2.2_rc48/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccp4-apps: PYTONPATH patch added -- thanks Donnie for pointing this out (Portage version: 2.2_rc47/git/Linux i686)  (Signed Manifest commit)
-  * sci-libs/cgnstools: Fixed problems with 2D meshes and cgns_to_vtk.
-  * dev-python/pythoncgns: Initial release for bug 291221
-  * apbs version bump (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sys-cluster/scalasca missing dep bug #290560 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * 64bit fix (Portage version: 2.2_rc46/git/Linux i686)  (Signed Manifest commit)
-  * app-arch/lbzip2 version bump (Portage version: 2.2_rc46/git/Linux i686)  (Signed Manifest commit)
-  * apbs version bump (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * fix for bug 289032 (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * fix for bug 290754 (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * import from stride
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * In main tree
-  * renamed patch which was missing
-  * nedit is fixed in tree
-  * smartgit version bump
-  * app-arch/lbzip2 version bump to 0.16 (Portage version: 2.2_rc46/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/ccpn python update (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/talos+  version bump fixes bug 289651
-  * sci-chemistry/nmrpipe version bump (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * talos missing RDEPEND added
-  * nmrpiep fixes (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/nmrpipe various fixes (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/tinker version bump fixes bug 290459 Thanks Ivan Fedyanin for providing a updated ebuild (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * app-editors/nedit missing die (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * dev-ml/mlgmpidl-1.1: fix depend variable
-  * wrong CAT name
-  * update gre-test digest (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * app-editors/nedit fix for bug 290337 (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * nedit import from portage
-  * New package, bug 155780. Ebuild written by me and dawe <daweonline@gmail.com>
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * more eapi2 updates
-  * various eapi2 updates
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/sage-bin: I stopped trying to make sage-bin work some time ago.  Upstream made it very difficult.  Ebuild not updated since then and now trying to work out an ebuild to compile sage rather than install the binaries.
-  * New package, bug 155780. Ebuild written by me and dawe <daweonline@gmail.com>
-  * version bump fix for upstream typo
-  * sci-electronics/linsmith version bump patch created by TomJBE (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * Added gcb
-  * Added classads
-  * sci-chemistry/polygon initial commit written by me (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * needed die added
-  * sci-libs/gmsh-9999: moved sources to svn repesitory
-  * app-arch/lbzip2 version bump to 0.16_rc1 Maintainer wrote me a mail. (Portage version: 2.2_rc46/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/refmac version bump (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * [sci-biology/sequin] Please dont brake metadata. Run repoman full before you commit something. Or use repoman commit it works with git too (Portage version: 2.2_rc46/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Add desktop shortcut
-  * Fix manifest
-  * New package, ebuild written by me
-  * sci-chemistry/molrep tests enhanced (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * version bump of pointless (Portage version: 2.2_rc46/git/Linux i686)  (Signed Manifest commit)
-  * molrep version bump (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * refmac version bump to 5.5.108 (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-libs/med-2.3.5 needs >=sci-libs/hdf5-2.6.4
-  * removed numeric dep (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-mathematics/apron/apron: fix ppl install on x86
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/gappa(lib-coq): bump version to 0.12(.1)
-  * sci-libs/gmsh-9999: removed keywords
-  * Manifest fix again (Portage version: 2.2_rc46/git/Linux i686)  (Signed Manifest commit)
-  * Cleaning and much QA, tested on amd64
-  * Manifest (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * tried to fix coot test
-  * qa
-  * sci-mathematics/why: fix search with pvs binary
-  * dropping sci-mathematics/pvs: unmaintained mainstream and PITA to maintain in portage
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/pvs: fix sbcl-patch on i*86
-  * sci-libs/gmsh: small corrections + version bump + nightly version
-  * sci-libs/cgnslib: fixed DEPEND and RDEPEND confusion
-  * sci-libs/med: Version bump + corrections, doc and examples USE flags added
-  * [sys-infiniband/ibutils] Fix bug 289037. thanks to Kacper Kowalik (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * Version bump to blcr-0.8.2.  Minor edits to remove unused vmadump module and unneeded sandbox warning.
-  * refmac version bump to 5.5.0107
-  * fix Manifest and remove old versions (Portage version: 2.2_rc46/git/Linux i686)  (Signed Manifest commit)
-  * manifest fix
-  * [sci-chemistry/ccpn] Fix manifest (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * new version needs testing
-  * ccpn update
-  * cctbx version bump
-  * refmac bump to 5.5.106
-  * coot libcurl dep added
-  * ccpn version bump to 2.1.1
-  * sci-mathematics/frama-c: varinfo_export patch dev-ml/ocamlgraph: eapi2 fix
-  * octave-epstk-2.1.ebuild -- fix for bug 288586 Some QA, rest is commented in the ebuild
-  * Bump ICC 10 series per bug 284801
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * Version bump, rewrite and rename to gbrowse
-  * ccpn update
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * New package, ebuild written by me
-  * Import of lwpr
-  * ccpn now includes updates from upstream which are not provided in the releases
-  * pointless tarball mirrored
-  * [eclass] Update openib eclass per bgreen mail
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * opendx changes now in main tree
-  * Bump sys-cluster/mpich2-1.2
-  * Added working docs from old gentooscience repo
-  * aplpy version bump
-  * vo version bump
-  * atpy bump
-  * sci-chemistry/mgltools-autodocktools Needs python[tk]
-  * sci-chemistry/autodock Qa and respect flags
-  * sci-chemistry/mgltools-autodocktools -- Added sci-chemistry/mgltools-support to RDEPEND
-  * removed icc idb ifc ipp now in main tree
-  * Some QA on coot
-  * fixed ChangeLog and Manifest
-  * coot fixes as-needed patch not needed anymore Same for reduce sed rappermc patch added
-  * molrep version bump to 10.2.34
-  * refmac version bump to 5.5.105
-  * [sci-biology/foldingathome] Version bump (Portage version: 2.2_rc43/git/Linux x86_64)  (Signed Manifest commit)
-  * Merge remote branch 'origin/master'
-  * Fixed bug in octave-forge eclass.
-  * Bumped remaining octave-forge ebuilds.
-  * [sci-biology/fasta] Fix manifest (Portage version: 2.2_rc42/git/Linux x86_64)  (Signed Manifest commit)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-visualization/ferret-bin:  Version bump to 6.3.
-  * In main tree
-  * Bumped additional octave-forge ebuilds.
-  * Manifest
-  * Fixing shaders patch
-  * Fixing pymol shaders patch.
-  * Bumped some of the octave-forge packages.
-  * In main tree
-  * pymol bump to 1.2.2
-  * sci-mathematics/netgen: fixed Manifest hopefully
-  * sci-mathematics/netgen: fixed Manifest and Changelog
-  * sci-mathematics/netgen: fixed libTogl location as it changed; removed old 4.4er patches
-  * sci-mathematics/netgen: Changed opencascade path to /opt/opencascade-6.3/ros 4.9.11; removed old 4.4er versions
-  * dev-tcltk/togl: Fixed install paths for togl-1.7; removed 2.0 as this is now in portage
-  * MANIFEST
-  * ccp4i should have been bumped before
-  * Merge git+ssh://kancheli/data/local/science into refmac
-  * refmac bump and cleanup
-  * version bump
-  * Add dep on sys-cluster/empi to mpi.eclass for classed packages.
-  * [dev-util/mercurial-server] Homepage updated (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * Remove incorrect blocker.
-  * clustalw-1.83-r3 is in the tree
-  * [dev-util/mercurial-server] Initial commit (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * In main tree
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * New package, ebuild written by me
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/frama-c: varinfo patch only to fix export
-  * [sys-block/tgt] Add missing rdepend (Portage version: 2.2_rc41/git/Linux x86_64)  (Unsigned Manifest commit)
-  * net-fs/glusterfs moved to tree as sys-cluster/glusterfs
-  * Another bunch of updates related to Frama-C
-  * Various updates related to Frama-C.
-  * removed h5py now in main tree
-  * removed h5py now in main tree
-  * coot -- upstream fixes COOT_TEST_DATA_DIR and included our patch for tests
-  * smartgit version bump
-  * dev-python/h5py: Version bump to 1.2.1.
-  * app-text/dgs: fix + modifs thanks to Olivier Huber
-  * New package: sci-mathematics/topcom-0.16.0 Bug #285619
-  * manifest
-  * manifest
-  * Manifest fix
-  * ccpn update
-  * smartgit versio bump
-  * smart-git version bump
-  * ccpn versionbump
-  * test
-  * ccpn minor fixes
-  * sci-chemistry/pymol-plugins-bni-tools added
-  * ccpn version bump and rewrittings
-  * sci-libs/gmsh: Reworked ebuild from Etienne Lorriaux
-  * sci-mathematics/netgen: Version bump
-  * tablelist: bump to 4.12.
-  * Bump mpich2-1.1.1_p1
-  * fixed env files for ifc and icc
-  * Replaced the broken opencascade-6.3 by opencascade-6.3-r1
-  * First import in science overlay as an opencascade dependency
-  * Cleaning  Committer: Etienne Lorriaux <etienne.lorriaux@gmail.com>  Changes to be committed: 	deleted:    Changelog 	modified:   Manifest 	modified:   med-2.3.1.ebuild 	modified:   med-2.3.4.ebuild
-  * Added correct manifest  Changes to be committed: 	modified:   Manifest  Changed but not updated: 	deleted:    Changelog
-  * Version bump + trivial changes for QA check  Committer: Etienne Lorriaux <etienne.lorriaux@gmail.com>  Changes to be committed: 	new file:   ChangeLog 	new file:   files/med-2.3.4-gcc-4.3.patch 	new file:   med-2.3.4.ebuild 	new file:   metadata.xml  Changed but not updated: 	deleted:    Changelog 	modified:   Manifest 	modified:   med-2.3.1.ebuild 	modified:   med-2.3.4.ebuild
-  * New package, thanks to Philippe Veber for the ebuild
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * New package, thanks to Philippe Veber for the ebuild
-  * HOMEPAGE corrected bug 285068 bumped prerelease to r2312 which will be the version of the second prerelease Included src_test in prerelease
-  * fix for bug 285068
-  * Gentoo is UNIX isn't it?
-  * sci-visualization/ferret-bin-6.2: Version bump plus much simpler because upstream generously changed download names.  Fixed some environment variables that didn't work in files/99ferret.
-  * coot working test revision to log added
-  * test-data was updated
-  * coot src_test cleanup
-  * src_test is working on coot
-  * prelimary src_test fix
-  * New package, ebuild written by me
-  * sci-mathematics/freefem++: version bump and cleanup.
-  * coot -- typo fixed
-  * coot -- use test condition missing for unpack
-  * coot -- src_test is working
-  * greg-1.5 added
-  * [dev-lang/ifc] Fix manifest; Please\! Dont commit ebuild with broken manifests\! (Portage version: 2.2_rc40/git/Linux x86_64)  (Signed Manifest commit)
-  * fix license
-  * fix license
-  * fix license
-  * missing quotations
-  * pointless -- version bump
-  * dev-scheme/greg added
-  * dev-util/smartgit version bump
-  * removed the env-update from pkg_postinstall
-  * Various updates related to sci-mathematics/frama-c
-  * New package, ebuild written by me
-  * Version bump
-  * Fixed closing quotations
-  * Modified env files for icc and ifc
-  * [dev-lang/ifc] Fix manifest (Portage version: 2.2_rc40/git/Linux x86_64)  (Signed Manifest commit)
-  * Fixed collision files among Intel packages
-  * fixed tagged source script
-  * Added numscons
-  * New ebuild for icc gathering all components
-  * New package: sci-mathematics/normaliz Bug #283676
-  * [sci-geosciencies/josm] New version
-  * sci-mathematics/netgen: Changed to slotted togl-1.7, minor changes for opencascade
-  * dev-tcltk/togl: Slotted ebuild for version 1.7
-  * readded togl
-  * coot Upstream fixed the check maketarget
-  * togl is fixed in the tree
-  * [sci-geosciences/qgis] Version bump. Ebuild fixed. Dropped postgis from dependencies. Delete gdal from overlay
-  * sci-mathematics/netgen: fixed netgen.desktop
-  * sci-mathematics/netgen: Version bump, make repoman happy; Thanks to Christoph Lehrenfeld, Adam Zdunek and Daniel Tourde
-  * dev-tcltk/togl: Reintroduced togl-1.7 as dependency for >netgen-4.9*
-  * sci-libs/cgnslib: Reintroduced cgnslib-2.5.3, as it needs <sci-libs/hdf5-1.8
-  * sci-libs/cgnslib: Needs now >=sci-libs/hdf5-1.8
-  * sci-libs/cgnstools: Corrected checksums, as upstream changed tarball.
-  * sci-libs/cgnslib: Corrected checksums, as upstream changed tarball.
-  * coot -- src_test developed
-  * version bump
-  * smartgit version bump
-  * ccp4i added crank_shelxd.tcl.patch QA removed WINDOWS and UNIX binary dirs cleaned up old versions
-  * talos+ version bump
-  * prelimary src_test support for coot
-  * sci-libs/driftwood written by me
-  * probcons ldflags and collision fix
-  * sci-chemistry/mosflm parallel cbf make patch
-  * QA on lbzip
-  * QA on my sci-libs packages
-  * superlu version bump
-  * fetch url fixed
-  * smartgit added
-  * lincense smartgit added
-  * sci-libs/calculix-cgx: Version bump.
-  * sci-libs/calculix-ccx: Version bump.
-  * sci-libs/cgnstools: Version bump
-  * sci-libs/cgnslib: Version bump, restricted to <sci-libs/hdf5-1.8
-  * [sci-chemistry/almost] Fix manifest (Portage version: 2.2_rc40/git/Linux x86_64)  (Signed Manifest commit)
-  * Bug #282174 was fixed. Removed workarounds from ebuild.
-  * Manifest
-  * sci-chemistry/mrbump superpose fix
-  * [eclass] Update openib.eclass
-  * [sys-block/tgt] we need to wait for 1 second to setup tgtd (Portage version: 2.2_rc38/git/Linux i686)  (Unsigned Manifest commit)
-  * [sys-block/tgt] update tgtd init.d (Portage version: 2.2_rc38/git/Linux i686)  (Unsigned Manifest commit)
-  * [sys-block/tgt] make ebuild eapi=2 (Portage version: 2.2_rc38/git/Linux i686)  (Unsigned Manifest commit)
-  * [sys-block/tgt] Update patch (Portage version: 2.2_rc38/git/Linux i686)  (Unsigned Manifest commit)
-  * sci-mathematics/pest-11.3: Updated copyright line in header
-  * sci-mathematics/pest-11.11: Version bump.  New web site and download.
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * [qgis-9999] when enabled, depend on python with sqlite support (needed for OSM plugin)
-  * fix for bug 282503
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * sci-libs/cbflib QA rpath and soname fixed
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * fixed bug 238300
-  * New package, ebuild written by me
-  * New package, ebuild written by me
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * [sys-infiniband] Update rds-tools
-  * [eclass] Update openib eclass
-  * [eclass] Update openib eclass
-  * [eclass] Update openib eclass
-  * [eclass] Update openib eclass
-  * [sys-infiniband] Add rds-tools
-  * [sys-infiniband] Add missing dep to ibutils
-  * [sys-infiniband] Add ibutils
-  * [sys-infiniband] Add ibutils
-  * [sys-infiniband] Add patch for OSM
-  * [sys-infiniband] Add patch for OSM
-  * [sys-infiniband] Update to OFED 1.4.1
-  * [sys-block/tgt] Version Bump to 0.9.8 (Portage version: 2.2_rc38/git/Linux i686)  (Unsigned Manifest commit)
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Rewritten version of sci-mathematics/Macaulay2 to fix QA issues.
-  * removed hdf5 now in main tree
-  * Add blocker against app-text/lcdf-typetools when vt is enabled. #281318
-  * Add blocker against app-text/lcdf-typetools when vt is enabled. #281318
-  * Remove -I hack for fortran
-  * manifest
-  * PYTHONPYTH fix and configure cut
-  * collision ccp4i and mrbump
-  * right clustalw added to overlay
-  * x11-libs/libjwc_f add patch until ccp4 6.1.2
-  * x11-libs/libjwc_cfixed the fix
-  * libjwc update to 6.1.2 and as-needed fix
-  * another blocker
-  * fix for bug 281734
-  * sci-chemistry/mrbump -- typo fixed in RDEPEND
-  * sci-chemistry/mrbump dependency added
-  * mrbump dependency fixed
-  * fixes mrbump collision fixes some variables
-  * [sys-infiniband/librdmacm] Add libibverbs to depend (Portage version: 2.2_rc38/git/Linux i686)  (Unsigned Manifest commit)
-  * sci-mathematics/freefem++: version bump.
-  * sci-chemistry/imosflm -- IMOSFLM_VERSION is set by sci-chemistry/imosflm
-  * sci-chemistry/ccp4-apps -- IMOSFLM_VERSION is set by sci-chemistry/imosflm
-  * Another git add . block for <sci-chemistry/ccp4-6.1.2
-  * sci-chemistry/imosflm rewritten compile phase
-  * ccp4 USE db renamed to balbesdb as suggested by Donnie and Afrever
-  * mmdb blocks !! ccp4-libs
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * ccp4-apps Manifest renewel due to merge
-  * ccp4i -- fixes to remove imosflm
-  * ccp4 setup.sh part 2
-  * imosflm bump and lib fix
-  * sci-chemistry/ccp4-apps fix for bash/sh compatibility
-  * .
-  * fix manifest
-  * keyworded ~amd64 after testing
-  * remove keywords. live version should not be installed by accident
-  * ingleborough is released
-  * balbes-db PDEPEND handled by sci-chemistry/ccp4
-  * ccp4 -- balbes is now optionall
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * sys-cluster/scalasca DOCDIR fix (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sys-cluster/scalasca version bump (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * trry to build libmmdb seperatly
-  * libmmdb build seperatly
-  * coot gcc-4.4 compatibility is fix by upstream
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * sync openmpi-1.3.3 with portage.
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * mmdb version bump added, needed for coot
-  * ccp4-6.1.2 tarball changes -- Manifest update
-  * pointless masked
-  * pointless version bump
-  * burrow-owl has some fixes from upstream now
-  * Adjusted DEPEND and RDEPEND.
-  * burrow-owl added from donnies overlay
-  * =sci-chemistry/burrow-owl-9999_pre15 masked
-  * ccp4-libs -- libccif.so gets build correctly on amd64
-  * reduce firxes for bug 280857 & 280858
-  * starparse keyworded for ~x86
-  * coot -- fixes for gcc4.4 and glibc-2.10
-  * where does  *.seave come from
-  * scale for 6.1.2!
-  * sci-libs/balbes-db ready for 6.1.2
-  * nmrpipe ver bump 5.0.2009.203.18.54
-  * repoman told about additional lines
-  * ccp4-apps imosflm excluded
-  * ccp4 cleanup and transmission to ccp4-6.1.2
-  * molrep version bump
-  * xia bump for ccp4-6.1.2
-  * ccp4-apps which I broke somehow are fixed now
-  * pointless bump
-  * guile-www bump
-  * ccp4-6.1.2 deps masked
-  * ccp4-apps transmission ccp4 --> ccp4-apps and ccp4 as meta package
-  * dev-tcltk/tablelist version bump
-  * sci-libs/med: Just updated SRC_URI; repoman is not yet happy :-S
-  * sci-libs/cgnsfoam: Initial import to science overlay
-  * sci-libs/libcgnsoo: Initial import to science overlay
-  * [sci-biology/wgs-assembler] Update manifest (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
-  * pymol-1.2.1 is in tree, lets remove it from Manifest
-  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
-  * Added to portage tree.
-  * removed keywords
-  * Version bump
-  * re-manifest
-  * Modified stuff and skymaker licenses
-  * the new ccp4-apps package masked
-  * ccp4i adapted to ccp4-apps
-  * ccp4 -- ccp4-apps
-  * RDEPEND fixed
-  * ccp4 --> ccp4-apps
-  * starparse Manifest fix and tree version removed
-  * netcdf removed and bug 279817 filed
-  * scala masked
-  * scala added -- to be excluded from ccp4
-  * pymol cleanup to move to the tree as requested by fauli in bug 269119
-  * [sys-infiniband] Deps cleanup
-  * version bump netcdf to 4.0.1 hdf5 support and any new features is not included yet
-  * molrep bump to 10.2.33
-  * ccp4-libs bumped to 6.1.2
-  * ccp4i bump to 6.1.2
-  * masked ccp4i-6.1.2
-  * here we can sort and store patches which are used by multiple packages to create tarballs out of them which can be mirrored
-  * update-monomers-db fixed --> sha256sum ouput
-  * automatic bump
-  * tinker now builds
-  * [sci-astronomy/skymaker] Update Manifest (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
-  * gabedit version bump requested by Maximilian Bräutigam bug 279438
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * suff initial import
-  * skymaker: version bump
-  * RASLIC license added
-  * balbes-db files permission QA
-  * Jligand has some internal wierdness
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * In main tree
-  * tinker bump to 5.0
-  * sci-chemistry/jligand -- written by me
-  * Version bump
-  * In main tree
-  * Revert "In main tree"
-  * In main tree
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * In main tree
-  * sci-chemmistry/rasmol version bump 2.7.5
-  * cbflib fix for fortran compatibility
-  * sci-libs/neartree written by me
-  * sci-libs/neartree written by me
-  * dev-libs/cvector written by me
-  * Merge branch 'freefem++-3.4'
-  * sci-mathematics/freefem++: fix dependencies for document building, cleanup  old files for freefem++-3.2.
-  * jana200 for Hannes Krüger
-  * changed sys-cluster to sys-infiniband in DEPEND
-  * updated Manifest
-  * changed "sys-cluster" to "sys-infiniband" in dependency spec.
-  * nmrpipe version bump
-  * remanifesting
-  * removed old cpl
-  * esorex version bump
-  * gasgano version bump
-  * added prroper license
-  * Initial import of kapteyn
-  * sci-libs/oasa: Version bump to 0.13.1
-  * sci-chemistry/wxmacmolplt: Version bump to 7.3
-  * sci-libs/cgnslib: executable rights for adf2hdf/hdf2adf
-  * [sys-infiniband] Move Infiniband Here
-  * [eclass] Update OpenIB eclass
-  * atpy initial import
-  * vo initial import
-  * add romio to mpi dep
-  * aplpy version bump
-  * pywcs version bump
-  * sci-libs/gmsh: Version bump; del hdf5 patch; dep fixes; EAPI=2
-  * Links now directly against libcgns; Changed to EAPI=2
-  * Installs ADF.h even without hdf5 USE-flag
-  * Added patches from debian; changed to EAPI=2
-  * version bump for cforms
-  * cbflib bump to 0.8.1
-  * Merge branch 'master' of ssh+git://134.94.85.9//data/local/science
-  * cbflib version bump
-  * sci-chemistry/openbabel-ruby: Version bump to 2.2.2
-  * sci-chemistry/openbabel-python: Version bump to 2.2.2
-  * sci-chemistry/openbabel-perl: Version bump to 2.2.2
-  * remove old version of cadabra
-  * update to cadabra 1.14
-  * Deleted old ebuild.
-  * Version bump.
-  * change Grass to wxwidgets USE flag
-  * add qgis libe ebuild for SVN trunk
-  * Fix up patch to apply to rc1
-  * Modified patch
-  * anifest
-  * add a copy of pymol-1.2_rc1-shaders.patch too...
-  * Changelog
-  * fix Manifest
-  * copy pymol-1.2_rc0-data-path.patch pymol-1.2_rc1-data-path.patch
-  * clipper bump
-  * mtz2sca DESCRITPION fixed
-  * mtz2sca added
-  * Initial add mtz2hkl Thanks to jlec for writting this ebuild pending bug is 278048
-  * fix manifests after merge conflict and wrong choice :-/
-  * change the postgres dep for qgis and grass
-  * now cns Manifest is fixed
-  * cns manifest fix
-  * fixed bug 277829
-  * clipper depends on fftw
-  * readded the j1 in ccp4
-  * Fix attribution
-  * New package, bug 119636
-  * live ebuilds are live ebuilds and do not have reviesions
-  * ccpn -- QA typo fixed and old patch removed
-  * clipper LDADD -> LIBADD
-  * ccp4 --disable-mosflm
-  * aria added to overlay
-  * fixed src-tarball name for aria
-  * cns -- aria support, ixes for bug 247579 and 276308, LDFLALGS are respected now, some QA
-  * ccpn -- python[ssl]
-  * fixed drawxtl dep to fltk:1,1
-  * pymol -- media-video/mpeg-tools dep added
-  * remove keywords
-  * make sure gdal does not compile against grass and make qgis depend on this fixed gdal version
-  * make sqlite optional for qgis-1.1.0 and clean up some issues
-  * sci-geosciences/qgis - remove unneeded patch, add development version
-  * update deps - in java overlay
-  * update deps - in java overlay
-  * initial import of new versions of Grass, QGIS, gdal and gdal-grass. The gdal-grass lib will resolve the current situation of circular dependencies between gdal and grass in portage and make depending on gdal-grass support easier.
-  * coor clipper dependency fixed
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * treectrl bump
-  * mpi.eclass:  mpi_doman fixes.
-  * Version bump. Changed dependency and added test (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
-  * pymol -- vmd and numpy support added
-  * mosflm CFLAGS fix -- Thanks Donnie for pointing that out
-  * In main tree
-  * pymol bump to secaond release candidate for 1.2
-  * drawxtl fix -- upstream ships objects
-  * drawxtl version bump thanks Hannes Krüger for the ebuild
-  * refmac version bump and test QA
-  * pymol has two buildsstems. We use the distutils one.
-  * rci ebuildlayout fixed
-  * resort dependencies in ccp4
-  * ccp4i depends on media-gfx/graphviz
-  * ccp4i baubles fix
-  * cctbx is depending on shelx for amd64
-  * pointless bump
-  * Donnie says pointless works for him
-  * xia doesn't use specific pointless version
-  * xdsi kpdf -> xpdf fix
-  * In gentoo-x86
-  * In gentoo-x86
-  * xdsi dep fix
-  * another syntax fix
-  * reverted
-  * CCP4_SCR fixed
-  * ccp4i -- superpose renamed to superpose-ccp4
-  * missing dep of xia2 added
-  * ccp4-libs aadditional bin installation
-  * xia license changed to BSD
-  * xia depends on right ccp4 version
-  * ccü4 needed for xia
-  * xia version bump
-  * balbes-db now in right place
-  * ccp4 userpriv and usersandbox fixed
-  * ccp4 upstream ctruncate patch included next version added
-  * caver bump
-  * cealign QA
-  * masked ccp4 6.1.2
-  * molrep bump
-  * sys-cluster/pyslice: Forgot to commit the ChangeLog.
-  * sys-cluster/pyslice: Version bump.  Fixed DEPEND and RDEPEND.
-  * sci-mathematics/mdp: Version bump.  Fixed DEPEND and RDEPEND.
-  * sci-geosciences/tappy: Version bump. Fixed DEPEND and RDEPEND.
-  * sci-geosciences/tappy: Version bump.  Fixed DEPEND and RDEPEND.
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * sci-mathematics/mdp: Version bump to 2.5.  Fixed DEPEND and RDEPEND.
-  * newbin > exeinto+newexe.  Thanks jlec
-  * refmac bump, test still broken
-  * Fix empi install location.
-  * pymol 1.2 rc0
-  * pymol nosplash fix for Je_fro
-  * refmac test.log patch fix
-  * metadata.xml fixed
-  * refmac test improved
-  * xdsi added
-  * xdsstat-bin added
-  * pymol src_unpack fix (thanks to Rene Meier)
-  * refmac bump
-  * empi:  Fix the location of the changelog.
-  * Bump mpi.eclass.  See sys-cluster/empi-0.6 ChangeLog for details.
-  * Remove app-admin/eselect-mpi, included in sys-cluster/empi.
-  * Bump empi-0.6, see included changelog for details.
-  * Version bump (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
-  * Initial import pywcs
-  * Initial import of aplpy
-  * Added dependency on libtool-2 and szip-2
-  * another pymol splash fix
-  * coot live fix
-  * refmac fixes and version bumps
-  * monomer fix
-  * refmac version bump hosting of apbs patch
-  * refmac -- make download of test sets conditionally
-  * test version of hdf5-1.8.x import
-  * test version of hdf5-1.8.x import
-  * refmac test case added
-  * monomer-db crap fixed
-  * refmac experimental version bump
-  * final fix for update-monomers-db
-  * automatic bump
-  * automatic bump
-  * automatic bump
-  * automatic bump
-  * automatic bump
-  * automatic bump
-  * automatic bump
-  * fix of update-monomers-db
-  * automatic bump
-  * talos+ QA
-  * refmac bump
-  * [metadata] add metadata layout.conf and git ingore for users who wants to use cache generated by layman
-  * refmac bump
-  * masked gromacs live ebuilds
-  * sci-chemistry/gromacs: added live ebuilds for old, stable, experimental branch (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * sci-chemistry/gromacs-4.0.4: Fixed some repoman errors (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
-  * in portage
-  * masked new monomer-db
-  * monomer-db reversioning and addition of "maybe" unstable monomer-db This has to be involved
-  * refmac unstable bump and dep to new monomer-db added
-  * dev-python/h5py-1.1.0:  Fix SRC_URI and digest.
-  * [sci-chemistry/icm] Add new ebuild (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
-  * keyworded coot-9999.ebuild and added new coot-data as dependency
-  * simplify apbs patch for pamol -- Donnie told to go the most easy way for the maintainer
-  * cara rdepend fixed
-  * sci-visualization/ferret-bin: Forgot to commit the Changelog.
-  * sci-geosciences/xtide: Fixed copyright years. Removed '~x86' from keywords because repoman complained.
-  * sci-libs/scikits_timeseries-0.91.1: Fixed DEPEND, RDEPEND, and metadata.xml.
-  * sci-visualization/ferret-bin-6.1: Fixed RDEPEND.
-  * sci-libs/scikits_timeseries-0.91.1.ebuild:  Initial ebuild.  Please file bugs at http://bugs.gentoo.org/show_bug.cgi?id=274430
-  * sci-visualization/ferret-bin-6.1.ebuild:  Initial ebuild.  Report bugs at http://bugs.gentoo.org/show_bug.cgi?id=274425
-  * pymol bump to beta7
-  * >=dev-lisp/cmucl-19e : needed by sci-mathematics/pvs
-  * Hopefully last patch to opendx for a while
-  * shiftx added
-  * digest
-  * Manifest
-  * fix patch
-  * Add fix from Christian Becke in bug #237634. Hopefully this doesn't break things for anyone else :)
-  * Remove old sys-cluster/hpl version.
-  * Sync sys-cluster/hpl with gentoo-cvs
-  * Remove old openmpi versions.
-  * Openmpi to EAPI=2, Sync ebuild with gentoo-cvs. Fix install location of vt include files when using empi.
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * Merge branch 'freefem++-3.3'
-  * sci-mathematics/freefem++: Version bump, now FHS comliant.
-  * ccp4 -- molref not installed anymore -> linked against libs we don't want to depend on
-  * frama-c: more clean ups.
-  * clean ups.
-  * sci-geosciences/tcd-utils: Correct bug in 20080820 ebuild, no longer needs $S specified.
-  * sci-geosciences/tcd-utils: Version bump to 20080820.  Updated copyright year.
-  * sci-geosciences/swmm: Missed the Manifest file.
-  * sci-geosciences/harmonics-dwf-free-noncomm: Fixed header copyright date.
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * sci-geosciences/harmonics-dwf-free: Version bump to 20081228.
-  * sci-geosciences/harmonics-dwf-free-noncomm: Version bump to 20081228.
-  * sci-geosciences/libtcd: Version bump to 2.2.4.  Add 'non-commercial' use flag to use.local.desc.
-  * ccp4libs cleanup
-  * pointless fix dependency
-  * ccp4-libs another linking problem fixed
-  * ccp4 examples are now optional
-  * another linking thing in ccp4-libs
-  * working pointless for Donnie
-  * pymol rekeyworded
-  * talos+ written
-  * [sys-block/tgt] Update deps (Portage version: 2.2_rc33/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sys-block/tgt] Update patch (Portage version: 2.2_rc33/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sys-block/tgt] Fix Makefile (Portage version: 2.2_rc33/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sys-block/tgt] Fix install (Portage version: 2.2_rc33/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sys-block/tgt] Fix install (Portage version: 2.2_rc33/git/Linux x86_64)  (Unsigned Manifest commit)
-  * [sys-block/tgt] Initial import (Portage version: 2.2_rc33/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-geosciences/swmm Version bump + minor change to edit Makefile
-  * dev-python/h5py: Version bump to 1.1.0
-  * masked pointless
-  * cctbx should be linkable now
-  * pointless added
-  * talos+ added
-  * nmrpipe is on the way to be fixed
-  * cctbx fixes
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * xds-bin: bump to 20090327.
-  * fixed coot KEYWORD
-  * mask live ebuilds
-  * live coot added
-  * pymol live ebuild added
-  * refmac bump and fix the eclass usage
-  * coot: fix as-needed build.
-  * Fix mrbayes building with mpi but without empi.
-  * coot fixed
-  * coot QA fixes and EAPI="2" for Donnie
-  * refmac qa
-  * Add a mpi.eclass version of mrbayes.
-  * rasmol QA
-  * cleaner glibc-2.10 fix in ccp4
-  * updated version of coot -- upstream includes our patches
-  * ccp4-libs version cleanup
-  * coot prereleases added
-  * ccp4-lins fix for glbic-2.10 (getline problem) bug 270615
-  * ccp4 glibc-2.10 getline fix bug 270617
-  * refmac experimental version bumped
-  * Fixing Manifest and EAPI location in LiE, modglue and cadabra
-  * mama manifest fixed
-  * opencascade now implictly rely on X when USE="opengl"
-  * phaser should work now
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * missing phaser patch added
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * phaser added thanks to Johan Hattne
-  * phaser licenses added
-  * old cctbx version removed
-  * refmac experimental version bump
-  * refmac bump to refmac-5.5.0095
-  * mmtk: set PYTHON_MODNAME.
-  * gabedit: new ebuild for a computational chemistry GUI.
-  * patch fixed
-  * mgltools manifest fixation
-  * nmrpipe version bump to 5.0.2009.103.20.08
-  * nmrpipe
-  * Manifest fix
-  * last fix of nmrpipe env, now it works
-  * another fix in the nmrpipe env file
-  * new nmrpipe env
-  * mmtk: fix location of .so modules, and dep on Scientific >=2.6.
-  * mmtk: bump to 2.6.0.
-  * manifest fix
-  * version bump of refmac A problem related with TLS has been fixed. The problem was that not in all cycle TLS contributions were added to B values and that could make refinement unstable.
-  * mgltools-webservices dependency fix
-  * zsi removed -- in tree
-  * clipper version bump
-  * sci-mathematics/freefem++: New ebuild for freefem++-3
-  * in tree
-  * Moving definition of INSPATH
-  * Add arches for testing
-  * Fix dying
-  * [sci-chemistry/pdb2pqr] Drop accidently added keywords and add gcc-4.4 patch (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
-  * masked nmrpipe-9.27.2009.120.14.28 for tsting
-  * prelimary ebuild of nmrpipe
-  * masked nmrpipe
-  * clipper version bump
-  * refmac version bump
-  * fixed a typo
-  * mask gnuplot-cvs
-  * added gnuplot-cvs ebuild (Portage version: 2.1.6.11/git/Linux i686)  (Signed Manifest commit)
-  * added dev-tex/picins (Portage version: 2.1.6.11/git/Linux i686)  (Signed Manifest commit)
-  * ccpn added missing dep and fixed python > 2.4 incompatibility
-  * added sci-libs/xdrfile-1.1b (Portage version: 2.1.6.11/git/Linux i686)  (Signed Manifest commit)
-  * Manifest fix
-  * fixed a typo in clipper-config and migrated frem sed to patch
-  * clipper-config changes included
-  * Add ~amd64 keyword and gcc-4.4 patch (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
-  * clipper-config fixed
-  * dev-tcltk/img_rotate added
-  * anigif update
-  * correct versioning of zsi in dev-python/opal-client
-  * sci-chemistry/mgltools fix USEdep
-  * sci-chemistry/mgltools-stride missing license added
-  * sci-chemistry/mgltools-utpackages missing license added
-  * UTPackages license added
-  * mgltools unmasked
-  * old togl removed
-  * sci-chemistry/mgltools-opengltk cannot depend on external togl
-  * dev-tcltk/togl-1.7 added, needed by mgltools
-  * dev-python/zsi upstream released the alpha
-  * mgltools-webservices another fix
-  * mgltools-volume another fix
-  * mgltools-visionlib another fix
-  * mgltools-vision another fix
-  * mgltools-viewer-framework another fix
-  * mgltools-utpackages another fix
-  * mgltools-symserv another fix
-  * mgltools-support another fix
-  * mgltools-stride another fix
-  * mgltools-sff another fix
-  * mgltools-scenario another fix
-  * mgltools-qslimlib another fix
-  * mgltools-pyglf another fix
-  * mgltools-pybabel another fix
-  * mgltools-pyautodock another fix
-  * mgltools-pmv another fix
-  * mgltools-opengltk another fix
-  * mgltools-networkeditor another fix
-  * mgltools-molkit another fix
-  * mgltools-mglutil another fix
-  * mgltools-gle another fix
-  * mgltools-geomutils another fix
-  * mgltools-dejavu another fix
-  * mgltools-cmolkit another fix
-  * mgltools-bhtree another fix
-  * mgltools-autodocktools another fix
-  * sci-chemistry/mgltools fixup
-  * sci-chemistry/mgltools-autodocktools fixup
-  * sci-chemistry/mgltools-bhtree fixup
-  * sci-chemistry/mgltools-cmolkit fixup
-  * sci-chemistry/mgltools-dejavu fixup
-  * sci-chemistry/mgltools-geomutils fixup
-  * sci-chemistry/mgltools-gle fixup
-  * sci-chemistry/mgltools-mglutil fixup
-  * sci-chemistry/mgltools-molkit fixup
-  * sci-chemistry/mgltools-networkeditor fixup
-  * sci-chemistry/mgltools-opengltk fixup
-  * sci-chemistry/mgltools-pmv fixup
-  * sci-chemistry/mgltools-pyautodock fixup
-  * sci-chemistry/mgltools-pybabel fixup
-  * sci-chemistry/mgltools-pyglf fixup
-  * sci-chemistry/mgltools-qslimlib fixup
-  * sci-chemistry/mgltools-scenario
-  * sci-chemistry/mgltools-sff fixup
-  * sci-chemistry/mgltools-stride fixup
-  * sci-chemistry/mgltools-support fixup
-  * sci-chemistry/mgltools-symserv fixups
-  * sci-chemistry/mgltools-utpackages fixups
-  * sci-chemistry/mgltools-viewer-framework fixup
-  * sci-chemistry/mgltools-vision misses file to install
-  * sci-chemistry/mgltools-vision fixup
-  * sci-chemistry/mgltools-visionlib fixup
-  * sci-chemistry/mgltools-volume fixup
-  * sci-chemistry/mgltools-webservices fix little typo
-  * sci-chemistry/mgltools-webservices fixup
-  * sci-chemistry/mgltools little fix
-  * sci-chemistry/mgltools masked for testing
-  * sci-chemistry/mgltools added
-  * manifest fix
-  * sci-chemistry/mgltools-autodocktools added
-  * sci-chemistry/mgltools-dejavu added
-  * sci-chemistry/mgltools-molkit added
-  * sci-chemistry/mgltools-networkeditor
-  * sci-chemistry/mgltools-pmv added
-  * sci-chemistry/mgltools-pyautodock added
-  * sci-chemistry/mgltools-pybabel added
-  * mgltools-qslimlib added
-  * mv libgfx from media-gfx to media-libs
-  * media-gfx/libgfx added
-  * sci-chemistry/mgltools-support added
-  * sci-chemistry/mgltools-utpackages aadded
-  * sci-chemistry/mgltools-viewer-framework added
-  * sci-chemistry/mgltools-vision added
-  * sci-chemistry/mgltools-visionlib added
-  * sci-chemistry/mgltools-volume added
-  * sci-chemistry/mgltools-WebServices added
-  * sci-chemistry/mgltools-bhtree added
-  * Manifest fix
-  * sci-chemistry/mgltools-cmolkit added
-  * sci-chemistry/mgltools-geomutils added
-  * sci-chemistry/mgltools-gle added
-  * mgltools-mglutil added
-  * Manifest fix
-  * sci-chemistry/mgltools-opengltk added
-  * togl updated
-  * Togl license removed as it is BSD
-  * sci-chemistry/mgltools-pyglf added
-  * sci-chemistry/mgltools-scenario added
-  * simpy version bump
-  * sff small change
-  * sci-chemistry/mgltools-sff added
-  * mgltools-samserv added
-  * little fix in mgltools-stride
-  * mgltools-stride added
-  * Update scalasca ebuild (Portage version: 2.1.6.11/git/Linux i686)  (Signed Manifest commit)
-  * refmac fix
-  * ccp4i manifest fix
-  * Added to portage
-  * fixed a bug in scalasca (Portage version: 2.1.6.11/git/Linux i686)  (Signed Manifest commit)
-  * sci-mathematics/freefem++: cleanup, fix copyright notice and Manifest
-  * app-vim/freefem++-syntax: cleanup, fix copyright notice and Manifest
-  * added scalasca licence
-  * added sys-cluster/scalasca ebuild (Portage version: 2.1.6.11/git/Linux i686)  (Signed Manifest commit)
-  * Added sci-physics/espresso ebuild (Portage version: 2.1.6.11/git/Linux i686)  (Signed Manifest commit)
-  * fix typo (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
-  * add mounting facility support for initscript in case of using nufa (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
-  * Update ebuild (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
-  * Update ebuild (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
-  * Update ebuild (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
-  * Update ebuild (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
-  * Add glusterfs. big #167955 (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
-  * QA review of dssp
-  * sci-chemistry/dssp added
-  * ccp4i clean up
-  * dssp license added
-  * Manifest fixed for updated patches
-  * ccp4 upstream patch included -- bug 269504
-  * ccp4 upstream patch included -- bug 269504
-  * ccp4 upstream patch included -- bug 269504
-  * ccp4i QA
-  * sci-chemistry/chooch autotools based build system fixed
-  * moved sci-libs/chooch to sci-chemistry/chooch part two
-  * moved sci-libs/chooch to sci-chemistry/chooch
-  * sci-libs/chooch unmasked
-  * chooch working verion ready
-  * fix opendx manifest before pushing to the overlay
-  * small fix to an opendx patch.
-  * Nothing in overlay should be executable
-  * patches should not be executable
-  * Licenses should not be executable
-  * secong typo fixed
-  * Manifest fixation (Portage version: 2.2_rc33/git/Linux x86_64)  (Unsigned Manifest commit)
-  * New package: sci-mathematics/4ti2 Corresponding bug is #269472
-  * fixed typo
-  * bump almost to adept to boost 1.3.6
-  * new revision of opendx and import of a new version of opendx-samples to cope with it.
-  * fixed bug 266470
-  * zsi SRC_URI fixed.
-  * direx unmasked
-  * direx license added
-  * direx ebuild completed
-  * thanks alexxy for breaking my push
-  * sorry for segf with eix
-  * Rename wrong ebuild (Portage version: 2.2_rc33/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * mask direx
-  * direx added but masked
-  * refmac Manifest fix
-  * refmac experimantel version bump
-  * Fix for bug #268064
-  * Updated a dependency
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * Fixes an issue with docs improved ebuild
-  * litlle QA
-  * updated digest. sorry.
-  * Proper patch for frama-c
-  * I've separated two patches for consistency.
-  * DESCRIPTION corrected
-  * DESCRIPTION corrected
-  * Fixed typos in Changelog
-  * New package sci-mathematics/polymake
-  * Latest added to portage, thanks!
-  * csrosetta-pdbh added
-  * csrosetta-angless cp section gives response now
-  * csrosetta-cs added
-  * csrosetta-angless added
-  * blast-db can include one db more
-  * RCI added
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * ntl --  bumped the ebuild to 5.5. Fixed error if LDFLAGS have "--" inside.
-  * Fix license
-  * New package sci-biology/newbler
-  * moving to portage
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * Moved to portage
-  * Moved exonerate to portage.
-  * perlprimer updated ~x86 added and one dep fixed
-  * cleand up
-  * adopted balbes-db to new monomers-db package
-  * Another fix of coot-data PATHs
-  * New package
-  * sci-biology/ncbi-tools++ fixed libdir (Portage version: 2.2_rc31/git/Linux i686)  (Unsigned Manifest commit)
-  * zsi SRC_URI changed
-  * update of update-monomer-db
-  * opal-python blocks sci-chemistry/apbs-1.1.0
-  * fix ccp4 data dir path in coot-data
-  * fix ccp4 data dir path in monomer-db
-  * fixed data dir path in ccp4-libs
-  * New package
-  * aloow tcl/tk-8.5 with imosflm
-  * rewind the mask of imosflm as it totally broken with tcl 8.5
-  * mask sci-chemistry/imosflm-1.0.0-r1.ebuild test version for tcl/tk-8.5
-  * refmac bump
-  * coot-data fix
-  * monomer-db install path corrected dudes be carefull when setting such things
-  * coot-data bumped to reflect the existence of sci-libs/monomer-db
-  * bumped experimental refmac and adopted patch
-  * cleaned molrep and added src_test
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * fix epatch (Portage version: 2.2_rc31/git/Linux x86_64)  (Signed Manifest commit)
-  * add block to apbs (Portage version: 2.2_rc31/git/Linux x86_64)  (Signed Manifest commit)
-  * needed apbs bump
-  * more molrep fixes
-  * molrep version bump and some fixes
-  * update-monomers-db added
-  * sci-libs/monomer-db added
-  * imosflm HOMEPAGE fixed
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * ccp4-libs: moved momoner-db to seprate ebuild
-  * refmac 5.6 masked
-  * refamc bumped to experimental version
-  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
-  * moved scripts from Documentation to scripts part 2
-  * moved scripts from Documentation to scripts
-  * New Package: sci-mathematics/Macaulay2 (Bug #246095)
-  * first version of automatic bump script for blast-dbs checked in
-  * fixed install phase (Portage version: 2.2_rc31/git/Linux x86_64)  (Unsigned Manifest commit)
-  * New package
-  * removed bundled opal and ZSI from apbs (Portage version: 2.2_rc31/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-chemistry/tinker ~amd64 added see bug 263006 (Portage version: 2.2_rc31/git/Linux x86_64)  (Unsigned Manifest commit)
-  * fix cadabra's manifest
-  * sci-chemistry/jmol update to 11.6
-  * sci-chemistry/tinker LDFLAGS respect added and X support removed because jav3d-bin is totaly broken but there is a src package in java-overlay dev-java/j3d-core
-  * bug 262905 digest thing fixed
-  * Manifest fix
-  * apbs checkin
-  * version bump of pdb2pqr
-  * dev-python/opal-client fix DEST PATH
-  * Manifest fix
-  * dev-perl/opelclient added
-  * ChnageLog entry added
-  * zsi version bump
-  * opal license added
-  * cleanup
-  * New package, bug 121921
-  * removed guile-gui as it is keyworded in the tree now
-  * Fix DEPEND line
-  * cleaning of the cadabra related ebuilds.
-  * continuing opendx renovation
-  * Important bump of ccpn which fixes the 1D bug
-  * Removed herwig and cernlib-montecarlo, changed applied to the tree
-  * New package
-  * Bump
-  * importing opend from the main tree
-  * fix coot license to GPL-3 which has been changed since 	 Jul 02, 2007
-  * Added zarja
-  * another qa for pymol Thanks bicatali
-  * QA on pymol
-  * removed flexdock as it is already in java-experimental
-  * app-arch/lbzip2 fixed src_test according to the suggestions of Daniel Lin
-  * Manifest fix
-  * fixes things from lbzip2
-  * removed additional patchs
-  * dev-java/flexdock-0.5.1 added It is a dep of the new scilab version
-  * removed use description from old packages
-  * lbzip2 version bump and src_test fix
-  * fix missing files in install
-  * app-arch/lbzip2 added
-  * rosetta USE="doc" is broken --> removed. See online docs instead https://www.rosettacommons.org/software/academic/3.0/rosetta3_user_guide/
-  *  "sci-chemistry/rosetta-tools added"
-  * refmac version bump to ...90
-  * sci-chemistry/rosetta added
-  * dev-libs/libunzip added
-  * renamed:    generate_tarball.sh -> generate_boinc-src_tarball.sh fixed:		libboinc_zip.a can now be build 			uses system libzip.a and libunzip.a
-  * To main tree
-  * sci-mathematics/freefem++: fix building the documentation with >=app-text/texlive-2008 app-vim/freefem++-syntax: moved download location to omploader
-  * pymol version bump to beta 6
-  * blast-db added
-  * rosetta-fragments added
-  * psipred added
-  * license psipred added
-  * rosetta-db DESCRIPTION changed
-  * fix some zip things in generate_tarball.sh
-  * Edited generate-tarball.sh so that only the bundled zip stuff is kicked out but the libboinc_zip.a could still be build
-  * cleaned the sci-libs/symmetrica ebuild by porting it to EAPI2
-  * changed the homepage for sci-libs/modglue
-  * Removed udav now in main tree
-  * Removed scidavis now in main tree
-  * rosetta licenses added
-  * sci-chemistry/ccpn version bump to 2.0.7
-  * removed libf2c, now in main tree
-  * phun-5.28.ebuild
-  * sci-chemistry/ambertools removed as I gave up getting chimera in
-  * added a patch for cadabra solving the --as-needed problem
-  * To main tree
-  * frama-c and why + dependencies new ebuilds
-  * To main tree
-  * New package sci-biology/mauve
-  * libmems, libmuscle, libgenome - deps of sci-biology/muscle
-  * updating manifest related to cadabra
-  * Importing cadabra and its dependencies modglue and lie
-  * Fix license
-  * New package sci-biology/shrimp
-  * New package sci-biology/mpiblast
-  * Removed mathgl, in main tree
-  * tnt version bump
-  * pyglet version bump
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * Fix manifest, again
-  * Remove envd file from ebuild and manifest as well.
-  * Remove envd file, no longer necessary.
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * sys-cluster/mpich2 Manifest fix
-  * sys-cluster/mpich2:  fix #259805 by backing out the site-packages fix.  It'll be better off just sent directly to upstream.
-  * Fix undeclared local variable.
-  * Phun version bump
-  * New package sci-biology/signalp
-  * New license signalp for package sci-biology/signalp
-  * pymol version cleanup and patch fix
-  * USE lua added to cara
-  * !media-libs/raptor removed from ccp4
-  * sci-chemistry/ccp4 unmacked
-  * sci-chemistry/ccp4i bump due to change in recmac5.tcl
-  * sci-chemistry/ambertools update but still problems
-  * reviewed version of clapack
-  * sci-libs/clapack RDEPEND missing
-  * sci-libs/clapack added
-  * removed .svn and added ChengeLog entry
-  * dev-libs/libf2c version bump
-  * sci-chemistry/ambertools added
-  * sci-chemistry/ambertools masked
-  * www-apps/SwishE added
-  * dev-scheme/guile-gui added for testing on ~amd64 pending bug is 259599
-  * tr src_install fixed
-  * sys-devel/ucpp added
-  * x11-libs/tr added
-  * mmtk Chnagelog added
-  * sci-libs/mmtk add with version bump and ~amd64
-  * Merge branch 'sci-libs/mmtk-import'
-  * sorry duplicated package to tree package
-  * sci-chmistry/mdtools added
-  * media-libs/freejpeg initial checkin
-  * sci-libs/msms added -> bug 209161
-  * dev-tcltk/togl added
-  * Removed ggobi, now in main tree
-  * apbs docs installation to the right place
-  * apbs: Ugly automagic removed make --> emake
-  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * add support for OFED-1.4.1-rc2
-  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
-  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
-  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
-  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
-  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
-  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
-  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
-  * fix openib-diags (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
-  * fix typo (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
-  * fix opensm (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-libs/libcmatrix license fixed
-  * sci-chemistry/gsim die added
-  * sci-chemistry/gsim added
-  * sci-libs/libcmatrix include destination fixed
-  * Fix digests for openmpi.
-  * sci-libs/libcmatrix added
-  * Bump openmpi-1.3.1
-  * apbs fix of doc installation dir
-  * tinker fix see bug 241180
-  * fix for apbs
-  * sci-chemistry/pymol APBS_PSIZE fix
-  * use deps fix in apbs
-  * sci-chemistry/apbs update Bug 262905
-  * dev-libs/punc created
-  * sci-libs/superlu update to 3.1
-  * sci-libs/libssm added (Portage version: 2.2_rc25/git/Linux x86_64)  (Unsigned Manifest commit)
-  * In main tree
-  * sci-chemistry/openbabel-python: Fix S
-  * Made some changes to the ebuild, do not configure in the src_unpack phase.
-  * sci-chemistry/pymol-plugins-cealign added
-  * sci-libs/balbes-db RESTRICT="binchecks strip" to save time
-  * sci-chemistry/refmac version bump to 5.5.0089 \n older versions removed (Portage version: 2.2_rc25/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Manifest fixed (Portage version: 2.2_rc25/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-chemistry/ccp4i conflict of rapper with media-libs/raptor (Portage version: 2.2_rc25/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-chemistry/ccp4 repper --> rappermc renaming
-  * sci-libs/cctbx another step to the end moved installdir from pothonsitedir to ${CCP4}/ (Portage version: 2.2_rc24/git/Linux x86_64)  (Unsigned Manifest commit)
-  * pdb-extract file collision conflict solved
-  * sci-visualization/xds-viewer uses new features from cmake-utils.eclass (Portage version: 2.2_rc24/git/Linux x86_64)  (Unsigned Manifest commit)
-  * cctbx fixing sinstalltion of some shell scripts
-  * xds input templat compression changed (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-libs/cctbx total rewrite of src_install (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * cctbx-2009.02.15.2320-r2 masked
-  * Change versioning to match internal package versioning
-  * New package sci-biology/miranda
-  * New package sci-biology/miranda
-  * sci-chemistry/xds-bin EPAI2fied (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-chemistry/pymol version bump to 1.2b5 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * sci-chemistry/phaser masked until all tests are passed
-  * New package sci-biology/infernal
-  * xds-viewer version bump to 0.6
-  * sci-chemistry/ccpn now respects LDFLAGS and is as-needed ready
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * cctbx scons fixes ASRP license added
-  * sci-libs/pycifrw initial checkin
-  * In gentoo-x86
-  * coot: update ccp4-libs/clipper deps to current versions.
-  * Remove -static
-  * Add metadata
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * cctbx now depends on system scons
-  * Remove webcheck option by default
-  * Fix changelog
-  * New package sci-biology/plink, bug 224017
-  * sci-libs/cctbx fixed and initial push Have fun and don't complain: THE BUILDSYSTEM IS CRAPPY!
-  * Merged sci-libs/cctbx from my overlay into sci overlay sci-chemistry/cbflib fixing LDFLAGS respect
-  * revert messed up commits
-  * sci-chemistry/xia version bump to 0.2.7.2 and fixing fperms --> chmod
-  * corrected linking gcc-config -X --> gcc-config -L
-  * ccp4i first patch set included
-  * sci-libs/balbes wierd code fixes
-  * sci-libs/clipper added as RDEPEND because it sin't build anymore
-  * New package sci-biology/mothur
-  * New package sci-biology/dotur
-  * New package sci-biology/dotur
-  * New package sci-biology/dotur
-  * sci-chemistry/openbabel-ruby: Version bump to 2.2.1
-  * sci-chemistry/openbabel-python: Version bump to 2.2.1
-  * sci-chemistry/openbabel-perl: Version bump to 2.2.1
-  * ccp4i: fixes for finding smartie.
-  * ccp4: try to get PYTHONPATH right.
-  * ccp4,ccp4i: rename truncate to ftruncate, build clipper progs, cleanup.
-  * clipper: bump, and stop installing examples.
-  * last cctbx changes
-  * libxdl_view: fix with --as-needed by linking libX11/libXt & adding deps.
-  * ccp4: reindent deps.
-  * ccp4: clean up cruft in weird places (files/delete/, *.bak).
-  * coot: pull in newly split clipper.
-  * ccp4-libs: make it suck less.
-  * clipper: bump to 20081201
-  * sci-chemistry/rasmol dep fix (x11-libs/vte)
-  * sci-libs/cbflib total cleanup include dir permissions fixed
-  * ccp4-libs nearly good linking
-  * rasmol fixed dep --> x11-libs/vte bug 238302
-  * sci-libs/cbflib cleanup
-  * coot: keyword ~amd64.
-  * sci-libs/chooch has automagic deps which aren't fixed --> masked
-  * Nessecary fixes in src. Should be fine now.
-  * cgraph.h installation fixed linking fixed
-  * sci-chemistry/Cgraph submitt
-  * sci-chemistry/ccp4 patch cleanup sci-chemiszty/chooch added sci-libs/cgraph added
-  * sci-chemistry/molrep added
-  * libjwc* docs not installed
-  * changed mosflm dep to build w/o ccp4
-  * x11-libs/libjwc_c/f added
-  * x11-libs/xdl_view added
-  * sci-chemistry/openbabel-ruby: Remove untested arches
-  * sci-chemistry/openbabel-perl: Remove untested arches
-  * sci-chemistry/openbabel-python: Add RDEPEND for OASA and PIL
-  * keyword amd64
-  * New package sci-biology/codonw
-  * sci-chemistry/openbabel-python: Fix ChangeLog
-  * sci-chemistry/openbabel-ruby: Fix ChangeLog
-  * sci-chemistry/openbabel-perl: Fix ChangeLog
-  * sci-chemistry/bkchem: Fix ChangeLog
-  * sci-chemistry/bkchem: Split out OASA library (now in sci-libs/oasa)
-  * New package sci-libs/oasa (split from BKChem)
-  * fix Manifest
-  * New package sci-biology/bowtie
-  * sci-libs/bables-db Changelog added
-  * Merged sci-libs/balbes-db in from dberkholz overlay
-  * Removed scamp, now in main tree
-  * masked ccp4
-  * Merge sci-chemistry/ccp4 from dberkholz overlay to sci fixed missing files in mrbump fixed msflm deps
-  * balbes-db clean up for merge
-  * sci-chemistry/xia2 metadata.xml added
-  * Merged sci-chemistry/xia2 from dberkholz overlay to sci
-  * sci-visualization/xds-viewer Good that no one tests my packages so typos won't harm. Typo in SRC_URI fixed
-  * Fixing dependencies of xds-viewer
-  * In gentoo-x86
-  * In gentoo-x86
-  * sci-biology/phred in gentoo-x86
-  * New package sci-biology/samtools
-  * sci-chemistry/refmac version bump to 5.5.0088
-  * QA and doc building
-  * QA and doc building
-  * sci-chemistry/xds version bump at 30 Jan 2009 and handling X changed
-  * sci-visulization/xds-viewer added
-  * sci-chemistry/chemtool: Fix ChangeLog
-  * sci-chemistry/chemtool: Remove unneeded files
-  * Manifest fixed
-  * sci-chemistry/cara keyworded for ~amd64
-  * Version bump (Portage version: 2.2_rc23/git/Linux i686)  (Unsigned Manifest commit)
-  * sci-chemistry/easychem: Fix strip, bug #252034
-  * sci-chemistry/chemtool: Add ebuilds from tree, bug #219528
-  * manifest fixed
-  * sci-chemistry/pymol version bump to 1.2beta4
-  * sci-chemistry/bkchem: Version bump to 0.13.0
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * fixed revision for pymol-1.2_beta3
-  * Adjusted Manifest
-  * Verion bump
-  * remove sed patch
-  * sci-libs/gmsh Version bump
-  * Push Vampir Trace includes to a subdir.  #257086
-  * sci-chemistry/stdinchi: Add doc use, fix prestriped files, make honor CFLAGS
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * Add 'append-ldflags' to facilitate building for users with --as-needed.
-  * New package sci-chemistry/stdinchi
-  * sci-chemistry/wxmacmolplt: Put -lGLU back in configure
-  * sci-chemistry/wxmacmolplt: Fix DEPEND vs RDEPEND
-  * sci-chemistry/wxmacmolplt: Set wxGTK opengl use dependency, flash use
-  * sci-chemistry/bkchem: Version bump to 0.12.6
-  * sci-chemistry/openbabel-ruby: Use EAPI=2, fix swig use
-  * sci-chemistry/openbabel-python: Use EAPI=2, fix swig use
-  * sci-chemistry/openbabel-perl: Use EAPI=2, fix swig use
-  * imosflm deps fixed and unmasked
-  * New package sci-chemistry/openbabel-ruby, #212212
-  * New package sci-chemistry/openbabel-python, #212212
-  * New package sci-chemistry/openbabel-perl, #212212
-  * dev-tcltk/anigif added
-  * dev-tcltk/combobox added to sci overlay
-  * sci-chemistry/openbabel-2.2.0-r1: New ebuild with doxyfile patch, #212212
-  * New package sci-chemistry/bkchem, #95178 (Thanks to Beda Kosata)
-  * Merge branch 'master' of ../asd
-  * dev-tcltk/tablelist added
-  * tktreectrl MANIFEST and Changelog fix
-  * Merged dev-tcltk/tktreectrl into sci overlay
-  * sci-chemistry/ghemical: Added ghemical package
-  * Imosflm checked in but masked because deps are missing or tbw
-  * mosflm Changelog and manifest fised
-  * Merged sci-chemistry/mosflm from dberkholz overlay to sci overlay
-  * mosflm cleaned for merge
-  * sci-chemistry/rasmol ChangeLog
-  * sci-chemistry/rasmol intial checkin
-  * sci-libs/cbflib added
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * Remove unused local use flag from metadata for sys-cluster/openmpi.
-  * Bump sys-cluster/openmpi-1.2.9.
-  * Version bump\! (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * fixed totaly messed up mrbump src_install
-  * Make libgmxmopac7.a -fpic library (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
-  * Fix typo (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * sci-chemistry/mrbump added to overlay
-  * Cleaned sci-chemistry/mrbump
-  * Add support for qm/mm with mopac7 for gromacs (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Add mopac7 with support library for gromacs (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/ccp4i  moved from Dberkholz overlayy to sci Thanks Donnie
-  * Manifest fixing
-  * New package sci-biology/phred
-  * sci-chemistry/ccp4i made ready for merge
-  * removed old versions of ccpn as they use hardcoded things and latest is okey
-  * Make tk verion not hardcodded (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
-  * Add ~amd64 kyword to ccpn; make python not hardocded (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
-  * Moved to tree
-  * sci-chemistry/pymol bumped to 1.2 beta 3
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * Version bump.
-  * fix manifests
-  * version bump
-  * version bump
-  * New packages sci-biology/pals, piler, pilercr
-  * New package sci-biology/mreps
-  * New package sci-biology/lagan
-  * New package sci-biology/lagan
-  * new package sci-biology/trf
-  * GAMESS - Version bump (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
-  * Forgot to block the ccp4-6.0* series
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * Merged sci-chemistry/coot from dberkholz-overlay to sci-overlay version bump to 0.5.2 We now build against ccp4-libs
-  * Missing line continuation, #259209.
-  * Merged dev-scheme/guile-lib-0.1.6 from dberkholz overlay to sci overlay We need this for coot
-  * Merged sci-chemistry/coot updates from my overlay into dberkholz-overlay
-  * Merged x11-libs/guile-gtk from my overlay into sci-overlay This is an updated version of the tree ebuild Bug is 251793
-  * Merged sci-libs/ccp4-libs from dberkholz-overlay to sci overlay Thanks Donnie for your work on this
-  * sci-libs/ccp4-libs bumped to 6.1.1 and cleaned for merge into sci-overlay
-  * Update HOMEPAGE for icm (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
-  * Update deps for icm (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/refmac merged from dberkholz-overlay to sci-overlay
-  * Fix syntax (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
-  * Update icon for icm-broser (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * sci-chemistry/refamc bumped to latest version (5.5.0085) and polished to submitt into sci overlay
-  * Update deps for icm-broser (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Update deps for icm-broser (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
-  * Add block to icm-broser (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Add icm-broser (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Add menuentry for icm (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Added herwig flag to cernlib, see bug #257732
-  * Added herwig
-  * removing, now in main tree
-  * Various QA fixes
-  * fix compilation of wxmacmolplt (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
-  * sci-chemistry/almost missed to install to headers which are needed to build sci-chemistry/aqva against it.
-  * sci-chemistry/azara Typo fix so that LDFLAGS are respected
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * sci-chemistry/ccpn version bump to 2.0.6.1
-  * Add patch for gcc 4.3 (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
-  * Add wxmacmolplt bug #197131 (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
-  * add MolSoft licence
-  * Add icm-pro (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
-  * Fix manifest for mpich2 (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
-  * Added the skel files from tree so that  we can use tools like echangelog.
-  * Fix the mpich2 pkgconfig file, #257921.  Mark patchses to be sent upstream.
-  * aria and cns changes
-  * Update boinc generator script. now server should build.
-  * sci-chemistry/procheck moved from Donnies overlay to sci overlay
-  * cctbx openmp depency fixed
-  * sci-chemistry/pymol-1.2_beta added. I will maintain all beta versions in sci overlay.
-  * cctbx fixes with donnie
-  * [QA]: Add missing diags USE flag to IUSE
-  * [QA]: Remove redundant src_compile, fix SRC_URI for new location
-  * [QA]: We need EAPI=1 for SLOT dependencies
-  * [QA]: Remove redundant src_compile
-  * [QA]: Remove redundant src_compile
-  * [QA]: Remove redundant src_compile
-  * [QA]: change RESTRICT=nomirror to RESTRICT=mirror
-  * [QA]: Remove redundant src_compile
-  * Fix Manifest.
-  * [QA]: Add test to IUSE
-  * [QA]: Order categories file
-  * some things added, nothing to mention
-  * x11-libs/xview bump and sci-chemistry/nmrpipe
-  * Revert "Revert "sci-chemistry/ccpn numpy USE flag removed""
-  * Revert "sci-chemistry/ccpn numpy USE flag removed"
-  * sci-chemistry/ccpn numpy USE flag removed (Portage version: 2.2_rc23/git/Linux i686)  (Unsigned Manifest commit)
-  * Add patch to fix crash on startup with tcl8.5 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Re-manifest
-  * Added gasgano
-  * cpl: added wcs and gasgano support
-  * sci-electronics/stage: add SLOT
-  * sci-electronics/player: add SLOT
-  * cdsclient: version bump
-  * cdsclient: version bump
-  * Added bug ref
-  * pyglet version bump
-  * Clean up
-  * Clean up
-  * move boinc to the tree.
-  * One more CUDA fix (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
-  * fix cuda support (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
-  * Same as previous commit but this time for normal boinc.
-  * Add things noted by bicatali
-  * Added ggobi
-  * sys-cluster/openmpi-1.3:  Don't build Vampir Trace on sparc, #256529.
-  * cuda++
-  * Add our bundled init script.
-  * Remove bundled init scripts
-  * Bit cleanup in boinc.
-  * sci-chemistry/ccpn version bump  to 2.0.6
-  * sci-chemistry/almost added to sci overlay, bug 248455 (Portage version: 2.2_rc23/git/Linux i686)  (Unsigned Manifest commit)
-  * sci-chemistry/pdb-extract-3.004.ebuild added for testing pending bug is 249933
-  * sci-chemistry/azara and sci-chemistry/ccpn added to overlay
-  * uncommited files
-  * Patch to fix when using libtool-2.2+, #228183.  Also remove sweep to avoid file conflict with media-libs/sweep, #245439 c2.
-  * First pass for boinc, NOTE: install is not done yet :]
-  * Update comments.
-  * Add some empty depend :]
-  * More boinc updates.
-  * Fix cuda stuff a bit :P
-  * Forget to add correct groups :P Now should cuda really work :]
-  * Update deps.
-  * Update generating script to hopefuly final version.
-  * matio-1.3.3 version bump
-  * Ups forgot one dep.
-  * Working cuda :]
-  * Update script.
-  * Umm. Fix breakage.
-  * Remove prerelease. We wont bother.
-  * More updates.
-  * Moar init fixups. (Portage version: 2.2_rc20/git/Linux 2.6.27-gentoo x86_64)  (Unsigned Manifest commit)
-  * Update boinc-bin a bit, fixup initscript severly. (Portage version: 2.2_rc20/git/Linux 2.6.27-gentoo x86_64)  (Unsigned Manifest commit)
-  * Update profiles/categories/ and add generate_tarball.sh for boinc (that script is heavy WIP)
-  * Update openib-osm ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Update openib-osm ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Update openib-osm ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Update openib-osm ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Update openib ebuild (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
-  * Update openib ebuild (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
-  * Update openib ebuild (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
-  * Update openib ebuild (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
-  * Update openib-files (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
-  * update eclass
-  * Update openib-files ebuild (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
-  * eclass update
-  * update
-  * Add metapackage for openib (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
-  * Add new openib-perf (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
-  * Add new openib-files (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
-  * Update ebuilds (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Add new diags (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Add new opensm (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * updaet eclass
-  * update ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * update ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * update ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * add libnes (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * update ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * add  driver for mlx4 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * update ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * update ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * updaet ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * update ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * update ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Add new libiubmad-1.2.3_p20081118 (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
-  * Add new libibmad-1.2.3_p20081118 (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
-  * Update libibcommon ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Add new libibcommon-1.1.2_20082010 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * update eclass
-  * Add new libibcm-1.0.4 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Add new libehca-1.2.1 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Update dapl ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Update librdmacm ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Update libibverbs ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Unmask for testing
-  * Update libibverbs ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Update librdmacm ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Update compat-dapl ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Update dapl ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Add librdmacm metapackage (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Update dapl ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Add libibverbs metapackage (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Add libibverbs metapackage (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * update dapl ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * add to pmask
-  * Add dapl compatibility layer (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * fix headers and ebuild to work with eclass (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Update ebuild according to eclass (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * update eclass a bit
-  * fix openib eclass
-  * add p.mask entry
-  * add experimental ebuild for dapl-2.0.15 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
-  * sys-cluster/mpich-1.0.8 bugfixes, no revbump.  Fix some doc file locations (#255748).  Fix sandbox errors (254167).
-  * fix typo
-  * add new openib eclass
-  * Add empty package.mask, for use by broken/in-development/9999 packages.
-  * Slightly update the previous commit.
-  * Fix bug 243194. Update init so it uses CFS. Hope it wont harm kittens looks fine now.
-  * Whitespacie notes.
-  * Update slightly initscript. Note: it (as whole) needs review
-  * Fix bug 137224. Wrong attach usage. Note: i will close it and when this boinc versions are passed to the tree it will be just updated.
-  * add boinc-bin. Cuda not created there is library ${S}/libcudart.so which needs to be placed somewhere. So somebody with nvidia, tweak yourself up :P
-  * Drop smp use flag since its defautl for openmpi (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * fix syntax
-  * initial version bump to 1.3 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Make it work with current libtool (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * We dont want static gromacs by default (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Fix headers (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Fix headers (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Fix syntax issues (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Fix syntax issues (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * Bump gromacs to 4.0.3 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * fix keywords and hader for gtk-gamess (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
-  * fix manifests
-  * dev-python/h5py - Bumped version to 1.0.0.
-  * gap:version bump
-  * Version bump
-  * Added ekee
-  * Update mpi.eclass.  Major changes include simplyfing use and allowing non empi builds to still get some information.  Also updated all related packages using this eclass.
-  * Header change w/o getting the 1000s commit
-  * Header change w/o getting the 1000s commit
-  * Header change in ./sci-libs/cctbx/cctbx-2008.05.19.2030.ebuild
-  * Header change in ./sci-libs/mmdb/mmdb-1.0.10.ebuild
-  * Finite state toolkit foma. Initial ebuild.
-  * Bump to OpenCascade 6.3 Needs testing...
-  * version bump
-  * In CVS
-  * In CVS
-  * http://bugs.gentoo.org/show_bug.cgi?id=251793 (Portage version: 2.2_rc17/svn/Linux 2.6.26-gentoo-r4-cdrom i686)
-  * phun: version bump
-  * cctbx update -- rosetta++ added from bug 250401
-  * intial checkin version bump which results in broken digest of ebuild in tree (bug 247788) (Portage version: 2.2_rc17/svn/Linux 2.6.26-gentoo-r4-noata i686)
-  * removing old version
-  * spr: fixed data files and added use flag description
-  * spr: initial import for testing
-  * sci-chemistry/cara-bin Initial checking in (Portage version: 2.2_rc17/svn/Linux 2.6.26-gentoo-r4 i686)
-  * CARA license added
-  * esorex: version bump
-  * cpl: version bump
-  * sci-mathematics/freefem++: fix a P1 FE bug and examples++-load
-  * Removed spooles USE-flag for sci-libs/calculix-ccx
-  * sci-libs/calculix-ccx: Removed spooles USE-flag, spooles is no longer optional
-  * sci-libs/gmsh: Version bump
-  * rasmol: bump to latest. also added new dep, cbflib. (#238302).
-  * rasmol: bump to latest. also added new dep, cbflib. (#238302).
-  * Force serial build of mpich2... Ironically.  #248456
-  * new USE-flag 'chaco' for sci-libs/gmsh
-  * sci-libs/gmsh: Fixed metis compilation problem and added chaco USE-flag
-  * app-vim/freefem++-syntax: version bump.
-  * sci-libs/gmsh: Improved typo
-  * sci-libs/gmsh: Version bump
-  * removed speedcrunch now in main tree
-  * sci-geosciences/tappy-0.8.1.ebuild - Version bump
-  * mosflm: bump to 7.0.4; parallel build is broken.
-  * Version bump.
-  * Fix 242180, comment 5 by just allocating a buffer for the string instead of trying to use PATH_MAX.
-  * sci-mathematics/sage-bin: Updated Manifest
-  * sci-mathematics/sage-bin: Version 3.1.2 no longer available for download.  Minor change in SRC.  Explicit installation of sage-* and explicit creation of /usr/bin/sage symlink.
-  * Updated mpi.eclass to handle packages with blockers and mpich2
-  * dev-python/h5py-0.3.1.ebuild Python interface to HDF5 files.  Initial ebuild.
-  * sys-cluster/mpe2 needs to handle building without empi.
-  * Integrate Joel's fixes for #220877 into mpich2 (fpic ->fPIC)
-  * Add empi-capable mpe2, tests pass with mpich2, some issues with openmpi
-  * Add empi-capable mpich2
-  * sci-misc/salome-med: Reordered dependencies
-  * sci-mathematics/freefem++: gcc-4.3 and no-X11R6 symlink fixes
-  * removed cgal, now in main tree
-  * removed cgal-python, now in main tree
-  * sci-misc/salome-kernel: Reordered dependencies
-  * deleted USE-flag 'corba' for sci-misc/salome-kernel
-  * sci-mathematics/mdp - Even though I couldn't reproduce the error, I updated the Manifest, per http://bugs.gentoo.org/show_bug.cgi?id=146976#c6
-  * Added patch to support hdf5-1.6.7
-  * Added support to VTK 5.2
-  * Added support to VTK 5.2
-  * Added support to VTK 5.2
-  * sci-mathematics/mdp-2.4.ebuild : A Python data processing framework. Bumped to version 2.4, updated DEPEND.
-  * removed plplot, now in main tree
-  * removed lasi, now in main tree
-  * ipython now in tree
-  * Fix bug #242574, version bump and gcc-4.3 patch.
-  * bump sys-cluster/openmpi-1.2.8 and clean up old version.
-  * new USE flags 'arpack' and 'spooles' for sci-libs/calculix-ccx
-  * sci-libs/calculix-cgx: Reworked ebuild for bug 125775, thanks to pva
-  * sci-libs/calculix-ccx: Reworked ebuild for bug 125773, thanks to pva
-  * sci-libs/spooles: Reworked ebuild for bug 125772, thanks to abraxxas and pva
-  * sci-geosciences/swmm Initial ebuild for SWMM - Storm Water Management Model, developed by the U.S. Environmental Protection Agency and Camp, Dresser, McKee (CDM).
-  * sci-mathematics/sage-bin This is the Sage binary package.  Sage is very difficult to tease out the sources to build separately and so I gritted my teeth and created this binary package ebuild.  See http://bugs.gentoo.org/show_bug.cgi?id=201321 for information on the conventional source based ebuild.
-  * Added Manifest for ipython
-  * Added ipython-0.9.1 for testing
-  * Automated script commit
-  * Automated script commit
-  * Probably the last fix. Fixing of path in right place' (Portage version: 2.2_rc11/svn/Linux 2.6.25-gentoo-r8 i686)
-  * Automated script commit
-  * aribas-1.63
-  * Automated script commit
-  * Removed superfluous files.
-  * Automated script commit
-  * Added second set of octave-forge updates.
-  * latest version
-  * Nearly ready
-  * Nearly ready
-  * Automated script commit
-  * Automated script commit
-  * Automated script commit
-  * Bump first batch of octave-forge packages to new revision.
-  * Removed octave since octave-3 has been merged to the main tree.
-  * Automated script commit
-  * cdsclient: bump to 3.01
-  * removed root, now in main tree
-  * sci-misc/salome-kernel: fixed dependency
-  * sci-misc/salome-kernel: Fixed typo in dependency
-  * gmpy-1.03 is now in the tree
-  * Bring in latest openmpi-1.2.7 with empi support.  Remove old 1.2.5, cleanup repoman warnings.
-  * upstream patched; redigest
-  * Version bump. Patch for gcc-4.3.
-  * Version bump; ensure python has tkinter
-  * manifest update
-  * In gentoo-x86
-  * New package, bug 236954
-  * sci-misc/salome-med: Added patch for >=dev-libs/boost-1.35.0
-  * sci-misc/salome-kernel: Fixed version dependency
-  * sci-misc/salome-kernel: Fixed version dependency
-  * sci-misc/salome-superv: Fixed typo in patch file
-  * sci-misc/salome-pycalculator: removed omniorb* dependencies, as they are already in salome-kernel
-  * sci-misc/salome-visu: removed omniorb* dependencies, as they are already in salome-kernel
-  * sci-misc/salome-superv: removed omniorb* dependencies, as they are already in salome-kernel; added omniorb_4.1.patch
-  * sci-misc/salome-component: removed omniorb* and med dependencies, as they are already in salome-kernel and salome-med
-  * sci-misc/salome-smesh: removed omniorb* dependencies, as they are already in salome-kernel
-  * sci-misc/salome-med: removed omniorb* dependencies, as they are already in salome-kernel
-  * sci-misc/salome-geom: removed omniorb* dependencies, as they are already in salome-kernel
-  * sci-misc/salome-gui: Most USE-flags doesn't seem to be optional, changed default settings; added pyobject.patch
-  * sci-misc/salome-kernel: Reworked USE-flags, changed default behaviour, added omniorb_4.1.patch
-  * pyglet-1.1.1.ebuild: version bump
-  * The GIS Django branch was merged into the trunk.
-  * +Manifest
-  * Initial commit for bug 221965, thanks to Marek Miller <mlm@ngc17.pl>
-  * root: added better emacs support
-  * dev-python/sympy is now in the main tree
-  * jama: cleaning
-  * tnt: version bump and fixes
-  * pythia now in main tree
-  * added root for test on extra patches
-  * pythia6: rev bump
-  * pythia6: added additional declarations for root
-  * sympy-0.6.2: with docs (using sphinx), mpmath and pyglet are internal so far
-  * Added USE-flags for the sci-misc/salome-* ebuilds
-  * sci-misc/salome-smesh: Now really removed fetch restriction
-  * sci-misc/salome-visu: Removed fetch restriction, removed hardcode
-  * sci-misc/salome-superv: Removed fetch restriction, removed hardcode
-  * sci-misc/salome-smesh: Removed fetch restriction, removed hardcode
-  * sci-misc/salome-pycalculator: Removed fetch restriction, removed hardcode
-  * sci-misc/salome-meta: Fixed repoman errors, removed hardcode
-  * sci-misc/salome-med: Removed fetch restriction, removed hardcode
-  * sci-misc/salome-gui: Removed fetch restriction, removed hardcode
-  * sci-misc/salome-geom: Removed fetch restriction, removed hardcode
-  * sci-misc/salome-component: Removed fetch restriction, removed hardcode
-  * sci-mathematics/netgen: Fixed dependency for opencascade
-  * Added corba and openpbs USE-flags for sci-misc/salome-kernel
-  * sci-misc/salome-kernel: Removed fetch restriction, added python-2.5 support, removed hardcode
-  * Added cgns, metis and opencascade USE-flags for sci-libs/gmsh
-  * sci-libs/cgnstools: New Ebuild for bug 176455
-  * sci-libs/cgnslib: New Ebuild for bug 176455
-  * sci-libs/gmsh: New Ebuild for bug 195980
-  * gmpy-1.03: an update to the package in the main tree
-  * pyglet-1.1: version bump
-  * avbin-bin-6: version bump
-  * sci-libs/mathgl-1.7.ebuild *1.7 version based on 1.6.2. *Removed unneeded patches and 'sed' commands, updated SRC_URI, added append-flags for CPPFLAGS and LDFLAGS.
-  * pythia-8: install data files
-  * sci-visualization/scidavis-0.1.3.ebuild - Changed two lines indented with spaces to indented with tabs.
-  * sci-visualization/nodemon-0.3.5.ebuild - Changed description to < 100 characters and updated copyright date.
-  * sci-misc/brlcad-7.10.4.ebuild - Removed BSD license which was for the BRLCAD wiki content and updated copyright year.
-  * sci-misc/simpy-1.9.1.ebuild - Initial ebuild for simpy, a process and event simulation system for Python.
-  * sci-geosciences/congen-1.6.ebuild - Congen calculates astronomic parameters necessary to analyse tides.
-  * ccp4: split out ccp4i into separate package.
-  * ccp4: split out ccp4i into separate package.
-  * coot: require librsvg (reported by Hari Jarayam).
-  * coot: also needs imlib.m4 or it fails on systems without imlib-1.
-  * app-office/texmacs is in the main tree
-  * Moved to portage
-  * Remove sys-cluster/ganglia as it's in the main tree.
-  * Fixed Manifests
-  * ccp4: pull in balbes-db.
-  * Add balbes-db, split out from ccp4.
-  * ccp4: pull in standalone xia2.
-  * Add split-out xia2 ebuild.
-  * refmac: install refmac5 symlink.
-  * ccp4: more fixes.
-  * ccp4: pull in standalone refmac.
-  * Add standalone refmac.
-  * ccp4: pull in imosflm.
-  * ccp4: pull in standalone mosflm.
-  * New package: standalone mosflm.
-  * ccp4: initial version that depends on ccp4-libs.
-  * Move ccp4-libs to sci-libs.
-  * ccp4: add imosflm deps. fix quoting syntax error.
-  * tktreectrl: dep for new ccp4, from bug #217706.
-  * Use category in has_version, thanks to filko on #-science for pointing it out.
-  * Add ganglia-3.1.0.  Python is not fully working yet, but everything else checks out.
-  * ccp4: bump to 6.0.99e, alpha ebuild.
-  * added ~x86
-  * minor fixes to symmetrica and cddlib
-  * Added givaro
-  * Added Symmetrica
-  * Added dev-libs/ntl-5.4.2
-  * minor change to gdmodule
-  * added fplll
-  * added m4ri
-  * added gdmodule
-  * added cddlib
-  * sci-mathematics/mdp * Added ~x86 per http://bugs.gentoo.org/show_bug.cgi?id=146976
-  * sci-mathematics/mdp * Initial ebuild
-  * coot: bump to 0.5_pre1-r1272.
-  * coot: Bump to 0.5_pre1-r1212, drop 0.4.1.
-  * Added pythia (6 and 8)
-  * gap-4.4.10: sysinfo.gap now installed
-  * removed libsdp-1.1.ebuild added libsdp-1.1.99.ebuild
-  * added libehca-1.2.ebuild removed libehca-1.1.ebuild
-  * manifest
-  * taking patch away
-  * svn housekeeping
-  * fix patch name
-  * Added surfer
-  * In the portage tree
-  * pyglet-1.1_beta2
-  * sci-mathematics/pest * Added '-j1' to MAKEOPTS to force correct compile order.
-  * bump as openmpi-1.2.6-r1 just hit the tree.
-  * sci-geosciences/pyslice * Added ~x86
-  * sci-geosciences/tappy * Added ~x86 as per https://bugs.gentoo.org/show_bug.cgi?id=138005#c8
-  * sci-geosciences/geodjango-svn * Added ~x86 per https://bugs.gentoo.org/show_bug.cgi?id=230880#c4
-  * Version bump
-  * fix digest
-  * version bump
-  * New package, bug 207250
-  * New license for sci-biology/mavid
-  * New package, bug 114089
-  * sys-cluster/hpl * Minor repoman edits.
-  * sys-cluster/pyslice * Initial ebuild entry.
-  * sci-geosciences/tappy * Added correct header.
-  * sys-cluster/blcr * Minor repoman edits.
-  * sci-geosciences/tappy * Initial ebuild.
-  * sci-geosciences/geodjango-svn * Initial import of GeoDjango branch.
-  * sci-geosciences/xtide * Added ~x86 per https://bugs.gentoo.org/show_bug.cgi?id=214868#c9
-  * manifest
-  * compressing the patch
-  * Updated the gcc-4.3 patch for salome-kernel (Thanks Bart K.)
-  * sci-geosciences/libtcd * Added ~x86 per http://bugs.gentoo.org/show_bug.cgi?id=214867#c4
-  * sci-geosciences/harmonics-dwf-free-noncomm * Added ~x86 per http://bugs.gentoo.org/show_bug.cgi?id=214873#c4
-  * sci-geosciences/tcd-utils * Added ~x86 per http://bugs.gentoo.org/show_bug.cgi?id=214875#c4
-  * sci-geosciences/xtide * Added required dependencies to fix   http://bugs.gentoo.org/show_bug.cgi?id=214868#c4
-  * patches
-  * Import for testing
-  * add metadata.xml
-  * Add changelog, and thanks to Jose Maria Fernandez Gonzalez
-  * Initial import.
-  * adding local variables myconf_s and myconf_d to keep track of flags
-  * fixing cases when all you want is double-precision, thanks to Shvetsov Alexey on bug #193532
-  * guile-lib: bump to 0.1.6.
-  * scamp:version bump and fixes
-  * coot: Bump to 0.5_pre1-r1192.
-  * openmotif, not motif
-  * openmotif, not motif
-  * openmotif, not motif
-  * switch virtual/motif to x11-libs/openmotif for bug #204249.
-  * switch virtual/motif to x11-libs/openmotif for bug #204249.
-  * switch virtual/motif to x11-libs/openmotif for bug #204249.
-  * new cluster, make license file
-  * note in license file this is for sci-biology/cluster
-  * License for sci-biology/cluster
-  * Remove opencv from overlay, it's now in gentoo-x86
-  * Made media-libs/lasi ebuild adhere to multilib-strict.
-  * sci-chemistry/drawxtl:  * Added metadata.xml
-  * sci-calculators/speedcrunch:  * Added metadata.xml
-  * sci-astronomy/scamp: Simple repoman inspired edit  * Changed copyright date
-  * dev-lang/aldor: Simple repoman inspired edits  * Updated copyright dates  * Removed unneeded 'cd "${S}"'
-  * dev-cpp/growler: Simple repoman inspired edits  * Changed copyright dates  * Shortened long DESCRIPTIONs to under 100 characters  * Fixed svn Headers
-  * app-office/texmacs: Simple repoman edit  * Added trailing semicolon in files/TeXmacs.desktop
-  * eselect-mpi: Simple repoman guided edits.  * Deleted trailing spaces  * Quote variables  * Added metadata.xml
-  * Update description
-  * add manifest
-  * New package
-  * In gentoo-x86
-  * Final fixes before eclass goes out for review.
-  * Latest gromacs for testing
-  * fix Manifest
-  * fix headers and utf
-  * added libsfmt and libdsfmt
-  * Remove unnecessary RESTRICT, keyword for x86 since pchrist tested it
-  * Bump eselect-mpi-0.0.4.  Adds /etc/profile.d support.  Thanks to Bryan Green for suggesting this.
-  * Fix step 6 in the README, paths were wrong.  Thanks again to Bryan Green.
-  * Fix a couple of bad csh environment var settings.  Thanks to Bryan Green for pointing this out, #226105
-  * Actually bump empi correctly.
-  * And add a missing patch, forgot to 'svn add'
-  * Fix ffmpeg linking with sws_getContext by adding -lswscale to FFMPEGLIBS, and fix up ffmpeg's configure checks as well
-  * Add demos USE flag for sample opencv applications, change to a better format(unified) for the cvcapffmpeg patch
-  * Add demos local USE flag description for opencv
-  * Fixxor AC_CONFIG_MACRO_DIR conflicts with ACLOCAL_AMFLAGS
-  * repoman fixups
-  * git-svn-id: svn+ssh://svn.j-schmitz.net/svn/portage-overlay/ebuilds@413 848b6a78-a7b0-4e08-a36b-699b422dbac5
-  * Initial import, bug #70506
-  * removed clhep, now in main tree
-  * removed geant, now in main tree
-  * removed dawn, now in main tree
-  * added openib.env per bug #223955 comment #17
-  * updates to several openib packages
-  * Final cleanup.
-  * added ebuilds for OFED/openib 1.2.5.5
-  * fixed doc install
-  * added speedcrunch
-  * Added patch to fix stdout problem in chi2rnd function.
-  * esorex: bump to 3.6.8
-  * cpl: version bump to 4.1
-  * geant: patch bump
-  * More cleanups.
-  * Added Gcc-4.3 support. Thanks to Bert K. for his patches!
-  * Added Gcc-4.3 support. Thanks to Bert K. for his patches!
-  * Added Gcc-4.3 support. Thanks to Bert K. for his patches!
-  * Added Gcc-4.3 support. Thanks to Bert K. for his patches!
-  * Added Gcc-4.3 support. Thanks to Bert K. for his patches!
-  * Corrected a minor bug
-  * Added Gcc-4.3 support. Thanks to Bert K. for his patches!
-  * Added Gcc-4.3 support. Thanks to Bert K. for his patches!
-  * Added the license file for OpenCascade. Corrected issues with the configuration of OpenCascade (Thanks Richard W.!)
-  * More manifest fixing
-  * fixing manifests and ebuild name
-  * new package: libibvpp
-  * Major ebuild cleanup. Disabled failing tests and added patched from debian svn.
-  * pyglet-1.1_beta1
-  * avbin-bin-3 (needed by pyglet)
-  * added openib-mvapich2-1.0.1-r1 to MPI_EMPI_COMPAT
-  * minor fix, added use of ${mpi_conf_args}
-  * added openib-mvapich2 to MPI_ALL_IMPS
-  * added ~x86 keyword, updated copyright dates
-  * added openib-mvapich2-1.0.1-r1.ebuild, added ~x86 keyword
-  * Initial import, thanks to Jan Marten Simons, Hannes Kruger, and Srebrodolskite.
-  * add menu entry
-  * Remove quotes
-  * Cleanup and add ApE license file.
-  * Initial import.
-  * In gentoo-x86
-  * Compilation and installation now properly takes place in src_compile and src_install. Also, make the compile and install phases more verbose.
-  * git-svn-id: svn+ssh://svn.j-schmitz.net/svn/portage-overlay/ebuilds@406 848b6a78-a7b0-4e08-a36b-699b422dbac5
-  * asciidata: version bump
-  * visual-4_beta26 now in main tree
-  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
-  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
-  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
-  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
-  * Modified a minor bug regarding the location of some python/salome shared directory
-  * gle is in the main tree now
-  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
-  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
-  * scidavis-0.1.3: translations are now handled correctly
-  * Added new octave-forge packages.
-  * Heavy rework of the ebuild and the associated epatches. WARNING: At the moment, OpenCascade support is broken (at least on amd64)
-  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
-  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
-  * Corrected a minor issue (the icon reference)
-  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
-  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
-  * Added ~x86 in the KEYWORDS list. I tested it, it seems to work correctly.
-  * Initial import. See bug #130502 for more info
-  * Bug correction. Thank you Dewald for testing and showing me how to solve it.
-  * scidavis-0.1.3
-  * qtiplot-0.9.6 is now in the main tree
-  * Initial import of xtide.  A tidal prediction program that has graphical interfaces and a web server.
-  * Utilities for the creation and restoration of Tidal Constituent Database files.
-  * Initial import of an ebuild for and graphical editor of Tidal Constituent Database files.
-  * Initial import of libtcd, a library for the editing of Tidal Constituent Database files.
-  * Initial import of Tidal Constituent Database. Dependency of other tide related programs (libtcd, tcd-editor, tcd-utils, xtide).
-  * Initial import of Tide Constituent Database ebuilds. Dependency of several tide related programs (libtcd, tcd-editor, tcd-utils, and xtide).
-  * Added sci-geosciences to add new ebuilds.
-  * Initial ebuild for the PEST model calibration, Parameter ESTimation, and uncertainty analysis tool.
-  * qwt-5.1.0: in the main tree
-  * qtiplot-0.9.6: dependencies corrected
-  * Committed new versions for octave-forge packages.
-  * bump to empi-0.4 fixing issue with directories in portage_confdir, reported by Radice David
-  * qtiplot-0.9.6
-  * qwt-5.1.0
-  * Added librdmacm-1.0.7.ebuild
-  * Fixed recursive dohtml (see bug #221905) in sci-libs/lapackpp.
-  * mmtk: bump to 2.5.23.
-  * Updated to netgen-4.4-r1
-  * Bump to opencascade-6.2-r1
-  * OpenCascade belongs to sci-libs, not sci-misc. OpenCascade being fundamentally a library....
-  * OpenCascade belongs to sci-libs, not sci-misc. OpenCascade being fundamentally a library....
-  * My first contrib on the science overlay is a library for DICOM files (Digital Imaging and COmmunications in Medecine)
-  * mathgl-1.6.2, udav-0.3.2: ~ppc added
-  * udav-0.3.2: several improvements
-  * mathgl-1.6.2: several improvements
-  * Bump to new versions.
-  * Added compatibility with new imagemagick to octave-forge-image.
-  * added libibverbs-1.2.2.ebuild
-  * keyworded amd64
-  * keyworded amd64
-  * freefem++ version bump, added freefem++-syntax
-  * Upstream changed tarballs again
-  * coot: bump to 0.5_pre1-r87, add gcc 4.3 patch.
-  * extrema is now in the main tree
-  * maxima-5.15.0 and wxmaxima-0.7.5 are in the main tree
-  * udav-0.3.2: cleanup
-  * mathgl-1.6.2 cleanup and improvements
-  * Don't spit out errors if people aren't using empi
-  * udav-0.3.2: Universal Data Array Visualization
-  * mathgl-1.6.2: Math Graphics Library
-  * maxima-5.15.0 and related stuff
-  * Call eautoreconf in every required directory by hand as AC_CONFIG_SUBDIRS isn't uses and autotools.eclass can't find everything.
-  *  Fix for gcc-4.3.0.  Change 'char * argv[]' to 'char **argv' in configure scripts.  Thanks to Peter Alfredsen (peter.alfredsen at gmail) for the fix.
-  * Version bump.
-  * added phun
-  * plplot: more use flags dep checking
-  * empi, add x86.  Thanks to Shvetsov Alexey (alexxyum at gmail) for testing.
-  * eselect-mpi, add x86.  Thanks to Shvetsov Alexey (alexxyum at gmail) for testing.
-  * bump openmpi to 1.2.6.  Thanks to    Shvetsov Alexey (alexxyum at gmail) for the note.
-  * Fixed incorrect package descriptions.
-  * geant4: fixed a wrong sed command
-  * checksum change
-  * geant4: fixed syntax
-  * geant4: new ebuild with exports
-  * point {do,new}bin to correct functions
-  * add missing mpi.eselect-0.0.3
-  * removed skycat now in main tree
-  * removed tkimg, now in main tree
-  * added slotted geant-3, data dir is now /usr/share/geant-4/data for geant-4
-  * geant4: fix a bad env name and removed and extra fi in the no-source patch
-  * Changelog
-  * fixing license
-  * Add license for sci-chemistry/modeller
-  * Initial import, added MY_PV, thanks to the prolific Justin Schmitz
-  * readded geant
-  * removed geant4
-  * geant-4: fixed data installation
-  * added geant-4
-  * added dawn
-  * plplot: more fixes on use flags and fortran
-  * plplot: add missing use, more fortran fixes
-  * Initial import, openFST finite state transducer toolkit
-  * Bump eselect-mpi.  Fix mpi.eclass so it correctly reports the mpi_dir when building implementations via empi.
-  * removed mkl, now in main tree
-  * cdsclient: bump
-  * removed parmetis, now in main tree
-  * imported lasi
-  * Add digest for blcr changelog too.
-  * Initial import of blcr.  Thanks to kuffs (Aaron Tygart) for the ebuild.
-  * bump empi-0.3.  See ChangeLog for details.
-  * visual-4_beta26
-  * Don't use eselect-mpi in get_mpi_dir if empi is not being used
-  * octave-forge.eclass now uses octave's pkg.m for compiling packages.
-  * coot: bump to 0.5_pre1-r875.
-  * gle-4.1.2b
-  * yorick-2.1.05: DEPEND corrected
-  * texmacs-1.0.6.14
-  * breqn-0.97a
-  * mkl: more polishing
-  * yorick-2.1.05
-  * Added patch to have 'pkg install' exit with error code if it can't find the source tarball.
-  * moved overlay to new directory
-  * coot: keyword ~amd64
-  * mmtk: Bump to 2.5.22
-  * ccp4: revbump with new upstream patches and Gentoo build fixes.
-  * Update coot to 0.4.1.
-  * Drop unneeded packages and packages that exist in other repos.
-  * move stuff to root
-  * deleted ifc and icc, now in main tree
-  * qtiplot-0.9 Depends on x11-libs/qwtplot3d built with qt-4 (bug #184652)!!!
-  * freemat in main tree
-  * harminv: fixed autotools
-  * freemat-3.5
-  * octave-2.9.14 (seems to work fine on my x86 without any patches)
-  * metis: fixed autotools patch and license
-  * fixed cxsparse autotools patch
-  * added cholmod and metis
-  * revert acml
-  * revert acml
-  * acml manifest fix
-  * extrema-4.2.8
-  * added: colamd ccolamd cxsparse camd
-  * removed blas-goto, updated in main tree
-  * added gsl-1.10 with cblas support
-  * *-atlas: set default fortran flags
-  * cleaning license and use flag
-  * removed cmt, now in main tree
-  * sci-mathematics/gretl: Fixed for lapack settings, removed tetex.
-  * removed maxima, now in main tree
-  * boa-constructor-0.6.1
-  * lapack-atlas: fixed clapack error
-  * sci-biology/sibsim4: version bump
-  * sci-biology/gmap: version bump
-  * removed cfitsio, now in main tree
-  * texmacs-1.0.6.11
-  * icc/ifc: few fixes with envd files
-  * delete numeric, now in main tree
-  * numeric: fix for 2.5
-  * ifc/icc: added rootpath in env files
-  * mkl: swap restrict fetch and mirror
-  * icc: added emul-linux-compat-x86
-  * maxima-5.13.0 and texmacs-1.0.6.10-r1 with a patch to run maxima-5.13.0
-  * added icc-10
-  * added ifc-10
-  * cleaning
-  * Added ipp
-  * cleaning
-  * removed root, geant, cernlib, cernlib-montecarlo, paw, now in main tree
-  * cleaning
-  * cleaning
-  * removed xbae, now in main tree
-  * removed numdisplay, now in main tree
-  * extrema-4.2.7: added ~amd64
-  * removed gdl, now in main tree
-  * extrema-4.2.7: data analysis and visualization
-  * removed gsl, now in main tree
-  * removed blas,cblas,lapack-reference, now in main tree
-  * lapackpp update
-  * lapackpp cleanup
-  * lapackpp: initial import
-  * {blas,lapack}-atlas: updated patch
-  * mkl: re-fix access violation and a comment
-  * mkl: lapack.pc fix
-  * mkl update
-  * updated virtual with deps
-  * atlas: fixed bug
-  * mkl update
-  * blas/lapack pkg-config file update
-  * fixed *.pc.in to work on x86
-  * added many updates to blas/lapack packages
-  * added new virtual blas, cblas and lapack
-  * cernlib.eclass: cleanup
-  * removed libctl, now in main tree
-  * removed pygsl, now in main tree
-  * removed muParser update, now in main tree
-  * Whoops! inherit autotools
-  * Fix typos
-  * Remove LICENSE until I have time to fix it.
-  * Initial import of cluster-1.36 thanks to Favero Francesco
-  * sci-physics/root: root: fixed Manifest
-  * Merged many things to gentoo-x86, mostly coot-related
-  * sci-astronomy/sextractor: filter optim flags
-  * removed ds9, now in main tree
-  * dev-lang/gdl: gdl: fftw>=3
-  * sci-astronomy/scamp: cleaning
-  * sci-astronomy/scamp: Version bump
-  * removed freemat, now in main tree
-  * dev-cpp/muParser: Version bump
-  * sci-astronomy/ds9: Version bump
-  * sci-astronomy/swarp: swarp: version bump
-  * dev-lang/gdl: added ChangeLog
-  * dev-lang/gdl: gdl: version update
-  * dev-python/pygsl: pygsl: version bump
-  * sci-physics/bullet: bullet version bump
-  * sci-physics/root: root:added patch release
-  * sci-physics/root: root: fixed CC -> CXX
-  * sci-physics/root: root: added truetype option, fixed intel and fortran compilers support
-  * cernlib.eclass cleanup
-  * sci-physics/cernlib: cernlib: fixed an ifc problem
-  * sci-physics/cernlib: cernlib:updated patch
-  * sci-physics/root: Version bump
-  * added makedepend dep on cernlib.eclass
-  * Making gtk-gamess ~amd64 only until I can fix up gamess to include the amd64 arch.
-  * Removing, as ghemical is now in the main tree.
-  * Removing as it's now in the tree.
-  * Removed apbs, as it made it into portage and was causing confusion.
-  * coot: pull guile 1.8 patch from upstream instead of our custom one.
-  * coot: fix build with guile 1.8 / gmp 4.2.1
-  * Changed to use markusle's octave ebuild.
-  * Deleted jmol as it's now in the tree.
-  * Replacing octave-2.9.12.ebuild with markusle's ebuild.
-  * Removing keywords.
-  * Fixing manifest.
-  * Bumping to octave-2.9.12
-  * add bullet
-  * Removed pymol as it's now in the main tree.
-  * Testing pymol-0.99_rc10.
-  * Coot: delete old snapshot, newer version's in portage.
-  * Add burrow-owl NMR package, and its new guile deps, bumps and patches.
-  * Fixed a typo in jmol.
-  * paw: version bump
-  * added root digest
-  * root: version bump
-  * Fix jmol digest
-  * sci-chemistry/jmol: changed to use sci-libs/jmol-acme
-  * More java cleanup thanks to nichoj.
-  * Depend on saxon-6.5 to generate documentation.
-  * sci-biology/gmap: upstream re-rolled tarball due to single bug, updating digests
-  * sci-biology/gmap: version bump
-  * sci-physics/root: root: mit-krb5 -> virtual/krb5
-  * sci-mathematics/gretl: gretl:initial import
-  * dev-python/numeric: dev-python/numeric: various new patches to work with python 2.5
-  * More cleanup...
-  * Cleanup and get ready for portage migration.
-  * Removing from overlay as it's now it portage. Getting ready to introduce JMol.
-  * Removing from here as it's in portage. Getting ready to introduce JMol.
-  * geant: debian patches update
-  * paw: fixed back to older debian cernlib
-  * sci-astronomy/scamp: scamp: version bump
-  * More appropriate file name for vecmath-objectclub.
-  * Took out the symlink to plugin.jar.
-  * Emptied KEYWORDS temporarily.
-  * Fixed all jars except for netscape.jar. Ugly hack used. :(
-  * Initial import.
-  * Initial import...comments welcome :D
-  * Adjusted $ARCH
-  * Moved jmol-acme as it fits better in sci-libs.
-  * Argh!
-  * Re-adding jmol-acme.
-  * Moving from sci-chemistry to sci-libs,
-  * More cleanup
-  * Fixing DEPEND
-  * Adding KEYWORDS
-  * Tidy up a bit.
-  * Improved the 11.0 build and removed 10.2
-  * Adding -sourcepath "" as per Caster's suggestion.
-  * Initial import.
-  * The patch has been applied upstream (without changing the version number)
-  * texmacs-1.0.6.10
-  * Manifest corrected
-  * sci-physics/root: bumped root from main tree with cernlib compatibility
-  * an attempt to solve the problem that /usr/share/maxima/5.12.0/doc/html/ is created twice on some systems
-  * added use local flag hdf5 for meep
-  * sci-physics/meep: added meep
-  * sci-physics/harminv: harminv: enabled shared library
-  * sci-libs/libctl: added libctl
-  * sci-physics/harminv: added harminv
-  * git-svn-id: http://overlays.gentoo.org/svn/proj/science/overlay@597 32389bae-6d03-0410-99cf-db05cde120eb
-  * sci-libs/cfitsio: Version bump
-  * Added a check that, if guile is 1.8, it is emerged with +deprecated
-  * Please don't leave inconsistent Manifest files in the tree!
-  * fixed for new debian directory structure
-  * texmacs-1.0.6.9-r1: support for maxima-5.12.0
-  * maxima-5.12.0
-  * Moved ebuild to portage.
-  * Getting rid of pymol since it's in the tree now...
-  * cernlib: version bump+cleaning
-  * qcl version bump and added amd64 for testing
-  * pygsl version bump. added src_test
-  * added muparser
-  * sci-biology/blat: version bump!
-  * Updated ChangeLog.
-  * Added ~amd64.
-  * Add changelog thanking hodak at ncsu.
-  * Importing pymol-0.99_rc8.
-  * Adding svn pymol build.
-  * add metatadata.xmls for all these poor souls
-  * Mass import from sunrise
-  * new use flag for sci-biology import
-  * new licenses for sci-biology
-  * new license gmap for sci-biology/gmap
-  * rkward now in main tree
-  * qwt was moved in main tree
-  * Manifest update.
-  * removed paraview, now in main tree
-  * vtk now in main tree
-  * mayavi-1.5 now in main tree
-  * minor cleanup
-  * jdk dep for vtk
-  * added mayavi
-  * added paraview
-  * vtk suite
-  * added new vtk
-  * liborigin now in main tree
-  * sci-astronomy/sextractor: sextractor: cleanup
-  * sci-astronomy/ds9: ds9: version bump
-  * aldor-1.1.0_rc
-  * sci-astronomy/skymaker: Initial import of skymaker
-  * sci-mathematics/rkward: rkward: version bump
-  * sci-mathematics/freemat: freemat: added post_install function
-  * sci-mathematics/freemat: freemat version bump
-  * maxima changes now in main tree
-  * removed obsolete itpp
-  * dev-util/cmt: Version bump
-  * final cernlib cleaning
-  * fixed keywording for cernlib eclass
-  * fixed keywording for cernlib packages
-  * cernlib now uses the cernlib.eclass
-  * added cernlib eclass
-  * fixed for type -P/which
-  * deleted geant321
-  * sci-physics/geant: geant: version cleaning and update
-  * sci-physics/cernlib: cleaning cernlib
-  * sci-physics/cernlib-montecarlo: cleaning cernlib-montecarlo
-  * sci-physics/paw: version adapted for cernlib-2006 paw new revision for cernlib-2006
-  * x11-libs/xbae: initial import
-  * sci-physics/cernlib-montecarlo: cleaning
-  * sci-physics/cernlib-montecarlo: version bump version bump
-  * sci-physics/cernlib: changelog commit
-  * sci-physics/cernlib: version bump
-  * cleaning old versions of cernlib packages
-  * sci-mathematics/maxima: maxima: added latex stuff from bug #169178.
-  * dev-tcltk/tkimg: cleaning tkimg
-  * sci-astronomy/swarp: cleaning swarp
-  * sci-astronomy/skycat: cleaning skycat
-  * sci-astronomy/stiff: cleaning
-  * sci-astronomy/sextractor: cleaning
-  * sci-astronomy/esorex: cleaning esorex
-  * sci-astronomy/scamp: scamp version bump
-  * esorex version bump
-  * cpl version bump
-  * bumped cdsclient
-  * cleaning
-  * removed arpack, now in main tree
-  * rkward: fixed rdeopend
-  * kayali version bump
-  * rkward version bump
-  * cleaning
-  * removed pspp from overlay, now in main tree
-  * Changed ARCH for jmol temporarily.
-  * removed pgplot, now in main tree
-  * Initial import of gromacs.
-  * Initial import...jmol-11.0.ebuild is NOT working yet...
-  * cleaning maxima, a few fixes
-  * Fix guile dep as per b.g.o bug 169488.
-  * removed root, now in main tree
-  * freemat-3.0
-  * cleanup
-  * fixed cfitsio
-  * root-5.14 fixes
-  * removed basemap, now in main tree
-  * added an updated version of root
-  * finalize apbs-0.5.0 cleanup
-  * cleaning Manifest and digests
-  * removed minuit, now in main tree
-  * removed root, now in portage
-  * removed hippodraw, now in portage
-  * Fixing apbs-0.5.0
-  * Fixing apbs-0.5.0
-  * removed wxmaxima, now in main tree
-  * removed imaxima, now in main tree
-  * removed qfits, now in main tree
-  * cleanup bogus patches
-  * removing umfpack now in main tree
-  * removing scipy, now in main tree
-  * asymptote is now in the main portage tree
-  * aldor-1.0.3 (binary, x86 only)
-  * aldor-1.0.3 (binary, x86 only)
-  * TeXmacs-1.0.6.9
-  * removed matplotlib (now in main tree)
-  * cleaning scipy
-  * removed numeric, now in main tree
-  * removed cfortran, now in main tree
-  * removed blas-docs and lapack-docs, now in main tree
-  * cleaned matplotlib
-  * removed pyfits (in main tree)
-  * removed numarray (in main tree)
-  * Initial apbs import.
-  * removed numpy (in main tree)
-  * removed libafterimage, now in main tree
-  * removed wcstools (in main tree)
-  * removed celestia (in main tree)
-  * TeXmacs-1.0.6.8-src.tar.gz has silently changed at ftp.texmacs.org
-  * asymptote-1.20: a fix in DEPEND
-  * maxima-5.11.0-r1: now depends on x11-misc/xdg-utils, sbcl-disable-debugger.patch dropped
-  * asymptote-1.20
-  * TeXmacs-1.0.6.8
-  * Use science for repo_name
-  * Adding categories and repo_name to profiles following glep 42 and reminded by dev-zero
-  * Whoops, putting mopac7 back :)
-  * Remove mopac7 from IUSE.
-  * Removed mopac7 USE flag.
-  * Add gtk-gamess to RDEPEND.
-  * Changed help browser to allow seamonkey or firefox.
-  * add ~amd64 to texmacs-1.0.6.7
-  * Fix for bug 162154.
-  * Corrected SRC_URI.
-  * Adding the forgotten metadata file.
-  * Initial cgal-python import
-  * initial import of the CGAL library
-  * Add dependency to RDEPEND.
-  * Initial import of ghemical-2.10 into sci overlay.
-  * Initial import of gtk-gamess.
-  * Bump coot to latest prerelease.
-  * added basemap
-  * agg removed, now in main tree
-  * hippodraw version 1.19.1 update
-  * hippodraw version 1.19.1 update
-  * removed scigraphica, now in main tree
-  * root-5.14.00 version update
-  * pspp cleaning
-  * wxmaxima version bump
-  * umfpack version update
-  * qfits manifest
-  * minuit version bump
-  * cleaning skycat
-  * cleaning swarp
-  * cleaning stiff
-  * cleaning scamp
-  * cleaning ds9
-  * cleaning esorex
-  * cleaning cpl
-  * cleaning sextractor
-  * wcstools-3.6.6 version bump
-  * removed icc flag, too buggy
-  * tclx now in main tree
-  * fixed some changelogs
-  * added asciidata
-  * cfortran: minor patch update
-  * imaxima version bump
-  * maxima-5.11.0: version bump
-  * texmacs-1.0.6.7: version bump
-  * cfitsio-3.030 update
-  * Add dev version of mmtk. PyMol plugins for it are available on the homepage.
-  * Add coot snapshots.
-  * fixed numpy changelog
-  * scipy version bump
-  * numpy version bump
-  * numpy: fixed lapack flag
-  * gle-4.0.12 with lots of new stuff (Qt4 GUI, etc.)
-  * dev-utils/cmt version bump to 1.19
-  * sci-libs/cfitsio version bump and cleaning
-  * asymptote-1.18: imported from bug 82871, with a fix for sandbox violation
-  * freemat-2.0: now builds with recent umfpack ebuilds
-  * qtiplot-0.8.8 depends on liborigin and qwt-5 (with USE=qt3); for now, emerge it with USE=-python
-  * qwt5: USE=qt3 builds a qt3-version needed for qtiplot
-  * muParser ebuild removed - now in the mainline tree
-  * a fix for muParser
-  * moving muParser, part 2
-  * moving muParser to dev-cpp
-  * Comment about rlwrap corrected
-  * matplotlib-0.87.7: version update
-  * added numpy-1.0
-  * cfortran: some cleanup
-  * imaxima: removed version in tree
-  * tclx-8.4: minor fixes
-  * remove SLOT and made sed statement more readable.
-  * misc cleanup and beautification
-  * fixed metadata.xml
-  * misc cleanup and beautification
-  * Fixes per bug #138619
-  * Initial import of jmol.
-  * Minor fix to comment.
-  * git-svn-id: http://overlays.gentoo.org/svn/proj/science/overlay@394 32389bae-6d03-0410-99cf-db05cde120eb
-  * OPJFile.h is now installed
-  * An improved liborigin ebuild by George Shapovalov
-  * added OpenIB-related USE-flags
-  * Initial import for OpenIB-/OFED-1.1
-  * Updated for 1.1 release of openib/OFED
-  * root-5.12: only use fortran when cern is selected
-  * hippodraw-1.19.0 version bump
-  * removed scientificpython, now in main tree
-  * removed orsa, now in main tree
-  * coot: merged to gentoo-x86
-  * ds9: fixed a typo and cflags
-  * tree cleaning: manifest, metadata, old versions.
-  * added esorex
-  * added cpl
-  * added qfits
-  * scamp, sextractor, stiff, swarp: removed flag filtering + cleaning
-  * root-5.12.00e-r1: fixes for asimage, xrootd and qt3
-  * hippodraw: cleanup
-  * hippodraw-1.18.6 version bump. updated license.
-  * geant321: removed ifc support for now
-  * paw-2.14.04-r1.ebuild: updated patches
-  * cernlib-montecarlo-2005-r1: updated patches
-  * cernlib-2005-r1: updated patches
-  * added umfpack use flag
-  * celestia: added cairo flag + fixes
-  * fixed deps for x11 modular
-  * oops
-  * wxmaxima-0.70a: version bump
-  * pspp: updated plotutils flag
-  * scipy: removed ppc (because of umfpack)
-  * arpack: clean up
-  * deleted mkl (now in main tree)
-  * cfitsio: depends on cfortran (better between arches)
-  * ds9-4.0_beta10: updated version and patches.
-  * git-svn-id: http://overlays.gentoo.org/svn/proj/science/overlay@360 32389bae-6d03-0410-99cf-db05cde120eb
-  * git-svn-id: http://overlays.gentoo.org/svn/proj/science/overlay@359 32389bae-6d03-0410-99cf-db05cde120eb
-  * git-svn-id: http://overlays.gentoo.org/svn/proj/science/overlay@358 32389bae-6d03-0410-99cf-db05cde120eb
-  * git-svn-id: http://overlays.gentoo.org/svn/proj/science/overlay@357 32389bae-6d03-0410-99cf-db05cde120eb
-  * scamp-1.2.11: added eselect deps.
-  * scamp-1.2.11: added warning if atlas is not selected
-  * orsa: added metadata.xml
-  * added wcstools-3.6.5
-  * imaxima-0.95 version bump
-  * cmt-1.18.20061003: version bump
-  * tclx-8.4: removed amd64 bad bit
-  * scientificpython: bumped stable 2.6
-  * matplotlib-0.87.6: proper commit this time
-  * numeric-24.2-r2: fixed lapack, added a math patch
-  * numarray-1.5.2-r1: fixed lapack stuff
-  * pygsl: updated gsl min version
-  * matplotlib-0.87.6: version bump
-  * added: liborigin-20060616
-  * added: muparser-1.25
-  * matio: minor cleanup
-  * wxmaxima/Manifest fixed
-  * Updated ChangeLog
-  * -libibverbs-1.0.9999.ebuild, -libibverbs-1.1.9999.ebuild
-  * Initial import
-  * hippodraw-1.18.3: added an addwrite for qt settings
-  * scipy-0.5.1-r1: fix a PIC for non-x86 arches
-  * umfpack-5.0.1: fixed an missing include file
-  * sync scipy with main tree, add one with umfpack
-  * redigesting
-  * added use flags for hippodraw
-  * deleted packages bumped in main tree
-  * added hippodraw-1.18.3
-  * readded minuit + version update to 5.12.00
-  * wxmaxima-0.7.0 is for the new maxima-5.10.0
-  * maxima-5.10.0: a major new version
-  * added cern use flag
-  * added numpy-1.0_rc1.ebuild
-  * matplotlib-0.87.5: removed ppc keywods (agg untested)
-  * scientificpython, cmt: changed license to CeCill-2
-  * Changed CeCiLL license, added agg use flag
-  * numarray-1.5.2.ebuild: fixed lapack and fortran deps
-  * umfpack: added a warning about upgrading. Is there a better solution??
-  * matio-1.3.1: version bump
-  * qcl ebuild now honours the user's $CXXFLAGS
-  * added a working celestia-1.4.1-r1
-  * added plplot use flag
-  * added sci-astronomy/scamp
-  * added sci-astronomy/cdsclient
-  * added sci-astronomy/stiff
-  * removed swarp-2.15.7, cleaning
-  * some cleaning
-  * updated metadata.xml
-  * added tclx-8.4 and tkimg-1.3
-  * added skycat-3.0.1
-  * orsa-0.7-r1: ebuild update
-  * orsa-0.7-r1: qt -> qt3 use flag
-  * deleted minuit (now in >=root-5)
-  * new ebuild for libafterimage
-  * major root-5.12.00e ebuild update, removed old one.
-  * scientificpython-2.5.11 update
-  * cleaning white spaces, digest and others.
-  * some cleaning
-  * version bump for openmpi+pg fortran compiler
-  * added new fortran eclass
-  * added matplotlib-0.87.5, removed old (buggy) 0.87.4-r1
-  * updated root to 5.12a and moved to sci-physics
-  * added geant321-3-21.14
-  * added cernlib-montecarlo-2005
-  * added paw-2.14.04
-  * split cernlib, updated ebuild and put it in sci-physics
-  * added scientificpython-2.4.11 and scientificpython-2.5.10
-  * added torque-2.1.2
-  * added scipy-0.5.1
-  * fixed a test in umfpack-5.0.1
-  * added umfpack-5.0.1
-  * added swarp-2.16.0
-  * added sextractor-2.5.0
-  * added cmt-1.18.20060606, removed old versions
-  * added numpy-1.0_beta5, removed old versions
-  * numarray-1.5.2: version update and clean
-  * added matplotlib-0.87.4-r1
-  * more flexibility to change versions of AMD and UFconfig
-  * coot: bump to 0.1.2
-  * added a forgotten file
-  * changed download url for UFconfig to a fixed version instead of current
-  * changed amd download url to a fixed version (1.2) instead of current
-  * matplotlib: updated to 0.87.4-r1, removed 0.87.3 and various cleanups
-  * agg: updated Manifest, removed agg-2.3
-  * fixed sandbox violation with USE flag doc
-  * matio-1.3.0 download url fixed
-  * matio-1.3.0 (version bump); freemat-2.0 (patch for building with matio-1.3.0)
-  * added texmacs-1.0.6.6
-  * Corrected herd in metadata.xml
-  * added qcl-0.6.2
-  * new version: texmacs-1.0.6.5
-  * new version: texmacs-1.0.6.5
-  * Added xspice and X use flag. See bug 140402
-  * New ebuild for gerbv-1.0.2
-  * removed old files
-  * Version bump to 0.99.1
-  * Version bump to 0.99.1
-  * Making repoman happy.
-  * Version bump. Removed old version
-  * Removed some ebuilds older than the ones in the tree
-  * added: freemat-2.0
-  * new version: texmacs-1.0.6.4
-  * Added initial ebuild for rkward
-  * Minor fixes to kayali in order to please repoman
-  * minor cleanups
-  * new version: texmacs-1.0.6.3
-  * Adding kayali ebuild
-  * Merged ccp4, coot and deps to gentoo-x86
-  * Merged ccp4, coot and deps to gentoo-x86
-  * bug fix in matio-1.1.4
-  * added matio-1.1.4, removed matio-1.0 (this last ebuild was unsatisfactory)
-  * There's a new coot 0.1.2-pre1 with fixed hydrogen hiding.
-  * added USE flags for texmacs
-  * added matio-1.0
-  * matplotlib: cleanup
-  * matplotlib-0.87.3-r1: fixed wxpython versioning, added patch for tcltk
-  * imaxima: changed ChangeLog
-  * imaxima-0.94b: added patch
-  * maxima-5.9.3-r1: fixed linguas, added new patches
-  * ccp4 double-defines gerror_ in library_f.c on ppc/gcc4
-  * pyfits-1.0.1: version bump
-  * numpy-0.9.8: fixed some typos
-  * Add missing patch
-  * Make coot prereleases work.
-  * ccp4: install everything formerly in /usr/lib/ccp4/ to /usr/share/ccp4/ with the exception of ccp4i, because it contains binaries and scripts. Fix installation of some html docs that tried going to /usr/html/. Fix generation of symlinks in /usr/lib/ccp4/ so ccp4i documentation works. Also sed MOLREPLIB in the setup scripts, so programs using it work.
-  * Minimal changes to get ccp4 6.0.1 working.
-  * Initial bump of coot to 0.1.2-pre1
-  * arpack: fixed typo
-  * added imaxima-0.94b
-  * added maxima-5.9.3-r1
-  * cfitsio: fix $PF to $ for docs
-  * Bump ccp4 to 6.0.1
-  * Instead of a hackish check for whether our rpaths will kills us, just add stricter to RESTRICT.
-  * agg-2.4: redigesting
-  * scigraphica: fixed ALL_LINGUAS
-  * libscigraphica: fixed ALL_LINGUAS
-  * matplotlib-0.87.3: version bump
-  * scigraphica & libscigraphica: major update
-  * sci-astronomy: cleanup
-  * umfpack: fixed a typo in libtool tag
-  * scipy-0.4.9: added swig dependency for umfpack bindings
-  * numeric-24.2-r1: cleaned, updated changelog.
-  * numpy-0.9.8: blocks f2py. tested with gcc-4.1
-  * added algae-4.3.6
-  * scipy-0.4.9: version bump + fixes
-  * dev-python: cleanup
-  * added numeric-24.2-r1: various fixes
-  * arpack96-r1: autotoolization
-  * Moved the the portage tree.
-  * Minor updates.
-  * cernlib-2005-r1: fixed cernlib script, added imake dep.
-  * added pgplot-5.2.2-r1
-  * Bump coot.
-  * Pull in coot-data, also add missing guile-gui dep
-  * cfitsio-3.006-r1: proper libtoolization
-  * numpy-0.9.8: version bump
-  * agg-2.4: updated for X modular
-  * orsa-0.7.0-r1: added patch to compile with for gcc-4.1
-  * added texmacs-1.0.6.2
-  * matplotlib-0.87.2-r2.ebuild: swap numeric/numpy
-  * wxmaxima: fixed for wxwidget versioning
-  * Moved to the main portage tree.
-  * added yorick-1.5.22
-  * added qtiplot-0.8.5
-  * added keyword -amd64
-  * Stop patching in gfortran 4.0 tarball and remove the associated patch. Bill Scott suggests the stuff's already in 6.0.
-  * numarray-1.5.1-r2: fixed for gcc-4.1, lapack and headers
-  * Add ccp4 patches from prerelease/ section. Pass --tmpdir so imake doesn't attempt to write to /imakeXXXXXX
-  * Forgot to add the ccp4 patch to fix builds w/ gcc 4.1
-  * added scigraphica-2.1.0 and libscigraphica-2.1.1
-  * torque: version bump to 2.1.0
-  * added blas-docs and lapack-docs
-  * agg-2.4: fixed virtual/x11
-  * agg: updated to 2.4
-  * wxmaxima: version bump to 0.6.5
-  * cmt-1.18: version bump and fixed emacs USE flag
-  * openmpi: fixed use fortran
-  * Update sauerbraten version. Add RMD160 and SHA256 digests to ccp4.
-  * cmt-1.18.20060301.ebuild: fixed CMTDIR
-  * Add gfortran to allowed compilers.
-  * Don't mirror this stuff.
-  * Since we install with insecure RPATH settings, add a check to see whether portage has been edited to allow it.
-  * Apply upstream patches.
-  * Set CCP4_LIB to try and get the X programs linking with libxdl_view.
-  * Try einstall instead of make install to see whether it improves rpath issues.
-  * Do a more generic sed to change CCP4_MASTER.
-  * Fix up some formatting.
-  * Add a ccp_patch() wrapper that makes it look like we're bulk patching.
-  * Minimal changes to get it working.
-  * Copy 5.99.5 to new version.
-  * added cmt-1.18.20060301
-  * minuit: fixed ChangeLog
-  * root-5.10.00: fixed CXXFLAGS, doc
-  * general cleaning
-  * root-5.10.00: added doc keyword and install
-  * cernlib-2005: fixed cfortran to use installed one.
-  * cernlib: fixed doc targets
-  * cfortran-4.4: updated debian patch
-  * root-5.10.00: fixed EXTRA_ECONF and some cleaning
-  * added root-5.10.00 (major version bump)
-  * cernlib-2005: fixed a doc installation
-  * added cernlib-2005
-  * added agg-2.3 (for matplotlib)
-  * matplotlib-0.87.2-r2: added agg support
-  * openmpi: fixed digest
-  * Removed src_compile
-  * removed useless src_compile
-  * Adding ebuild for generecon
-  * Merge in comet overlay.
-  * Initial commit of portage overlay.
-  * Initial commit of portage overlay.
-  * arpack cleaning
-  * openmpi-1.0.2: version bump
-  * major update for umfpack-4.6
-  * arpack: fixed a bunch of things, new blas flag, libtoolization.
-  * added mkl-8.0.2.004.ebuild (simple version bump)
-  * Moved to the main portage tree.
-  * Added ebuild for magic-7.4.2
-  * Adding new ebuild for octave-epstk
-  * added mkl-8.1.014 (working experimental version)
-  * Fixed documentation issue
-  * Moved to the main portage tree.
-  * Cleaning up as they are now in the main portage tree.
-  * cleaned to sync with portage
-  * added gle-4.0.11
-  * Fixed IUSE line
-  * Various small cleanups of the ebuild, added examples USE flag and marked ~amd64.
-  * Version bump
-  * maxima-5.9.3: removed unicode patch
-  * various ebuild cleaning
-  * swarp-2.15.7 version bump
-  * cleaned numdisplay
-  * added numpy-0.9.6-r1
-  * pruned old numpy and added numpy-0.9.6-r1
-  * cleaned cfortran and pruned R
-  * Removed previous linsmith versions
-  * Version bump for linsmith-0.9.4
-  * Version bump for linsmith-0.9.4
-  * Version bump for linsmith-0.9.4
-  * maxima-5.9.3: version bump, fixes + removed 5.9.2
-  * matplotlib/Manifest: fixed
-  * added an ATLAS check. corrected some path in site.cfg
-  * mkl-8.0.1.006.ebuild: added env.d and a few cleaning
-  * openmpi-1.0.1.ebuild: fixed links added noexecstack and
-  * numarray-1.5.1-r1.ebuild: put lapack sed in src_unpack
-  * openmpi-1.0.1.ebuild: fix USE flags, links
-  * cleaning
-  * torque-2.0.0_p8.ebuild: now pic only for libpbs with a patch
-  * torque-2.0.0_p8.ebuild: forced fPIC and added PBS_SERVER_NAME
-  * openmpi-1.0.1.ebuild: removed warning if not pic
-  * arpack-96.ebuild: fortran and mpi fixes
-  * numpy-0.9.6.ebuild: fix atlas/lapack again
-  * removed src_test
-  * added scipy-0.4.8.ebuild with proper fftw and atlas treatment
-  * added matplotlib-0.87.2.ebuild, also with wxpython flag
-  * scipy-0.4.6.ebuild: removed ifc flag
-  * torque-2.0.0_p8.ebuild: changed pic and tcltk behaviour, added netkit-rsh
-  * openmpi-1.0.1.ebuild: slight more info on pic behaviour
-  * scipy-0.4.6.ebuild: removed eselect dependencies
-  * fixed pic behaviour for openmpi and torque
-  * added openpbs-common-1.1.1
-  * deleted torque-2.0.0_p7.ebuild and changed DEPENDS for torque-2.0.0_p8.ebuild
-  * white space cleaning for torque-2.0.0_p8.ebuild
-  * added torque-2.0.0_p8.ebuild and patches
-  * openmpi-1.0.1.ebuild: removed pic flag, forced -fPIC for amd64
-  * scipy-0.4.6.ebuild: fixed threaded-ATLAS directory
-  * scipy-0.4.6.ebuild: eselect corrections
-  * openmpi-1.0.1.ebuild: added pic use flag and corrected fortran stuff
-  * bumped numpy-0.9.6
-  * added matplotlib-0.87.1 patches
-  * added sys-cluster/{torque,openmpi} very experimental ebuilds
-  * matplotlib-0.87.1 version bump and doc clean
-  * added numpy/ChangeLog
-  * changed lapack config: added use flag. removed test for now.
-  * added numarray-1.5.1-r1
-  * added matplotlib-0.87
-  * added cfitsio-3.006
-  * forgot scipy-0.4.6 digest
-  * added numpy-0.9.5
-  * scipy-0.4.6 version bump
-  * general cleaning (licenses, USE flags descriptions, headers)
-  * orsa-0.7.0.ebuild: removed useless USE flags
-  * cfortran-4.4.ebuild: fixed error in license
-  * scipy-0.4.4: lapack-atlas instead of virtual/lapack
-  * mkl: added blas/lapack routines files for shared libs
-  * Adding new freehdl from bug 122790
-  * mkl-8.0.1.006.ebuild: make shared libs, removed cpu detection, threading by default
-  * mkl: removing threaded scripts and c-lapack
-  * local USE flags description file added
-  * updated license and metadata.xml
-  * scipy/scipy-0.4.4.ebuild: changed fortran
-  * added scipy-0.4.4
-  * mkl-8.0.1.006.ebuild: improved cpu detection
-  * mkl-8.0.1.006: config scripts, license stuff
-  * added licenses directory and AURA, mkl licenses
-  * mkl: reworked ebuild: +fortran95, rpm work and install, not yet operational
-  * mkl-8.0.1.006.ebuild: reworked lib install + tests
-  * mkl/mkl-8.0.1.006.ebuild: corrected some installation bugs
-  * added experimental mkl-8.0.1.006
-  * Version bump
-  * maxima-5.9.2.ebuild: changed gnuplot category for sci-visualisation
-  * maxima-5.9.2.ebuild: changed gnuplot dep for sci-visualisation
-  * maxima-5.9.2: final fixes for ebuild and updated metadata.xml
-  * maxima-5.9.2.ebuild: some cleaning
-  * maxima-5.9.2.ebuild: gcl use flag is back.
-  * maxima-5.9.2: added patches (browser+emaxima) + cleaning
-  * gdl in portage
-  * maxima-5.9.2.ebuild: forced >=sbcl-0.9.4, and rlwrap change
-  * maxima-5.9.2.ebuild: put back the eautoreconf to build on x86
-  * Adding geos-2.2.1 Bug 120479
-  * Adding geos-2.2.1 Bug 120479
-  * Adding a new patch to configure.ac
-  * ebuild cleaning
-  * added maxima-5.9.2
-  * added wxmaxima package
-  * Adding a missing digest
-  * pspp-0.4.0.ebuild: emacs now uses elisp-common stuff
-  * added package dev-python/numdisplay
-  * Adding the path posted in the bug modified to work with 7.6.6. It does not solve the TK problem
-  * orsa-0.7.ebuild: change MPI stuff
-  * umfpack/umfpack-4.4.ebuild: changed doc behaviour and removed harcoded -j1
-  * sci-astronomy/orsa/orsa-0.7.0.ebuild: restored lam-mpi
-  * added sci-astronomy/orsa-0.7.0
-  * Very initial import of brlcad, from bug 77197. Does not compile here yet - needs work.
-  * fixed for USE=examples
-  * removed celestia (in portage)
-  * added package arpack (version -96)
-  * celestia/celestia-1.4.0.ebuild: fixed USE=kde deps.
-  * cleaning metadata and ebuild
-  * ebuild cleaning
-  * ebuild cleaning
-  * ebuild cleaning
-  * In the main portage tree.
-  * Moved to the main portage tree.
-  * Several minor corrections and enhancements.
-  * added package pygsl
-  * pyfits/pyfits-1.0.ebuild: license info
-  * Moved veusz to the main repo - thanks.
-  * Cleaned up some white space issues.
-  * Corrected a few whitespace issues, added doc to IUSE.
-  * sci-astronomy/celestia/celestia-1.4.0.ebuild: dependencies cleaning
-  * ds9-4.0_beta7.ebuild: added () for dohtml
-  * added celestia-1.4.0.ebuild
-  * added veusz-0.8.ebuild
-  * Added pspp-0.4.0.ebuild
-  * minuit-1.7.9 version bump
-  * minuit-1.7.9 version bump
-  * minuit-1.7.9.ebuild version bump
-  * minuit-1.7.6.ebuild: added insinto for doc, cfortran-4.4.ebuild added a link for cfortran.h
-  * New ebuild added: cfortran
-  * Small fix to header too...
-  * Tweaking dep.
-  * Initial import from bug 50565.
-  * IDL_STARTUP + cosmetics
-  * added umfpack-4.4.ebuild
-  * change gdl category to dev-lang + slight ebuild update
-  * minuit: pdf doc with DISTDIR
-  * cosmetics + RDEPEND without icc
-  * Added new ebuild for swarp-2.15.6
-  * Added new ebuild for ds9-4.0_beta7
-  * Adding ebuild for kseg
-  * added pyfits-1.0.ebuild
-  * added examples to test even without doc flag
-  * USE flags cleaning (ncurses, imagemagick and python)
-  * Adding linsmith patch
-  * Added new ebuild for minuit-1.7.6
-  * Added new ebuild for gdl-0.8.11
-  * Added new ebuild for sextractor-2.4.4
-  * Adding linsmith-0.9.2.ebuild
-  * Adding emu-1.10 form bug #98051
-  * Added new ebuild for linsmith-0.9.2
-  * Adding R-2.2.0 ebuild from bug 112022
-  * Adding kst-1.1.1
-  * New ebuild for linsmith-0.9.1
-  * Removed boinc -> moved to main tree.
-  * Cleaned up deps on X and modular X, bug 110606.
-  * Add experimental boinc ebuild to the overlay for testing.
-  * Moved to portage main tree.
-  * Small cleanup.
-  * Forgot to add the revbumped kst ebuild...
-  * Clean up old ebuilds not changed in overlay, revision bump, reset keywords and a few small ebuild cleanups.
-  * new ebuild for another smith chart calculation program
-  * New patch to really fix bug 104617
-  * Added media-gfx/kst with patch to fix bug #104617
-  * Fixed some errors in the ebuild and in the ChangeLog
-  * Adding new ebuild for gsmc-1.0
-  * Created initial directory structure.
 # ChangeLog for <CATEGORY>/<PACKAGE_NAME>
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
 *<PACKAGE_NAME>-<PACKAGE_VERSION>-<PACKAGE_RELEASE> (DD MMM YYYY)

diff --git a/skel.ebuild b/skel.ebuild
index 6c9dc85..93f5e16 100644
--- a/skel.ebuild
+++ b/skel.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 

diff --git a/skel.metadata.xml b/skel.metadata.xml
index 4dcddcb..17b08b4 100644
--- a/skel.metadata.xml
+++ b/skel.metadata.xml
@@ -1,34 +1,20 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<!--
-$Header: /var/cvsroot/gentoo-x86/skel.metadata.xml,v 1.21 2012/02/07 00:03:15 idl0r Exp $
-
-This is the example metadata file.
-The root element of this file is <pkgmetadata>. Within this element a
-number of subelements are allowed: herd, maintainer, and
-longdescription. herd is a required subelement.
-
-For a full description look at:
-http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml?part=2&chap=4
-
-
-Before committing, please remove the comments from this file. They are
-not relevant for general metadata.xml files.
--->
 <pkgmetadata>
-	<herd>sci</herd>
+
+<herd>sci-blah</herd>
 <maintainer>
-	<email>@gentoo.org</email>
-<!--  <description>Description of the maintainership</description> -->
+  <email>my.email@blah.doh</email>
 </maintainer>
-<!-- <longdescription>Long description of the package</longdescription> -->
-<!--
+
+<longdescription>
+  Long description of the package. Check the homepage. Make it useful
+  for users.
+</longdescription>
 <use>
-	<flag name="flag">Description of how USE='flag' affects this package</flag>
-	<flag name="userland_GNU">Description of how USERLAND='GNU' affects this
-		package</flag>
-	<flag name="aspell">Uses <pkg>app-text/aspell</pkg> for spell checking.
-		Requires an installed dictionary from <cat>app-dicts</cat></flag>
+  <flag name="flag">Description of how USE='flag' affects this package</flag>
 </use>
--->
+<upstream>
+  <remote-id type="blah">name-of-package-in-blah</remote-id>
+</upstream>
 </pkgmetadata>

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     52856f2bdf0d60884389fb5362340c64e693f6e6
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Mon Apr 29 06:32:16 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Apr 29 06:32:16 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=52856f2b

Merge pull request #65 from gentryx/master

New ebuild: VampirTrace


 dev-util/VampirTrace/Manifest                  |    1 +
 dev-util/VampirTrace/VampirTrace-5.14.3.ebuild |   33 ++++++++++++++++++++++
 dev-util/VampirTrace/metadata.xml              |   13 ++++++++
 licenses/vampir                                |   36 ++++++++++++++++++++++++
 sys-apps/likwid/files/use_uncore.patch         |   12 ++++++++
 sys-apps/likwid/likwid-3.0.ebuild              |    5 ++-
 sys-apps/likwid/metadata.xml                   |    7 +++-
 7 files changed, 103 insertions(+), 4 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     6d23e13180fb3099af32a680e3a94a26d53a7160
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed Apr 24 11:49:52 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Apr 24 11:49:52 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6d23e131

Merge branch 'master' of https://github.com/gentoo-science/sci


 app-doc/root-docs/ChangeLog                        |    9 +-
 app-doc/root-docs/Manifest                         |    3 +-
 app-doc/root-docs/root-docs-5.32.04.ebuild         |   96 -
 ...ocs-5.34.03.ebuild => root-docs-5.34.05.ebuild} |    5 +-
 app-doc/root-docs/root-docs-9999.ebuild            |    3 +-
 app-doc/scalapack-docs/ChangeLog                   |    7 +-
 app-doc/scalapack-docs/metadata.xml                |    3 +-
 app-doc/scalapack-docs/scalapack-docs-2.0.ebuild   |    6 +-
 app-forensics/vine/ChangeLog                       |   11 +
 app-forensics/vine/Manifest                        |    1 +
 app-forensics/vine/files/vine-1.0-binutils.patch   |   16 +
 app-forensics/vine/files/vine-1.0-gcc46.patch      |   37 +
 app-forensics/vine/files/vine-1.0-install.patch    |   89 +
 .../vine/files/vine-1.0-ocamlgraph182.patch        |   68 +
 {dev-lang/ispc => app-forensics/vine}/metadata.xml |    0
 app-forensics/vine/vine-1.0.ebuild                 |   40 +
 app-portage/g-octave/ChangeLog                     |    6 +-
 app-portage/g-octave/g-octave-9999.ebuild          |   44 +-
 app-portage/g-octave/metadata.xml                  |   10 +-
 app-text/jabref/ChangeLog                          |   12 +
 app-text/jabref/Manifest                           |    1 +
 ...{jabref-2.9.2-r1.ebuild => jabref-2.10b.ebuild} |   13 +-
 app-text/jabref/jabref-2.9.2-r1.ebuild             |    9 +-
 dev-db/cppdb/ChangeLog                             |   26 +
 dev-db/cppdb/Manifest                              |    1 +
 dev-db/cppdb/cppdb-0.3.1-r1.ebuild                 |   50 +
 dev-db/cppdb/metadata.xml                          |   13 +
 dev-java/flexdock/Manifest                         |    2 +-
 ....2-nodemo.patch => flexdock-1.2.3-nodemo.patch} |    0
 ...flexdock-1.2.2.ebuild => flexdock-1.2.3.ebuild} |    8 +-
 dev-java/gluegen/ChangeLog                         |    4 +
 dev-java/gluegen/gluegen-2.0_rc8.ebuild            |    2 +-
 dev-java/gluegen/metadata.xml                      |    4 +-
 dev-java/jcip-annotations/ChangeLog                |    6 +-
 dev-java/jcip-annotations/Manifest                 |    2 +-
 .../jcip-annotations-1.0-r1.ebuild                 |    7 +-
 dev-java/jcip-annotations/metadata.xml             |   13 +-
 dev-java/jlatexmath-fop/Manifest                   |    3 +-
 .../files/jlatexmath-fop-1.0.2-fixpaths.patch      |   13 +
 dev-java/jlatexmath-fop/files/version.xml          |    5 +
 .../jlatexmath-fop/jlatexmath-fop-0.9.7.ebuild     |   52 -
 .../jlatexmath-fop/jlatexmath-fop-1.0.0.ebuild     |   52 -
 .../jlatexmath-fop/jlatexmath-fop-1.0.2.ebuild     |   45 +
 dev-java/jlatexmath/Manifest                       |    3 +-
 dev-java/jlatexmath/jlatexmath-1.0.0.ebuild        |   32 -
 ...exmath-0.9.7.ebuild => jlatexmath-1.0.2.ebuild} |   22 +-
 dev-java/jogl/ChangeLog                            |    4 +
 dev-java/jogl/jogl-2.0_rc8-r1.ebuild               |    2 +-
 dev-java/jogl/metadata.xml                         |   10 +-
 dev-java/netcdf/Manifest                           |    2 +-
 dev-java/scirenderer/Manifest                      |    2 +-
 ...derer-1.0.5.ebuild => scirenderer-1.1.0.ebuild} |    4 +-
 dev-java/xmlgraphics-commons/Manifest              |    1 +
 .../files/disable-iccprofile-test.patch            |   38 +
 .../xmlgraphics-commons}/metadata.xml              |    2 +-
 .../xmlgraphics-commons-1.5.ebuild                 |   58 +
 dev-lang/berkeley_upc/ChangeLog                    |   10 +
 dev-lang/berkeley_upc/Manifest                     |    1 +
 dev-lang/berkeley_upc/berkeley_upc-2.16.0.ebuild   |   55 +
 dev-lang/berkeley_upc/metadata.xml                 |   25 +
 dev-lang/berkeley_upc_translator/ChangeLog         |   11 +
 dev-lang/berkeley_upc_translator/Manifest          |    1 +
 .../berkeley_upc_translator-2.16.0.ebuild          |   30 +
 ...keley_upc_translator-2.16.0-stackoverflow.patch |   18 +
 .../berkeley_upc_translator}/metadata.xml          |    4 +-
 dev-lang/julia/files/julia-nopatchelf.patch        |   14 +
 dev-lang/julia/julia-9999.ebuild                   |   28 +-
 dev-lang/julia/metadata.xml                        |    8 +-
 dev-lang/vtune/ChangeLog                           |    8 +-
 dev-lang/vtune/Manifest                            |    4 +-
 dev-lang/vtune/metadata.xml                        |    8 +-
 dev-lang/vtune/vtune-11.0.7.221625.ebuild          |   69 -
 dev-lang/vtune/vtune-13.1.4.270817.ebuild          |   38 +
 dev-libs/double-conversion/ChangeLog               |   10 +-
 dev-libs/double-conversion/Manifest                |    2 +-
 ...n-1.1.ebuild => double-conversion-1.1.1.ebuild} |    8 +-
 ...s.patch => double-conversion-1.1.1-scons.patch} |    0
 dev-libs/fortrancl/ChangeLog                       |    8 +
 dev-libs/fortrancl/fortrancl-0.1_alpha3.ebuild     |    5 +-
 dev-libs/fortrancl/metadata.xml                    |   12 +-
 dev-libs/libpfm/ChangeLog                          |   12 +
 dev-libs/libpfm/Manifest                           |    1 +
 dev-libs/libpfm/libpfm-4.3.0.ebuild                |   35 +
 .../envytools => dev-libs/libpfm}/metadata.xml     |    0
 dev-libs/mathjax/ChangeLog                         |   10 -
 dev-libs/mathjax/Manifest                          |    1 -
 dev-libs/mathjax/mathjax-2.0.ebuild                |   50 -
 dev-libs/mathjax/metadata.xml                      |   17 -
 dev-libs/papi/ChangeLog                            |    9 +
 dev-libs/papi/Manifest                             |    1 +
 {x11-misc/envytools => dev-libs/papi}/metadata.xml |    0
 dev-libs/papi/papi-5.1.0.2.ebuild                  |   30 +
 dev-ml/lacaml/ChangeLog                            |    6 +-
 dev-ml/lacaml/lacaml-7.0.3.ebuild                  |   12 +-
 dev-ml/lacaml/metadata.xml                         |    4 +-
 dev-ml/zarith/ChangeLog                            |    3 +
 dev-ml/zarith/Manifest                             |    3 -
 dev-ml/zarith/metadata.xml                         |   16 +-
 dev-ml/zarith/zarith-1.1.ebuild                    |   31 +-
 dev-perl/DBIx-DBStag/ChangeLog                     |    6 +-
 dev-perl/DBIx-DBStag/DBIx-DBStag-0.12.ebuild       |    9 +-
 dev-perl/DBIx-DBStag/Manifest                      |    2 +-
 dev-perl/DBIx-DBStag/metadata.xml                  |   10 +-
 dev-perl/Log-Cabin/ChangeLog                       |    9 +-
 dev-perl/Log-Cabin/Log-Cabin-0.06.ebuild           |    9 +-
 dev-perl/Log-Cabin/Manifest                        |    2 +-
 dev-perl/Log-Cabin/metadata.xml                    |   10 +-
 dev-perl/Text-ParseWords/ChangeLog                 |    6 +-
 dev-perl/Text-ParseWords/Manifest                  |    2 +-
 .../Text-ParseWords/Text-ParseWords-3.27.ebuild    |    6 +-
 dev-perl/Text-ParseWords/metadata.xml              |   10 +-
 dev-perl/Time-Progress/ChangeLog                   |    6 +-
 dev-perl/Time-Progress/Manifest                    |    2 +-
 dev-perl/Time-Progress/Time-Progress-1.7.ebuild    |    6 +-
 dev-perl/Time-Progress/metadata.xml                |   10 +-
 dev-perl/go-perl/ChangeLog                         |    6 +-
 dev-perl/go-perl/Manifest                          |    2 +-
 dev-perl/go-perl/go-perl-0.13.ebuild               |   10 +-
 dev-perl/go-perl/metadata.xml                      |   10 +-
 dev-python/Forthon/ChangeLog                       |    8 +
 dev-python/Forthon/Forthon-0.8.11.ebuild           |   11 +-
 .../files/Forthon-0.8.11-fix_options_parser.patch  |   17 +
 dev-python/Forthon/metadata.xml                    |    8 +-
 dev-python/GOGrapher/ChangeLog                     |    6 +-
 dev-python/GOGrapher/GOGrapher-9999.ebuild         |   10 +-
 dev-python/GOGrapher/metadata.xml                  |   10 +-
 dev-python/RecSQL/ChangeLog                        |   18 +
 dev-python/RecSQL/RecSQL-9999.ebuild               |   33 +
 .../libcmatrix => dev-python/RecSQL}/metadata.xml  |    3 +-
 dev-python/pymvpa/ChangeLog                        |    6 +-
 dev-python/pymvpa/metadata.xml                     |    4 +-
 dev-python/pymvpa/pymvpa-0.4.4.ebuild              |   30 +-
 dev-python/pythonocc/ChangeLog                     |   17 +-
 dev-python/pythonocc/Manifest                      |    2 +-
 dev-python/pythonocc/metadata.xml                  |    2 +-
 .../{pythonocc-0.4.ebuild => pythonocc-0.5.ebuild} |   19 +-
 licenses/ECL-2.0                                   |   97 +
 licenses/blasr                                     |   65 +
 licenses/mgltools                                  |   42 +
 media-gfx/PhiloGL/ChangeLog                        |    6 +-
 media-gfx/PhiloGL/PhiloGL-1.4.3.ebuild             |    6 +-
 media-gfx/PhiloGL/metadata.xml                     |    8 +-
 media-gfx/librecad/ChangeLog                       |   11 +-
 media-gfx/librecad/Manifest                        |    7 +-
 media-gfx/librecad/librecad-1.0.2.ebuild           |   10 +-
 ...librecad-1.0.1.ebuild => librecad-1.0.3.ebuild} |   15 +-
 media-gfx/librecad/librecad-2.0.0_alpha3.ebuild    |   48 -
 ...0_alpha4.ebuild => librecad-2.0.0_beta5.ebuild} |   10 +-
 media-gfx/librecad/librecad-9999.ebuild            |    8 +-
 media-gfx/librecad/metadata.xml                    |   18 +-
 profiles/arch.list                                 |   44 +
 profiles/hardened/package.mask                     |   27 -
 profiles/package.mask                              |   12 +
 sci-astronomy/astrometry/ChangeLog                 |    6 +-
 sci-astronomy/astrometry/astrometry-0.38.ebuild    |    9 +-
 sci-astronomy/astrometry/metadata.xml              |    4 +-
 sci-astronomy/eye/ChangeLog                        |    4 +-
 sci-astronomy/eye/eye-9999.ebuild                  |    3 +-
 sci-astronomy/eye/metadata.xml                     |    4 +-
 sci-astronomy/stiff/ChangeLog                      |    5 +-
 sci-astronomy/stiff/metadata.xml                   |    4 +-
 sci-astronomy/stiff/stiff-9999.ebuild              |   23 +-
 sci-astronomy/zebra/ChangeLog                      |    5 +-
 sci-astronomy/zebra/metadata.xml                   |    4 +-
 sci-astronomy/zebra/zebra-1.01.ebuild              |   16 +-
 sci-biology/Gambit/ChangeLog                       |    8 +
 sci-biology/Gambit/Gambit-0.4.145.ebuild           |    6 +-
 sci-biology/Gambit/Manifest                        |    4 +-
 sci-biology/Gambit/metadata.xml                    |   10 +-
 sci-biology/YASRA/ChangeLog                        |    5 +-
 sci-biology/YASRA/YASRA-2.1.ebuild                 |    4 +-
 sci-biology/YASRA/metadata.xml                     |   10 +-
 sci-biology/amos/ChangeLog                         |    8 +-
 sci-biology/amos/amos-9999.ebuild                  |   47 +-
 sci-biology/amos/metadata.xml                      |   17 +-
 sci-biology/artemis-bin/ChangeLog                  |    6 +-
 sci-biology/artemis-bin/Manifest                   |    2 +-
 sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild |    3 +-
 sci-biology/artemis-bin/metadata.xml               |   10 +-
 sci-biology/blasr/ChangeLog                        |    8 +-
 sci-biology/blasr/Manifest                         |    3 -
 sci-biology/blasr/blasr-9999.ebuild                |   13 +-
 sci-biology/blasr/metadata.xml                     |   10 +-
 sci-biology/cluster/ChangeLog                      |    6 +-
 sci-biology/cluster/cluster-1.50-r1.ebuild         |    4 +-
 sci-biology/cluster/cluster-1.50.ebuild            |    4 +-
 sci-biology/cluster/metadata.xml                   |   12 +-
 sci-biology/consed-bin/ChangeLog                   |    8 +
 sci-biology/consed-bin/Manifest                    |    4 +-
 sci-biology/consed-bin/consed-bin-20.ebuild        |    4 +-
 sci-biology/consed-bin/metadata.xml                |   10 +-
 sci-biology/estscan/ChangeLog                      |    5 +-
 sci-biology/estscan/Manifest                       |   18 +-
 sci-biology/estscan/metadata.xml                   |   16 +-
 sci-biology/hydra-sv/ChangeLog                     |    8 +
 sci-biology/hydra-sv/Manifest                      |    2 +-
 sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild         |   11 +-
 .../hydra-sv}/metadata.xml                         |    0
 sci-biology/manatee-igs/ChangeLog                  |    6 +-
 sci-biology/manatee-igs/Manifest                   |    4 +-
 sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild  |    4 +-
 sci-biology/manatee-igs/metadata.xml               |   10 +-
 sci-biology/mira/ChangeLog                         |   11 +-
 sci-biology/mira/Manifest                          |    7 +-
 .../mira/files/mira-3.4.0.2-boost-1.50.patch       |   24 +
 sci-biology/mira/mira-3.4.1.1.ebuild               |   61 +
 sci-biology/mira/mira-3.9.9.ebuild                 |   61 +
 sci-biology/ncbi-tools++/ChangeLog                 |   21 +
 .../files/ncbi-tools++-9.0.0-as-needed.patch       |  758 +-
 sci-biology/ncbi-tools++/metadata.xml              |   39 +
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |   95 +-
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild |    6 +-
 sci-biology/sra_sdk/ChangeLog                      |    6 +-
 sci-biology/sra_sdk/metadata.xml                   |   10 +-
 sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild           |    6 +-
 sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild          |    6 +-
 sci-biology/wcd/ChangeLog                          |    8 +-
 sci-biology/wcd/Manifest                           |    2 +-
 sci-biology/wcd/files/wcd-0.6.0-impl-decl.patch    |   15 +
 sci-biology/wcd/files/wcd-0.6.0-ldflags.patch      |   16 +
 sci-biology/wcd/metadata.xml                       |   10 +-
 sci-biology/wcd/wcd-0.6.0.ebuild                   |   41 +-
 sci-chemistry/GromacsWrapper/ChangeLog             |   25 +
 .../GromacsWrapper/GromacsWrapper-9999.ebuild      |   41 +
 .../files/0001-Drop-chmod-hack.patch               |   28 +
 .../GromacsWrapper}/metadata.xml                   |    3 +-
 sci-chemistry/ambertools/ChangeLog                 |   14 +-
 sci-chemistry/ambertools/ambertools-1.5-r2.ebuild  |  156 -
 sci-chemistry/ambertools/ambertools-1.5-r3.ebuild  |  158 -
 sci-chemistry/ambertools/ambertools-1.5-r4.ebuild  |   10 +-
 sci-chemistry/ambertools/ambertools-12.ebuild      |   16 +-
 sci-chemistry/ambertools/metadata.xml              |   10 +-
 sci-chemistry/ball/ChangeLog                       |    5 +-
 sci-chemistry/ball/ball-9999.ebuild                |   16 +-
 sci-chemistry/ball/metadata.xml                    |   20 +-
 sci-chemistry/burrow-owl/ChangeLog                 |    6 +-
 sci-chemistry/burrow-owl/burrow-owl-9999.ebuild    |    6 +-
 sci-chemistry/burrow-owl/metadata.xml              |    8 +-
 sci-chemistry/camshift/ChangeLog                   |    6 +-
 sci-chemistry/camshift/Manifest                    |    2 +-
 sci-chemistry/camshift/camshift-1.35.0.ebuild      |   45 +-
 sci-chemistry/camshift/files/1.35.0-gcc47.patch    |  148 +
 sci-chemistry/camshift/files/1.35.0-gentoo.patch   |   38 +
 sci-chemistry/camshift/metadata.xml                |    8 +-
 sci-chemistry/chooch/ChangeLog                     |    7 +-
 sci-chemistry/chooch/Manifest                      |    2 +-
 sci-chemistry/chooch/chooch-5.0.2-r1.ebuild        |   47 +-
 sci-chemistry/chooch/metadata.xml                  |    8 +-
 sci-chemistry/concoord/ChangeLog                   |    8 +-
 sci-chemistry/concoord/Manifest                    |    2 +
 .../{concoord-2.1.ebuild => concoord-2.1.2.ebuild} |   13 +-
 sci-chemistry/concoord/concoord-2.1.ebuild         |    4 +-
 sci-chemistry/concoord/metadata.xml                |    8 +-
 sci-chemistry/cs-rosetta/ChangeLog                 |   18 +
 sci-chemistry/cs-rosetta/Manifest                  |    3 +
 .../cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild |  104 +
 .../{phenix-bin => cs-rosetta}/metadata.xml        |    0
 sci-chemistry/curvefit/ChangeLog                   |    6 +-
 sci-chemistry/curvefit/curvefit-1.40.ebuild        |    6 +-
 sci-chemistry/curvefit/metadata.xml                |    2 +-
 sci-chemistry/freeon/ChangeLog                     |    7 +-
 sci-chemistry/freeon/freeon-9999.ebuild            |   21 +-
 sci-chemistry/freeon/metadata.xml                  |   12 +-
 sci-chemistry/gamess/ChangeLog                     |    6 +-
 .../gamess/files/gamess-20120501.1.gentoo.patch    |    4 +-
 sci-chemistry/gamess/gamess-20120501.1.ebuild      |    3 +-
 sci-chemistry/gamess/metadata.xml                  |   20 +-
 sci-chemistry/gnome-chemistry-utils/ChangeLog      |   20 +
 sci-chemistry/gnome-chemistry-utils/Manifest       |    1 +
 .../gnome-chemistry-utils-0.14.2.ebuild            |   44 +
 sci-chemistry/gnome-chemistry-utils/metadata.xml   |   11 +
 sci-chemistry/gromacs/ChangeLog                    |   18 +
 sci-chemistry/gromacs/Manifest                     |    2 -
 sci-chemistry/gromacs/gromacs-4.5.9999.ebuild      |  238 -
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild      |   47 +-
 sci-chemistry/gromacs/gromacs-9999.ebuild          |    1 -
 sci-chemistry/gromacs/metadata.xml                 |    1 -
 sci-chemistry/hydronmr/ChangeLog                   |   10 +
 sci-chemistry/hydronmr/Manifest                    |   13 +
 sci-chemistry/hydronmr/hydronmr-7c.ebuild          |   57 +
 .../{phenix-bin => hydronmr}/metadata.xml          |    0
 sci-chemistry/jligand/ChangeLog                    |    6 +-
 sci-chemistry/jligand/Manifest                     |    2 +-
 sci-chemistry/jligand/jligand-1.0.19.ebuild        |    4 +-
 sci-chemistry/jligand/metadata.xml                 |    8 +-
 sci-chemistry/mgltools-autodocktools/ChangeLog     |   16 +
 sci-chemistry/mgltools-autodocktools/Manifest      |    3 +-
 .../mgltools-autodocktools-1.5.4-r2.ebuild         |    4 +-
 ....ebuild => mgltools-autodocktools-1.5.6.ebuild} |    5 +-
 .../mgltools-autodocktools-1.5.6_rc2.ebuild        |   71 -
 sci-chemistry/mgltools-bhtree/ChangeLog            |   14 +
 sci-chemistry/mgltools-bhtree/Manifest             |    3 +-
 .../mgltools-bhtree-1.5.4-r1.ebuild                |    4 +-
 ...5.6_rc3.ebuild => mgltools-bhtree-1.5.6.ebuild} |    5 +-
 .../mgltools-bhtree-1.5.6_rc2.ebuild               |   48 -
 sci-chemistry/mgltools-cadd/ChangeLog              |   12 +
 sci-chemistry/mgltools-cadd/Manifest               |    3 +-
 ...1.5.6_rc3.ebuild => mgltools-cadd-1.5.6.ebuild} |    5 +-
 .../mgltools-cadd/mgltools-cadd-1.5.6_rc2.ebuild   |   48 -
 sci-chemistry/mgltools-cmolkit/ChangeLog           |   14 +
 sci-chemistry/mgltools-cmolkit/Manifest            |    3 +-
 .../mgltools-cmolkit-1.5.4-r1.ebuild               |    4 +-
 ....6_rc3.ebuild => mgltools-cmolkit-1.5.6.ebuild} |    5 +-
 .../mgltools-cmolkit-1.5.6_rc2.ebuild              |   48 -
 sci-chemistry/mgltools-dejavu/ChangeLog            |   14 +
 sci-chemistry/mgltools-dejavu/Manifest             |    3 +-
 .../mgltools-dejavu-1.5.4-r1.ebuild                |    4 +-
 ...5.6_rc3.ebuild => mgltools-dejavu-1.5.6.ebuild} |    5 +-
 .../mgltools-dejavu-1.5.6_rc2.ebuild               |   51 -
 sci-chemistry/mgltools-geomutils/ChangeLog         |   14 +
 sci-chemistry/mgltools-geomutils/Manifest          |    3 +-
 .../mgltools-geomutils-1.5.4-r1.ebuild             |    4 +-
 ..._rc3.ebuild => mgltools-geomutils-1.5.6.ebuild} |    5 +-
 .../mgltools-geomutils-1.5.6_rc2.ebuild            |   49 -
 sci-chemistry/mgltools-gle/ChangeLog               |   13 +
 sci-chemistry/mgltools-gle/Manifest                |    3 +-
 .../mgltools-gle/mgltools-gle-1.5.4-r1.ebuild      |    4 +-
 ...-1.5.6_rc3.ebuild => mgltools-gle-1.5.6.ebuild} |    5 +-
 .../mgltools-gle/mgltools-gle-1.5.6_rc2.ebuild     |   48 -
 sci-chemistry/mgltools-mglutil/ChangeLog           |   14 +
 sci-chemistry/mgltools-mglutil/Manifest            |    3 +-
 .../mgltools-mglutil-1.5.4-r1.ebuild               |    4 +-
 ....6_rc3.ebuild => mgltools-mglutil-1.5.6.ebuild} |    5 +-
 .../mgltools-mglutil-1.5.6_rc2.ebuild              |   51 -
 sci-chemistry/mgltools-molkit/ChangeLog            |   14 +
 sci-chemistry/mgltools-molkit/Manifest             |    3 +-
 .../mgltools-molkit-1.5.4-r1.ebuild                |    4 +-
 ...5.6_rc3.ebuild => mgltools-molkit-1.5.6.ebuild} |    5 +-
 .../mgltools-molkit-1.5.6_rc2.ebuild               |   50 -
 sci-chemistry/mgltools-networkeditor/ChangeLog     |   16 +
 sci-chemistry/mgltools-networkeditor/Manifest      |    3 +-
 .../mgltools-networkeditor-1.5.4-r1.ebuild         |    4 +-
 ....ebuild => mgltools-networkeditor-1.5.6.ebuild} |    5 +-
 .../mgltools-networkeditor-1.5.6_rc2.ebuild        |   50 -
 sci-chemistry/mgltools-opengltk/ChangeLog          |   14 +
 sci-chemistry/mgltools-opengltk/Manifest           |    3 +-
 .../mgltools-opengltk-1.5.4-r2.ebuild              |    4 +-
 ...6_rc3.ebuild => mgltools-opengltk-1.5.6.ebuild} |    5 +-
 .../mgltools-opengltk-1.5.6_rc2.ebuild             |   68 -
 sci-chemistry/mgltools-pmv/ChangeLog               |   13 +
 sci-chemistry/mgltools-pmv/Manifest                |    3 +-
 .../mgltools-pmv/mgltools-pmv-1.5.4-r1.ebuild      |    4 +-
 ...-1.5.6_rc3.ebuild => mgltools-pmv-1.5.6.ebuild} |    5 +-
 .../mgltools-pmv/mgltools-pmv-1.5.6_rc2.ebuild     |   52 -
 sci-chemistry/mgltools-pyautodock/ChangeLog        |   15 +
 sci-chemistry/mgltools-pyautodock/Manifest         |    3 +-
 .../mgltools-pyautodock-1.5.4-r1.ebuild            |    4 +-
 ...rc3.ebuild => mgltools-pyautodock-1.5.6.ebuild} |    5 +-
 .../mgltools-pyautodock-1.5.6_rc2.ebuild           |   48 -
 sci-chemistry/mgltools-pybabel/ChangeLog           |   14 +
 sci-chemistry/mgltools-pybabel/Manifest            |    3 +-
 .../mgltools-pybabel-1.5.4-r1.ebuild               |    4 +-
 ....6_rc3.ebuild => mgltools-pybabel-1.5.6.ebuild} |    5 +-
 .../mgltools-pybabel-1.5.6_rc2.ebuild              |   50 -
 sci-chemistry/mgltools-pyglf/ChangeLog             |   14 +
 sci-chemistry/mgltools-pyglf/Manifest              |    3 +-
 .../mgltools-pyglf/mgltools-pyglf-1.5.4-r1.ebuild  |    4 +-
 ....5.6_rc3.ebuild => mgltools-pyglf-1.5.6.ebuild} |    5 +-
 .../mgltools-pyglf/mgltools-pyglf-1.5.6_rc2.ebuild |   48 -
 sci-chemistry/mgltools-qslimlib/ChangeLog          |   14 +
 sci-chemistry/mgltools-qslimlib/Manifest           |    3 +-
 .../mgltools-qslimlib-1.5.4-r1.ebuild              |    4 +-
 ...6_rc3.ebuild => mgltools-qslimlib-1.5.6.ebuild} |    5 +-
 .../mgltools-qslimlib-1.5.6_rc2.ebuild             |   52 -
 sci-chemistry/mgltools-scenario/ChangeLog          |    4 +
 .../mgltools-scenario-1.5.4-r1.ebuild              |    4 +-
 sci-chemistry/mgltools-scenario2/ChangeLog         |   13 +
 sci-chemistry/mgltools-scenario2/Manifest          |    3 +-
 ..._rc3.ebuild => mgltools-scenario2-1.5.6.ebuild} |    5 +-
 .../mgltools-scenario2-1.5.6_rc2.ebuild            |   50 -
 sci-chemistry/mgltools-sff/ChangeLog               |   13 +
 sci-chemistry/mgltools-sff/Manifest                |    3 +-
 .../mgltools-sff/mgltools-sff-1.5.4-r1.ebuild      |    4 +-
 ...-1.5.6_rc3.ebuild => mgltools-sff-1.5.6.ebuild} |    5 +-
 .../mgltools-sff/mgltools-sff-1.5.6_rc2.ebuild     |   49 -
 sci-chemistry/mgltools-stride/ChangeLog            |    6 +
 .../mgltools-stride-1.5.4-r1.ebuild                |    4 +-
 sci-chemistry/mgltools-support/ChangeLog           |   14 +
 sci-chemistry/mgltools-support/Manifest            |    3 +-
 .../mgltools-support-1.5.4-r1.ebuild               |    4 +-
 ....6_rc3.ebuild => mgltools-support-1.5.6.ebuild} |    5 +-
 .../mgltools-support-1.5.6_rc2.ebuild              |   49 -
 sci-chemistry/mgltools-symserv/ChangeLog           |   12 +
 sci-chemistry/mgltools-symserv/Manifest            |    3 +-
 .../mgltools-symserv-1.5.4-r1.ebuild               |    4 +-
 ....6_rc3.ebuild => mgltools-symserv-1.5.6.ebuild} |    5 +-
 .../mgltools-symserv-1.5.6_rc2.ebuild              |   48 -
 sci-chemistry/mgltools-utpackages/ChangeLog        |   15 +
 sci-chemistry/mgltools-utpackages/Manifest         |    3 +-
 .../mgltools-utpackages-1.5.4-r1.ebuild            |    4 +-
 ...rc3.ebuild => mgltools-utpackages-1.5.6.ebuild} |    5 +-
 .../mgltools-utpackages-1.5.6_rc2.ebuild           |   49 -
 sci-chemistry/mgltools-viewer-framework/ChangeLog  |   17 +
 sci-chemistry/mgltools-viewer-framework/Manifest   |    3 +-
 .../mgltools-viewer-framework-1.5.4-r2.ebuild      |    4 +-
 ...uild => mgltools-viewer-framework-1.5.6.ebuild} |    5 +-
 .../mgltools-viewer-framework-1.5.6_rc2.ebuild     |   53 -
 sci-chemistry/mgltools-vision/ChangeLog            |   14 +
 sci-chemistry/mgltools-vision/Manifest             |    3 +-
 .../mgltools-vision-1.5.4-r1.ebuild                |    4 +-
 ...5.6_rc3.ebuild => mgltools-vision-1.5.6.ebuild} |    5 +-
 .../mgltools-vision-1.5.6_rc2.ebuild               |   59 -
 sci-chemistry/mgltools-visionlib/ChangeLog         |   14 +
 sci-chemistry/mgltools-visionlib/Manifest          |    3 +-
 .../mgltools-visionlib-1.5.4-r1.ebuild             |    4 +-
 ..._rc3.ebuild => mgltools-visionlib-1.5.6.ebuild} |    5 +-
 .../mgltools-visionlib-1.5.6_rc2.ebuild            |   48 -
 sci-chemistry/mgltools-volume/ChangeLog            |   14 +
 sci-chemistry/mgltools-volume/Manifest             |    3 +-
 .../mgltools-volume-1.5.4-r1.ebuild                |    4 +-
 ...5.6_rc3.ebuild => mgltools-volume-1.5.6.ebuild} |    5 +-
 .../mgltools-volume-1.5.6_rc2.ebuild               |   50 -
 sci-chemistry/mgltools-webservices/ChangeLog       |   11 +
 sci-chemistry/mgltools-webservices/Manifest        |    3 +-
 .../mgltools-webservices-1.5.4-r2.ebuild           |    4 +-
 ...c3.ebuild => mgltools-webservices-1.5.6.ebuild} |    5 +-
 .../mgltools-webservices-1.5.6_rc2.ebuild          |   49 -
 sci-chemistry/mgltools/ChangeLog                   |   10 +
 sci-chemistry/mgltools/Manifest                    |    3 +-
 sci-chemistry/mgltools/mgltools-1.5.4.ebuild       |    4 +-
 ...ools-1.5.6_rc3.ebuild => mgltools-1.5.6.ebuild} |    5 +-
 sci-chemistry/mgltools/mgltools-1.5.6_rc2.ebuild   |   39 -
 sci-chemistry/modelfree/ChangeLog                  |    6 +-
 sci-chemistry/modelfree/metadata.xml               |    8 +-
 sci-chemistry/modelfree/modelfree-4.20.ebuild      |    6 +-
 sci-chemistry/nmrpipe/ChangeLog                    |   10 +
 sci-chemistry/nmrpipe/Manifest                     |    4 +-
 ...ebuild => nmrpipe-7.9.2013.021.23.09-r2.ebuild} |    8 +-
 sci-chemistry/nwchem/ChangeLog                     |   10 +-
 sci-chemistry/nwchem/metadata.xml                  |   16 +-
 sci-chemistry/nwchem/nwchem-6.1.1.ebuild           |   91 +-
 sci-chemistry/phenix-bin/ChangeLog                 |    6 +
 sci-chemistry/phenix-bin/Manifest                  |    4 +-
 ....1.1168.ebuild => phenix-bin-1.8.2.1309.ebuild} |   28 +-
 sci-chemistry/pymol-plugins-ezviz/ChangeLog        |    5 +-
 sci-chemistry/pymol-plugins-ezviz/Manifest         |    2 +-
 sci-chemistry/pymol-plugins-ezviz/metadata.xml     |   11 +-
 sci-chemistry/pymol-plugins-psico/ChangeLog        |    6 +-
 sci-chemistry/pymol-plugins-psico/metadata.xml     |    8 +-
 .../pymol-plugins-psico-9999.ebuild                |    4 +-
 sci-chemistry/pymol/ChangeLog                      |   16 +
 sci-chemistry/pymol/files/pymol-9999-flags.patch   |   19 -
 sci-chemistry/pymol/files/pymol-9999-prefix.patch  |   41 -
 sci-chemistry/pymol/metadata.xml                   |    3 +-
 sci-chemistry/pymol/pymol-9999.ebuild              |   43 +-
 sci-chemistry/rosetta/ChangeLog                    |   25 +-
 sci-chemistry/rosetta/Manifest                     |    2 +-
 .../rosetta/files/3.0-user-settings.patch          |   26 -
 .../{3.0-boinc.patch => rosetta-3.4-boinc.patch}   |    0
 .../rosetta/files/rosetta-3.4-boost.patch          |   16 +
 ....patch => rosetta-3.4-fix-scons-warnings.patch} |    0
 ...lgrind.patch => rosetta-3.4-fix-valgrind.patch} |    0
 .../rosetta/files/rosetta-3.4-gcc4.7.patch         |   32 +
 ...0-platform.patch => rosetta-3.4-platform.patch} |    0
 .../rosetta/files/rosetta-3.4-unbundle.patch       |   47 +
 .../rosetta/files/rosetta-3.4-user-settings.patch  |   29 +
 .../{3.0-zlib.patch => rosetta-3.4-zlib.patch}     |    0
 sci-chemistry/rosetta/metadata.xml                 |   25 +-
 .../{rosetta-3.0-r1.ebuild => rosetta-3.4.ebuild}  |  102 +-
 sci-chemistry/simpson/ChangeLog                    |   11 +-
 sci-chemistry/simpson/files/3.0.1-gentoo.patch     |    2 +-
 sci-chemistry/simpson/files/3.1.0-gentoo.patch     |    2 +-
 sci-chemistry/simpson/files/3.1.2-gentoo.patch     |    2 +-
 sci-chemistry/simpson/metadata.xml                 |    2 +-
 sci-chemistry/simpson/simpson-3.0.1.ebuild         |    8 +-
 sci-chemistry/simpson/simpson-3.1.0.ebuild         |    8 +-
 sci-chemistry/simpson/simpson-3.1.2.ebuild         |    8 +-
 sci-chemistry/specView/ChangeLog                   |    6 +-
 sci-chemistry/specView/metadata.xml                |    2 +-
 sci-chemistry/specView/specView-1.0.2.ebuild       |   16 +-
 sci-chemistry/usf-tools/ChangeLog                  |    8 +-
 sci-chemistry/usf-tools/metadata.xml               |    5 +-
 sci-chemistry/usf-tools/usf-tools-9999.ebuild      |    4 +-
 sci-chemistry/votca-csg/ChangeLog                  |    3 +
 sci-chemistry/votca-csg/votca-csg-9999.ebuild      |    4 +-
 sci-geosciences/fullprof-bin/ChangeLog             |   10 +
 sci-geosciences/fullprof-bin/Manifest              |    1 +
 .../fullprof-bin/fullprof-bin-2012.11.ebuild       |   66 +
 sci-geosciences/fullprof-bin/metadata.xml          |   16 +
 sci-geosciences/qgis/ChangeLog                     |    5 +-
 sci-geosciences/qgis/Manifest                      |    2 +-
 sci-geosciences/qgis/metadata.xml                  |   11 +-
 sci-geosciences/qgis/qgis-9999.ebuild              |   12 +-
 sci-libs/Cgraph/Cgraph-2.04.ebuild                 |    5 +-
 sci-libs/Cgraph/ChangeLog                          |    6 +-
 sci-libs/Cgraph/Manifest                           |    2 +-
 sci-libs/Cgraph/metadata.xml                       |    8 +-
 sci-libs/acml/ChangeLog                            |    3 +
 sci-libs/acml/acml-5.3.0.ebuild                    |    1 +
 sci-libs/amdlibm/ChangeLog                         |    9 +-
 sci-libs/amdlibm/amdlibm-3.0.2.ebuild              |   23 +-
 sci-libs/amdlibm/metadata.xml                      |    4 +-
 sci-libs/armadillo/ChangeLog                       |   13 +
 sci-libs/armadillo/Manifest                        |    2 +-
 ...o-3.6.2-r1.ebuild => armadillo-3.6.3-r1.ebuild} |   13 +-
 sci-libs/armadillo/metadata.xml                    |   10 +-
 sci-libs/atlas/ChangeLog                           |    8 +
 sci-libs/atlas/atlas-3.10.1-r1.ebuild              |  281 +
 sci-libs/bigdft/ChangeLog                          |   23 +-
 sci-libs/bigdft/Manifest                           |    1 -
 sci-libs/bigdft/bigdft-1.6.0-r2.ebuild             |   18 +-
 sci-libs/bigdft/bigdft-1.6_pre1-r4.ebuild          |  130 -
 sci-libs/bigdft/bigdft-1.7_pre12.ebuild            |   33 +-
 .../bigdft/files/bigdft-1.7-dev.12-GPUlink.patch   |   12 +
 sci-libs/bigdft/metadata.xml                       |   20 +-
 sci-libs/blas-reference/ChangeLog                  |    6 +-
 .../blas-reference/blas-reference-20120925.ebuild  |    5 +-
 .../blas-reference/blas-reference-99999999.ebuild  |    7 +-
 sci-libs/blas-reference/metadata.xml               |    4 +-
 sci-libs/blastdb/blastdb-9999.ebuild               |   27 +
 skel.metadata.xml => sci-libs/blastdb/metadata.xml |    0
 sci-libs/calculix-ccx/ChangeLog                    |    8 +-
 sci-libs/calculix-ccx/Manifest                     |    6 +-
 sci-libs/calculix-ccx/calculix-ccx-2.2.ebuild      |   19 +-
 sci-libs/calculix-ccx/metadata.xml                 |    8 +-
 sci-libs/coinor-bonmin/ChangeLog                   |    5 +-
 sci-libs/coinor-bonmin/metadata.xml                |    7 +-
 sci-libs/coinor-cppad/ChangeLog                    |    4 +
 sci-libs/coinor-cppad/coinor-cppad-20130127.ebuild |    7 +-
 sci-libs/coinor-cppad/metadata.xml                 |    4 +-
 sci-libs/cs-rosetta-db/ChangeLog                   |   14 +
 sci-libs/cs-rosetta-db/Manifest                    |    7 +
 .../cs-rosetta-db-1.01.2009.1109.11.ebuild         |   61 +
 .../cs-rosetta-db}/metadata.xml                    |    0
 sci-libs/csrosetta-angless/ChangeLog               |   14 -
 sci-libs/csrosetta-angless/Manifest                |    1 -
 .../csrosetta-angless-2009.05.01.ebuild            |   24 -
 sci-libs/csrosetta-angless/metadata.xml            |    8 -
 sci-libs/csrosetta-cs/ChangeLog                    |   14 -
 sci-libs/csrosetta-cs/Manifest                     |    1 -
 .../csrosetta-cs/csrosetta-cs-2009.05.01.ebuild    |   24 -
 sci-libs/csrosetta-cs/metadata.xml                 |    8 -
 sci-libs/csrosetta-pdbh/ChangeLog                  |   14 -
 sci-libs/csrosetta-pdbh/Manifest                   |    1 -
 .../csrosetta-pdbh-2009.05.01.ebuild               |   24 -
 sci-libs/csrosetta-pdbh/metadata.xml               |    8 -
 sci-libs/gmsh/ChangeLog                            |    5 +-
 sci-libs/gmsh/gmsh-2.5.0.ebuild                    |    3 +-
 sci-libs/gmsh/metadata.xml                         |   24 +-
 sci-libs/gsl/ChangeLog                             |    6 +-
 sci-libs/gsl/gsl-1.15-r3.ebuild                    |    8 +-
 sci-libs/gsl/metadata.xml                          |   10 +-
 sci-libs/lapack-reference/ChangeLog                |    5 +-
 sci-libs/lapack-reference/metadata.xml             |   13 +-
 sci-libs/lemon/ChangeLog                           |    6 +-
 sci-libs/lemon/lemon-1.2.3.ebuild                  |   20 +-
 sci-libs/lemon/metadata.xml                        |   10 +-
 sci-libs/libcmatrix/ChangeLog                      |   69 -
 sci-libs/libcmatrix/Manifest                       |    1 -
 sci-libs/libcmatrix/files/3.11.0-shared.patch      |   80 -
 sci-libs/libcmatrix/files/3.2.1-atlas.patch        |   33 -
 sci-libs/libcmatrix/files/3.2.1-gcc4.4.patch       |   12 -
 sci-libs/libcmatrix/files/3.2.1-gcc4.6.patch       |   16 -
 sci-libs/libcmatrix/files/3.2.1-gcc4.7.patch       |  227 -
 sci-libs/libcmatrix/files/3.2.1-minuit2.patch      |   14 -
 sci-libs/libcmatrix/files/3.2.1-shared.patch       |   80 -
 sci-libs/libcmatrix/files/3.9.0-atlas.patch        |   24 -
 sci-libs/libcmatrix/libcmatrix-3.11.0.ebuild       |   55 -
 sci-libs/libspatialindex/ChangeLog                 |    6 +-
 sci-libs/libspatialindex/Manifest                  |    2 +-
 .../libspatialindex/libspatialindex-1.6.1.ebuild   |   17 +-
 sci-libs/libspatialindex/metadata.xml              |    2 +-
 sci-libs/magma/ChangeLog                           |    5 +
 sci-libs/magma/Manifest                            |    1 -
 .../files/magma-1.2.1-duplicate-symbols.patch      |  612 -
 sci-libs/magma/magma-1.2.1.ebuild                  |  139 -
 sci-libs/magma/magma-1.3.0.ebuild                  |   17 +-
 sci-libs/magma/metadata.xml                        |   12 +-
 sci-libs/mlpack/ChangeLog                          |   17 +
 sci-libs/mlpack/Manifest                           |    1 +
 sci-libs/mlpack/files/mlpack-1.0.4-libdir.patch    |   13 +
 sci-libs/mlpack/metadata.xml                       |   13 +
 sci-libs/mlpack/mlpack-1.0.4-r1.ebuild             |   49 +
 sci-libs/modglue/ChangeLog                         |    6 +-
 sci-libs/modglue/Manifest                          |    2 +-
 sci-libs/modglue/metadata.xml                      |   14 +-
 sci-libs/modglue/modglue-1.16.ebuild               |   15 +-
 sci-libs/o2scl/ChangeLog                           |    8 +-
 sci-libs/o2scl/Manifest                            |    2 +-
 .../{o2scl-0.911.ebuild => o2scl-0.912.ebuild}     |    7 +-
 sci-libs/openblas/ChangeLog                        |   11 +-
 sci-libs/openblas/Manifest                         |    2 +-
 ...openblas-0.2.5.ebuild => openblas-0.2.6.ebuild} |    0
 sci-libs/openblas/openblas-9999.ebuild             |   12 +-
 sci-libs/openlibm/ChangeLog                        |   10 +
 .../files/openlibm-respect-toolchain.patch         |   32 +
 sci-libs/openlibm/files/openlibm-soname.patch      |   11 +
 sci-libs/openlibm/metadata.xml                     |   18 +
 sci-libs/openlibm/openlibm-9999.ebuild             |   43 +
 sci-libs/optpp/ChangeLog                           |   11 +-
 sci-libs/optpp/metadata.xml                        |    2 +-
 sci-libs/optpp/optpp-2.4.ebuild                    |   15 +-
 sci-libs/parmetis/ChangeLog                        |    6 +-
 sci-libs/parmetis/metadata.xml                     |   12 +-
 sci-libs/parmetis/parmetis-4.0.2.ebuild            |    6 +-
 sci-libs/starparse/ChangeLog                       |    6 +-
 sci-libs/starparse/Manifest                        |    2 +-
 sci-libs/starparse/metadata.xml                    |    8 +-
 sci-libs/starparse/starparse-1.0.ebuild            |   25 +-
 sci-libs/starparse/starparse-9999.ebuild           |    8 +-
 sci-libs/starparse/starparse-9999_pre10.ebuild     |   22 +-
 sci-libs/tmglib/ChangeLog                          |    6 +-
 sci-libs/tmglib/metadata.xml                       |    4 +-
 sci-libs/tmglib/tmglib-3.4.2.ebuild                |    6 +-
 sci-libs/trilinos/ChangeLog                        |   12 +-
 sci-libs/trilinos/Manifest                         |    1 +
 .../files/trilinos-11.0.3-fix-install-paths.patch  |   76 +
 sci-libs/trilinos/metadata.xml                     |   37 +-
 sci-libs/trilinos/trilinos-10.10.1.ebuild          |   26 +-
 ...linos-10.10.1.ebuild => trilinos-11.0.3.ebuild} |   35 +-
 sci-libs/wannier90/ChangeLog                       |    7 +-
 sci-libs/wannier90/Manifest                        |    2 +-
 sci-libs/wannier90/metadata.xml                    |    8 +-
 sci-libs/wannier90/wannier90-1.2.ebuild            |   51 +-
 sci-libs/xblas/ChangeLog                           |    6 +-
 sci-libs/xblas/metadata.xml                        |    4 +-
 sci-libs/xblas/xblas-1.0.248.ebuild                |    8 +-
 sci-libs/zarja/ChangeLog                           |    7 +-
 sci-libs/zarja/Manifest                            |    2 +-
 sci-libs/zarja/metadata.xml                        |    4 +-
 sci-libs/zarja/zarja-1.1.1.ebuild                  |   22 +-
 sci-mathematics/Macaulay2/ChangeLog                |    8 +
 sci-mathematics/Macaulay2/Macaulay2-9999.ebuild    |   23 +-
 sci-mathematics/Macaulay2/Manifest                 |    4 +-
 sci-mathematics/Macaulay2/files/9999-lapack.patch  |    2 +-
 sci-mathematics/Macaulay2/metadata.xml             |   18 +-
 sci-mathematics/algae/ChangeLog                    |   18 -
 sci-mathematics/algae/Manifest                     |    1 -
 sci-mathematics/algae/algae-4.3.6.ebuild           |   55 -
 sci-mathematics/algae/files/Makefile.in-doc.patch  |    5 -
 sci-mathematics/algae/files/Makefile.in-src.patch  |    4 -
 sci-mathematics/algae/files/configure.in.patch     |   10 -
 sci-mathematics/algae/files/unbundle.patch         |   41 +
 sci-mathematics/algae/metadata.xml                 |   16 -
 sci-mathematics/alt-ergo/ChangeLog                 |    4 +
 sci-mathematics/alt-ergo/Manifest                  |    3 -
 sci-mathematics/alt-ergo/alt-ergo-0.95.ebuild      |   28 +-
 sci-mathematics/alt-ergo/metadata.xml              |   18 +-
 sci-mathematics/bertini/ChangeLog                  |    6 +-
 sci-mathematics/bertini/bertini-1.3.1.ebuild       |    3 +-
 sci-mathematics/bertini/metadata.xml               |   10 +-
 sci-mathematics/cadabra/ChangeLog                  |    8 +-
 sci-mathematics/cadabra/Manifest                   |    1 +
 sci-mathematics/cadabra/cadabra-1.31.ebuild        |   83 +
 sci-mathematics/cdfplayer/ChangeLog                |    7 +
 sci-mathematics/cdfplayer/Manifest                 |    2 +-
 ...fplayer-9.0.0.ebuild => cdfplayer-9.0.1.ebuild} |    2 +-
 ...aller.patch => cdfplayer-9.0.1-installer.patch} |    4 +-
 sci-mathematics/dsfmt/ChangeLog                    |    5 +-
 sci-mathematics/dsfmt/dsfmt-2.2.ebuild             |   11 +-
 sci-mathematics/dsfmt/metadata.xml                 |    4 +-
 sci-mathematics/flocq/ChangeLog                    |    4 +
 sci-mathematics/flocq/Manifest                     |    3 -
 sci-mathematics/flocq/flocq-2.1.0.ebuild           |   13 +-
 sci-mathematics/flocq/metadata.xml                 |   10 +-
 sci-mathematics/freefem++/ChangeLog                |    8 +-
 sci-mathematics/freefem++/Manifest                 |    3 +-
 .../files/freefem++-3.4.2-no-doc-autobuild.patch   |   30 -
 sci-mathematics/freefem++/freefem++-3.5.ebuild     |  156 -
 sci-mathematics/freefem++/freefem++-3.8.ebuild     |   18 +-
 sci-mathematics/freefem++/metadata.xml             |    4 +-
 sci-mathematics/gambit/ChangeLog                   |    6 +-
 sci-mathematics/gambit/Manifest                    |    2 +-
 sci-mathematics/gambit/gambit-0.2010.09.01.ebuild  |    4 +-
 sci-mathematics/gambit/metadata.xml                |   16 +-
 sci-mathematics/gappalib-coq/ChangeLog             |    4 +
 sci-mathematics/gappalib-coq/Manifest              |    4 -
 .../gappalib-coq/gappalib-coq-0.18.0.ebuild        |   28 +-
 sci-mathematics/gappalib-coq/metadata.xml          |   10 +-
 sci-mathematics/giac/ChangeLog                     |    3 +
 sci-mathematics/giac/Manifest                      |    3 -
 sci-mathematics/giac/giac-1.0.0.ebuild             |   33 +-
 sci-mathematics/giac/metadata.xml                  |   20 +-
 sci-mathematics/lattE-macchiato/ChangeLog          |    6 +-
 sci-mathematics/lattE-macchiato/Manifest           |    2 +-
 .../lattE-macchiato/lattE-macchiato-0.9.3.ebuild   |    5 +-
 sci-mathematics/lattE-macchiato/metadata.xml       |   12 +-
 sci-mathematics/mdp/ChangeLog                      |    5 +-
 sci-mathematics/mdp/mdp-9999.ebuild                |   12 +-
 sci-mathematics/mdp/metadata.xml                   |   12 +-
 sci-mathematics/petsc/ChangeLog                    |   14 +-
 sci-mathematics/petsc/Manifest                     |    2 -
 .../petsc/files/petsc-3.1_p8-configure-pic.patch   |   11 -
 .../petsc/files/petsc-3.1_p8-disable-rpath.patch   |   16 -
 .../petsc/files/petsc-3.2_p7-configure-pic.patch   |   11 -
 .../files/petsc-3.2_p7-disable-env-warnings.patch  |   13 -
 .../petsc/files/petsc-3.2_p7-disable-rpath.patch   |   16 -
 sci-mathematics/petsc/metadata.xml                 |   19 +-
 sci-mathematics/petsc/petsc-3.1_p8-r1.ebuild       |  202 -
 sci-mathematics/petsc/petsc-3.2_p7.ebuild          |  215 -
 sci-mathematics/petsc/petsc-3.3_p5.ebuild          |    6 +-
 sci-mathematics/pff/ChangeLog                      |    3 +
 sci-mathematics/pff/Manifest                       |    3 -
 sci-mathematics/pff/metadata.xml                   |   10 +-
 sci-mathematics/pff/pff-8.4.ebuild                 |   17 +-
 sci-mathematics/polymake/ChangeLog                 |    8 +
 sci-mathematics/polymake/metadata.xml              |   18 +-
 sci-mathematics/polymake/polymake-2.11-r1.ebuild   |    4 +-
 sci-mathematics/rstudio/ChangeLog                  |   19 -
 sci-mathematics/rstudio/Manifest                   |    7 -
 .../rstudio/files/rstudio-0.97.237-prefs.patch     |   20 -
 .../rstudio/files/rstudio-linker_flags.patch       |   13 -
 sci-mathematics/rstudio/files/rstudio-paths.patch  |  106 -
 sci-mathematics/rstudio/files/rstudio-prefs.patch  |   20 -
 .../rstudio/files/rstudio-rserver.initd            |   15 -
 .../rstudio/files/rstudio.desktop.patch            |   16 -
 sci-mathematics/rstudio/metadata.xml               |   13 -
 sci-mathematics/rstudio/rstudio-0.96.316.ebuild    |  141 -
 sci-mathematics/rstudio/rstudio-0.96.331.ebuild    |  141 -
 sci-mathematics/rstudio/rstudio-0.97.237.ebuild    |  139 -
 sci-mathematics/scilab/ChangeLog                   |    6 +-
 sci-mathematics/scilab/metadata.xml                |   16 +-
 sci-mathematics/scilab/scilab-5.3.3-r1.ebuild      |   26 +-
 sci-mathematics/scilab/scilab-5.4.0.ebuild         |   19 +-
 sci-mathematics/surfer/ChangeLog                   |    6 +-
 sci-mathematics/surfer/Manifest                    |    2 +-
 sci-mathematics/surfer/metadata.xml                |    2 +-
 sci-mathematics/surfer/surfer-0.0.197.ebuild       |   21 +-
 sci-mathematics/why/ChangeLog                      |    5 +-
 sci-mathematics/why/Manifest                       |    6 +-
 sci-mathematics/why/metadata.xml                   |   26 +-
 sci-mathematics/why/why-2.30.ebuild                |   74 +-
 sci-mathematics/yorick/ChangeLog                   |    6 +-
 sci-mathematics/yorick/Manifest                    |    2 +-
 sci-mathematics/yorick/metadata.xml                |   12 +-
 sci-mathematics/yorick/yorick-2.1.06.ebuild        |   29 +-
 sci-misc/foma/ChangeLog                            |    6 +-
 sci-misc/foma/foma-0.9.14_alpha.ebuild             |    4 +-
 sci-misc/foma/foma-0.9.16_alpha.ebuild             |    4 +-
 sci-misc/foma/metadata.xml                         |    6 +-
 sci-misc/hfst/ChangeLog                            |    6 +-
 sci-misc/hfst/hfst-3.0.2.ebuild                    |    4 +-
 sci-misc/hfst/hfst-3.3.12.ebuild                   |    6 +-
 sci-misc/hfst/metadata.xml                         |   16 +-
 sci-misc/openfst/ChangeLog                         |    6 +-
 sci-misc/openfst/metadata.xml                      |    6 +-
 sci-misc/openfst/openfst-1.2.7.ebuild              |    4 +-
 sci-misc/openfst/openfst-1.3.2.ebuild              |    4 +-
 sci-misc/praat/ChangeLog                           |    6 +-
 sci-misc/praat/Manifest                            |    4 +-
 sci-misc/praat/metadata.xml                        |    8 +-
 sci-misc/praat/praat-5.1.00.ebuild                 |   23 +-
 sci-misc/praat/praat-5.1.15.ebuild                 |   23 +-
 sci-misc/salome-component/ChangeLog                |    6 +-
 sci-misc/salome-component/Manifest                 |    4 +-
 sci-misc/salome-component/metadata.xml             |    2 +-
 .../salome-component/salome-component-5.1.3.ebuild |    8 +-
 .../salome-component/salome-component-5.1.4.ebuild |    8 +-
 sci-misc/salome-geom/ChangeLog                     |    6 +-
 sci-misc/salome-geom/Manifest                      |    4 +-
 sci-misc/salome-geom/metadata.xml                  |    2 +-
 sci-misc/salome-geom/salome-geom-5.1.3.ebuild      |   10 +-
 sci-misc/salome-geom/salome-geom-5.1.4.ebuild      |   10 +-
 sci-misc/salome-gui/ChangeLog                      |    6 +-
 sci-misc/salome-gui/Manifest                       |    4 +-
 sci-misc/salome-gui/metadata.xml                   |    2 +-
 sci-misc/salome-gui/salome-gui-5.1.3.ebuild        |   10 +-
 sci-misc/salome-gui/salome-gui-5.1.4.ebuild        |   10 +-
 sci-misc/salome-med/ChangeLog                      |    6 +-
 sci-misc/salome-med/Manifest                       |    4 +-
 sci-misc/salome-med/metadata.xml                   |   10 +-
 sci-misc/salome-med/salome-med-5.1.3.ebuild        |    8 +-
 sci-misc/salome-med/salome-med-5.1.4.ebuild        |    8 +-
 sci-misc/salome-smesh/ChangeLog                    |    6 +-
 sci-misc/salome-smesh/Manifest                     |    4 +-
 sci-misc/salome-smesh/metadata.xml                 |    2 +-
 sci-misc/salome-smesh/salome-smesh-5.1.3.ebuild    |    8 +-
 sci-misc/salome-smesh/salome-smesh-5.1.4.ebuild    |    8 +-
 sci-misc/salome-visu/ChangeLog                     |    6 +-
 sci-misc/salome-visu/Manifest                      |    4 +-
 sci-misc/salome-visu/metadata.xml                  |    2 +-
 sci-misc/salome-visu/salome-visu-5.1.3.ebuild      |    8 +-
 sci-misc/salome-visu/salome-visu-5.1.4.ebuild      |    8 +-
 sci-misc/salome-yacs/ChangeLog                     |    6 +-
 sci-misc/salome-yacs/Manifest                      |    4 +-
 sci-misc/salome-yacs/metadata.xml                  |    2 +-
 sci-misc/salome-yacs/salome-yacs-5.1.3.ebuild      |    8 +-
 sci-misc/salome-yacs/salome-yacs-5.1.4.ebuild      |    8 +-
 sci-misc/sfst/ChangeLog                            |    6 +-
 sci-misc/sfst/metadata.xml                         |   10 +-
 sci-misc/sfst/sfst-1.4.2.ebuild                    |    4 +-
 sci-misc/sfst/sfst-1.4.6g.ebuild                   |    4 +-
 sci-physics/abinit/ChangeLog                       |   13 +
 sci-physics/abinit/Manifest                        |    2 +-
 sci-physics/abinit/abinit-7.0.4.ebuild             |   27 +-
 ...abinit-6.12.3-r2.ebuild => abinit-7.0.5.ebuild} |   63 +-
 sci-physics/abinit/metadata.xml                    |   74 +-
 sci-physics/atompaw/ChangeLog                      |    5 +
 sci-physics/atompaw/atompaw-3.0.1.9.ebuild         |   14 +-
 sci-physics/atompaw/metadata.xml                   |   14 +-
 sci-physics/atompaw2abinit/ChangeLog               |    7 +-
 sci-physics/atompaw2abinit/Manifest                |    2 +-
 .../atompaw2abinit/atompaw2abinit-3.3.0-r1.ebuild  |   19 +-
 sci-physics/atompaw2abinit/metadata.xml            |    8 +-
 sci-physics/elk/ChangeLog                          |    6 +-
 sci-physics/elk/elk-1.4.22.ebuild                  |   92 +-
 sci-physics/elk/metadata.xml                       |   10 +-
 sci-physics/espresso/ChangeLog                     |    5 +-
 sci-physics/espresso/espresso-9999.ebuild          |   14 +-
 sci-physics/herwig++/ChangeLog                     |    7 +
 sci-physics/herwig++/Manifest                      |    2 +-
 ...ptools.patch => herwig++-2.6.3-looptools.patch} |    0
 ...herwig++-2.6.2.ebuild => herwig++-2.6.3.ebuild} |    2 +-
 sci-physics/openmx/ChangeLog                       |    8 +
 .../phenix-bin => sci-physics/openmx}/metadata.xml |    0
 sci-physics/openmx/openmx-3.6.ebuild               |   42 +-
 sci-physics/root/ChangeLog                         |   10 +
 sci-physics/root/Manifest                          |    4 +-
 .../root/files/root-5.34.05-nobyte-compile.patch   |  137 +
 sci-physics/root/metadata.xml                      |   38 +-
 .../{root-5.34.03.ebuild => root-5.34.05.ebuild}   |   19 +-
 sci-physics/root/root-9999.ebuild                  |   12 +-
 sci-physics/thepeg/ChangeLog                       |    7 +
 sci-physics/thepeg/Manifest                        |    6 +-
 ...eg-1.8.2-java.patch => thepeg-1.8.3-java.patch} |    0
 .../{thepeg-1.8.2.ebuild => thepeg-1.8.3.ebuild}   |    2 +-
 sci-visualization/ferret-bin/ChangeLog             |    7 +-
 sci-visualization/ferret-bin/Manifest              |   10 +-
 .../ferret-bin/ferret-bin-6.6.4.ebuild             |   52 +-
 sci-visualization/ferret-bin/metadata.xml          |   12 +-
 sci-visualization/gnuplot/ChangeLog                |   18 +-
 sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild  |  213 +-
 sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild  |  202 +-
 sci-visualization/gnuplot/metadata.xml             |   26 +-
 sci-visualization/paraview/ChangeLog               |    6 +-
 sci-visualization/paraview/metadata.xml            |   36 +-
 sci-visualization/paraview/paraview-3.10.1.ebuild  |   28 +-
 sci-visualization/paraview/paraview-3.12.0.ebuild  |   26 +-
 .../paraview/paraview-3.14.1-r4.ebuild             |   16 +-
 sci-visualization/v_sim/ChangeLog                  |    6 +-
 sci-visualization/v_sim/Manifest                   |    4 +-
 sci-visualization/v_sim/metadata.xml               |   26 +-
 sci-visualization/v_sim/v_sim-3.5.1.ebuild         |   80 -
 sci-visualization/v_sim/v_sim-3.5.2.ebuild         |   87 -
 sci-visualization/v_sim/v_sim-3.6.0.ebuild         |    4 +-
 sci-visualization/yt/yt-9999.ebuild                |    3 +-
 skel.ChangeLog                                     | 8022 ++++++++
 sys-cluster/blcr/ChangeLog                         |    5 +-
 sys-cluster/blcr/blcr-0.8.4.ebuild                 |    3 +-
 sys-cluster/blcr/metadata.xml                      |    4 +-
 sys-cluster/empi/ChangeLog                         |   10 +-
 .../empi/{empi-0.7.ebuild => empi-0.8.ebuild}      |    2 +-
 sys-cluster/empi/files/ChangeLog-0.7               |  164 -
 sys-cluster/empi/files/ChangeLog-0.8               |   68 +
 sys-cluster/empi/files/empi-0.7                    |  408 -
 sys-cluster/empi/files/empi-0.8                    |  492 +
 .../files/{eselect.mpi-0.7 => eselect.mpi-0.8}     |    2 +-
 sys-cluster/hpl/ChangeLog                          |    9 +-
 sys-cluster/hpl/Manifest                           |    2 +-
 sys-cluster/hpl/hpl-2.0-r1.ebuild                  |   20 +-
 sys-cluster/hpl/metadata.xml                       |   12 +-
 sys-cluster/lustre/ChangeLog                       |  333 +
 ...ld-make-AC-check-for-linux-arch-sandbox-f.patch |   95 +
 ...rnel-3.0-SuSE-and-3.6-FC18-server-patches.patch |21302 ++++++++++++++++++++
 ...nel-sock_map_fd-replaced-by-sock_alloc_fi.patch |  137 +
 ...6-kernel-Kernel-update-for-3.7.2-201.fc18.patch |  184 +
 ...pat-posix_acl_-to-from-_xattr-take-user_n.patch |  159 +
 ...006-LU-2800-llite-introduce-local-getname.patch |   91 +
 .../files/0007-LU-2987-llite-rcu-free-inode.patch  |   89 +
 ...50-kernel-3.8-upstream-removes-vmtruncate.patch |   83 +
 ...-2850-kernel-3.8-upstream-kills-daemonize.patch | 2966 +++
 ...rnel-3.9-hlist_for_each_entry-uses-3-args.patch |  115 +
 ...79-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch |   82 +
 ...fids-fix-compilation-error-with-gcc-4.7.2.patch |   29 +
 ...7-build-zfs-0.6.1-kmod-dkms-compatibility.patch | 1038 +
 sys-cluster/lustre/lustre-9999.ebuild              |   94 +-
 sys-cluster/lustre/metadata.xml                    |    3 +
 sys-cluster/mvapich2/ChangeLog                     |    7 +
 sys-cluster/mvapich2/Manifest                      |    2 +-
 sys-cluster/mvapich2/mvapich2-1.6-r1.ebuild        |    4 +-
 sys-cluster/openmpi/ChangeLog                      |    6 +
 sys-cluster/openmpi/Manifest                       |    2 +-
 .../{openmpi-1.6.3.ebuild => openmpi-1.6.4.ebuild} |    7 +-
 sys-cluster/ovis/ChangeLog                         |    5 +-
 sys-cluster/ovis/metadata.xml                      |   10 +-
 sys-cluster/ovis/ovis-3.0.1.ebuild                 |    6 +-
 virtual/blas/ChangeLog                             |    2 +-
 virtual/lapack/ChangeLog                           |    8 +-
 virtual/lapack/lapack-3.3.ebuild                   |   23 -
 virtual/lapack/lapack-3.4.ebuild                   |   23 +
 virtual/lapack/metadata.xml                        |    3 +-
 virtual/scalapack/ChangeLog                        |    9 +-
 virtual/scalapack/metadata.xml                     |    4 +-
 .../{scalapack-1.8.ebuild => scalapack-2.0.ebuild} |    6 +-
 x11-libs/xview-bin/ChangeLog                       |    9 +-
 x11-libs/xview-bin/Manifest                        |    2 +-
 x11-libs/xview-bin/metadata.xml                    |   10 +-
 x11-libs/xview-bin/xview-bin-3.2_p1428.ebuild      |    6 +-
 x11-libs/xview/ChangeLog                           |   12 +-
 x11-libs/xview/Manifest                            |    1 +
 x11-libs/xview/metadata.xml                        |   10 +-
 x11-libs/xview/xview-3.2-r6.ebuild                 |    4 +-
 x11-libs/xview/xview-3.2-r7.ebuild                 |    4 +-
 .../{xview-3.2-r7.ebuild => xview-3.2-r8.ebuild}   |    8 +-
 894 files changed, 42959 insertions(+), 9213 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     4873ee2bc60d04d34ab4a70d7b4e19dfeee51b83
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Apr 24 15:29:10 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Wed Apr 24 15:29:10 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4873ee2b

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 dev-java/flexdock/Manifest                         |    2 +-
 ....2-nodemo.patch => flexdock-1.2.3-nodemo.patch} |    0
 ...flexdock-1.2.2.ebuild => flexdock-1.2.3.ebuild} |    8 ++--
 dev-java/jlatexmath-fop/Manifest                   |    3 +-
 .../files/jlatexmath-fop-1.0.2-fixpaths.patch      |   13 +++++
 dev-java/jlatexmath-fop/files/version.xml          |    5 ++
 .../jlatexmath-fop/jlatexmath-fop-0.9.7.ebuild     |   52 ------------------
 .../jlatexmath-fop/jlatexmath-fop-1.0.0.ebuild     |   52 ------------------
 .../jlatexmath-fop/jlatexmath-fop-1.0.2.ebuild     |   45 +++++++++++++++
 dev-java/jlatexmath/Manifest                       |    3 +-
 dev-java/jlatexmath/jlatexmath-1.0.0.ebuild        |   32 -----------
 ...exmath-0.9.7.ebuild => jlatexmath-1.0.2.ebuild} |   22 ++++----
 dev-java/scirenderer/Manifest                      |    2 +-
 ...derer-1.0.5.ebuild => scirenderer-1.1.0.ebuild} |    4 +-
 dev-java/xmlgraphics-commons/Manifest              |    1 +
 .../files/disable-iccprofile-test.patch            |   38 +++++++++++++
 .../{jrosetta => xmlgraphics-commons}/metadata.xml |    1 -
 .../xmlgraphics-commons-1.5.ebuild                 |   58 ++++++++++++++++++++
 18 files changed, 181 insertions(+), 160 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     519b986cb390aecc8fcd7907b1987c7763e9d424
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 23 19:50:14 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Apr 23 19:50:14 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=519b986c

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 sys-cluster/lustre/ChangeLog                       |   19 +++++++
 ...ld-make-AC-check-for-linux-arch-sandbox-f.patch |    2 +-
 ...rnel-3.0-SuSE-and-3.6-FC18-server-patches.patch |    2 +-
 ...nel-sock_map_fd-replaced-by-sock_alloc_fi.patch |    2 +-
 ...6-kernel-Kernel-update-for-3.7.2-201.fc18.patch |    2 +-
 ...pat-posix_acl_-to-from-_xattr-take-user_n.patch |    6 +-
 ...006-LU-2800-llite-introduce-local-getname.patch |    2 +-
 .../files/0007-LU-2987-llite-rcu-free-inode.patch  |    2 +-
 ...50-kernel-3.8-upstream-removes-vmtruncate.patch |    2 +-
 ...-2850-kernel-3.8-upstream-kills-daemonize.patch |   55 +++++++++-----------
 ...rnel-3.9-hlist_for_each_entry-uses-3-args.patch |    2 +-
 ...79-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch |    2 +-
 ...ids-fix-compilation-error-with-gcc-4.7.2.patch} |    4 +-
 ...-build-zfs-0.6.1-kmod-dkms-compatibility.patch} |    4 +-
 sys-cluster/lustre/lustre-9999.ebuild              |   14 +----
 15 files changed, 62 insertions(+), 58 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     81ca88ca5c51675f546d289e70446b93c30da9e3
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 15 15:43:32 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Apr 15 15:43:32 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=81ca88ca

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 licenses/{MGLTOOLS => mgltools}                    |    3 +-
 media-gfx/librecad/ChangeLog                       |    4 +
 media-gfx/librecad/Manifest                        |    5 +-
 ...librecad-1.0.2.ebuild => librecad-1.0.3.ebuild} |    4 +-
 ....0_beta2.ebuild => librecad-2.0.0_beta5.ebuild} |    2 +-
 sci-chemistry/mgltools-autodocktools/ChangeLog     |   16 +
 sci-chemistry/mgltools-autodocktools/Manifest      |    3 +-
 .../mgltools-autodocktools-1.5.4-r2.ebuild         |    4 +-
 ....ebuild => mgltools-autodocktools-1.5.6.ebuild} |    5 +-
 .../mgltools-autodocktools-1.5.6_rc2.ebuild        |   71 -
 sci-chemistry/mgltools-bhtree/ChangeLog            |   14 +
 sci-chemistry/mgltools-bhtree/Manifest             |    3 +-
 .../mgltools-bhtree-1.5.4-r1.ebuild                |    4 +-
 ...5.6_rc3.ebuild => mgltools-bhtree-1.5.6.ebuild} |    5 +-
 .../mgltools-bhtree-1.5.6_rc2.ebuild               |   48 -
 sci-chemistry/mgltools-cadd/ChangeLog              |   12 +
 sci-chemistry/mgltools-cadd/Manifest               |    3 +-
 ...1.5.6_rc3.ebuild => mgltools-cadd-1.5.6.ebuild} |    5 +-
 .../mgltools-cadd/mgltools-cadd-1.5.6_rc2.ebuild   |   48 -
 sci-chemistry/mgltools-cmolkit/ChangeLog           |   14 +
 sci-chemistry/mgltools-cmolkit/Manifest            |    3 +-
 .../mgltools-cmolkit-1.5.4-r1.ebuild               |    4 +-
 ....6_rc3.ebuild => mgltools-cmolkit-1.5.6.ebuild} |    5 +-
 .../mgltools-cmolkit-1.5.6_rc2.ebuild              |   48 -
 sci-chemistry/mgltools-dejavu/ChangeLog            |   14 +
 sci-chemistry/mgltools-dejavu/Manifest             |    3 +-
 .../mgltools-dejavu-1.5.4-r1.ebuild                |    4 +-
 ...5.6_rc3.ebuild => mgltools-dejavu-1.5.6.ebuild} |    5 +-
 .../mgltools-dejavu-1.5.6_rc2.ebuild               |   51 -
 sci-chemistry/mgltools-geomutils/ChangeLog         |   14 +
 sci-chemistry/mgltools-geomutils/Manifest          |    3 +-
 .../mgltools-geomutils-1.5.4-r1.ebuild             |    4 +-
 ..._rc3.ebuild => mgltools-geomutils-1.5.6.ebuild} |    5 +-
 .../mgltools-geomutils-1.5.6_rc2.ebuild            |   49 -
 sci-chemistry/mgltools-gle/ChangeLog               |   13 +
 sci-chemistry/mgltools-gle/Manifest                |    3 +-
 .../mgltools-gle/mgltools-gle-1.5.4-r1.ebuild      |    4 +-
 ...-1.5.6_rc3.ebuild => mgltools-gle-1.5.6.ebuild} |    5 +-
 .../mgltools-gle/mgltools-gle-1.5.6_rc2.ebuild     |   48 -
 sci-chemistry/mgltools-mglutil/ChangeLog           |   14 +
 sci-chemistry/mgltools-mglutil/Manifest            |    3 +-
 .../mgltools-mglutil-1.5.4-r1.ebuild               |    4 +-
 ....6_rc3.ebuild => mgltools-mglutil-1.5.6.ebuild} |    5 +-
 .../mgltools-mglutil-1.5.6_rc2.ebuild              |   51 -
 sci-chemistry/mgltools-molkit/ChangeLog            |   14 +
 sci-chemistry/mgltools-molkit/Manifest             |    3 +-
 .../mgltools-molkit-1.5.4-r1.ebuild                |    4 +-
 ...5.6_rc3.ebuild => mgltools-molkit-1.5.6.ebuild} |    5 +-
 .../mgltools-molkit-1.5.6_rc2.ebuild               |   50 -
 sci-chemistry/mgltools-networkeditor/ChangeLog     |   16 +
 sci-chemistry/mgltools-networkeditor/Manifest      |    3 +-
 .../mgltools-networkeditor-1.5.4-r1.ebuild         |    4 +-
 ....ebuild => mgltools-networkeditor-1.5.6.ebuild} |    5 +-
 .../mgltools-networkeditor-1.5.6_rc2.ebuild        |   50 -
 sci-chemistry/mgltools-opengltk/ChangeLog          |   14 +
 sci-chemistry/mgltools-opengltk/Manifest           |    3 +-
 .../mgltools-opengltk-1.5.4-r2.ebuild              |    4 +-
 ...6_rc3.ebuild => mgltools-opengltk-1.5.6.ebuild} |    5 +-
 .../mgltools-opengltk-1.5.6_rc2.ebuild             |   68 -
 sci-chemistry/mgltools-pmv/ChangeLog               |   13 +
 sci-chemistry/mgltools-pmv/Manifest                |    3 +-
 .../mgltools-pmv/mgltools-pmv-1.5.4-r1.ebuild      |    4 +-
 ...-1.5.6_rc3.ebuild => mgltools-pmv-1.5.6.ebuild} |    5 +-
 .../mgltools-pmv/mgltools-pmv-1.5.6_rc2.ebuild     |   52 -
 sci-chemistry/mgltools-pyautodock/ChangeLog        |   15 +
 sci-chemistry/mgltools-pyautodock/Manifest         |    3 +-
 .../mgltools-pyautodock-1.5.4-r1.ebuild            |    4 +-
 ...rc3.ebuild => mgltools-pyautodock-1.5.6.ebuild} |    5 +-
 .../mgltools-pyautodock-1.5.6_rc2.ebuild           |   48 -
 sci-chemistry/mgltools-pybabel/ChangeLog           |   14 +
 sci-chemistry/mgltools-pybabel/Manifest            |    3 +-
 .../mgltools-pybabel-1.5.4-r1.ebuild               |    4 +-
 ....6_rc3.ebuild => mgltools-pybabel-1.5.6.ebuild} |    5 +-
 .../mgltools-pybabel-1.5.6_rc2.ebuild              |   50 -
 sci-chemistry/mgltools-pyglf/ChangeLog             |   14 +
 sci-chemistry/mgltools-pyglf/Manifest              |    3 +-
 .../mgltools-pyglf/mgltools-pyglf-1.5.4-r1.ebuild  |    4 +-
 ....5.6_rc3.ebuild => mgltools-pyglf-1.5.6.ebuild} |    5 +-
 .../mgltools-pyglf/mgltools-pyglf-1.5.6_rc2.ebuild |   48 -
 sci-chemistry/mgltools-qslimlib/ChangeLog          |   14 +
 sci-chemistry/mgltools-qslimlib/Manifest           |    3 +-
 .../mgltools-qslimlib-1.5.4-r1.ebuild              |    4 +-
 ...6_rc3.ebuild => mgltools-qslimlib-1.5.6.ebuild} |    5 +-
 .../mgltools-qslimlib-1.5.6_rc2.ebuild             |   52 -
 sci-chemistry/mgltools-scenario/ChangeLog          |    4 +
 .../mgltools-scenario-1.5.4-r1.ebuild              |    4 +-
 sci-chemistry/mgltools-scenario2/ChangeLog         |   13 +
 sci-chemistry/mgltools-scenario2/Manifest          |    3 +-
 ..._rc3.ebuild => mgltools-scenario2-1.5.6.ebuild} |    5 +-
 .../mgltools-scenario2-1.5.6_rc2.ebuild            |   50 -
 sci-chemistry/mgltools-sff/ChangeLog               |   13 +
 sci-chemistry/mgltools-sff/Manifest                |    3 +-
 .../mgltools-sff/mgltools-sff-1.5.4-r1.ebuild      |    4 +-
 ...-1.5.6_rc3.ebuild => mgltools-sff-1.5.6.ebuild} |    5 +-
 .../mgltools-sff/mgltools-sff-1.5.6_rc2.ebuild     |   49 -
 sci-chemistry/mgltools-stride/ChangeLog            |    6 +
 .../mgltools-stride-1.5.4-r1.ebuild                |    4 +-
 sci-chemistry/mgltools-support/ChangeLog           |   14 +
 sci-chemistry/mgltools-support/Manifest            |    3 +-
 .../mgltools-support-1.5.4-r1.ebuild               |    4 +-
 ....6_rc3.ebuild => mgltools-support-1.5.6.ebuild} |    5 +-
 .../mgltools-support-1.5.6_rc2.ebuild              |   49 -
 sci-chemistry/mgltools-symserv/ChangeLog           |   12 +
 sci-chemistry/mgltools-symserv/Manifest            |    3 +-
 .../mgltools-symserv-1.5.4-r1.ebuild               |    4 +-
 ....6_rc3.ebuild => mgltools-symserv-1.5.6.ebuild} |    5 +-
 .../mgltools-symserv-1.5.6_rc2.ebuild              |   48 -
 sci-chemistry/mgltools-utpackages/ChangeLog        |   15 +
 sci-chemistry/mgltools-utpackages/Manifest         |    3 +-
 .../mgltools-utpackages-1.5.4-r1.ebuild            |    4 +-
 ...rc3.ebuild => mgltools-utpackages-1.5.6.ebuild} |    5 +-
 .../mgltools-utpackages-1.5.6_rc2.ebuild           |   49 -
 sci-chemistry/mgltools-viewer-framework/ChangeLog  |   17 +
 sci-chemistry/mgltools-viewer-framework/Manifest   |    3 +-
 .../mgltools-viewer-framework-1.5.4-r2.ebuild      |    4 +-
 ...uild => mgltools-viewer-framework-1.5.6.ebuild} |    5 +-
 .../mgltools-viewer-framework-1.5.6_rc2.ebuild     |   53 -
 sci-chemistry/mgltools-vision/ChangeLog            |   14 +
 sci-chemistry/mgltools-vision/Manifest             |    3 +-
 .../mgltools-vision-1.5.4-r1.ebuild                |    4 +-
 ...5.6_rc3.ebuild => mgltools-vision-1.5.6.ebuild} |    5 +-
 .../mgltools-vision-1.5.6_rc2.ebuild               |   59 -
 sci-chemistry/mgltools-visionlib/ChangeLog         |   14 +
 sci-chemistry/mgltools-visionlib/Manifest          |    3 +-
 .../mgltools-visionlib-1.5.4-r1.ebuild             |    4 +-
 ..._rc3.ebuild => mgltools-visionlib-1.5.6.ebuild} |    5 +-
 .../mgltools-visionlib-1.5.6_rc2.ebuild            |   48 -
 sci-chemistry/mgltools-volume/ChangeLog            |   14 +
 sci-chemistry/mgltools-volume/Manifest             |    3 +-
 .../mgltools-volume-1.5.4-r1.ebuild                |    4 +-
 ...5.6_rc3.ebuild => mgltools-volume-1.5.6.ebuild} |    5 +-
 .../mgltools-volume-1.5.6_rc2.ebuild               |   50 -
 sci-chemistry/mgltools-webservices/ChangeLog       |   11 +
 sci-chemistry/mgltools-webservices/Manifest        |    3 +-
 .../mgltools-webservices-1.5.4-r2.ebuild           |    4 +-
 ...c3.ebuild => mgltools-webservices-1.5.6.ebuild} |    5 +-
 .../mgltools-webservices-1.5.6_rc2.ebuild          |   49 -
 sci-chemistry/mgltools/ChangeLog                   |   10 +
 sci-chemistry/mgltools/Manifest                    |    3 +-
 sci-chemistry/mgltools/mgltools-1.5.4.ebuild       |    4 +-
 ...ools-1.5.6_rc3.ebuild => mgltools-1.5.6.ebuild} |    5 +-
 sci-chemistry/mgltools/mgltools-1.5.6_rc2.ebuild   |   39 -
 sci-libs/blastdb/blastdb-9999.ebuild               |   27 +
 skel.metadata.xml => sci-libs/blastdb/metadata.xml |    0
 sci-mathematics/algae/files/unbundle.patch         |   41 +
 skel.ChangeLog                                     | 8022 ++++++++++++++++++++
 146 files changed, 8619 insertions(+), 1570 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     d645d94489cb8e42cb7acf88bdf06360c5d49571
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 22 16:34:23 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Apr 22 16:34:23 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d645d944

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci


 dev-java/netcdf/Manifest                           |    2 +-
 sci-libs/trilinos/ChangeLog                        |    3 +
 sci-libs/trilinos/Manifest                         |    1 +
 .../files/trilinos-11.0.3-fix-install-paths.patch  |   76 +
 ...linos-10.10.1.ebuild => trilinos-11.0.3.ebuild} |   41 +-
 sci-mathematics/Macaulay2/Macaulay2-9999.ebuild    |    4 +-
 sci-mathematics/Macaulay2/Manifest                 |    4 +-
 sci-visualization/gnuplot/ChangeLog                |    4 +
 sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild  |   10 +-
 sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild  |    2 +-
 sys-cluster/lustre/ChangeLog                       |  112 +
 ...ld-make-AC-check-for-linux-arch-sandbox-f.patch |    6 +-
 ...rnel-3.0-SuSE-and-3.6-FC18-server-patches.patch |21302 ++++++++++++++++++++
 ...cfs-use-sock_alloc_file-instead-of-sock_m.patch |  124 -
 ...nel-sock_map_fd-replaced-by-sock_alloc_fi.patch |  137 +
 ...-kernel-Kernel-update-for-3.7.2-201.fc18.patch} |  145 +-
 ...at-posix_acl_-to-from-_xattr-take-user_n.patch} |   12 +-
 ...06-LU-2800-llite-introduce-local-getname.patch} |    6 +-
 ...tch => 0007-LU-2987-llite-rcu-free-inode.patch} |   12 +-
 ...0-kernel-3.8-upstream-removes-vmtruncate.patch} |   29 +-
 ...2850-kernel-3.8-upstream-kills-daemonize.patch} |  115 +-
 ...ubuntu-Fix-build-failures-on-Ubuntu-12.04.patch |   58 -
 ...3077-build-fix-warnings-in-client-modules.patch |   34 -
 ...nel-3.9-hlist_for_each_entry-uses-3-args.patch} |   18 +-
 ...9-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch} |   12 +-
 ...7-build-zfs-0.6.1-kmod-dkms-compatibility.patch | 1038 +
 ...fids-fix-compilation-error-with-gcc-4.7.2.patch |   29 +
 sys-cluster/lustre/lustre-9999.ebuild              |   42 +-
 28 files changed, 22947 insertions(+), 431 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     0f3c50e562d5974b4eea266b3f45525dc8d96d95
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Apr  8 15:51:29 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Apr  8 15:51:29 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0f3c50e5

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 sci-chemistry/gnome-chemistry-utils/ChangeLog      |   20 +++++++
 sci-chemistry/gnome-chemistry-utils/Manifest       |    1 +
 .../gnome-chemistry-utils-0.14.2.ebuild            |   44 +++++++++++++++
 sci-chemistry/gnome-chemistry-utils/metadata.xml   |   11 ++++
 sci-chemistry/hydronmr/ChangeLog                   |   10 ++++
 sci-chemistry/hydronmr/Manifest                    |   13 +++++
 sci-chemistry/hydronmr/hydronmr-7c.ebuild          |   57 ++++++++++++++++++++
 .../hydronmr}/metadata.xml                         |    0
 8 files changed, 156 insertions(+), 0 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     6f522aeb712f2fd3d959df76388a27812c147e98
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Fri Apr  5 20:28:31 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Fri Apr  5 20:28:31 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6f522aeb

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 app-text/jabref/ChangeLog                          |    5 +++++
 app-text/jabref/Manifest                           |    1 +
 ...{jabref-2.9.2-r1.ebuild => jabref-2.10b.ebuild} |    0
 3 files changed, 6 insertions(+), 0 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     021424868626a1328eb2b2ab1b3e4d2b036a8f49
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Apr  9 16:33:25 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Apr  9 16:33:25 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=02142486

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 app-text/jabref/ChangeLog                          |    4 ++++
 app-text/jabref/jabref-2.10b.ebuild                |    4 ++--
 sys-cluster/openmpi/ChangeLog                      |    6 ++++++
 sys-cluster/openmpi/Manifest                       |    2 +-
 .../{openmpi-1.6.3.ebuild => openmpi-1.6.4.ebuild} |    7 +++++--
 5 files changed, 18 insertions(+), 5 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     1bc2ddef619ca94f3b2005c042ee82bc7d56ab19
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Apr  2 16:34:41 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Apr  2 16:34:41 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1bc2ddef

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 dev-lang/julia/files/julia-nopatchelf.patch        |   14 +++
 dev-lang/julia/julia-9999.ebuild                   |   28 ++---
 dev-lang/julia/metadata.xml                        |    8 +-
 dev-libs/double-conversion/ChangeLog               |   10 ++-
 dev-libs/double-conversion/Manifest                |    2 +-
 ...n-1.1.ebuild => double-conversion-1.1.1.ebuild} |    8 +-
 ...s.patch => double-conversion-1.1.1-scons.patch} |    0
 sci-biology/ncbi-tools++/ChangeLog                 |    7 +
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |   87 ++++++++------
 sci-mathematics/cadabra/ChangeLog                  |    8 +-
 sci-mathematics/cadabra/Manifest                   |    1 +
 .../{cadabra-1.28.ebuild => cadabra-1.31.ebuild}   |   40 +++----
 sys-cluster/lustre/ChangeLog                       |   69 +++++++++++
 ...d-make-AC-check-for-linux-arch-sandbox-f.patch} |   22 ++--
 ...fs-use-sock_alloc_file-instead-of-sock_m.patch} |    8 +-
 ...at-posix_acl_-to-from-_xattr-take-user_n.patch} |   16 ++--
 ...004-LU-2800-llite-introduce-local-getname.patch |    6 +-
 ...d-check-header-files-in-generated-uapi-d.patch} |   28 +++---
 ...0-kernel-3.8-upstream-removes-vmtruncate.patch} |   30 ++---
 ...2850-kernel-3.8-upstream-kills-daemonize.patch} |  123 +++++---------------
 ...ld-fix-unused-uninitilized-virables-error.patch |   30 -----
 ...tch => 0008-LU-2987-llite-rcu-free-inode.patch} |    8 +-
 ...ubuntu-Fix-build-failures-on-Ubuntu-12.04.patch |   58 +++++++++
 ...3077-build-fix-warnings-in-client-modules.patch |   34 ++++++
 ...nel-3.9-hlist_for_each_entry-uses-3-args.patch} |   54 +++++++--
 ...50-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch |   82 +++++++++++++
 sys-cluster/lustre/lustre-9999.ebuild              |   35 ++++--
 sys-cluster/lustre/metadata.xml                    |    3 +
 28 files changed, 514 insertions(+), 305 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     0463cfab77f3349cd7606a202dfc15bdd41c8771
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 26 17:40:05 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Tue Mar 26 17:40:05 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0463cfab

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 dev-python/RecSQL/ChangeLog                        |    4 ++
 dev-python/RecSQL/RecSQL-9999.ebuild               |    8 ++--
 dev-python/RecSQL/metadata.xml                     |   10 ++--
 sci-chemistry/GromacsWrapper/ChangeLog             |   10 +++++
 .../GromacsWrapper/GromacsWrapper-0.3.1.ebuild     |   40 --------------------
 .../GromacsWrapper/GromacsWrapper-9999.ebuild      |   11 +++--
 sci-chemistry/GromacsWrapper/Manifest              |    1 -
 sci-chemistry/GromacsWrapper/metadata.xml          |   10 ++--
 sci-chemistry/pymol/ChangeLog                      |    3 +
 sci-chemistry/pymol/metadata.xml                   |    1 +
 sci-chemistry/pymol/pymol-9999.ebuild              |   33 +++++++++++++---
 11 files changed, 65 insertions(+), 66 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     1b1cc53a0ad314b316f465609987bb6c64575823
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Mar 25 16:39:00 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Mar 25 16:39:00 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1b1cc53a

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 dev-python/RecSQL/ChangeLog           |    4 ++++
 dev-python/RecSQL/Manifest            |    1 -
 dev-python/RecSQL/RecSQL-0.7.8.ebuild |   31 -------------------------------
 dev-python/RecSQL/RecSQL-9999.ebuild  |    4 +++-
 4 files changed, 7 insertions(+), 33 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Sebastien Fabbro]

commit:     b045257bbbc03183b054f6f92c99000131d43055
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 23 14:43:47 2013 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Sat Mar 23 14:43:47 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b045257b

Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci


 dev-python/RecSQL/ChangeLog                        |   10 +
 dev-python/RecSQL/Manifest                         |    1 +
 dev-python/RecSQL/RecSQL-0.7.8.ebuild              |   31 +++
 dev-python/RecSQL/RecSQL-9999.ebuild               |   31 +++
 .../libpfm => dev-python/RecSQL}/metadata.xml      |    0
 sci-chemistry/GromacsWrapper/ChangeLog             |   15 ++
 .../GromacsWrapper/GromacsWrapper-0.3.1.ebuild     |   40 ++++
 .../GromacsWrapper/GromacsWrapper-9999.ebuild      |   40 ++++
 sci-chemistry/GromacsWrapper/Manifest              |    1 +
 .../files/0001-Drop-chmod-hack.patch               |   28 +++
 .../GromacsWrapper}/metadata.xml                   |    0
 sci-chemistry/cs-rosetta/ChangeLog                 |    4 +
 .../cs-rosetta/cs-rosetta-1.01.2009.1109.11.ebuild |    2 +-
 sci-libs/cs-rosetta-db/ChangeLog                   |    4 +
 .../cs-rosetta-db-1.01.2009.1109.11.ebuild         |   18 +-
 sys-cluster/lustre/ChangeLog                       |   27 +++
 ...ld-check-header-files-in-generated-uapi-d.patch |    4 +-
 ...pat-posix_acl_-to-from-_xattr-take-user_n.patch |  159 ++++++++++++++
 ...-kernel-3.7-kernel-posix-acl-needs-userns.patch |  128 -----------
 ...cfs-use-sock_alloc_file-instead-of-sock_m.patch |  124 +++++++++++
 ...3-LU-2850-kernel-3.7-uneports-sock_map_fd.patch |  121 ----------
 ...004-LU-2800-llite-introduce-local-getname.patch |   91 ++++++++
 ...rnel-3.7-get-putname-uses-struct-filename.patch |  231 --------------------
 ...50-kernel-3.8-upstream-removes-vmtruncate.patch |   20 +-
 ...-2850-kernel-3.8-upstream-kills-daemonize.patch |  102 +++++++--
 ...ld-Fix-warning-with-gcc-4.6-in-mdt_handle.patch |   38 ----
 .../files/0007-LU-2987-llite-rcu-free-inode.patch  |   89 ++++++++
 ...ld-fix-unused-uninitilized-virables-error.patch |   30 +++
 ...rnel-3.9-hlist_for_each_entry-uses-3-args.patch |   87 ++++++++
 sys-cluster/lustre/lustre-9999.ebuild              |   10 +-
 30 files changed, 920 insertions(+), 566 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     ff203adb5ad7adf5665409404fe79d1867bc5e49
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 22 01:40:12 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Apr 22 01:40:12 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ff203adb

Merge ssh://github.com/gentoo-science/sci


 sci-libs/trilinos/ChangeLog                        |    3 +
 sci-libs/trilinos/Manifest                         |    1 +
 .../files/trilinos-11.0.3-fix-install-paths.patch  |   76 ++++++++++++++++++++
 ...linos-10.10.1.ebuild => trilinos-11.0.3.ebuild} |   41 ++++++-----
 sys-cluster/lustre/lustre-9999.ebuild              |   10 ++-
 5 files changed, 108 insertions(+), 23 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     bdf8d31a9e3664c4f499977b4bef48c3c663fc1f
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Wed Apr 17 14:28:00 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Apr 17 14:28:00 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bdf8d31a

Merge pull request #63 from ryao/lustre

Stop duplicating ${myconf}


 sys-cluster/lustre/lustre-9999.ebuild |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     32e19bd173cefb94a312c07e72968b8b67f00266
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Wed Apr 17 14:14:47 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Apr 17 14:14:47 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=32e19bd1

Merge pull request #62 from ryao/lustre

Lustre


 sys-cluster/lustre/ChangeLog                       |   45 +
 ...ld-make-AC-check-for-linux-arch-sandbox-f.patch |    4 +-
 ...rnel-3.0-SuSE-and-3.6-FC18-server-patches.patch |21302 ++++++++++++++++++++
 ...el-sock_map_fd-replaced-by-sock_alloc_fi.patch} |    4 +-
 ...-kernel-Kernel-update-for-3.7.2-201.fc18.patch} |    6 +-
 ...at-posix_acl_-to-from-_xattr-take-user_n.patch} |   10 +-
 ...06-LU-2800-llite-introduce-local-getname.patch} |    4 +-
 ...tch => 0007-LU-2987-llite-rcu-free-inode.patch} |    8 +-
 ...0-kernel-3.8-upstream-removes-vmtruncate.patch} |   27 +-
 ...2850-kernel-3.8-upstream-kills-daemonize.patch} |   10 +-
 ...rnel-3.9-hlist_for_each_entry-uses-3-args.patch |  115 +
 ...79-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch |   82 +
 ...-build-zfs-0.6.1-kmod-dkms-compatibility.patch} |   67 +-
 sys-cluster/lustre/lustre-9999.ebuild              |   33 +-
 14 files changed, 21651 insertions(+), 66 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Christoph Junghans]

commit:     7d44ea834f79009e1f48605847417ac56091f536
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Wed Apr 17 05:48:34 2013 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Apr 17 05:48:34 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7d44ea83

Merge pull request #59 from tamiko/bump-trilinos

Bump trilinos to version 11.0.3


 sci-libs/trilinos/ChangeLog                        |    3 +
 sci-libs/trilinos/Manifest                         |    1 +
 .../files/trilinos-11.0.3-fix-install-paths.patch  |   76 ++++++++++++++++++++
 ...linos-10.10.1.ebuild => trilinos-11.0.3.ebuild} |   41 ++++++-----
 4 files changed, 102 insertions(+), 19 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     0d9d8867156da0f627b35d00a5c5cb314329e6c4
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 15 06:17:19 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Apr 15 06:17:19 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0d9d8867

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci: (58 commits)
  media-gfx/librecad: version bump: 1.0.3, 2.0.0beta5
  sci-chemistry/mgltools-stride: Fix license, thanks ulm looking for correct licensing
  sci-chemistry/mgltools-webservices: Correct license
  sci-chemistry/mgltools-volume: Correct license
  sci-chemistry/mgltools-visionlib: Correct license
  sci-chemistry/mgltools-vision: Correct license
  sci-chemistry/mgltools-viewer-framework: Correct license
  sci-chemistry/mgltools-utpackages: Correct license
  sci-chemistry/mgltools-symserv: Correct license
  sci-chemistry/mgltools-support: Correct license
  sci-chemistry/mgltools-stride: Correct license
  sci-chemistry/mgltools-sff: Correct license
  sci-chemistry/mgltools-scenario2: Correct license
  sci-chemistry/mgltools-scenario: Correct license
  sci-chemistry/mgltools-qslimlib: Correct license
  sci-chemistry/mgltools-pyglf: Correct license
  sci-chemistry/mgltools-pybabel: Correct license
  sci-chemistry/mgltools-pyautodock: Correct license
  sci-chemistry/mgltools-pmv: Correct license
  sci-chemistry/mgltools-opengltk: Correct license
  ...

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

Conflicts:
	sci-chemistry/mgltools-symserv/ChangeLog
	sci-chemistry/mgltools-webservices/ChangeLog


 licenses/{MGLTOOLS => mgltools}                    |    3 +-
 media-gfx/librecad/ChangeLog                       |    4 +
 media-gfx/librecad/Manifest                        |    5 +-
 ...librecad-1.0.2.ebuild => librecad-1.0.3.ebuild} |    4 +-
 ....0_beta2.ebuild => librecad-2.0.0_beta5.ebuild} |    2 +-
 sci-chemistry/mgltools-autodocktools/ChangeLog     |    8 +
 .../mgltools-autodocktools-1.5.4-r2.ebuild         |    4 +-
 .../mgltools-autodocktools-1.5.6.ebuild            |    5 +-
 sci-chemistry/mgltools-bhtree/ChangeLog            |    7 +
 .../mgltools-bhtree-1.5.4-r1.ebuild                |    4 +-
 .../mgltools-bhtree/mgltools-bhtree-1.5.6.ebuild   |    5 +-
 sci-chemistry/mgltools-cadd/ChangeLog              |    6 +
 .../mgltools-cadd/mgltools-cadd-1.5.6.ebuild       |    5 +-
 sci-chemistry/mgltools-cmolkit/ChangeLog           |    7 +
 .../mgltools-cmolkit-1.5.4-r1.ebuild               |    4 +-
 .../mgltools-cmolkit/mgltools-cmolkit-1.5.6.ebuild |    5 +-
 sci-chemistry/mgltools-dejavu/ChangeLog            |    7 +
 .../mgltools-dejavu-1.5.4-r1.ebuild                |    4 +-
 .../mgltools-dejavu/mgltools-dejavu-1.5.6.ebuild   |    5 +-
 sci-chemistry/mgltools-geomutils/ChangeLog         |    7 +
 .../mgltools-geomutils-1.5.4-r1.ebuild             |    4 +-
 .../mgltools-geomutils-1.5.6.ebuild                |    5 +-
 sci-chemistry/mgltools-gle/ChangeLog               |    7 +
 .../mgltools-gle/mgltools-gle-1.5.4-r1.ebuild      |    4 +-
 .../mgltools-gle/mgltools-gle-1.5.6.ebuild         |    5 +-
 sci-chemistry/mgltools-mglutil/ChangeLog           |    7 +
 .../mgltools-mglutil-1.5.4-r1.ebuild               |    4 +-
 .../mgltools-mglutil/mgltools-mglutil-1.5.6.ebuild |    5 +-
 sci-chemistry/mgltools-molkit/ChangeLog            |    7 +
 .../mgltools-molkit-1.5.4-r1.ebuild                |    4 +-
 .../mgltools-molkit/mgltools-molkit-1.5.6.ebuild   |    5 +-
 sci-chemistry/mgltools-networkeditor/ChangeLog     |    8 +
 .../mgltools-networkeditor-1.5.4-r1.ebuild         |    4 +-
 .../mgltools-networkeditor-1.5.6.ebuild            |    5 +-
 sci-chemistry/mgltools-opengltk/ChangeLog          |    7 +
 .../mgltools-opengltk-1.5.4-r2.ebuild              |    4 +-
 .../mgltools-opengltk-1.5.6.ebuild                 |    5 +-
 sci-chemistry/mgltools-pmv/ChangeLog               |    7 +
 .../mgltools-pmv/mgltools-pmv-1.5.4-r1.ebuild      |    4 +-
 .../mgltools-pmv/mgltools-pmv-1.5.6.ebuild         |    5 +-
 sci-chemistry/mgltools-pyautodock/ChangeLog        |    8 +
 .../mgltools-pyautodock-1.5.4-r1.ebuild            |    4 +-
 .../mgltools-pyautodock-1.5.6.ebuild               |    5 +-
 sci-chemistry/mgltools-pybabel/ChangeLog           |    7 +
 .../mgltools-pybabel-1.5.4-r1.ebuild               |    4 +-
 .../mgltools-pybabel/mgltools-pybabel-1.5.6.ebuild |    5 +-
 sci-chemistry/mgltools-pyglf/ChangeLog             |    7 +
 .../mgltools-pyglf/mgltools-pyglf-1.5.4-r1.ebuild  |    4 +-
 .../mgltools-pyglf/mgltools-pyglf-1.5.6.ebuild     |    5 +-
 sci-chemistry/mgltools-qslimlib/ChangeLog          |    7 +
 .../mgltools-qslimlib-1.5.4-r1.ebuild              |    4 +-
 .../mgltools-qslimlib-1.5.6.ebuild                 |    5 +-
 sci-chemistry/mgltools-scenario/ChangeLog          |    4 +
 .../mgltools-scenario-1.5.4-r1.ebuild              |    4 +-
 sci-chemistry/mgltools-scenario2/ChangeLog         |    6 +
 .../mgltools-scenario2-1.5.6.ebuild                |    5 +-
 sci-chemistry/mgltools-sff/ChangeLog               |    7 +
 .../mgltools-sff/mgltools-sff-1.5.4-r1.ebuild      |    4 +-
 .../mgltools-sff/mgltools-sff-1.5.6.ebuild         |    5 +-
 sci-chemistry/mgltools-stride/ChangeLog            |    6 +
 .../mgltools-stride-1.5.4-r1.ebuild                |    4 +-
 sci-chemistry/mgltools-support/ChangeLog           |    7 +
 .../mgltools-support-1.5.4-r1.ebuild               |    4 +-
 .../mgltools-support/mgltools-support-1.5.6.ebuild |    5 +-
 sci-chemistry/mgltools-symserv/ChangeLog           |    9 +-
 .../mgltools-symserv-1.5.4-r1.ebuild               |    4 +-
 .../mgltools-symserv/mgltools-symserv-1.5.6.ebuild |    5 +-
 sci-chemistry/mgltools-utpackages/ChangeLog        |    8 +
 .../mgltools-utpackages-1.5.4-r1.ebuild            |    4 +-
 .../mgltools-utpackages-1.5.6.ebuild               |    5 +-
 sci-chemistry/mgltools-viewer-framework/ChangeLog  |    9 +
 .../mgltools-viewer-framework-1.5.4-r2.ebuild      |    4 +-
 .../mgltools-viewer-framework-1.5.6.ebuild         |    5 +-
 sci-chemistry/mgltools-vision/ChangeLog            |    7 +
 .../mgltools-vision-1.5.4-r1.ebuild                |    4 +-
 .../mgltools-vision/mgltools-vision-1.5.6.ebuild   |    5 +-
 sci-chemistry/mgltools-visionlib/ChangeLog         |    7 +
 .../mgltools-visionlib-1.5.4-r1.ebuild             |    4 +-
 .../mgltools-visionlib-1.5.6.ebuild                |    5 +-
 sci-chemistry/mgltools-volume/ChangeLog            |    7 +
 .../mgltools-volume-1.5.4-r1.ebuild                |    4 +-
 .../mgltools-volume/mgltools-volume-1.5.6.ebuild   |    5 +-
 sci-chemistry/mgltools-webservices/ChangeLog       |    8 +-
 .../mgltools-webservices-1.5.4-r2.ebuild           |    4 +-
 .../mgltools-webservices-1.5.6.ebuild              |    5 +-
 sci-chemistry/mgltools/ChangeLog                   |    4 +
 sci-chemistry/mgltools/mgltools-1.5.4.ebuild       |    4 +-
 sci-chemistry/mgltools/mgltools-1.5.6.ebuild       |    2 +-
 sci-libs/blastdb/blastdb-9999.ebuild               |   27 +
 skel.metadata.xml => sci-libs/blastdb/metadata.xml |    0
 sci-mathematics/algae/files/unbundle.patch         |   41 +
 skel.ChangeLog                                     | 8022 ++++++++++++++++++++
 92 files changed, 8408 insertions(+), 143 deletions(-)

diff --cc sci-chemistry/mgltools-symserv/ChangeLog
index b500bf5,4161623..8d87844
--- a/sci-chemistry/mgltools-symserv/ChangeLog
+++ b/sci-chemistry/mgltools-symserv/ChangeLog
@@@ -2,13 -2,17 +2,18 @@@
  # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
  # $Header: $
  
- *mgltools-symserv-1.5.6 (15 Apr 2013)
- 
 -  14 Apr 2013; Justin Lecher <jlec@gentoo.org>
 -  mgltools-symserv-1.5.4-r1.ebuild, mgltools-symserv-1.5.6.ebuild:
 -  Correct license
 +  15 Apr 2013; Justin Lecher <jlec@gentoo.org>
 +  -mgltools-symserv-1.5.6_rc2.ebuild, -mgltools-symserv-1.5.6_rc3.ebuild,
 +  +mgltools-symserv-1.5.6.ebuild:
 +  Version Bump, drop old
  
+ *mgltools-symserv-1.5.6 (14 Apr 2013)
+ 
+   14 Apr 2013; Justin Lecher <jlec@gentoo.org>
+   -mgltools-symserv-1.5.6_rc2.ebuild, -mgltools-symserv-1.5.6_rc3.ebuild,
+   +mgltools-symserv-1.5.6.ebuild:
+   Fix SRC_URI
+ 
  *mgltools-symserv-1.5.6_rc3 (27 Jan 2013)
  
    27 Jan 2013; Justin Lecher <jlec@gentoo.org>
diff --cc sci-libs/blastdb/blastdb-9999.ebuild
index 0000000,0000000..18d29af
new file mode 100644
--- /dev/null
+++ b/sci-libs/blastdb/blastdb-9999.ebuild
@@@ -1,0 -1,0 +1,27 @@@
++# Copyright 1999-2013 Gentoo Foundation
++# Distributed under the terms of the GNU General Public License v2
++# $Header: $
++
++EAPI=5
++
++# inherit
++
++DESCRIPTION="The BLAST NR database"
++HOMEPAGE="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=ProgSelectionGuide"
++SRC_URI=""
++
++SLOT="0"
++LICENSE="alrights-resevered"
++KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
++IUSE=""
++
++RDEPEND=""
++DEPEND="${RDEPEND}"
++
++src_unpack() {
++	if [[ -n ${ESLEEP} ]]; then
++		elog "Will sleep for ${ESLEEP}"
++		sleep ${ESLEEP}
++	fi
++	update_blastdb.pl --verbose --verbose --decompress nr || die
++}
diff --cc sci-mathematics/algae/files/unbundle.patch
index 0000000,0000000..9457bdd
new file mode 100644
--- /dev/null
+++ b/sci-mathematics/algae/files/unbundle.patch
@@@ -1,0 -1,0 +1,41 @@@
++ Makefile.in | 16 +++-------------
++ 1 file changed, 3 insertions(+), 13 deletions(-)
++
++diff --git a/Makefile.in b/Makefile.in
++index 8887b2e..61d185d 100644
++--- a/Makefile.in
+++++ b/Makefile.in
++@@ -112,7 +112,7 @@ SHELL = /bin/sh
++ 
++ # Subdirectories to make recursively.
++ BINSUBDIRS = doc etc examples src test timing tools
++-SUBDIRS = blas lapack superlu arpack fpe $(BINSUBDIRS)
+++SUBDIRS = fpe $(BINSUBDIRS)
++ 
++ # Files in the source distribution from this directory.
++ DISTFILES = COPYING INSTALL LICENSE Makefile.in NEWS PROBLEMS README \
++@@ -149,22 +149,12 @@ configure: configure.in
++ 
++ # Compile the source code.
++ 
++-source: @BLAS@ @LAPACK@
++-	cd superlu; $(MAKE) RC0=$(RC0)
++-	cd arpack; $(MAKE)
++-	cd src; $(MAKE) RC0=$(RC0)
+++source: 
+++	$(MAKE) -C src RC0=$(RC0)
++ .PHONY: source
++ 
++ # Compile the BLAS and LAPACK libraries, if required.
++ 
++-xblas:
++-	cd blas; $(MAKE)
++-.PHONY: xblas
++-
++-xlapack:
++-	cd lapack; $(MAKE)
++-.PHONY: xlapack
++-
++ check: source
++ times: source
++ 
diff --cc skel.ChangeLog
index e41b557,e41b557..66ff00c
--- a/skel.ChangeLog
+++ b/skel.ChangeLog
@@@ -1,3 -1,3 +1,8025 @@@
++
++n.n.n / 2013-04-11 
++==================
++
++  * Bump, workaround #462602
++  * Jabref-2.10b does not build anymore with Java 6.
++  * Merge branch 'master' of github.com:gentoo-science/sci
++  * sci-chemistry/hydronmr: New addition
++  * Merge pull request #60 from lilrc/master
++  * sci-chemistry/gnome-chemistry-utils: Migrate to gnome2 eclass. Sort inherits. Add slots where suitable.
++  * Fix missing inherit.
++  * sci-chemistry/gnome-chemistry-utils: initial ebuild
++  * Adding jabref-2.10b (beta) ebuild.
++  * dev-lang/julia update dependency and remove useflag
++  * dev-libs/double-conversion version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/ncbi-tools++: Some Prefix love
++  * Add patches for gcc-4.8 and linux-3.9
++  * Enable more options
++  * Add patch to fix as-needed issue
++  * Fix autogen
++  * build was renamed to config
++  * Merge remote-tracking branch 'github/master'
++  * Update rebased patches
++  * Merge pull request #58 from jauhien/cadabra-1.31
++  * sci-mathematics/cadabra-1.31: new line fixes, thanks to jlec
++  * sci-mathemtics/cadabra-1.31: different fixes, thanks to jlec
++  * Update patches
++  * sci-chemistry/GromacsWrapper: Drop py 2.5 support
++  * sci-chemistry/GromacsWrapper: Enhance python r1 eclass usage
++  * dev-python/RecSQL: Enhance python r1 eclass usage
++  * sci-chemistry/GromacsWrapper: Drop in tree version
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Update deps
++  * sci-chemistry/pymol: Sync with tree
++  * Add patch to fix hack
++  * Add Gromacs Python wrapper
++  * Add RecSQL to tree
++  * sci-mathematics-cadabra-1.31: bump to EAPI-5
++  * Update patches for 3.9
++  * Merge remote-tracking branch 'github/master'
++  * Update patches for 3.8
++  * sci-chemistry/cs-rosetta: Missing exec bit for pdbrms
++  * sci-libs/cs-rosetta-db: Correct installation directory to mach the main package
++  * sci-mathematics/cadabra: version bump
++  * sci-chemistry/rosetta: Fix for mpi
++  * Merge pull request #57 from jauhien/thepeg-1.8.3_herwig++-2.6.3
++  * sci-physics/thepeg: manifest fix
++  * sci-chemistry/cs-rosetta: Use Fortran eclass
++  * sci-chemistry/rosetta: Use system path
++  * sci-chemistry/rosetta: Rename USE custom-flags -> custom-cflags
++  * sci-chemistry/cs-rosetta: New addition
++  * sci-libs/cs-rosetta-db: New addition
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * $PWD dont needed in automake invocation
++  * Fix escape sequence
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-chemistry/rosetta: Version Bump
++  * Merge pull request #56 from jauhien/berkeley_upc_translator-2.16.0
++  * dev-lang/berkeley_upc_translator: new ebuild for bug#462296, thanks to Paul H. Hargrove
++  * aggregated into sci-chemistry/cs-rosetta
++  * sci-biology/amos: Bump to latest git HEAD, fixes qt problems, #348031
++  * Update patches
++  * Merge remote-tracking branch 'github/master'
++  * Fix some install path
++  * Add gentoo style configure
++  * Fix error in mdt_handler.c
++  * Update metadata.xml
++  * Update berkeley_upc-2.16.0.ebuild
++  * Merge pull request #55 from jauhien/berkeley_upc-2.16.0
++  * dev-db/cppdb: Import from sunrise
++  * Update patch
++  * Update patch
++  * Add patch sended upstream
++  * Update patch
++  * Fix sandbox violation during configure
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Update lustre patches
++  * dev-lang/berkeley_upc: install into libexec
++  * dev-lang/berkeley_upc: New ebuild for bug#462026
++  * Merge ssh://github.com/gentoo-science/sci
++  * initial commit
++  * Update deps. thanks to Richard Yao
++  * Update media-gfx/librecad ebuilds.
++  * Make client and utils as default flags
++  * Update to reflect latest zfs changes
++  * nvcc flags dont needed anymore here
++  * Fix build with cuda enabled
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Drop Werror hack
++  * Now it builds and loads with 3.8
++  * More updates to lustre patches
++  * Update lustre patches. Now it builds against linux 3.8
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Improving mpi linking. It will now work with openmpi as well.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge ssh://github.com/gentoo-science/sci
++  * fix build without emacs
++  * sci-chemistry/usf-tools: Update license
++  * sci-chemistry/usf-tools: Drop myself as maintainer
++  * Merge pull request #53 from jauhien/cdfplayer-9.0.1
++  * Merge pull request #54 from jauhien/thepeg-1.8.3_herwig++-2.6.3
++  * sci-physics/herwig++: version bump
++  * sci-physics/thepeg: version bump
++  * sci-mathematics/cdfplayer: version bump
++  * sci-chemistry/phenix-bin: Version BUmp
++  * sci-chemistry/concoord: Version Bump; switch license to all-rights-reserved
++  * added cuda build fix from gx86
++  * sync with gx86
++  * fix doc build on darwin
++  * fixed deps + doc build on darwin
++  * Newer version in CVS
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sync wit gx86
++  * Fix typo
++  * Fix typo
++  * Realy add patches to ebuild
++  * Add patches for kernels 3.7 and 3.8
++  * sync with gx86 + clean up
++  * merge slew of jlec small fixes
++  * sci-libs/optpp: Removed uneeded python eclass, keyword for prefix
++  * sci-libs/o2scl: Version bump
++  * sci-libs/openblas: Version bump
++  * sci-libs/openlibm: Initial import
++  * Mask several package due to different QA issues
++  * sci-chemistry/ambertools: Add missing multilib.eclass
++  * sci-mathematics/yorick: Move to EAPI=5; add missing multilib.eclass
++  * sci-chemistry/jligand: Fix version of refmac dep
++  * sci-chemistry/pymol-plugins-psico: Rename sci-chemistry/mmtk to sci-libs/mmtk
++  * sci-geosciences/qgis: Update to new qt deps names
++  * sci-libs/lapack-reference: Add unocumented USE to metadata.xml
++  * sci-biology/estscan: Add local USE to metadata.xml
++  * sci-libs/coinor-bonmin: Add unocumented USE to metadata.xml
++  * sci-biology/ncbi-tools++: Document USE
++  * sci-chemistry/pymol-plugins-ezviz: Fix missing DOCTYPE
++  * sci-chemistry/pymol: Fix missing DOCTYPE
++  * dev-libs/fortrancl: Clean whitespace errors
++  * dev-ml/zarith: Clean wrong space and blank lines; move EAPI=5
++  * media-gfx/PhiloGL: Move to EAPI=5 and fix quoting
++  * sci-astronomy/astrometry: Clean wrong space and blank lines
++  * sci-libs/amdlibm: Updated download page and prefix'ed
++  * sci-astronomy/eye: Clean wrong space and blank lines
++  * sci-astronomy/stiff: Move to EAPI=5 and autotools-utils
++  * sci-chemistry/nmrpipe: Fix quoting
++  * sci-biology/artemis-bin: Clean whitespace errors
++  * sci-biology/ncbi-tools++: Clean whitespace errors
++  * sci-biology/sra_sdk: Drop useless blank line
++  * sci-chemistry/specView: Fix quoting
++  * sci-libs/amdlibm: Clean wrong space and blank lines
++  * sci-libs/coinor-cppad: Drop useless blank line
++  * sci-mathematics/alt-ergo: Move to EAPI=5; clean quoting and ebuild syntax and indention
++  * sci-libs/parmetis: Drop useless blank line
++  * sci-mathematics/giac: Drop useless blank line
++  * sci-mathematics/bertini: Clean wrong space and blank lines
++  * sci-mathematics/mdp: Clean wrong space and blank lines
++  * sys-cluster/blcr: Drop useless blank line
++  * sys-cluster/hpl: Sort *DEPEND correctly
++  * sci-libs/lemon: Move to EAPI=5; sort *DEPEND correctly
++  * sci-biology/ncbi-tools++: Add metadata.xml
++  * sci-biology/hydra-sv: Add metadata.xml; move to EAPI=5; cleaned ebuild syntax
++  * x11-libs/xview: Fix header
++  * x11-libs/xview-bin: Fix header
++  * sci-mathematics/gambit: Fix header and move to EAPI=5
++  * sci-libs/libspatialindex: Fix header and move to EAPI=5: cleaned ebuild syntax
++  * sci-mathematics/dsfmt: Fix header and move to EAPI=5; cleaned ebuild syntax
++  * dev-perl/go-perl: Fix header and move to EAPI=5
++  * dev-perl/Time-Progress: Fix header and move to EAPI=5
++  * dev-perl/Log-Cabin: Fix header and move to EAPI=5
++  * dev-perl/Text-ParseWords: Fix header and move to EAPI=5
++  * dev-perl/DBIx-DBStag: Fix header and move to EAPI=5
++  * sci-libs/zarja: Move to EAPI=5; fix slot for fftw dep; move to virtual/pkgconfig; clean ebuild syntax
++  * sci-libs/modglue: Move to EPAI=5 and virtual/pkgconfig; clean usage of autotools-utils.eclass
++  * sci-libs/blas-reference: Cleaned deps
++  * sci-chemistry/burrow-owl: Bump to EPAI=5 and move to virtual/pkgconfig
++  * sci-biology/manatee-igs: Shorten DESCRIPTION
++  * sci-physics/openmx: Move to EAPI=5 and shorten DESCRIPTION
++  * sci-chemistry/nwchem: Move to EAPI=5 and clean ebuild syntax style
++  * Add new license
++  * dev-python/Forthon: Correct license name
++  * dev-java/jcip-annotations: Correct license name
++  * sys-cluster/mvapich2: Add missing flag-o-matic.eclass
++  * sci-mathematics/polymake: Add missing multilib.eclass
++  * sci-libs/starparse: Add missing multilib.eclass; move to EAPI=5 and autotools-utils.eclass
++  * dev-lang/vtune: Version Bump; move to parallel studio tarball; add missing multilib.eclass
++  * sci-chemistry/modelfree: Add missing multilib.eclass; move to EAPI=5
++  * sci-chemistry/ambertools: Add missing multilib.eclass
++  * sci-biology/wcd: Add missing multilib.eclass; move to EAPI=5 and autotools-utils.eclass; simplify ebuild syntax; fix for ld.gold; fix implicid declarations
++  * correct license
++  * add new license
++  * sci-biology/blasr: Migrate to git2 eclass and EAPI=5
++  * app-portage/g-octave: Migrate to new python eclasses, git2 eclass and EAPI=5
++  * dev-python/GOGrapher: Set license to GPL-2
++  * sci-mathematics/flocq: Move to EAPI=5; assign RDEPEND explicitatly
++  * sys-cluster/ovis: Update to new qt deps names
++  * sci-visualization/paraview: Update to new qt deps names
++  * sci-visualization/gnuplot: Update to new qt deps names
++  * sci-chemistry/ball: Update to new qt deps names
++  * sci-biology/amos: Update to new qt deps names
++  * dev-python/pymvpa: Move to new python eclasses
++  * sci-misc/hfst: Add ~amd64 or ~x86 keywords for revdeps
++  * sci-misc/foma: Add ~amd64 or ~x86 keywords for revdeps
++  * sci-misc/sfst: Add ~amd64 or ~x86 keywords for revdeps
++  * sci-misc/openfst: Add ~amd64 or ~x86 keywords for revdeps
++  * sci-visualization/ferret-bin: Move to EAPI=5; clean ebuild style; add missing die; remove portage-internal (env-update)
++  * sci-mathematics/why: Drop ppc as deps are not keyworded; move to EAPI=5 and autotools-utils.eclass
++  * sci-mathematics/gappalib-coq: Drop pcc and sparc keywords as deps are not keyworded; move to EAPI=5
++  * sci-mathematics/lattE-macchiato: Fix rename of USE nocxx to cxx for dev-libs/gmp
++  * sci-mathematics/pff: Drop pcc and sparc keywords as deps are not keyworded; move to EAPI=5
++  * sci-mathematics/surfer: Move to autotools-utils.eclass; use virtual/pkgconfig
++  * sci-misc/praat: Update to new qt deps names; remove virtual/x11
++  * sci-misc/salome-geom: Update to new qt deps names
++  * sci-misc/salome-component: Update to new qt deps names
++  * sci-misc/salome-gui: Update to new qt deps names
++  * sci-misc/salome-med: Update to new qt deps names
++  * sci-misc/salome-smesh: Update to new qt deps names
++  * sci-misc/salome-visu: Update to new qt deps names
++  * sci-misc/salome-yacs: Update to new qt deps names
++  * sci-physics/abinit: Drop old
++  * sci-physics/root: Update to new qt deps names
++  * sci-libs/trilinos: Update to new qt deps names
++  * dev-perl/Log-Cabin: Add ~amd64 or ~x86 keywords for revdeps
++  * We can't do profile specific masks
++  * imported latest arch.list from gx86
++  * sci-chemistry/curvefit: Correct lib name of ref blas
++  * sci-biology/consed-bin: Correct motif dep naming
++  * sci-biology/cluster: Correct motif dep naming
++  * sci-biology/YASRA: Drop keywords as deps are unkeyworded
++  * sci-biology/Gambit: Update to new qt deps names
++  * dev-python/pythonocc: Version BUmp; change license; move to new python eclasses
++  * dev-python/pythonocc: Version BUmp; change license; move to new python eclasses
++  * media-gfx/librecad: Update to new qt deps names; drop old
++  * dev-java/jogl: Keyworded for ~x86
++  * dev-java/gluegen: Keyworded for ~x86
++  * sci-libs/bigdft: Fix issue 52
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * Initial import
++  * Add ~x86
++  * Initial import
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * sci-libs/mlpack: Added a patch to respect libdir, and debug flag for profiling and debugging (thanks Ryan Curtin)
++  * sci-libs/armadillo: Small prefix fix
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * sci-mathematics/Macaulay2: Use PKG_CONFIG instead of generic pkg-config
++  * sci-chemistry/simpson: Use PKG_CONFIG instead of generic pkg-config
++  * sci-chemistry/gamess: Use PKG_CONFIG instead of generic pkg-config
++  * sci-chemistry/nmrpipe: Fix broken Manifest, #458928
++  * sci-libs/acml: Add -lm -lrt for static linking on pc file
++  * sci-libs/openblas: Move threads to Libs.private in pc file
++  * x11-libs/xview: Version Bump
++  * x11-libs/xview-bin: Version Bump
++  * sci-libs/Cgraph: Add blocker
++  * sci-libs/mlpack: Initial import
++  * sci-libs/armadillo: Version bump. Respect libdir
++  * sci-libs/atlas: Switched threads libraries to Libs.private in pkg-config files
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * app-doc/root-docs: version bump
++  * sci-physics/root: version bump
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * sci-libs/tmglib: Add missing dep on virtual/blas
++  * sci-chemistry/freeon: Add missing dep on virtual/pkgconfig; bump to eapi=5; use pkg-config to detect blas
++  * sci-libs/gmsh: Add missing dep on virtual/pkgconfig
++  * sci-geosciences/fullprof-bin: Indent with tabs instead of spaces; use QA_PREBUILT for binary packages; restrict all arches but x86/amd64; bump EAPI to 5; clean DESCRIPTION; fix quoting
++  * Merge branch 'master' of github.com:gentoo-science/sci
++  * Merge pull request #28 from jamasi/master
++  * sci-visualization/v_sim: Drop old; add missing multilib.eclass
++  * Bundles all numeric libs, which are not easily unbundlable Various other QA issues
++  * sci-libs/trilinos: Correct USE dependency for virtual/pkgconfig; bump EAPI to 5
++  * sci-libs/armadillo: Correct USE dependency for virtual/pkgconfig
++  * sci-chemistry/simpson: Add missing dep on virtual/pkgconfig
++  * sci-chemistry/chooch: Bump to EAPI=5; add missing deps; drop additional virtual which aren't needed; move to autotools-utils
++  * sci-chemistry/camshift: Bump to EAPI=5; add missing deps; fix for gcc-4.7
++  * dev-ml/lacaml: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
++  * Revert "Merge branch 'jlec' of github.com:gentoo-science/sci"
++  * Revert "dev-ml/lacaml: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config"
++  * Merge branch 'master' of github.com:gentoo-science/sci
++  * Merge branch 'jlec' of github.com:gentoo-science/sci
++  * dev-ml/lacaml: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
++  * sci-astronomy/zebra: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
++  * sci-chemistry/ambertools: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
++  * sci-libs/bigdft: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; drop old
++  * sci-libs/calculix-ccx: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; bump to EAPI=5; add missing dep on virtual/pkgconfig; use pkgconfig to detect arpack
++  * sci-libs/gsl: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
++  * sci-libs/magma: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; drop old
++  * sci-libs/optpp: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; bump to EAPI=5; move to new python eclasses
++  * sci-libs/wannier90: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; bump to EAPI=5
++  * sci-libs/xblas: Bump EAPI to 5
++  * sci-mathematics/freefem++: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; drop old
++  * sci-mathematics/Macaulay2: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config#
++  * sci-mathematics/petsc: Drop unused local USE-description: 'metis'
++  * sci-mathematics/petsc: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; drop old
++  * sci-mathematics/scilab: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config
++  * sci-physics/atompaw: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; correct dep for pkgconfig to virtual
++  * sci-physics/atompaw2abinit: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; correct dep for pkgconfig to virtual
++  * sci-physics/abinit: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; correct dep for pkgconfig to virtual; fix openmp compatibility detection
++  * empi:  bump 0.8
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * sci-biology/mira: current stable and development version bumps
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * First working patch
++  * sci-physics/elk: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; add missing dep on virtual/pkgconfig; cleaning of ebuild
++  * sci-physics/elk: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; add missing dep on virtual/pkgconfig; cleaning of ebuild
++  * sci-physics/openmx: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; add missing dep on virtual/pkgconfig
++  * sys-cluster/hpl: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; add missing dep on virtual/pkgconfig
++  * mathjax now in main tree
++  * app-doc/scalapack-docs: Cleaning and keywording for prefix
++  * virtual/scalapack: Bump to latest scalapack reference
++  * virtual/lapack: Bump to latest reference
++  * [dev-python/Forthon] Fix option parser to take into account that wrapper filename may have a suffix, use dodoc/docinto. Thanks to Michał Górny <mgorny@gentoo.org> for his help on this
++  * [sci-visualization/yt] update
++  * sci-libs/atlas: Move -lm -latlas to Libs.private in all pkg-config files
++  * app-text/jabref: Fixed doc generation, keyword amd64-linux and x86-linux
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * The setup of python for the compilation of the GPU support in sci-libs/bigdft-1.7_pre12 improved.
++  * Added sci-physics/abinit-7.0.5, compilation of GPU support in sci-libs/bigdft-1.7_pre12 improved.
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * rstudio now in main tree
++  * sci-chemistry/pymol: Fix sed syntax
++  * sci-chemistry/pymol: Fix sed syntax
++  * sci-chemistry/pymol: Adapt to current HEAD
++  * version bump
++  * Update live ebuild
++  * Update live ebuild
++  * newer version in the tree
++  * Added ~x86 KEYWORD and API/README do docs.
++  * Merge branch 'master' of github.com:gentoo-science/sci
++  * sci-chemistry/pymol: adopt to current HEAD
++  * Typo
++  * Added changes suggested by Christoph Junghans <ottxor@gentoo.org>.
++  * Adding first draft version of jabref-2.9.2 ebuild.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/mkl: Version Bump
++  * Fix probable trailing / in EROOT
++  * Prepare alternatives-2.eclass for the main tree
++  * sci-libs/mkl: Add KEYWORDS, #342185
++  * sse41 -> sse4_1 (bug #456886) + ninja has missing keywords
++  * added warning about petsc threads support
++  * Merge remote-tracking branch 'github/master'
++  * [sys-cluster/lustre] Update lustre ebuild
++  * Merge pull request #49 from gentryx/master
++  * Merge /usr/local/portage/andis_overlay
++  * moved fperms to correct ebuild phase
++  * Merge branch 'master' of https://github.com/gentoo-science/sci
++  * Merge /usr/local/portage/andis_overlay
++  * reverted to calling cutils eclass functions
++  * Merge /usr/local/portage/andis_overlay
++  * adapting to standard order of definitions, dropped some default-equivalent function definitions, re-added test build functions as tests wouldn't otherwise be run
++  * fixed petsc compile issue reported by disperato
++  * Merge /usr/local/portage/andis_overlay
++  * dropped superfluous vcs-snapshot eclass and functions equivalent to default
++  * minor improvements
++  * added linebreaks where necessary
++  * Merge ../sci.bitbucket
++  * Merge branch 'master' of https://github.com/gentoo-science/sci
++  * added proper quotes for variables, use fperms in favor of chmod
++  * updated Manifest
++  * fixed indenting, descriptions and updated to EAPI 5
++  * updated EAPI, dropped versionator eclass, added shortcut for package name
++  * added missing metadata.xml
++  * using new EAPI and skipping superfluous die
++  * adapted coding style to appease repoman
++  * resolved various warnings reported by repoman for LibGeoDecomp and HPX, also fixed shortcomings as requested by jlec in https://github.com/gentoo-science/sci/pull/49/files#r2931081
++  * Merge ../sci.bitbucket
++  * sci-libs/armadillo: Version bump
++  * Merge branch 'master' of https://github.com/gentoo-science/sci
++  * Merge branch 'master' of github.com:gentoo-science/sci
++  * virtual/blas: Rise eigen version in deps
++  * Merge pull request #48 from jauhien/thepeg_182_herwig_262
++  * sci-physics/herwig++: version bump
++  * sci-physics/thepeg: version bump
++  * Next couple of fixes
++  * Merge branch 'master' of https://github.com/gentoo-science/sci
++  * And another step forward
++  * dev-java/jogl import from the java-overlay
++  * dev-java/gluegen import from java-overlay
++  * Fixed name in ChangeLog and metadata.xml
++  * Removed CMAKE_VERBOSE=1 from libSUFR ebuilds
++  * clean up package.mask
++  * sci-chemistry/votca-csg-tutorials is part of sci-chemistry/votca-csg
++  * app-doc/votca-csg-manual is part of sci-chemistry/votca-csg
++  * Some more patching
++  * More work on as-needed problems
++  * fixed path
++  * set SUID bit for access daemon
++  * access-daemon needs a full path, thus we're hardcoding /usr to shut it up
++  * don't hardcode absolute patch for access daemon
++  * clean up + merge csg-{manual,tutorials}
++  * added subslot, removed gromacs-manual blocker
++  * gromacs-manual: got merged in gromacs ebuild
++  * clean up
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * sci-libs/coinor-csdp: use generic pkg-config
++  * sci-libs/coinor-blis: Add missing coinor-bcps dependency
++  * sci-libs/coinor-alps: Add missing coinor-cgl dependency for tests
++  * sci-libs/coinor-netlib: no more empty doc
++  * sci-libs/coinor-sample: no more empty doc
++  * my version
++  * fixed compilation with newer cmake, removed currently unused use flags
++  * sci-libs/ipopt: Version bump
++  * sci-libs/coinor-utils: Version bump
++  * sci-libs/coinor-symphony: Version bump
++  * sci-libs/coinor-sample: Version bump
++  * sci-libs/coinor-osi: Version bump
++  * sci-libs/coinor-netlib: Version bump
++  * sci-libs/coinor-cppad: Version bump
++  * sci-libs/coinor-couenne: Version bump
++  * sci-libs/coinor-clp: Version bump
++  * sci-libs/coinor-cgl: Version bump
++  * sci-libs/coinor-blis: Version bump
++  * added likwid ebuild
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-chemistry/pymol: Bump python eclass
++  * Merge pull request #45 from jhcloos/openmx
++  * Merge branch 'master' of https://github.com/gentoo-science/sci
++  * fixed copyright note
++  * unmask scilab-5.4
++  * sci-mathematics/scilab cleanup ebuild
++  * sci-libs/atlas: Version bump
++  * [sci-biology/psychopy] fix typo in inherit, add metadata, make repoman happy
++  * [dev-python/Forthon] version bump, add modified version of BSD license, port to distutils-r1
++  * Merge remote-tracking branch 'upstream/master'
++  * added app-doc/gromacs-manual in here
++  * Merge branch 'master' of github.com:gentoo-science/sci
++  * sci-chemistry/mgltools: Allow multiple py ABIs install
++  * sci-chemistry/mgltools: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-webservices: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-volume: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-visionlib: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-vision: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-viewer-framework: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-utpackages: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-symserv: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-support: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-stride: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-sff: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-scenario2: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-scenario: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-qslimlib: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-pyglf: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-pybabel: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-pyautodock: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-pmv: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-opengltk: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-networkeditor: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-molkit: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-mglutil: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-gle: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-geomutils: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-dejavu: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-cmolkit: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-cadd: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-bhtree: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-autodocktools: Version Bump; move to distutils-r1.eclass
++  * sci-chemistry/mgltools-autodocktools: Version Bump; move to distutils-r1.eclass
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge pull request #43 from TheChymera/master
++  * sync with gx86
++  * Inherited gnome2-utils and called cache update from pkg_postrm as well
++  * used gnome2-utils.eclass function instead of touch to update cache
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/libcmatrix: fixed
++  * merging github && overlays.g.o
++  * sci-libs/acml: Version bump, now fetch restricted.
++  * app-admin/eselect: Cleaned old
++  * alternatives-2: update eselect min version
++  * sci-libs/armadillo: Version bump
++  * sci-chemistry/nmrpipe: Upstream changed tarballs
++  * sci-mathematics/giac: it's supposed to be frozen...
++  * Already in the tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * sci-chemistry/nmrpipe: Version BUmp; drop fetch restriction as upstream provides and promotes direct access
++  * added missing manifest
++  * added ebuild for libgeodecomp 0.1.0
++  * added LibGeoDecomp ebuild which tracks the trunk on Bitbucket
++  * cosmetics
++  * Fix bug 452806
++  * cleaning ebuild
++  * added ebuild for HPX
++  * sci-chemistry/gromacs: use cuda.eclass
++  * replaced src_install with python_install_all
++  * fixed sci-chemistry/gromacs[test]
++  * sci-physics/geant-vmc: source geant4 shell script before compiling
++  * Updated minimum geant4 version
++  * [sci-chemistry/gromacs] Drop restrict test for 4.6
++  * [sci-chemistry/gromacs] Update 4.6 series ebuild
++  * Corrected source repository Had been changed for testing.
++  * Added pkg_postinst() in order  to refresh the timestamp and make the desktop environment regenerate the chace - otherwise the icon doesn't show up appropriately
++  * sci-physics/openmx:  Fix fftw dependency.
++  * dev-java/flexdock version bump
++  * dev-java/scirenderer version bump
++  * sci-mathematics/scilab update dependencies
++  * virtual/geant: Initial import
++  * Initial import
++  * virtual/geant:3 work
++  * sci-physics/geant-vmc: Initial import
++  * Added src_install() script to make a launcher and assign an icon to it.
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * In sci-physics/abinit-7.0.4 missing makefile sources for the gui added from the 6.12.3 version.
++  * yet another update for git
++  * Fperms instead of Chmod
++  * Merge ssh://github.com/gentoo-science/sci
++  * live ebuild update
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * sci-physics/openmx added, version 3.6. sci-physics/atompaw version bumped to 3.0.1.9. New versions of sci-physics/abinit and sci-libs/bigdft added, but sci-libs/bigdft-1.7_pre12 is a version from the Abinit site, and the bigdft support in sci-physics/abinit-7.0.4 segfaults; on the other hand abinit-7.0.4 supports openmp. GPU support in sci-libs/bigdft-1.7_pre12 and sci-physics/abinit-7.0.4 not yet tested.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-chemistry/phenix-bin: Add new dep on libtinfo.so
++  * sci-astronomy/galfit-bin: Since #452532 we have libtinfo.so in the tree
++  * Merge pull request #44 from jhcloos/cgns-tcltk
++  * sci-libs/cgnstools: Add patch for current tcl/tk.
++  * Added run permissions for the package's executable file Also upgraded to distutils-r1 and made other minor improvements to python-related metadata
++  * Executable priviledges for /app/psychopyApp.py Also generally improved 9999 build (many thanks to prometheanfire from #gentoo-dev-help!)
++  * dev-util/ndiff: updated DESCRIPTION and ebuild comments
++  * Merge pull request #41 from AstroFloyd/master
++  * Removed CMAKE_VERBOSE=1 in pg2plplot-0.2.0.ebuild
++  * Initial upload of sci-libs/libmatheval (bug 181417)
++  * moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/pff: version bump
++  * sci-mathematics/giac: version bump
++  * sci-mathematics/gappalib-coq: version bump
++  * sci-mathematics/gappa: version bump
++  * sci-mathematics/frama-c: version bump
++  * sci-mathematics/flocq: version bump
++  * sci-mathematics/alt-ergo: initial commit
++  * dev-ml/zarith: initial commit
++  * dev-ml/ocamlgraph: version bump
++  * moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * sci-libs/coinor-cbc: Version Bump
++  * sci-mathematics/pulp: Move to EAPI=5, distutils-r1.eclass and virtual/pyparsing, #449564; unbundle sci-libs/coinor-cbc
++  * inCvs Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-chemistry/nmrpipe: Version Bump
++  * Created first ebuild for PG2PLplot and added it to repo
++  * Upgraded to sci-libs/libsufr-0.4.1.ebuild; added ChangeLog to repo
++  * mpi.eclass:  fix whitespace
++  * moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * migrate to git-2 eclass, fix lapack support
++  * sync with gentoo-x86
++  * Merge pull request #40 from jauhien/LoopTools_manifest
++  * sci-physics/LoopTools: manifest fixed forever, thanks to jlec
++  * Merge pull request #39 from jauhien/cdfplayer_9_0_0
++  * sci-mathematics/cdfplayer: use domenu
++  * fixed python dep
++  * sci-mathematics/scilab-5.4.0 cleanup dependencies
++  * dev-java/scirenderer version bump
++  * dev-java/flexdock version bump
++  * dev-java/jrosetta fix ant build files
++  * reverting to --no-as-needed LDFLAG
++  * reverting to --no-as-needed LDFLAG
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * fixed repman issues
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * put back in the --as-needed LDFLAG to yield hopefully smaller executables; recreating the patch so that it applies automatically
++  * upated to latest petsc 3.3 release
++  * updated to latest petsc 3.2 release
++  * app-admin/eselect: Version Bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/ncbi-tools++-9.0.0: although masked a not passing repoman checks this ebuild works for me, finally. All patches from upstream.
++  * dev-lang/julia fix emacs filename
++  * dev-lang/julia fix version in previous update
++  * dev-lang/julia update dependencies
++  * sci-mathematics/cdfplayer: version bump
++  * sci-astronomy/lephare: Fixed manifest and removed patch, thanks James Cloos
++  * sci-libs/magma: Fixed URL, thanks James Cloos
++  * Merge pull request #37 from xhub/master
++  * update EHG_REPO_URI
++  * update EHG_REPO_URI
++  * update EHG_REPO_URI
++  * update EHG_REPO_URI
++  * update EHG_REPO_URI
++  * further clean up
++  * version bump
++  * Merge pull request #30 from jauhien/cdfplayer
++  * fixed build with newer mkl
++  * dev-util/ccache: fixed clang links
++  * sci-biology/ncbi-tools++-9.0.0: a sketch of an updated ebuild, bug #279606, does not pass repoman checks due to IUSE items
++  * sci-biology/sra_sdk-2.2.2a: a version bump, still requires MAKEOPTS=-j1 and copies softlinks to binaries and libraries as files, so everything is in 3 physical copies
++  * sci-libs/magma: Bump
++  * added for testing
++  * masked dev-util/ccache use flags
++  * sci-chemistry/gromacs: clean up
++  * ccache-{clang,icc} are part of ccache now
++  * fixed openmm suffix
++  * fixed another typo
++  * fixed typo
++  * Added mkl support
++  * added ~amd64
++  * updated profile
++  * added ~amd64
++  * version bump
++  * fix build with !cuda and python=3 + qa
++  * sync with gx86
++  * reworked emacs issue (bug #444526#c3) + move to git
++  * sync with gx86
++  * [sys-cluster/lustre] Add missing patch
++  * [sys-cluster/lustre] Fix disabling
++  * [sys-cluster/lustre] Disable Werror
++  * [sys-cluster/lustre] All patches for 3.6 was merge into mainline
++  * fortran is gone
++  * Remove last instances of vtkNetCDF from paraview-3.14
++  * Add cblas-external USE flag to sci-libs/gsl
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * dev-lang/julia add emacs config file
++  * dev-lang/julia new ebuild
++  * sci-libs/o2scl: Initial import
++  * Sort webkit dep in paraview 3.14
++  * Moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * sci-libs/scalapack: Use latest pkg-config, removed old
++  * sci-libs/lapackpp: Use latest pkg-config
++  * sci-libs/atlas: Update for lapack-3.4.2
++  * dev-cpp/eigen: Removed old
++  * sci-libs/acml: Removed old
++  * sci-libs/cblas-reference: Fixed pkg-config and fortran use
++  * sci-libs/blas-reference: Removed unused dependencies
++  * Removed unused dependencies
++  * sci-libs/levmar: Use virtual/pkgconfig and prefix keywords
++  * sci-libs/openblas: Version bump. Link latest version to live one
++  * sci-libs/armadillo: Version bump
++  * in Cvs, this was just a test Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Include suggestions from g-dev review
++  * Renamed eclass Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * sci-libs/mumps: Install libpord, force -j1 on makefile because of random parallel build failures, separate dummy sequential mpi library from the common mumps library
++  * sci-mathematics/rstudio: version bump
++  * InCvs Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * Drop nasty MAC crap Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * Update skel files Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * In Cvs Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * In Cvs Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * In Cvs Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * In Cvs Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * inCvs Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * sci-libs/mkl: Version BUmp
++  * sci-libs/ipp: Version BUmp
++  * sci-biology/pybrain: Drop comments from metadata.xml; drop keywords from live ebuild
++  * Merge branch 'master' of github.com:gentoo-science/sci
++  * Merge pull request #36 from TheChymera/master
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * updated + fix for bug #444526
++  * CMAKE_BUILD_DIR -> BUILD_DIR
++  * ran repoman -vdx fix as per jlec'S recommendation
++  * sci-chemistry/avogadro: Add patch to avoid textrels on i686, #439410
++  * sci-chemistry/avogadro: Restrict test phase https://sourceforge.net/p/avogadro/bugs/653/
++  * sci-chemistry/avogadro: Fix openbabel version, #442154
++  * Merge branch 'master' of github.com:gentoo-science/sci
++  * Moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * Moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * Moved to tree Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * sci-chemistry/openbabel: Add missing dep for USE=doc
++  * Update README.md
++  * Create README.md
++  * Added live ebuild for pybrain
++  * updated deps
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * dev-lang/idb: Version bump
++  * [sci-chemistry/nwchem] Initial import from bug #393139. Mpi still doesnt work
++  * moved to gx86
++  * moved to gx86 profile
++  * sync with gx86
++  * use T for temp file
++  * remove graphical tools when -X
++  * version bump + improved ebuild for fullprof
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * dev-java/hdf-java: cleaned for old version, buggy
++  * fix typo in intel-sdp_pkg_pretend
++  * updated deps
++  * sci-chemistry/mddnmr: Version BUmp
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Drop stupid static-libs idea again Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * Last remaning underscored removed Signed-off-by: Justin Lecher <jlec@gentoo.org>
++  * sci-chemistry/vmd: Drop dep on old tk
++  * random files
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci into pkg-config
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/tmglib: Initial import
++  * removed mac files from jlec
++  * sci-astronomy/starlink-bin: Version bump
++  * sci-libs/plasma: Version bump. Introduce testing
++  * sci-libs/lapacke-reference: added tmg for testing, cleaning up ebuild
++  * sci-libs/lapack-reference: removed tmg flag, now separate ebuild
++  * sci-libs/lapack-reference: tmg flag description
++  * sci-libs/lapack-reference: Added tmg use flag, fix a failing post command test
++  * sci-libs/mmdb: Test version for new eclass
++  * Keep order in pc file
++  * full featured
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-chemistry/mddnmr: Version Bump
++  * Work in progress
++  * Implemented comments from g-dev review
++  * Be bin package friendly
++  * Fix typo in Copyright year
++  * Implemented comments from g-dev review
++  * Only handle documentation if present
++  * intel-sdp.eclass: fix install on x86 + qa
++  * updated license
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * * intel:   Drop USE=doc and add static-libs support   Speed up unpacking #431614   Drop additional blank lines.   Drop old testing functions   Resort general functions and variables at the beginning   Add descriptions to standard phase functions.   declare local variables at once   Use clear += insteat of repeating variables   Drop version restriction of rpm2targz   Drop Sebastien as maintainer   Enhancement of intel-sdp.eclass   dev-lang/icc: Version Bump   dev-lang/ifc: Version Bump   imported from tree   dev-libs/intel-common: Version Bump; drop creation of license dir   Imported from tree   import from tree
++  * dev-python/pytools: fix test related stuff and license
++  * Drop USE=doc and add static-libs support
++  * Speed up unpacking #431614
++  * Drop additional blank lines.
++  * Drop old testing functions
++  * Resort general functions and variables at the beginning
++  * Add descriptions to standard phase functions.
++  * declare local variables at once
++  * Use clear += insteat of repeating variables
++  * Drop version restriction of rpm2targz
++  * Drop Sebastien as maintainer
++  * Enhancement of intel-sdp.eclass
++  * dev-lang/icc: Version Bump
++  * dev-lang/ifc: Version Bump
++  * imported from tree
++  * dev-libs/intel-common: Version Bump; drop creation of license dir
++  * Imported from tree
++  * import from tree
++  * Merge pull request #33 from xhub/master
++  * dev-python/pytools: fix test related stuff and license
++  * added openmm support
++  * mask sci-chemistry/gromacs[openmm]
++  * re-added for gromacs
++  * sci-mathematics/scilab various fixes
++  * dev-python/pycuda: Bump EAPI to 5; add missing dep on dev-python/mako; use cuda.eclass and make use of cuda_gccbindir
++  * dev-python/pytools: Bump EAPI to 5; add missing dep for tests
++  * dev-python/pycuda: bump and add tests
++  * dev-python/pytools: bump and add tests
++  * # By Justin Lecher (20) and Olivier Huber (1) * cuda: (21 commits)   dev-util/nvidia-cuda-sdk: Version Bump, inclusive cuda.eclass usage   sci-chemistry/vmd: Using new cuda.eclass   Imported from tree   Preparing Version Bump   dev-util/nvidia-cuda-toolkit: Merge change in both versions; fix whitespace error   Correcting whitespace problem   Minor fixes   Be a little more informative.   do not call pkg_setup from cuda.eclass   Move pkg_postinst to dev-util/nvidia-cuda-toolkit   Adding ignores for Mac   Add comments and streamline   dev-util/nvidia-cuda-sdk: Preparing Version Bump   Add pkg_setup and gcc bindir detection   dev-util/nvidia-cuda-toolkit: Enhancing cuda-config   dev-util/nvidia-cuda-sdk: Reverted changes to bicatalis commit; Moving to cuda.eclass   dev-util/nvidia-cuda-toolkit: Version Bump   preliminary cuda.eclass   Work in progress towards cuda eclass usage   dev-util/nvidia-cuda-toolkit: Use cuda.eclass; install cuda-config; install doc and html into system pat
 h to support portages file filter   ...
++  * Merge github.com:gentoo-science/sci
++  * dev-util/nvidia-cuda-sdk: Version Bump, inclusive cuda.eclass usage
++  * sci-chemistry/vmd: Using new cuda.eclass
++  * Imported from tree
++  * Preparing Version Bump
++  * dev-util/nvidia-cuda-toolkit: Merge change in both versions; fix whitespace error
++  * Correcting whitespace problem
++  * Minor fixes
++  * Be a little more informative.
++  * do not call pkg_setup from cuda.eclass
++  * Move pkg_postinst to dev-util/nvidia-cuda-toolkit
++  * Adding ignores for Mac
++  * Add comments and streamline
++  * dev-util/nvidia-cuda-sdk: Preparing Version Bump
++  * Add pkg_setup and gcc bindir detection
++  * dev-util/nvidia-cuda-toolkit: Enhancing cuda-config
++  * dev-util/nvidia-cuda-sdk: Reverted changes to bicatalis commit; Moving to cuda.eclass
++  * dev-util/nvidia-cuda-toolkit: Version Bump
++  * preliminary cuda.eclass
++  * Work in progress towards cuda eclass usage
++  * dev-util/nvidia-cuda-toolkit: Use cuda.eclass; install cuda-config; install doc and html into system path to support portages file filter
++  * Misc fixes for sci-libs/magma
++  * * cuda:   dev-util/nvidia-cuda-sdk: Version Bump, inclusive cuda.eclass usage   sci-chemistry/vmd: Using new cuda.eclass   Imported from tree   Preparing Version Bump   dev-util/nvidia-cuda-toolkit: Merge change in both versions; fix whitespace error   Correcting whitespace problem   Minor fixes   Be a little more informative.   do not call pkg_setup from cuda.eclass   Move pkg_postinst to dev-util/nvidia-cuda-toolkit   Adding ignores for Mac   Add comments and streamline   dev-util/nvidia-cuda-sdk: Preparing Version Bump   Add pkg_setup and gcc bindir detection   dev-util/nvidia-cuda-toolkit: Enhancing cuda-config   dev-util/nvidia-cuda-sdk: Reverted changes to bicatalis commit; Moving to cuda.eclass   dev-util/nvidia-cuda-toolkit: Version Bump   preliminary cuda.eclass   Work in progress towards cuda eclass usage   dev-util/nvidia-cuda-toolkit: Use cuda.eclass; install cuda-config; install doc and html into system path to support portages file filter
++  * sci-chemistry/openbabel: Add test phase, check openmp correctly
++  * sci-biology/staden: Version Bump, move to sane portage like building
++  * sci-chemistry/nmrpipe: Version BUmp
++  * Misc fixes for sci-libs/magma
++  * dev-util/nvidia-cuda-sdk: Version Bump, inclusive cuda.eclass usage
++  * sci-chemistry/vmd: Using new cuda.eclass
++  * Imported from tree
++  * Preparing Version Bump
++  * hdf-java: version bump
++  * flexdock: fix outdated SRC_URI and broken Manifest
++  * Merge pull request #31 from xhub/master
++  * dev-util/nvidia-cuda-toolkit: Merge change in both versions; fix whitespace error
++  * Merge branch 'master' into cuda
++  * Correcting whitespace problem
++  * Merge branch 'cuda' of github.com:gentoo-science/sci into cuda
++  * Minor fixes
++  * Misc fixes for sci-libs/magma
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * Ignore .DS_Store
++  * Merge branch 'master' into cuda
++  * Merge branch 'master' into pkg-config
++  * First scratch of new pkgconfig.eclass
++  * sci-mathematics/cdfplayer: installation of desktop file/other fixes
++  * Be a little more informative.
++  * do not call pkg_setup from cuda.eclass
++  * Move pkg_postinst to dev-util/nvidia-cuda-toolkit
++  * Adding ignores for Mac
++  * Add comments and streamline
++  * sci-mathematics/cdfplayer: installation path fixed
++  * sci-mathematics/cdfplayer: new ebuild for bug #421019
++  * improved ebuild for fullprof, added docs + examples useflags
++  * Merge pull request #29 from jauhien/master
++  * sci-physics/LoopTools: Manifest fixed
++  * fixing manifest
++  * removed g-cran, broken
++  * Merge pull request #26 from TheChymera/master
++  * Re-manifesting
++  * dev-cpp/eigen: Version bump
++  * improved ebuild for fullprof
++  * improved ebuild for fullprof
++  * added an ebuild for fullprof
++  * Merge pull request #27 from wking/master
++  * live ebuild update
++  * updated build and deps
++  * dev-java/netcdf: Add the netCDF licence (which is *not* MIT)
++  * dev-util/nvidia-cuda-sdk: Preparing Version Bump
++  * Add pkg_setup and gcc bindir detection
++  * dev-util/nvidia-cuda-toolkit: Enhancing cuda-config
++  * dev-util/nvidia-cuda-sdk: Reverted changes to bicatalis commit; Moving to cuda.eclass
++  * dev-util/nvidia-cuda-toolkit: Version Bump
++  * preliminary cuda.eclass
++  * Work in progress towards cuda eclass usage
++  * dev-util/nvidia-cuda-toolkit: Use cuda.eclass; install cuda-config; install doc and html into system path to support portages file filter
++  * sci-chemistry/avogadro: Add test phase
++  * sci-chemistry/simpson: Fix underlinking
++  * Fix underlinking
++  * Move to dev-libs
++  * initial import of libcuda
++  * initial import of libgdev
++  * dev-lang/idb: in main tree
++  * Moved to Tree
++  * sci-chemistry/phenix-bin: Make no-fetch msg better understandable
++  * sci-chemistry/phenix-bin: Fix deps
++  * sci-chemistry/chimera-bin: Add dep on virtual/opengl
++  * sci-chemistry/chimera-bin: Fix deps
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Update live ebuild for latest Normaliz
++  * sci-libs/gmsh: Add another dep for opengl support
++  * sci-libs/gmsh: Addmissing dep on virtual/opengl
++  * Added live ebuild for MDP
++  * sci-libs/gmsh: Fix link problems with gold
++  * sci-libs/med: Fix SRC_URI; move to EAPI=5
++  * Fix dep on gmp[cxx] (Thanks Gerhard Bräunlich)
++  * x11-libs/xview-bin: Update to latest debian patches
++  * openbabel-python: Enter BUILD_DIR in src_install
++  * Merge pull request #24 from TheChymera/master
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * sci-biology/bamtools: Drop tree version, merge changes into live version
++  * Merge pull request #25 from jauhien/thepeg-herwig-version-bump
++  * sci-physics/herwig++: version bump
++  * sci-physics/thepeg: version bump
++  * sci-chemistry/ambertools: Add another fix for blas/lapack
++  * Revert "Update Copyright"
++  * Fix DEP on eselect
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * Update Copyright
++  * Merge pull request #21 from fredricj/master
++  * version bump
++  * Merge remote-tracking branch 'remotes/github/master'
++  * bump
++  * renamed dependency from openmotif to motif
++  * Fix linking against arbitrary lapack implementation
++  * net-fs/cvmfs: now in main tree
++  * Proper DEPEND list and eclass info
++  * Added MY_P key to SRC_URI path
++  * Defined general MY_P
++  * Removed redundant S= from git version, fixed faulty S= specification in 1.75.01
++  * New ebuild for stable psychopy version + manifest
++  * Ebuild improvements as per jauhien's instructions.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * New ebbuild for sci-biology/psychopy
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-physics/root: remove unused patch
++  * sci-chemistry/nmrpipe: Version Bump
++  * sci-chemistry/wxmacmolplt: Fix prefix awareness; correct desktop file creation
++  * sci-physics/root, app-doc/root-doc: update Manifest
++  * ambertools: export AMBERHOME in ebuild
++  * gamess: Version bump to 20120501.1
++  * sci-libs/mkl: Fix size of builddir
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/lapacke-reference: Version bump. Restore the reflapack library name instead of lapack
++  * sci-libs/lapack-reference: Version bump. Restore the reflapack library name instead of lapack
++  * Merge blas to master
++  * sci-physics/root: Drop virtual/fortran from DEP as it is provided by the fortran-2.eclass
++  * sys-cluster/mpich2: Move to EAPI=5, use fortran-2.eclass correctly
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * app-doc/root-docs: version bump
++  * sci-physics/root: version bump
++  * sci-astronomy/zpeg: Drop unnessecarry virtual/fortran dep
++  * dev-util/f90cache: Use fortran-2.eclass
++  * dev-python/inference: Move to EAPI=5; correct usage of fortran-2.eclass
++  * dev-python/ffnet: Move to EAPI=5; use distutils-r1.eclass; correct usage of fortran-2.eclass
++  * dev-cpp/growler-link: Fix for gcc-4.7; correct fortran-2.eclass usage; move to autotools-utils.eclass
++  * dev-cpp/eigen: Use vcs-snapshot.eclass, correct usage of fortran-2.eclass, some layout improvements
++  * Update M2 live ebuild
++  * inCvs
++  * sci-libs/inchi: Straighten out some minor things, respect AR and RANLIB
++  * app-admin/eselect: Bump to tree version
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * version bump
++  * vmd: Fix netcdf config, bug #406737
++  * wxmacmolplt: Version bump to 7.4.3
++  * sci-libs/blas-reference: Version bump, revert to change soname to refblas
++  * ambertools: Fix parallel tests
++  * ambertools: Version bump to 12
++  * avogadro: Version bump to 1.1.0
++  * app-doc/root-docs: version bump
++  * sci-physics/root: version bump
++  * openbabel-python: Fix typo
++  * openbabel-python: Add PYTHON_DEPS
++  * inchi: Add static-libs USE flag
++  * openbabel-python: Version bump to 2.3.2
++  * openbabel-perl: Version bump to 2.3.2
++  * openbabel: Version bump to 2.3.2
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-mathematics/scilab] revert part of commit 033255b367
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-mathematics/scilab] remove virtual/fortran
++  * [sci-mathematics/scilab] remove virtual/fortran
++  * Merge pull request #22 from jauhien/master
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-physics/LoopTools-2.8: Manifest fixed
++  * [sci-libs/openblas] Solved problem with fetching
++  * sci-chemistry/pymol: Add mime type definition
++  * Merge branch 'master' of github.com:gentoo-science/sci
++  * [sci-mathematics/scilab] fix slot dependencies
++  * Merge pull request #18 from jauhien/herwig
++  * bump boehm-gc, fix python
++  * Fix deps of live ebuild
++  * [x11-misc/envytools] There is no opcodes
++  * [x11-misc/envytools] Allow to build with recent bison
++  * [x11-misc/envytools] Add envytools
++  * improve live ebuild
++  * Removed the TODO item for the desktop file
++  * Added rstudio-0.96.331 and desktop file fix
++  * [sci-chemistry/trajng] Fix ebuild
++  * [sci-chemistry/trajng] Add keywords
++  * [sci-chemistry/xdrfile] Add keywords
++  * [sci-chemistry/trajng] Add to repo
++  * [sci-chemistry/xdrfile] actualy allow optional fortran
++  * [sci-chemistry/xdrfile] Add to repo
++  * inCVS
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * sci-chemistry/phenix-bin: Version Bump
++  * [app-vim/vim-gromacs] Fix typo
++  * [app-vim/vim-gromacs] Update vim syntax repo uri
++  * initial commit (thx to Torsten Stuehn)
++  * package.mask: added sci-physics/espresso++
++  * sync with gx86
++  * [sci-libs/openblas] Version bump
++  * [sys-cluster/lustre] Update patches
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * fix to build petsc in Gentoo Prefix (thanks to Matthias Maier)
++  * live ebuild update
++  * live ebuild update
++  * updated package.mask
++  * cmake-utils.eclass got merged in gx86
++  * hybrid stuff got merged
++  * [sci-mathematics/scilab] fix errors in previous commit
++  * [sci-mathematics/scilab] version bump
++  * [dev-java/scirenderer] version bump
++  * version bump
++  * app-benchmarks/numbench: Updated dependency for eselect alternatives
++  * sci-libs/mkl: Version bump
++  * sci-libs/acml: Version bump
++  * [sci-mathematics/scilab] update dependencies
++  * [dev-java/scirenderer] version bump
++  * [dev-java/jlatexmath-fop] version bump
++  * [dev-java/jlatexmath] version bump
++  * app-admin/eselect: rev-bumped to avoid conflict with tree
++  * sci-chemistry/specView: Needs webkit support in pyside
++  * sci-chemistry/chemBuild: Needs webkit support in pyside
++  * sci-chemistry/specView: Prefix offset for header dirs
++  * sci-chemistry/specView: Copile py code
++  * sci-chemistry/chemBuild: New addition
++  * import latest skel data from tree
++  * sci-chemistry/specView: New addition
++  * sci-chemistry/phenix-bin: Add missing dep
++  * sci-chemistry/chimera-bin: Don't strip
++  * sci-chemistry/chimera-bin: Set rpath on prefix
++  * sci-chemistry/phenix-bin: Don't double prefix
++  * sci-chemistry/phenix-bin: Not everyone installs on my box
++  * Version Bump
++  * [sys-cluster/lustre] call apply_user_patches
++  * [sys-cluster/lustre] Initial import
++  * in Cvs
++  * in Cvs
++  * in Cvs
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * new addition
++  * new addition
++  * new license
++  * new license
++  * change one useflag name in paraview 3.14.1
++  * in CVS
++  * in CVS
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * Enable postscript support in paraview 3.14.1 through gl2ps
++  * app-admin/eselect: Version BUmp
++  * sci-physics/herwig++: move sed stuff to pkg_preinst and change $D to $ED
++  * sci-chemistry/curvefit: Quote sed correctly
++  * sci-chemistry/curvefit: And it sits in EPREFIX
++  * sci-chemistry/curvefit: We have ls in usr/bin
++  * sci-chemistry/curvefit: Also include gcc-4.1 libdir in rpath
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * sci-chemistry/curvefit: New addition
++  * Merge pull request #19 from jauhien/looptools-2.8
++  * Bump iml to the same level as s-o-g overlay, make it work on prefix including OS X.
++  * sci-physics/LoopTools: version bump
++  * sci-physics/herwig++: RDEPEND fixed
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * dummy files added to make pcheck happy
++  * Merge pull request #17 from jauhien/thepeg
++  * New Ebuild for bug #433060
++  * sci-physics/thepeg: maintainer email fixed
++  * sci-physics/thepeg: DEPEND fixed
++  * New Ebuild for bug #424003 thanks to hasufell, mgorny and xarthisius.
++  * dev-python/astlib: Version bump
++  * sci-libs/exodusii: Version Bump
++  * Patches for sci-libs/bigdft to install GPU support corrected not to break linking against the compiled libraries
++  * unbundle netcdf from paraview
++  * update descriptions
++  * Bunch of fix and ubundling for paraview 3.14.1
++  * enabled commit signing
++  * add empty files for pcheck
++  * sci-chemistry/ligplot+: New addition
++  * a license is a license not an eclass
++  * add license
++  * sci-chemistry/ssp: Fix offset of reference CS DB
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * sci-chemistry/ssp: New addition
++  * Merge pull request #16 from jauhien/LoopTools_so_fortran
++  * ambertools: Add bugfix 28
++  * sci-physics/LoopTools: shared library generation and dependency on virtual/fortran added
++  * Merge branch 'master' of git+ssh://github.com/gentoo-science/sci
++  * [app-benchmarks/numbench] Version bump.
++  * paraview 3.14.1 initial import to greater masses
++  * sync with gx86
++  * better version in tree
++  * Merge pull request #15 from jauhien/master
++  * manifest fixed
++  * renamed -bin
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * Merge remote-tracking branch 'github/master'
++  * [sci-libs/openblas] Version bump
++  * update to EAPI=4, cosmetics, deps
++  * sci-chemistry/usf-tools: Bump to latest release
++  * Merge git+ssh://paul/local/overlays/sci
++  * ucsf-tools
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge pull request #14 from xhub/github-master
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * [dev-python/Forthon] version bump
++  * sci-chemistry/pymol: Correct Desktop entry
++  * Enable cross-compilation of {CBLAS,LAPACK}-reference
++  * [sci-mathematics/scilab] version bump
++  * [dev-java/scirenderer] version bump
++  * [dev-ml/zarith] fix license
++  * [dev-ml/gsl-ocaml] new package
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * sci-chemistry/nmrpipe: no function called from prefix.eclass; please drop
++  * sci-chemistry/nmrpipe: Enhancing prefix support
++  * x11-libs/xview-bin: Add stupid binary package
++  * use ninja if available
++  * cmake-utils.eclass: added ninja support
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * [sci-mathematics/scilab] live ebuild update
++  * [app-benchmarks/numbench] New revision, directory cleaned up.
++  * [app-benchmarks/numbench] Updated live ebuild.
++  * Update live dependencies
++  * [app-benchmarks/numbench] Version bump.
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * dev-java/scirenderer version bump
++  * dev-ml/lacaml version bump and cleanup old version
++  * dev-java/scirenderer version bump
++  * scotch in main tree
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * Version bump sfst to 1.4.6g
++  * Bump foma to version 0.9.16alpha.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Version bump hfst to 3.3.12
++  * x11-libs/xview: Add missing inherit of multilib
++  * x11-libs/xview: Use everything from debian; build only 32bit libs everywhere; be carefully this is very hacky approach
++  * sci-chemistry/nmrpipe: Version Bump, bring x11-libs/xview back into the game
++  * Version bump.
++  * sci-astronomy/galfit-bin: renamed to binary package
++  * Update live ebuild
++  * sci-astronomy/galfit: add links to ncurses/tinfo
++  * sci-astronomy/psfex: fixed for newer plplot
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * sci-astronomy/galfit: manifest/new tar file
++  * dev-java/scirenderer version bump
++  * dev-java/jgraphx version bump
++  * dev-java/flexdock version bump
++  * sci-mathematics/scilab live ebuild update
++  * updated min eselect version
++  * sci-libs/atlas: added a generic flag for more generic architectures, and possibility for user to pass configure options via standard EXTRA_ECONF flags
++  * sci-astronomy/zpeg: Initial import
++  * dev-cpp/eigen: Version bump. Changed license to MPL-2
++  * fix deps
++  * net-fs/cvmfs: fixed client init and setup, added config stage
++  * added ~x86-macos
++  * package.mask: removed obsolete entries
++  * sync with gx86
++  * sync with gx86
++  * sync with gx86
++  * sync with gx86
++  * sync with gx86
++  * net-fs/cvmfs: Initial import, need more work
++  * sci-chemistry/concoord: Use QA_PREBUILT for binary packages
++  * sci-physics/root: update User's Guide
++  * app-doc/root-docs: remove Manifest
++  * incvs
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * sci-physics/root-docs: version bump
++  * sci-physics/root: version bump
++  * sci-physics/root: improve cling support
++  * app-doc/root-docs: update live ebuild
++  * sci-physics/root: update live ebuild
++  * sci-physics/root: fix bug 426432
++  * sci-libs/armadillo: Adapted for new atlas
++  * sci-libs/coinor-dip: Initial import
++  * fixed license to CPL
++  * sci-libs/coinor-csdp: Initial import
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * [dev-util/nvidia-cuda-sdk] fix asneeded issues
++  * sci-libs/coinor-os: Initial import
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * added plcol patch with increased diff line count, bug #391669; same patch needs to go into offical emboss-6.3.1_p4
++  * sci-libs/coinor-cppad: Initial import
++  * sci-libs/coinor-couenne: Initial import
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * InCvs
++  * sci-libs/coinor-vol: Fixed for occasional parallel install breaks
++  * fixed description
++  * sci-libs/coinor-bonmin: Initial import
++  * sci-libs/coinor-bcp: Initial import
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * live ebuild update
++  * live ebuild update
++  * sci-chemistry/votca-{ctp,kmc,moo}: removed never realy used
++  * sci-astronomy/lephare: prefix keywording, version fix
++  * [dev-libs/fortrancl] fix patch
++  * sci-libs/coinor-symphony: Initial import
++  * sci-libs/coinor-mp: Initial import
++  * [sci-visualization/yt] update dependencies
++  * [dev-python/Forthon] version bump
++  * syntax error in passing lapack
++  * sci-libs/ipopt: Initial import
++  * sci-libs/coinor-blis: Initial import
++  * sci-libs/coinor-bcps: Initial import
++  * sci-libs/coinor-alps: Initial import
++  * sci-libs/coinor-cbc: Initial import
++  * sci-libs/coinor-cgl: Initial import
++  * sci-libs/coinor-clp: Initial import
++  * sci-libs/coinor-dylp: Initial import
++  * sci-libs/coinor-vol: Initial import
++  * sci-libs/coinor-osi: Initial import
++  * sci-libs/coinor-utils: Initial import
++  * sci-libs/coinor-netlib: Initial import
++  * sci-libs/coinor-sample: Initial import
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * Merge pull request #12 from xhub/0825f16ab3ec153827d9aadc60880028d81a9efe
++  * Add support for x32 ABI
++  * sci-libs/mumps: Merge dummy sequential mpi into sequential mumps
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * media-gfx/librecad: dependency fix, bug#426730
++  * clean up
++  * initial commit
++  * sci-libs/mumps: fix underlinking for sequential library
++  * sci-libs/magma: Shared library fixes, prefix love and ebuild cleanup
++  * sci-libs/xblas: Shared library fixes, prefix love and ebuild cleanup
++  * sci-libs/plasma: Shared library fixes and prefix love
++  * sci-libs/scotch: Shared library fixes and prefix love
++  * sci-libs/mumps: Shared library fixes and prefix love
++  * sci-libs/mpiblacs: Shared library fixes and prefix love
++  * sci-libs/fdlibm: Shared library fixes and prefix love
++  * sci-libs/cblas-reference: Shared library fixes and prefix love
++  * sci-libs/scalapack: dependencies fix, removed old
++  * sci-libs/mumps: prefix love
++  * remove duplicate
++  * dev-libs/double-conversion: Initial import
++  * sci-mathematics/dsfmt: Initial import
++  * sci-libs/fdlibm: Initial import
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * Made dev-util/nvidia-cuda-sdk-4.2.9 compile with USE=opencl
++  * [dev-java/scirenderer] version bump
++  * [sci-mathematics/scilab-5.3.999] test ebuild for 5.4 branch
++  * [dev-java/jrosetta] version bump
++  * sci-libs/atlas: Version bump, this is a stable release.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * The bigdft-1.6-tuto.1-GPUlibs.patch of sci-libs/bigdft-1.6_pre1-r3 updated not to forget the pkg-config file
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * remove old
++  * more sci-astronomy live ebuild masking
++  * sci-astronomy/stiff: live version, prefix keywording
++  * sci-astronomy/missfits: live version, prefix keywording
++  * sci-astronomy/weightwatcher: live version, prefix keywording
++  * sci-astronomy/eye: live version, prefix keywording
++  * prefix keywording
++  * prefix keywording
++  * sci-libs/openblas: version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * dev-cpp/eigen: version bump and more test fixes
++  * sci-libs/adolc: to main tree
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * sci-libs/dsdp: changes incorporated in main tree
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * pfft: removed - never used
++  * layout.conf: updated manifest-hashes
++  * version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * The version of sci-physics/elk bumped to 1.4.22, the old ones removed.
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * sync hash with new portage
++  * dev-java/jlatexmath-fop: remove old
++  * dev-java/jlatexmath: do not compile examples, bug #421743
++  * sci-libs/hdf5: in main tree
++  * Fixed typo.
++  * Moved prefix to /opt.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * Merge branch 'master' of github.com:gentoo-science/sci
++  * Updated DEPEND.
++  * Adding live build.
++  * Added package mask for live ebuild, sci-chemistry/freeon-9999.
++  * Merge pull request #9 from jauhien/master
++  * Added modules-3.2.9c-r1.ebuild.
++  * update metadata
++  * New ebuild sci-physics/LoopTools-2.7 for bug#424860
++  * root-docs: clean version moved to portage
++  * Mask live ebuilds from sci-astronomy
++  * sci-astronomy/stuff: Live version. Prefix love
++  * no blas
++  * Live version. Prefix love
++  * sci-astronomy/sextractor: cblas -> atlas
++  * sci-astronomy/scamp: cblas -> atlas
++  * sci-astronomy/psfex: live version
++  * sci-astronomy/swarp: added live version
++  * sci-astronomy/scamp: live version
++  * sci-astronomy/sextractor: Live version, introduced prefix love
++  * dev-util/nvidia-cuda-sdk: Adapted to newer nvidia-cuda-sdk
++  * dev-util/nvidia: rewrote ebuild
++  * a blind attempt to get from a pull-push confusion
++  * sci-libs/bigdft-1.6_pre1 from -r2 to -r3: patched to install necessary libraries for GPU support and to compile with gcc-4.6
++  * dev-util/nvidia-cuda-toolkit: This package is prebuilt so we are using QA_PREBUILT for everything
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/atlas: version bump. Adapt calls to compilers. Inherit multilib
++  * dev-util/nvidia-cuda-toolkit: fix for amd64-linux
++  * dev-util/nvidia-cuda-toolkit: fix for amd64-linux
++  * sci-libs/magma: Version bump. Updated patches
++  * dev-util/nvidia-cuda-toolkit: more prefix fixes
++  * dev-util/nvidia-cuda-sdk: import/clean/bump
++  * dev-util/nvidia-cuda-toolkit: import/clean/bump
++  * sci-chemistry/coot: Gcc-4.7 support included upstream
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-physics/root: backport fixes from the portage
++  * app-doc/root-docs: backport fixes from portage
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * more comments, .Rhistory
++  * sci-mathematics/rstudio: initial import
++  * dev-libs/mathjax: Initial import
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Moved to tree
++  * dev-python/bitarray: New package requested by jamasi on irc
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * dev-cpp/eigen: version bump
++  * keyword amd64-linux and x86-linux
++  * add pthread for as-needed
++  * fix license and add flag desc
++  * initial import
++  * sci-physics/root: Drop in tree versions
++  * [dev-python/pyhdf] whitespace
++  * [dev-python/pyhdf] initial import wrt #423953. Ebuild written by Paweł Rumian <gorkypl@gmail.com> with my modifications
++  * updated to petsc-3.3_p1
++  * sci-libs/openblas: fixed soname
++  * sci-libs/atlas: version bump
++  * sci-libs/atlas: version bump
++  * sci-libs/openblas: remove test flag
++  * sci-libs/openblas: version bump
++  * Merge github.com:gentoo-science/sci
++  * sci-libs/magma: Initial import
++  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci into overlay
++  * [sci-libs/libxc] add ~amd64-linux
++  * [sci-libs/libxc] add ~amd64-linux
++  * [sci-libs/bigdft] add ~amd64-linux
++  * [sci-libs/wannier90] add ~amd64-linux
++  * [sci-libs/fox] make it prefix aware
++  * Merge pull request #8 from nicolasbock/master
++  * Added libX11 dependency.
++  * [dev-java/joda-convert] add missing dependency on junit:4
++  * Merge branch 'master' of https://github.com/wking/science into wking-hdfview
++  * dev-java/hdf-java-2.8: fix hdfview script (quotes and sh-bang)
++  * dev-java/hdf-java-2.8: explicitly build packages for hdfview
++  * dev-java/hdf-java: fix HOMEPAGE in v2.8 ebuild.
++  * Fixed package description.
++  * First commit for modules package.
++  * app-doc/root-docs: backport htmldoc generation fixes
++  * sci-physics/root: backport htmldoc fixes to 5.32 branch
++  * sci-physics/root: remove redundant virtualx
++  * sci-physics/root: reuse htmldoc patch
++  * app-doc/root-docs: version bump for 5.34.00
++  * sci-physics/root: version bump for 5.34.00
++  * app-doc/root-docs: separate htmldoc from root package
++  * sci-physics/root: fix repoman warnings and update manifest
++  * sci-physics/root: separate htmldoc package
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Reflect the split of the fortran interface out of sci-libs/netcdf in sci-libs/bigdft and sci-libs/etsf_io. The version of sci-physics/elk bumped to 1.4.22, the old ones removed.
++  * [sci-chemistry/gromacs] Add new acceleration use flags for gromacs
++  * Reflect the split of the fortran interface out of sci-libs/netcdf in sci-physics/abinit-6.12.3-r2
++  * Merge github.com:gentoo-science/sci
++  * sci-libs/atlas: Version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * fixed redundant license (bug #421401)
++  * fixed redundant license (bug #421401)
++  * sci-geosciences/harmonics-dwf-20120302: Fixed problem where "S" directory wasn't found.
++  * Merge branch 'master' of github.com:gentoo-science/sci
++  * sci-geosciences/xtide: Version bump.  Removed "non-commercial" use since upstream received take-down notice and that dataset is no longer available.
++  * sci-geosciences/libtcd: Version bump.  Removed "non-commercial" use since upstream received a take-down notice and the "non-commercial" dataset is no longer available.
++  * sci-geosciences/harmonics-dwf-free: Version bump.
++  * dev-perl/Const-Fast, dev-perl/File-Map, dev-perl/OpenGL, dev-perl/PDL, dev-perl/PerlIO-Layers: now in main tree
++  * dev-perl/PerlIO-Layers: Initial import
++  * dev-perl/OpenGL: Initial import
++  * dev-perl/File-Map: Initial import
++  * dev-perl/Const-Fast: Initial import
++  * dev-perl/PDL: Version bump
++  * sci-astronomy/scamp: Fixed patch name
++  * sci-astronomy/lephare: Initial import
++  * sci-physics/root: update live ebuild
++  * initial commit
++  * masked dev-lang/ispc-9999
++  * sci-chemistry/coot: Fix for gcc-4.7
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-physics/root: sync with tree
++  * Masks moved to tree
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [dev-java/scirenderer] new ebuild
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * add support for new hybrid kernels
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/cluster: Correct masking, #419999
++  * added missing private headers
++  * added petsc-3.3-p0 ebuild
++  * sci-chemistry/mgltools-opengltk: Add missing dep on media-libs/glew and fix underlinking problem
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sys-devel/gdebugger: Fix Manifest
++  * sci-libs/atlas: Version bump
++  * Add missing hashes
++  * Drop unused licenses
++  * sci-biology/cluster: Rename cluster to cluster3, #419999
++  * Merge branch 'master' of github.com:gentoo-science/sci
++  * sci-chemistry/mgltools-qslimlib: Fix for gcc-4.7
++  * fixed info install
++  * sci-chemistry/mgltools-pmv: Fix for bytecompiling
++  * app-admin/eselect: Fix eaclocal call
++  * Mask old dssp and make sci overlay user to tester
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * improved die() message to inform user that gcc-4.5.3 does not work while gcc-4.3.6 does
++  * sci-chemistry/nmrview: Move to EAPI=4, specify QA_PREBUILT
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-physics/root: use virtualx eclass for Xvfb
++  * sci-chemistry/simpson: Correct blas to cblas for linking
++  * [sci-mathematics/scilab] force jgraphx version
++  * sci-physics/root: html documentation generation
++  * initial commit
++  * fixed EAPI bump
++  * initial commit
++  * sci-mathematics/scilab: fix bug #375769
++  * dev-java/jogl: adapted gluegen dependency
++  * sci-mathematics/scilab: fixed gui/xcos deps
++  * dev-java/gluegen: sync version with java-overlay
++  * sci-mathematics/scilab: complete ebuild revamp
++  * sci-physics/root: sync live ebuild with upstream
++  * [sys-cluster/hpl] add -Lflags from lapack and blas, fixes #400785 by Aleksandr Yakimov <yaleks@gentoo.ru>
++  * sci-biology/cluster: Version Bump, Move to EAPI=4
++  * dev-java/hdf-java: add hack for hdf5[mpi]
++  * dev-java/hdf-java: fixed missing use
++  * dev-java/flexdock: add missing jgoodies-looks dependency
++  * [dev-lang/path64] remove epause along with eutils.eclass since it does nothing for EAPI>2. Thanks to Jeremy Olexa <darkside@gentoo.org> for noticing
++  * [net-misc/dhcp] add user.eclass for enew{user,group}
++  * [sci-physics/root] add user.eclass for enew{user,group}
++  * [sys-cluster/condor] add user.eclass for enew{user,group}
++  * [dev-lang/path64] add eutils.eclass for epause
++  * [dev-util/smartgit] add eutils.eclass for make_desktop_entry
++  * [media-gfx/librecad] add eutils.eclass for make_desktop_entry
++  * [sci-mathematics/petsc] add eutils.eclass for epatch
++  * [sci-geosciences/qgis] add eutils.eclass for make_desktop_entry
++  * sci-physics/root: update User's Guide
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-astronomy/topcat: Initial import
++  * sci-libs/exodusii: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
++  * sci-libs/lapacke-reference: Add missing eutils.eclass
++  * sci-libs/scalapack: Add missing eutils.eclass
++  * sci-mathematics/dolfin: Add missing eutils.eclass, bump to EAPI=4
++  * sci-physics/abinit: Add missing eutils.eclass
++  * sci-physics/atompaw: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
++  * sys-cluster/ovis: Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; fix installation of envd file; correct leading spaces
++  * sci-astronomy/stilts: Initial import
++  * sys-cluster/ovis: Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; fix installation of envd file; correct leading spaces
++  * sys-cluster/ovis: Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; fix installation of envd file; correct leading spaces
++  * sci-physics/root: Add missing eutils.eclass
++  * sys-cluster/ovis: Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; fix installation of envd file; correct leading spaces
++  * sci-libs/cgnslib: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
++  * sci-libs/blas-reference: Add missing eutils.eclass
++  * sci-libs/bigdft: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
++  * sci-biology/mira: Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; drop old
++  * sci-biology/gbrowse: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
++  * sci-biology/est2uni: Bump to EAPI=4, remove unnecessary bits
++  * sci-biology/emboss: Add missing eutils.eclass
++  * sci-biology/amos: Bump to EAPI=4, remove unnecessary bits
++  * dev-perl/Bio-BigFile: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
++  * dev-java/jogl: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
++  * dev-java/flexdock: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
++  * Mask old version schema of ncbi-tools to make overlay user to be tester
++  * [dev-java/hdf-java] remove stray quotes
++  * media-gfx/librecad: added freetype to DEPS
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Mask >=sci-libs/arpack-96 to make overlay users to tester
++  * Fix repoman warning about position off EAPI
++  * sci-astronomy/starlink-bin: Initial import
++  * sci-astronomy/zebra: Initial import
++  * sci-libs/optpp: Initial import
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * dev-java/gluegen: Fix repoman warning about position off EAPI
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-physics/root: version bump
++  * sci-physics/abinit-6.12.3-r1 modified to accept revisions of sci-libs/bigdft-1.6_pre1
++  * The pkg-config file of sci-libs/bigdft corrected.
++  * masked scilab-5.4*
++  * dev-java/joda-time: import from wtk overlay
++  * dev-java/joda-convert: import from the java overlay
++  * dev-java/jrosetta: import from the java overlay
++  * dev-java/jogl: import from the java overlay
++  * dev-java/jcip-annotations: import from the java overlay
++  * dev-java/gluegen: import from the java overlay
++  * dev-java/jlatexmath-fop: Version bump
++  * dev-java/jlatexmath: Version bump
++  * dev-java/jeuclid-core: Version bump
++  * dev-java/hdf-java: Version bump. Added use flag hdfview. Adapted from the wtk overlay
++  * dev-java/netcdf: import to the science overlay and bump
++  * dev-java/fits: quotes
++  * dev-java/fits: updated herd and description
++  * dev-java/fits: Version bump and import to the science overlay
++  * sci-mathematics/flocq: QA fixe
++  * sci-mathematics/flocq: Various QA fixes
++  * [dev-python/cosmocalc] bump to eapi4, allow multiple python abis, call 2to3 for python3 support, reorder variables, add pypi to HOMEPAGE and SRC_URI, drop empty {R,}DEPEND
++  * [dev-python/asciidata] Reorder vars to comply with ebuild.skel, drop redundant PYTHON_DEPEND (already done via distutils.eclass) and src_test, add pyfits to RDEPEND, numpy is RDEPEND only, build docs instead of downloading them, bump to EAPI4
++  * [sci-mathematics/flocq] Fix ebuild eapi parsing and other minor issues
++  * [metadata] Enable md5-cache
++  * [dev-java/jgraphx] Fix ebuild eapi parsing and other minor issues
++  * [dev-lang/vtune] Fix ebuild eapi parsing and other minor issues
++  * sci-astronomy/galfit: Initial import
++  * sci-astronomy/eazy: Initial import
++  * sci-astronomy/bpz: Initial import
++  * sci-libs/scalapack: Version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-astronomy/astrometry: Initial import
++  * sci-mathematics/apron: fixes conflict of USE flags
++  * [sci-libs/atlas] Version bump.
++  * [sci-libs/openblas] Removed old alpha versions.
++  * [sci-libs/openblas] Version bump.
++  * sync with gx86
++  * [dev-python/astropy] fix depends, drop keywords from live ebuild to make repoman happy, whitespaces
++  * [dev-python/astropy] initial import, ebuild written by me
++  * [sys-devel/gdebugger] slight improvements, add proper depends
++  * Merge branch 'gdebugger' of https://github.com/nbigaouette/sci into nbigaouette-gdebugger
++  * Version bump, drop old, don't install unnecessary doc files
++  * sci-chemistry/pymol: Fix for latest HEAD
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Fix live ebuild
++  * sci-chemistry/nmrpipe: Version Bump, use QA_PREBUILT
++  * Bundled in nmrpipe
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Revert "Don't use "cp" for copying files/folders into ${D}, use insinto/doins -r instead."
++  * Assert sed execution with "die".
++  * Don't use "cp" for copying files/folders into ${D}, use insinto/doins -r instead. Note that an "mv" seems nessary to rename the installed folder (${My_PN} instead of ${My_PN}${PV}-${_arch}) and new variables ${_dest_folder} and ${_extracted_folder} are now used to prevent having ugly "basename" and "dirname" calls.
++  * Create directories just before installing files to them.
++  * Create destination directory just before first file copy.
++  * Go into WORKDIR instead of ".."
++  * Create .desktop file using "cat >> <<- EOF" instead of "echo".
++  * No need for a dot at end of description; not a sentence.
++  * Don't use html2text to create the license. Use the license from the overlay.
++  * Added license for sys-devel/gdebugger
++  * Add app-vim/vim-gromacs
++  * sci-chemistry/nmrpipe: Use QA_PREBUILT instead of QA_FLAGS_IGNORED
++  * sci-chemistry/nmrpipe: Version Bump, handle all binary files correctly for QA checks
++  * New ebuild: AMD gDEBugger version 6.2.438, an OpenCL and OpenGL debugger and memory analyzer.
++  * The dependence of sci-physics/abinit on sci-libs/fox corrected.
++  * mask =sci-libs/mmdb-1.24.20111208, no pkg-confiles installed
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-chemistry/gromacs] add more mirrors
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-chemistry/mgltools-webservices: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-volume: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-visionlib: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-vision: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-viewer-framework: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-utpackages: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-symserv: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-support: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-stride: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-sff: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-scenario2: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-scenario: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-qslimlib: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-pyglf: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-pybabel: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-pyautodock: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-pmv: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-opengltk: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-networkeditor: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-molkit: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-mglutil: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-gle: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-geomutils: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-dejavu: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-cmolkit: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-cadd: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-bhtree: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools-autodocktools: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-chemistry/mgltools: Add 2.7-pypy-* to RESTRICT_PYTHON_ABIS
++  * sci-libs/msms: RESTRICT pypy
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * Merge pull request #2 from nbigaouette/vtune
++  * Put symbolic links in /usr/bin and create .desktop file.
++  * Added ebuild for vtune 11.0.7.221625 using the "intel-sdp" eclass.
++  * Don't hardcode "rpm" as being the archive subdirectory where RPMs are to be found. Instead, define "INTEL_RPMS_DIRS" in the ebuild and loop over searching for the RPM. If unset, defaults to "rpm".
++  * Matching the archive for ".tgz" specifically breaks VTune which has .tar.gz as archive. Instead, remove everything after the first dot (the .tar.gz or .tgz part).
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/blas-reference: applied lapack patch to not compile tmglib when not needed
++  * sci-libs/lapack-reference: fixed patch for testing
++  * fixed patch for testing
++  * sci-chemistry/coot: Drop libpng-1.5 patch, included upstream
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/blas-reference: Fix manifest
++  * sci-libs/lapack-reference: Fix manifest
++  * sci-libs/blas-reference: Clean checksums
++  * sci-libs/lapack-reference: Clean checksums
++  * sci-libs/lapacke-reference: Version bump
++  * sci-libs/lapack-reference: Version bump
++  * sci-libs/blas-reference: Version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/libxc version bumped to 1.2.0.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sys-cluster/ovis] Masked for testing.
++  * [sys-cluster/ovis] Initial ebuild.
++  * Fix docdir for prefix.  Thanks to Robert McGehee for reporting.
++  * in main tree
++  * dev-python/emcee: Initial import
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * dev-python/astlib: Version bump
++  * Minor improvements related to sci-libs/fox.
++  * sci-physics/abinit-6.12.* improved to find uudecode, a patch created for that by mistake removed once more. Several packages related to Abinit, including sci-physics/elk, version-bumped.
++  * [sci-chemistry/gromacs] Also add http mirror git uri
++  * Merge branch 'master' into overlay
++  * Merge branch 'master' of github.com:gentoo-science/sci
++  * media-gfx/librecad: version bumped 1.0.2 2.0.0_alpha3
++  * in main tree
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-physics/abinit bumped to 6.12.3, a patch file removed by mistake put back.
++  * sci-libs/levmar: Initial import
++  * Merge git+ssh://git.overlays.gentoo.org/proj/sci
++  * Fix test in dsdp
++  * Merge branch 'master' of github.com:gentoo-science/sci
++  * sci-geosciences/pydap and pydap plugins:
++  * [dev-java/hdf-java] updates SRC_URI
++  * [app-benchmarks/numbench] Version bump.
++  * [sci-libs/trilinos] Solved many issues.
++  * [sci-libs/trilinos] Masked for testing.
++  * [sci-libs/trilinos] Initial ebuild.
++  * Import dsdp to include a huge number of fixes and improvement
++  * sci-physics/root: Drop in tree version
++  * sci-physics/root: Fix EAPI=4 usage, don't mix CFLAGS/CXXFLAGS, respect LD
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-physics/root: fix bug 408987
++  * [dev-libs/fortrancl] version bump
++  * Merge branch 'master' of github.com:gentoo-science/sci
++  * [dev-python/Forthon] re-add as it is now released under BSD terms
++  * sci-physics/root: version bump
++  * [dev-python/Forthon] re-add as it is now released under BSD terms
++  * sci-physics/root: version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * media-gfx/librecad: version bumped 2.0.0_alpha2
++  * media-gfx/librecad: version bumped to 1.0.0_alpha2
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-libs/hdf5] snapshot bump
++  * [sci-libs/amdlibm] drop old, fix manifest
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/bigdft & sci-physics/abinit clean-up after sci-physics/abinit version bump to 6.12.2 and tests
++  * [dev-ml/zarith] version bump
++  * [dev-ml/lacaml] moved to new oasis eclass
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * correct URI for icons
++  * Add new icon files provided by Ramiro Téllez Sanz
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * Import tree changes
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * media-gfx/brlcad: file cleanup
++  * media-gfx/brlcad: added a missing patch
++  * media-gfx/brlcad: added missing patch
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * Fix patches to be in line with tree
++  * Correct usage of python.eclass
++  * New addition, written by me, #406401
++  * [dev-cpp/eigen] Added 3.1.0_alpha2 version. Uncomplete lapack implementation.
++  * [sci-libs/atlas] Version bump.
++  * Fixes bug #405455, again
++  * Fixes bug #405455, again
++  * Fixes bug #405455, again
++  * [sci-libs/openblas] Updated patch and removed useless and unclear ewarn.
++  * [sci-libs/openblas] First stable version.
++  * using PATCHES variable instead of epatch
++  * sci-physics/root: fix Manifest
++  * sci-physics/root: switch to virtual/shadow
++  * [sci-libs/hdf5] add developement snapshot
++  * sci-physics/abinit-6.12.1 fortran setup improvement corrected, gui preparation corrected
++  * sci-physics/abinit metadata updated (libabinit USE flag), sci-physics/abinit-6.12.1 fortran setup improved
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * Version Bump
++  * [sci-libs/amdlibm] version bump wrt #405803 by Matthias Dahl <ua_gentoo_bugzilla@binary-island.eu>
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * fix manifest
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Bump intel compiler suite
++  * New package, ebuild written by me
++  * sci-libs/bigdft-1.6.0 corrected, sci-physics/abinit-6.12.1 added and moved to autotools-utils, sci-libs/bigdft-1.6_pre1 it depends on added. Old versions of bigdft needed by old versions of abinit ressurected.
++  * version bump
++  * sci-physics/root: updave live ebuild
++  * sci-physics/root: bug fix for #406817
++  * New addition, written by me, #408995
++  * This version and newer is in the tree
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * pandas: bump to 0.7.2.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-libs/amdlibm] remove SRC_URI wrt #405803, add valid 'amdlibm' license (copied to txt from pdf)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/frama-c: fix install with doc USE flag
++  * dev-libs/simclist: version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/atlas: Version bump
++  * sci-libs/openblas: Version bump
++  * Drop gl and test patch -> included upstream
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/mosaik: masking mosaik-2.1.33 mosaik-9999
++  * Merge github.com:gentoo-science/sci
++  * Add a band aid to eselect's alternative2 framework for prefix
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/sra_sdk-2.1.9: added missing insinto
++  * Final fixes for OS X in gotoblas2
++  * correct small error
++  * switch to multilib in openblas, gotoblas2 will come later as it needs another fix
++  * [net-misc/dhcp] Import more patches to make also client work
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/sra_sdk-2.1.9: use EAPI=4 hoping it will handle symlinks in bin/ and lib/ directories properly (but it does not, bug #408199
++  * [net-misc/dhcp] Import patches from F17
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sys-cluster/blcr: added ' || die' calls
++  * [sci-mathematics/polymake] add missing metadata.xml
++  * [net-misc/dhcp] once again
++  * [net-misc/dhcp] once again
++  * [net-misc/dhcp] wrong one =D
++  * [net-misc/dhcp] Opps fix patch
++  * [net-misc/dhcp] Enable infiniband in new version
++  * sci-biology/mosaik: version bump for 2.1.33 and GIT HEAD, neither compiles so far; upstream re-contacted
++  * version bump, added the pdf documentation to SRC_URI, the compile process leaks through many 'Fastq.cpp:224: error: conditional expression between distinct pointer types 'gzFile_s*' and 'FILE*' lacks a cast' messages in Fastq.cpp:224, Fastq.cpp:226, Fasta.cpp:258, Fasta.cpp:260, Fasta.cpp:266, Fasta.cpp:268, but the package itself installs and executes at least
++  * Merge branch 'polymake' of https://github.com/burcin/sci
++  * add *-macos prefix support to gotblas2
++  * Add *-macos prefix support to openblas
++  * Remove old polybori ebuild from the tree. Get new stuff from sage-on-gentoo
++  * Make sci-mathematics/polymake work with gentoo-prefix.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-visualization/gnuplot: clean up
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/mumps: Fixed for sequential (non mpi) libraries
++  * sci-libs/scalapack: remove mpi from pc file
++  * sci-libs/mumps: only allow earlier metis versions
++  * sci-libs/scotch: added 64bits integer flag and described the tools flag
++  * sci-libs/parmetis: added 64bits integer and double precision flags
++  * masked parmetis-4
++  * imported mumps
++  * [sci-chemistry/simpson] fix metadata.xml wrt bug 407877 by Patrick Lauer <patrick@getnoo.org>
++  * sci-libs/parmetis: bump
++  * sci-libs/scotch bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-physics/root: add live ebuild
++  * sci-physics/root: fix llvm support
++  * sci-physics/root: version bump and bugfix
++  * sys-cluster/blcr: update SRC_HOME, SRC_URI and added a check for kernel version <2.6.30, resp. <2.6.38, a version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [dev-python/pysolar] version bump
++  * sci-libs/lemon: shortened DESCR line
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Removed maintainer, as herd is enough
++  * Enable all fortran with single USE flag, fix license.
++  * fixed petsc 3.1 ebuild (missing patch files)
++  * disabled imagemagick, fixed lib configuring
++  * moved comments out of the argument list
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * sci-mathematics/petsc: more cleaning
++  * fix missing linking if hypre and superlu enabled
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * added superlu on activated hypre flag
++  * got sparse flag working
++  * disabled non-working dependencies
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * Moved to tree
++  * moved to tree
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * fixed undefined reference when using afterimage
++  * Moved to tree
++  * Block pypy usage
++  * Added sci-libs/libsufr-0.3.2
++  * removed obsolete call to env-update
++  * reworked fortran and openmp support
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * sci-chemistry/ambertools: Add another buffer overflow patch
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * fixed disable X option and use deps
++  * sci-chemistry/ambertools: Add bugfixes 22-27
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * sci-libs/lemon: added a note how to eventually create a shared library
++  * added optional boost and afterimage dep
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * sci-libs/inchi: Version bump, new licence
++  * further simplification, added more optional deps
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * fixed banned dosed, added more comments
++  * reworked configure function
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * sci-biology/cutadapt: new package
++  * sci-biology/phylobayes: new package, no explicit LICENSE stated
++  * sci-biology/phylobayes: new package, no explicit LICENSE stated
++  * sci-biology/cufflinks: new package
++  * sci-libs/lemon: new package, required by sci-biology/cufflinks
++  * [media-gfx/PhiloGL] version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [dev-ml/zarith] new ebuild
++  * [dev-ml/lacaml] version bump
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * added new petsc 3.2-p6 ebuild
++  * Update deps in M2 live ebuild
++  * sci-physics/root: fix repoman warning
++  * sci-physics/root: version bump
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * [sci-libs/fgsl] add prefix love
++  * updated Manifest
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * [app-benchmarks/numbench] Updated live ebuild.
++  * [app-benchmarks/numbench] Version 0.2_beta1.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * sci-biology/sra_sdk-2.1.9: remove trailing whitespace
++  * sci-biology/sra_sdk-2.1.9: almost working ebuild
++  * sci-biology/gbrowse-2.48: added dependency on <=sci-biology/primer3-2, per http://generic-model-organism-system-database.450254.n5.nabble.com/PrimerDesigner-working-in-2-40-tp4724773p5479669.html
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * fixed hypre dependency
++  * sci-physics/root: fix build on non-english locales
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; github.com:gentoo-science/sci
++  * [dev-lang/path64] add use.flag description
++  * Commit package.mask as well, was missing in last commit
++  * Dropped eapi again, zmedico: you don't need EAPI 4-python, when the ::repo is implied rather than explicit; masked sci-bioligy/amboss as well
++  * Correct masking, thanks zmedico for help, bump EAPI to 4-python
++  * Cleaned old patches, added goocanvas config option
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * [dev-lang/path64] update metadata.xml
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * sci-libs/plasma: fixed some as-needed issues
++  * sci-libs/plasma: Initial import
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * making cblas-reference OS X aware
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * sci-libs/gsl: Fixed gsl-config/pkg-config issues
++  * sci-libs/atlas: Version bump
++  * app-doc/scalapack-docs: Bumping to match scalapack-2 which include blacs quick reference sheets
++  * sci-libs/mpiblacs: Removed old, blocking scalapack > 2
++  * sci-libs/scalapack: Version bump. CMake based building, BLACS is now included with ScaLAPACK
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * Correct usage of autotools-eclass, prevents double call of elibtoolize
++  * Keyworded for ~-linux prefix
++  * Keyworded for ~-linux prefix
++  * Keyworded for ~-linux prefix
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Keyworded for ~-linux prefix
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * Workaround file collision, #404257
++  * intermidiate commit
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-libs/mpiblacs] Install blacs headers.
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * sci-libs/atlas: Reverted to older lapack
++  * Correct masking syntax
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Mask all emboss and embassy packages from overlay
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [dev-python/dimensionful] initial import, ebuild written by me
++  * [sci-libs/atlas] correct Manifest
++  * Fix for current HEAD, correct desktop entry generation
++  * Drop Keywords from live version
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Move to EAPI=4 and autotools-util.eclass
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * fixed manifest
++  * sci-libs/lapacke-reference: Fixed pkg-config
++  * sci-libs/lapack-reference: Fixed pkg-config
++  * sci-libs/blas-reference: Fixed pkg-config
++  * [media-gfx/PhiloGL] don't mess with paths and follow upstream as close as possible
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * eapi4 goodness
++  * sci-libs/ipp: Bump
++  * add units
++  * sci-libs/mkl: Version bump
++  * dev-lang/idb: Version bump
++  * dev-lang/ifc: Version bump
++  * dev-lang/icc: Version bump
++  * dev-libs/intel-common: Version bump
++  * [media-gfx/PhiloGL] Initial import, ebuild written by me
++  * Remove Forthon until legal issues are cleared
++  * [dev-python/Forthon] initial import, ebuild written by me
++  * sci-libs/atlas: bump
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * sci-libs/lapacke-reference: bump, with home patches
++  * sci-libs/lapack-reference: bump, with home patches
++  * sci-libs/blas-reference: bump, with home patches
++  * Drop python herd from remaining packages
++  * Remove python herd from metadata per djc request
++  * Fix for HEAD
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * Update to latest head
++  * in main tree
++  * app-admin/eselect: sync with tree
++  * sci-libs/libsufr: added ebuild for new version 0.3.1
++  * sci-chemistry/gromacs: clean up
++  * media-gfx/brlcad: removed old version
++  * sci-chemistry/gromacs: fixed threads and mpi
++  * media-gfx/brlcad: fixed as-needed filtering
++  * [dev-cpp/eigen] version bump.
++  * [dev-python/coards] also fix this in similar way
++  * [sci-misc/salome*] Fix python depend
++  * [metadata] Enable git signed commits
++  * Moved to autotools-utils, some more sanity
++  * Remove double prefix
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Add this nasty binary package
++  * dev-perl/Bio-DB-Das-Chado-0.32: added the LICENSE line and require DBD-Pg to be installed before compiling this packge
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * dev-perl/Bio-BigFile: new package, initial ebuild, see bug #402835
++  * some clean up in paraview 3.12.0
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * EROOT fix
++  * fixing a missing EROOT
++  * Fix Jon's name
++  * Bertini-1.3.1 added
++  * [sci-libs/gmsh] bump to EAPI4 for required use, removed unused call to flag-o-matic.eclass, shorten description, fix dependencies on libpng and zlib, remove redundant dependency on cmake, use PATCHES instead of calling src_unpack, mycmakeargs is now bash array, remove obsolete dies, compile doc during src_compile
++  * Added gmsh-2.5.0-r1 to work with libpng-1.5. I also removed the 'png' and 'zlib' use flage as the two libraries are hard included in upstream code
++  * [sys-cluster/scalasca] removed
++  * Paraview 3.12.0 is in. ugly right now will shape it a bit better.
++  * sci-biology/artemis: adjust ebuild based on upstream providing a Makefile
++  * sci-biology/artemis: adjust ebuild based on upstream providing a Makefile
++  * sci-biology/apollo: new package
++  * sci-biology/tablet-bin: adjust PATH to point to the installation place
++  * adjust PATH to point to the installation place, few comment lines changes
++  * sci-biology/tablet-bin-1.11.11.01: make use of the TMPDIR variable
++  * added the addpredict() trick from tablet-bin*.ebuild to make the ACCESS DENIED messages quiet, bugs #402507 (learned from bug #387227)
++  * added the addpredict() trick from tablet-bin*.ebuild to make the ACCESS DENIED messages quiet, bugs #402507 (learned from bug #387227)
++  * sci-biology/OBO-Edit: more attempts to get rid of sandbox ACCESS VIOLATION SUMMARY errors
++  * sci-biology/OBO-Edit: more attempts to get rid of sandbox ACCESS VIOLATION SUMMARY errors
++  * sci-biology-sra_sdk-2.1.9: preserve libs written directly into  at the end of src_compile() and install them later on
++  * sci-biology/sra_sdk-2.1.6: dropping an old crap
++  * two more Makefiles needed a DESTDIR patch, in conjunction with an ugly symlink hack in  one can build the stuff; dobin does not transfer symliks so every binary appears installed 3 times; upstream bug http://jira.be-md.ncbi.nlm.nih.gov/browse/TR-10207
++  * sci-mathematics/why: version bump
++  * sci-mathematics/pff: version bump
++  * sci-mathematics/ltl2ba: QA fixe
++  * sci-mathematics/giac: QA fixes
++  * sci-mathematics/gappalib-coq: version bump
++  * sci-mathematics/gappa: version bump
++  * sci-mathematics/frama-c: version bump
++  * sci-mathematics/flocq: QA Fixes
++  * sci-mathematics/apron: QA fixes
++  * dev-ml/mlgmpidl: SRC_URI now uses HTTPS
++  * dev-ml/ocamlgraph: version bump
++  * sci-biology/sra_sdk-2.1.9: version bump and almost correct DESTDIR patch
++  * handle new vmd detection
++  * media-gfx/brlcad: version bumped 7.20.4
++  * media-gfx/librecad: version bumped to 1.0.1
++  * added openmp support
++  * Adding kash (binary version only)
++  * Add kash licence
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [zfs,spl] They are in tree already
++  * updated eselect dependency
++  * sci-biology/seaview: and the path to the helpfile was corrected in the Makefile to match intended location specified in ebuild
++  * sci-biology/seaview: version bump; add missing symlink so that the C++ header can be found; remove calll to xft-config and use pkg-config instead; set our Gentoo FLTK path (not include path) to /usr/include/fltk-1 so that svg.o gets included during linking, otherwise we get undefined reference to svg_tree_save(FD_nj_plot*)
++  * Added first ebuild for k3match, version 1.0
++  * Updated Manifest for ndiff-2.00
++  * Added an ebuild for ndiff-2.00
++  * sync with tree and bug #400999#c7
++  * sci-biology/wgs-assembler-7.0: version bump, would be nice if we could stop compilation of the kmer/ subdir (an r1916 snapshot) and DEPEND on the external http://kmer.sourceforge.net complete bundle instead
++  * updated package.mask
++  * version bump
++  * sci-libs/lapack-reference: Version bump
++  * sci-libs/blas-reference: Version bump
++  * [sci-visualization/yt] update deps, add pyx remove zlib
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/acml: Version bump
++  * sci-libs/lapackpp: Version bump
++  * Dropped DOCS as it is handled by default
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * CCP4 upstream took over the real maintance
++  * sci-libs/atlas: Version bump
++  * switched to main tree hypre
++  * now in main tree
++  * app-admin/eselect: merge with main tree
++  * [sci-visualization/labplot] Add live ebuild
++  * sci-physics/root: fix Manifest
++  * sci-physics/root: fix cfitsio linking
++  * cleanup xrootd removal
++  * [dev-java/flexdock] version bump
++  * [dev-python/astlib] Version bump, drop old
++  * version bump and some fixes so that it works with webappconfig again?
++  * [sci-visualization/yt] initial import, ebuild written by me
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * New addition
++  * sci-biology/lastz: A pairwise DNA sequence aligner (also chromosome to chromosome), a BLASTZ replacement
++  * sci-biology/YASRA: Yet Another Short Read Assembler to reference using LASTZ
++  * sci-biology/gbrowse: added dev-perl/TermReadKey to dependencies
++  * sci-biology/libgtextutils: Gordon text utils library
++  * [dev-libs/fortrancl] initial import, ebuild written by me
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Call python_pkg_setup always
++  * Convert to thin manifests (as suggested by alexxy and jlec)
++  * Removed because the sources cannot be fetched
++  * Removed because the file is non-fetchable
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * tweaks to mpich2
++  * mpich2:  add link to upstream report
++  * Now in main tree
++  * Move sci-misc/simpy -> dev-python/simpy
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Version Bump
++  * Remove patch, fixed upstream
++  * Drop failing tests for now, fix #393361
++  * Version bump
++  * Bumped EAPI to 4 and added new eautoreconf handling of autotools-utils.eclass
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Fix double installation of spectrum.h
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/artemis-bin: DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool
++  * sci-biology/artemis: DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * dev-python/GOGrapher: more robust version from same author is at https://github.com/ntamas/biopython/blob/gosupport which is a rewrite of https://github.com/gotgenes/biopython
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/manatee-igs: new package for prokaryotic genome annotation and editing using chado
++  * sci-biology/manatee-igs: new package for prokaryotic genome annotation and editing using chado
++  * dev-perl/Log-Cabin: new package, required by sci-biology/manatee-igs
++  * Bumped to new upstream repo uri
++  * Drop double call of emake in src_configure
++  * Bumped to new upstream repo uri
++  * New package, ebuild written by me
++  * in main tree
++  * now in main tree
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * moved to tree
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Version Bump, #373679
++  * Added DEP on dev-python/simpy
++  * CAT move for simpy package
++  * Add missing fortran support
++  * Initial commit
++  * blas svn
++  * switch sci herd to sci-* sub herds, full overlay re-manifest
++  * plplot-5.9.9 compatibility
++  * move dependency for xrootd from main tree
++  * move dependency for xrootd from main tree
++  * move dependency for xrootd from main tree
++  * nco in tree
++  * documented status of go-parser (as a very simple implementation) which should be dropped once its successor code get into biopython
++  * dev-python/go-parser: a Gene Ontology OBO file format parser
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Sync ebuild to use install4j as in sci-biology/tablet-bin. Awaiting a fix from upstream so that the installer really respects --destination or -dir options.
++  * sci-chemistry/nmrpipe: Remove dep on xview
++  * sci-chemistry/nmrpipe: Always use bundled xview
++  * sci-mathematics/scilab-5.3.3 fixes for jdk-1.7
++  * Fix digest
++  * [dev-java/flexdock] version bump to 1.1
++  * Version Bump
++  * eigen: version bump
++  * New package, ebuild written by me
++  * New package, ebuild written by me
++  * sci-physics/atompaw2abinit-3.3.0-r1.ebuild reflects the new structure of the abinit web
++  * media-gfx/brlcad: use system libraries for svn version
++  * media-gfx/brlcad: version bumped to 7.20.4
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/libxc-1.1.0-r1 forces compilation with -fPIC for sci-physics/atompaw-3.0.1.3 not to complain
++  * sci-physics/root: fix clarens dependency
++  * sci-phzsics/elk Manifest broken by mistake, now corrected
++  * media-gfx/librecad: version bumped to 1.0.0
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-physics/elk adapted to accept sci-libs/libxc-1.1.0 and upgraded to 1.4.5
++  * sci-physics/abinit updated to 6.10.3, sci-libs/bigdft to 1.2.0.5, and sci-libs/libxc to 1.1.0
++  * sci-geosciences/xtide: Moved the setting of the HFILE_PATH environment variable back to the xtide ebuild.  Made HFILE_PATH point to a standard directory /usr/share/harmonics.  Version bump to install xtide with new HFILE_PATH and all dependencies. sci-geosciences/libtcd: Version bump to reinstall dependencies. sci-geosciences/harmonics-dwf-free: Moved location of database file to /usr/share/harmonics sci-geosciences/harmonics-dwf-free-noncomm: Moved location of database file to /usr/share/harmonics
++  * media-gfx/librecad: version bump to 2.0.0_alpha1
++  * ebuild doc cleanup
++  * A seed-driven progressive assembly program
++  * sci-biology/estscan: added Manifest file
++  * added configuration.php.patch for VHOSTS setup
++  * sci-biology/est2uni: example of necessary config changes for vhosts setup
++  * removed arches for this -9999 ebuild for sanity
++  * fix determination of svn-based checkout number required for building
++  * remove offending double-quotes
++  * ebuild cleanup, works, releasing for testing
++  * fix sanbox violations on some systems
++  * added MYPV to the ebuild to make it more easily re-usable
++  * sci-physics/root: add ~x86-linux keyword
++  * sci-biology/tablet-bin: ebuild cleanup, version bump
++  * sci-biology/tablet-bin: ebuild cleanup, version bump
++  * sci-biology/tablet-bin: ebuild cleanup, version bump, #348029
++  * sci-biology/tablet-bin: ebuild cleanup, version bump
++  * sci-biology/mira: version bump
++  * sci-biology/biopython: 1.58 version bump
++  * Version Bump
++  * Fix pymol-9999-setup.py.patch for current HEAD
++  * sci-physics/root: fix afs patch
++  * sci-physics/root: new production release bump
++  * sci-physics/xrootd: unbundled package from ROOT
++  * app-doc/root-docs: version bump
++  * sci-mathematics/pulp: Initial ebuild.
++  * Another Version bump
++  * Version BUmp, added missing dep, found by louic and reported in irc
++  * New package, ebuild written by me
++  * fixed astromatic packages for recent ATLAS
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * dev-python/pandas: Version bump.
++  * [sci-physics/espresso] live ebuild update
++  * casacore now in main tree
++  * sci-physics/root: version bump
++  * + sci-geosciences/harmonics-dwf-free and + sci-geosciences/harmonics-dwf-free-noncomm: Now create /etc/env.d/50xtide_harm in both of these ebuilds which contains HFILE_PATH environment variable used by the xtide suite of programs to locate the tidal constituent databases.  Concluded that this was better suited here than in the xtide ebuild. + sci-geosciences/libtcd: Trivial change updating DEPEND to bring in the latest harmonics-dwf* versions. + sci-geosciences/xtide: Version bump.  Eliminated creation of /etc/xtide.conf by using HFILE_PATH environment variable created by the harmonics-dwf* ebuilds.
++  * Fix manifest for sci-geosciences/pydap_handlers_nca
++  * Changed my e-mail address...
++  * sci-mathematics/mdp: Version bump.
++  * sci-misc/simpy: Version bump.
++  * sci-geosciences/pydap_handlers_sqlite: Initial build.
++  * sci-geosciences/pydap_handlers_sql: Version bump.
++  * sci-geosciences/pydap_handlers_hdf5: Initial ebuild
++  * sci-geosciences/pydap_handlers_cdms: Version bump.
++  * [sci-libs/hdf5] drop old
++  * Fixed digest, #390723
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-geosciences/pydap: Version bump.
++  * Corrected Slotting of media-libs/libpng and media-libs/tiff
++  * [sci-mathematics/scilab] 5.3.3 version bump
++  * [dev-ml/lacaml] initial import
++  * openbabel-perl: Redigest
++  * Version Bump
++  * Masked sco-chemistry/nmrpipe where ever needed
++  * mask nmrpipe on multilib
++  * Fix blas + lapack for hpl
++  * openbabel-perl: Version bump to 2.3.1
++  * openbabel-python: Version bump to 2.3.1
++  * openbabel: Version bump to 2.3.1
++  * [sci-libs/libsufr] initial import
++  * sci-libs/bigdft Manifest broken by mistake, now corrected
++  * sci-physics/abinit bumped to 6.10.2, sci-physics/atompaw to 3.0.1.3
++  * lapack-docs: fix file clash with blas-docs
++  * initial commit
++  * fixed desc
++  * initial commit
++  * initial commit
++  * updated package.mask
++  * multilib support
++  * multilib support
++  * EAPI bump + multilib support
++  * live ebuild update
++  * live ebuild update
++  * live ebuild update
++  * live ebuild update
++  * Live ebuild updates
++  * Corrected email adress in ChangeLog entry
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * remanifest
++  * sci-chemistry/ambertools: Fix possible buffer overflow
++  * sci-chemistry/ambertools: Add bugfixes up to 21, other fixes
++  * Updated license
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Version Bump
++  * Removed no-herd from herd tag in metadata.xml
++  * Version Bump
++  * Removed no-herd from herd tag in metadata.xml
++  * Version Bump
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * fix usage of check-reqs.eclass Adopt changes in new intel tarball
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * Removed no-herd from herd tag in metadata.xml
++  * media-gfx/librecad: version bumped to 1.0.0_rc4
++  * fixed typo
++  * Fixed usage of check_reqs.eclass
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-physics/root: switch to EAPI 4
++  * sci-physics/root: remove old versions
++  * sci-physics/root: update to 5.30.03
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-geosciences/tappy: Version bump.
++  * Bump do fit with embassy-6.4.0
++  * [sci-libs/atlas] Version bump
++  * Fix undefined symbols because of missing gslcblas lib during linking
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * media-gfx/librecad: Cleaned up old versions
++  * In main tree
++  * sci-physics/root: 5.28.00g update
++  * [dev-cpp/eigen] Version bump
++  * Added dep on >=sys-devel/libtool-2.4-r2
++  * Moved to autotools-utils.eclass in order to have correct .a/la file handling, #385865; added png15 patch
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Add png15 support and don't build static libs
++  * media-gfx/librecad: added boost to DEPS
++  * Use virtualx.eclass
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-physics/root: version bump to 5.30.02
++  * [sci-chemistry/gromacs] added 4.6 live version
++  * updated package.mask
++  * [app-admin/eselect] Version bump
++  * sci-physics/abinit bumped to 6.8.2.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * dev-python/pandas: Initial ebuild. Pandas is a data analysis toolkit. Bug report page is https://bugs.gentoo.org/show_bug.cgi?id=384583
++  * media-gfx/brlcad: included patch for 7.20.2, bug#378273
++  * Fix live ebuild
++  * Fix tests better
++  * Use Fedora hosting because unpstream removed the patches
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/sra_sdk-2.1.6: adjust to altered source tree strcuture, add weird ncbi/ subdirs to be installed, more comments in the ebuild
++  * sci-biology/sra_sdk-2.1.6: version bump
++  * media-gfx/librecad: fixed a missing file
++  * media-gfx/librecad: fixed manifests
++  * [sci-mathematics/scilab] install scilab mimetype
++  * Updated to new revision scheme
++  * Download tarballs with package revision
++  * Silent upstream bump
++  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci
++  * media-gfx/librecad: version bump to 1.0.0_rc3
++  * [sci-libs/scilab] Various fixes
++  * [sci-libs/openmm] version 2.0 is not supported by upstream anymore
++  * [sci-libs/xdrfile] removed it was never really stable
++  * [sci-libs/nfft] updated metadata
++  * [dev-tex/picins] not needed by gnuplot anymore
++  * [sys-cluster/nullmpi] updated metadata
++  * Add $(use_enable debug) on request from mgorny
++  * [dev-python/astlib] bump
++  * update pest manifest (changelog wasn't matching)
++  * sci-mathematics/pest - Version bump to 12.2.
++  * [sci-libs/pfft] version bump
++  * media-gfx/librecad: fixed manifests
++  * removed unneeded entries to blas-reference
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Version bump with new buildsystem
++  * [sci-chemistry/votca-csg] remove obsolete bash-completion_pkg_postinst
++  * [sci-chemistry/votca-csg] Migrate to the bash-completion-r1 eclass
++  * [sci-chemistry/gromacs] Migrate to the bash-completion-r1 eclass
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * moved to new release download link and version bump, documented that included JsonCPP is a modified version
++  * media-gfx/librecad: remove qt3support dependency
++  * update pest manifest
++  * Point to current HOMEPAGE
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * updated dependencies
++  * upgrade version
++  * [app-admin/eselect] Fix manifest
++  * prefix fix and number update
++  * updated eselect dependency
++  * bump
++  * bump
++  * bump
++  * Version bump.
++  * [sci-chemistry/votca-csg] updates
++  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci
++  * media-gfx/librecad: qt3support not needed anymore
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Initial commit
++  * [sci-libs/wannier90] Fix blas stuff
++  * sci-mathematics/htk: metadata cleanup
++  * sci-mathematics/htk: fixed license filenames
++  * sci-mathematics/htk: new package, #245595
++  * media-gfx/librecad: more cleanup for metadata
++  * media-gfx/librecad: updated metadata
++  * [sys-infiniband/librxe] Add sw driver for roce
++  * [sci-libs/fftw] in tree
++  * Moved to tree
++  * In the tree
++  * Version Bump
++  * Latest changes on HEAD
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Corrected doc installation, thanks James Cloos for the fix
++  * Version bump.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-chemistry/votca-csgapps] use default instead of tip
++  * [sci-chemistry/votca-csg-tutorials] use default instead of tip
++  * [app-doc/votca-csg-manual] use default instead of tip
++  * Cleaned up ebuild
++  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci
++  * media-gfx/librecad: ebuild cleanup for 1.0.0_rc2
++  * [app-doc/votca-csg-manual] fixed deps
++  * >sci-libs/blas-reference-20
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-chemistry/votca-csgapps] fixed a typo
++  * [sci-chemistry/votca-csg] changes due to 1.2.1 release
++  * sci-chemistry/votca-csg-apps -> sci-chemistry/votca-csgapps
++  * sci-chemistry/votca-csg-apps -> sci-chemistry/votca-csgapps
++  * sci-chemistry/votca-csg-apps -> sci-chemistry/votca-csgapps
++  * [virtual] Add ~amd64-linux keywords
++  * sci-physics/root: version bump
++  * [sci-visualization/paraview] Drop old, fix building with gcc-4.6, add missing dependency on PyQt4
++  * adding old blas to properly mask
++  * mask blas-reference from tree
++  * fix manifest
++  * added num library docs
++  * added virtuals
++  * added gsl
++  * added mpiblacs
++  * added xblas
++  * added cblas-reference
++  * added mkl
++  * added lapacke
++  * added acml
++  * added gotoblas2
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * In main tree
++  * updated package.mask
++  * [sci-libs/fftw] version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Keywork-mask eigen-9999.
++  * Added svn version for lapack-reference.
++  * Fix Manifest.
++  * Added blas-reference form bicatali overlay.
++  * Added lapack-reference from bicatali overlay.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Added eigen-3.0.1-r2.
++  * Added eigen-9999.
++  * media-gfx/librecad: ebuild cleanup for 9999 version
++  * media-gfx/brlcad: fixed building issue for 9999 svn live build
++  * Fixed patches
++  * Fix manifest
++  * fixed pkgconfig cflags
++  * correct pkgconfig in openblas
++  * Updated manifest for numbench.
++  * numbench now uses distutils.
++  * media-gfx/brlcad: removed cmake version for 7.20.2
++  * media-gfx/brlcad: removed cmake ebuild for 7.20.2
++  * sci-mathematics/acl2: fixed broken git merge
++  * sci-mathematics/acl2: fixed manifest
++  * sci-mathematics/acl2: updated metadata
++  * [dev-python/numscons] obsolete
++  * [sys-cluster/openmpi] redundant cd ${S} statement on line
++  * [dev-java/vecmath] Useless blank line on last line
++  * [dev-java/hdf-java] Trailing whitespace
++  * Remove unused local USE-description: 'xblas'
++  * fix metadata
++  * fix metadata
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Cleaned ebuilds
++  * media-gfx/brlcad: allow using of system tcl/tk
++  * [dev-lang/path64] Apply fix for bug #377111, use direct path for crt1.o
++  * Added sample configuration files to numbench.
++  * [sci-chemistry/votca-csg] renamed boost useflag
++  * [sci-libs/votca-tools] renamed boost useflag
++  * Updated numbench.
++  * [sys-cluster/openmpi] Add slurm support by Nicolas Bigaouette <nbigaouette@gmail.com>
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Update use.local.desc
++  * Fix categories
++  * [sys-cluster/open-mx] Add different mtu support
++  * [sys-cluster/open-mx] Add new version of open-mx
++  * Masked live builds, librecad and brlcad
++  * media-gfx/brlcad: fixed libpng-1.5, added version 9999 back
++  * media-gfx/brlcad: No need to include cmake in deps
++  * manifest
++  * adjusting boehm-gc source file
++  * [sci-visualization/gri] newer version in tree
++  * round of manifest
++  * [app-admin/eselect] Add prefix ~amd64-linux
++  * [sci-libs/atlas] Add prefix ~amd64-linux
++  * numbench depends on btl
++  * Added BTL.
++  * Restored atlas-3.8.4 from bicatali.
++  * Version bump atlas
++  * updating skel files
++  * manifest
++  * cleaning
++  * [sci-astronomy/weightwatcher] switch herd
++  * [sci-astronomy/stuff] switch herd
++  * [sci-astronomy/skymaker] switch herd
++  * [sci-astronomy/psfex] switch herd
++  * [sci-astronomy/missfits] switch herd
++  * [sci-astronomy/eye] switch herd
++  * [sci-astronomy/casacore] switch herd
++  * [dev-python/pysolar] switch herd
++  * [dev-python/cosmocalc] switch herd
++  * [dev-python/coords] switch herd
++  * [dev-python/astropysics] switch herd
++  * [dev-python/astlib] switch herd
++  * [dev-python/asciidata] switch herd
++  * Dependency to eselect updated.
++  * Added versioned openblas. Import from the bicatali overlay.
++  * Version bump. atlas imported from the bicatali overlay.
++  * alternatives-2 imported from bicatali and intel-sdp corrected
++  * eselect-1.2.16-r1 imported from the bicatali overlay
++  * autobench renamed to numbench to avoid conflicts.
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * [media-libs/OpenMOIV] Initial import per bug #239321
++  * Use rpath if prefix is enabled.
++  * Version bump, see bug 374859.
++  * Fix commiter information in the ChangeLog
++  * Version bump based on bug 374709.
++  * New package
++  * Revert "New package"
++  * New package
++  * Make sure portage does not run gbrowse_metadb_config.pl otherwise sandbox violation occurs when modifying /var/www/gbrowse2/databases/users.sqlite* file, maybe we could copy these during src_install to the {}, fix there and copy back to live filesystem? Improve error handling in gbrowse_metadb_config.pl. Fix symlink creation during install procedure.
++  * sci-biology/gbrowse: add missing brackets cause a perl error while exporting a PNG image
++  * sci-biology/gbrowse: fix typo in an ewarn() message
++  * sci-biology/gbrowse: fix typo in an ewarn() message
++  * sci-biology/gbrowse: added support for --destdir, patch sent to upstream
++  * sci-biology/go-db-perl to dev-perl/go-db-perl move
++  * sci-biology/go-db-perl to dev-perl/go-db-perl move
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * backbone of a new package, should probably use a lot of stuff from ncbi-tools++ ebuild
++  * msms: build with 3.x kernels.
++  * update Manifest checksums
++  * backbone of a new package, should probably use a lot of stuff from ncbi-tools++ ebuild
++  * some ebuild cleanup
++  * sci-biology/est2uni: pushing out more patches albeit ugly
++  * version bump but still need to rewrite upstream's install procedure to prevent 'mkdir /var/lib/gbrowse2' from happening
++  * dev-perl/Bio-DB-Das-Chado: new package required by sci-biology/gbrowse
++  * [sci-physics/fastjet] general QA
++  * sci-physics/fastjet: No need to enable plugins individually
++  * sci-physics/fastjet: Added maintainer
++  * sci-physics/fastjet: new package, #375575
++  * [dev-lang/path64] move snapshot to g-x86
++  * Add script for generating path64 snapshots
++  * Mask live version of path64
++  * Moved to tree
++  * [sci-chemistry/acpype] Initial import
++  * [dev-lang/path64] Fix SRC_URI for snapshot
++  * [dev-lang/path64] Add snapshot
++  * Also moved to tree
++  * [sci-chemistry/ambertools] Moved to tree =D
++  * [sci-chemistry/ambertools] Update patch
++  * [sci-chemistry/ambertools] Fix typo
++  * [sci-chemistry/ambertools] Updates for ambertools and gcc-4.6
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Add missing LDPATH to env file
++  * now in main tree
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Removed lpsolve, better version is in tree.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Fixed Manifest
++  * [dev-lang/path64] Add valgrind IUSE for debugging
++  * Move dev-lang/ekopath-bin to dev-lang/ekopath
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [dev-lang/path64] Unset all env vars that may cause trouble, prevent stripping source when build with Release, clean up
++  * Migrating gap-guava from s-o-g to sci: an example of gap package.
++  * Addd package.use.mask. Mask dev-lang/path64[assembler]
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [dev-lang/path64] Change lib -> get_libdir
++  * [dev-lang/path64] gcc:4.2 is no longer a strict dep
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [dev-lang/path64] Unset all fortran vars
++  * [dev-lang/path64] Fix fortran specific env handling
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [dev-lang/path64] Add env file
++  * [dev-lang/path64] Promote native to prefereed, add assembler flag (not working at the moment), remove needless dep on gcc for native
++  * Grap some fedora stuff, fix shadrers patch for current head
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [dev-lang/path64] Add fortran,openmp,debugger to IUSE
++  * [dev-lang/path64] Add native use flag for release build
++  * [dev-lang/path64] Initial import, only debug version (compiled with gcc) is working now
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-chemistry/gromacs] sync with tree
++  * [eclass] Moved cmake-utils.eclass to main tree
++  * [dev-util/cmake] Moved to main tree
++  * Improve variables names
++  * Improve variable names
++  * cmake should of course install all modules
++  * Actually make it possible to disable the module removal
++  * Fix missing bracket
++  * Move module removal into configure phase (otherwise it might never be called), no src_prepare again
++  * Same magic for LAPACK
++  * Same magic for LAPACK
++  * Add CMAKE_REMOVE_MODULES feature
++  * Copied eclass from main tree
++  * Patch FindBLAS to prefer PkgConfig over all tests, for the sci guys
++  * [sci-chemistry/votca-csg] Added IUSE=extras
++  * [sci-chemistry/votca-csg-apps] initial commit
++  * added sci-chemistry/votca-csg-apps to package.mask
++  * [sci-chemistry/votca-csg] Added IUSE=examples
++  * [sci-chemistry/votca-csg-tutorials] initial commit
++  * added votca-csg-tutorial to package.mask
++  * Install demos through USE=examples, #374187
++  * Adopt to unbundled ssm
++  * inCvs
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * libssm bump
++  * sci-geosciences/cdat-lite: Version bump.
++  * Updated SRC_URI
++  * Clean up - old version that I renamed, but git didn't delete.
++  * sci-geosciences/swmm: Version bump.
++  * sci-mathematics/mdp: Version bump and added all supported Python versions.
++  * Mmdb fix
++  * media-gfx/brlcad: Fixed a config time error when building
++  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci
++  * media-gfx/brlcad: Added back virtual/jre deps
++  * [dev-python/astropysics] Update dependencies, move to git repo
++  * media-gfx/brlcad: folder cleanup
++  * media-gfx/brlcad: Switch to cmake as supported by upstream
++  * [sys-cluster/open-mx] Update init.d
++  * [sys-cluster/open-mx] Update init.d
++  * [sys-cluster/open-mx] Update init.d
++  * [sys-cluster/open-mx] Update init.d
++  * [sys-cluster/open-mx] Initial import
++  * Update ocfs2
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * Update ocfs2
++  * app-benchmarks/autobench imported from proj/auto-numerical-bench.
++  * Autobench imported from proj/auto-numerical-bench
++  * media-gfx/brlcad: version bump to 7.20.2
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Moved to tree
++  * [sci-chemistry/icm] Version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Restored the MPI support in sci-libs/bigdft-1.2.0.2, broken by the introduction of the fortran-2.eclass.
++  * sci-biology/gbrowse-2.38: added URL to Bio::DB::Sam
++  * sci-biology/staden: Documented that we have to install somehow /usr/share/doc/staden/manual/gap4.index which is looked up when user accesses built-in help menu item
++  * sci-biology/gbrowse-2.38: Documented dependency on >=perl-gcpan/Text-ParseWords-3.27, documented requirement of Bio::Root::Version >= 1.0069
++  * Removed old version and fixed deps of live version
++  * Removing long old version of normaliz
++  * sci-mathematics/acl2: updated ChangeLog
++  * sci-mathematics/acl2: version bump to 4.3
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Version Bump
++  * sci-biology/mira-3.2.1.20: version bump
++  * Moved to tree
++  * Update gentoo defconfig
++  * Fix permissions
++  * Enable maui support
++  * Add maui with slurm and pbs integration
++  * [slurm] one more update to init.d
++  * Fix typo
++  * Update init.d
++  * Fix order
++  * Add init.d and conf.d files
++  * Fix cgroup location
++  * Also install sample config files
++  * Fix collisions with mpi implentations
++  * Enable pbs compatibility
++  * More cleaning
++  * use eapi4 feature
++  * s/contrib/contribs/
++  * Enable pam module
++  * Another typo with hwloc
++  * Another typo with pam
++  * Fix typo =D
++  * [sys-cluster/slurm] Initial import
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * formated skel-metadata.xml
++  * Metadata for sci-physics/elk added to appease repoman.
++  * New ebuild sci-physics/elk-1.3.15 added (a GPL-3 all-electron FP-LAPW code, used for example by sci-physics/abinit developers for comparison).
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Fix manifest
++  * Drop old OFED
++  * [sys-cluster/mvapich2] Update to eapi4
++  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci
++  * Moved to tree
++  * Keep old stuff here for some time
++  * media-gfx/librecad: QA cleanup
++  * [sys-infiniband/srptools] Fix ofed suffix
++  * [sys-infiniband/openib] add srp tools use
++  * [sys-infiniband/srptools] Add x86 keyword for srptools
++  * [sys-infiniband/perftest] Some docs doesnt exist
++  * [sys-infiniband/libmlx4] Tarball doesnt have changelog
++  * [sys-infiniband] Fix unapck logic
++  * [eclass] Fix unpack logic
++  * [eclass] add missing inherit
++  * [eclass] Update OFED eclass
++  * [eclass,profiles] Updates to ib stuff
++  * [sys-infiniband] Updates to infiniband stuff
++  * [sys-cluster/mvapich2] Move and version bump for mvapich2
++  * [virtual/mpi] Update virtual mpi
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [scilab-5.3.2] fixed xcos dependency
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci into guillaume
++  * [media-gfx/librecad]: upgraded to EAPI=4
++  * test
++  * [sys-cluster/ganglia_jobmonarch] Dont need to compile
++  * [sys-cluster/ganglia_jobmonarch] Drop unneded patch
++  * [sys-cluster/ganglia_jobmonarch] Import per bug #297587
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Yet another quick version bump, no improvement to the ebuild. Compiles well for me but has problems testing. The fault may be just in my openmpi installation but use with caution.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Imported changes from tree
++  * Restored the support for threaded fftw. Works for me. NEVER DISABLE FEATURES FOR OTHERS.
++  * [sci-mathematics/scilab] fix patch name wrt bug 237572#c218
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Version Bump
++  * [sci-chemistry/jmol] Fix manifest
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Cleanup
++  * Manifest
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Latest version.
++  * Version Bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Cleaned ebuild
++  * Cleaned ebuild
++  * Cleaned ebuild
++  * Cleaned ebuild
++  * migrate from 'git' to 'git-2'
++  * Cleaned ebuild
++  * Cleaned ebuild
++  * Cleaned ebuild
++  * Cleaned ebuild
++  * Cleaned ebuild
++  * Cleaned ebuild
++  * Version Bump
++  * Version Bump
++  * removed .#Manifest.1.21
++  * Cleaned ebuild, unused local USE-description
++  * migrate from 'git' to 'git-2'
++  * Fixed Malformed CVS Header on line: 3
++  * Fixed dep on openfoam
++  * no non-qt3 build available
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * migrate from 'git' to 'git-2'
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * migrate from 'git' to 'git-2'
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * Cleaned ebuild
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035
++  * Cleaned ebuild
++  * Cleaned ebuild
++  * Cleaned ebuild
++  * mv 0.1-build.patch 110625-build.patch
++  * Cleaned ebuild
++  * Cleaned ebuild
++  * Cleaned ebuild, 'http://search.cpan.org/CPAN' found in thirdpartymirrors
++  * Cleaned ebuild
++  * Cleaned ebuild, 'http://search.cpan.org/CPAN' found in thirdpartymirrors
++  * Cleaned ebuild
++  * Cleaned ebuild,  no eauto* function called
++  * Cleaned ebuild, unused local USE-description: 'plplot'
++  * empty dir
++  * 'http://pypi.python.org/packages/source' found in thirdpartymirrors
++  * 'http://pypi.python.org/packages/source' found in thirdpartymirrors
++  * 'http://pypi.python.org/packages/source' found in thirdpartymirrors
++  * Dropped keywords because deps are missing
++  * Fixed malformat CVS line in header
++  * migrate from 'git' to 'git-2'
++  * migrate from 'git' to 'git-2'
++  * RDEPEND is not explicitly assigned -> fixed
++  * migrate from 'git' to 'git-2'
++  * RDEPEND is not explicitly assigned -> fixed
++  * RDEPEND is not explicitly assigned -> fixed
++  * RDEPEND is not explicitly assigned -> fixed
++  * RDEPEND is not explicitly assigned -> fixed
++  * RDEPEND is not explicitly assigned -> fixed
++  * RDEPEND is not explicitly assigned -> fixed
++  * Version Bump, cleaned old
++  * Version Bump, cleaned old
++  * Cleaned ebuild
++  * Cleaned repoman issues, don't know if ebuild is still working
++  * Cleaned ebuild and fixed LICENSE
++  * Cleaned ebuild and fixed LICENSE
++  * [sys-cluster/nullmpi] migrate to git-2
++  * Cleaned ebuild and add USE description to metadata.xml
++  * Cleaned ebuild and add USE description to metadata.xml
++  * Added local USE description
++  * [sci-chemistry/gromacs] migrate to git-2
++  * [sci-physics/espresso] migrate to git-2
++  * [app-doc/gromacs-manual] migrate to git-2
++  * Define EAPI after inherit
++  * Fixed herd entry in metadata.xml
++  * Fixed herd entry in metadata.xml
++  * Fixed herd entry in metadata.xml
++  * Fixed herd entry in metadata.xml
++  * Fixed herd entry in metadata.xml
++  * Fixed herd entry in metadata.xml
++  * Fixed herd entry in metadata.xml
++  * Fixed herd entry in metadata.xml
++  * Fixed herd entry in metadata.xml
++  * Fixed herd entry in metadata.xml
++  * Cleaned ebuild
++  * Some ebuild cleaning
++  * Some ebuild cleaning
++  * Some ebuild cleaning
++  * Some ebuild cleaning
++  * Some ebuild cleaning
++  * Moved to EAPI=4
++  * Manifest fix
++  * SOme ebuild cleaning
++  * Moved from 'git' to 'git-2'
++  * Corrected ChangeLog
++  * Corrected ChangeLog
++  * Corrected ChangeLog
++  * Cleaned ebuild
++  * Fixed Manifest and cleaned ebuild
++  * Shorten Summary
++  * Manifest fix
++  * Manifest fix
++  * Manifest fix
++  * Manifest fix
++  * Manifest fix
++  * Manifest fix
++  * Manifest fix
++  * Manifest fix
++  * Fix repoman warnings
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Mask sci-visualization/vtkPOFFReader as paraview-3.8 is masked
++  * QA on package.mask
++  * sources are dead
++  * Sources not available anymore
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Dropped ~ppc as many deps aren't keyworded
++  * Dropped ~ppc as many deps aren't keyworded
++  * removed uneeded entry
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * broken old version
++  * QA on why
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * mask sci-libs/pfft as fftw-3.3 is masked
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Fix CVS Header , remove LICENSE from installation
++  * Sort inherit and/or USE
++  * metadata.xml added
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * EAPI bump
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Version Bump
++  * Streamlined fortran-2 eclass usage
++  * Sort inherit and/or USE
++  * Streamlined fortran-2 eclass usage
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Streamlined fortran-2 eclass usage
++  * Sort inherit and/or USE
++  * Streamlined fortran-2 eclass usage
++  * Sort inherit and/or USE
++  * Streamlined fortran-2 eclass usage
++  * Streamlined fortran-2 eclass usage
++  * Sort inherit and/or USE
++  * Streamlined fortran-2 eclass usage
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Streamlined fortran-2 eclass usage
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Streamlined fortran-2 eclass usage
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Sort inherit and/or USE
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/mira: libtool.m4 fix so we can safely run eautoreconf and a version bump
++  * Streamlined fortran-2 eclass usage
++  * Streamlined fortran-2 eclass usage
++  * Streamlined fortran-2 eclass usage
++  * Streamlined fortran-2 eclass usage
++  * Streamlined fortran-2 eclass usage
++  * Streamlined fortran-2 eclass usage
++  * Streamlined fortran-2 eclass usage
++  * Streamlined fortran-2 eclass usage
++  * And one more
++  * One more fix
++  * Fix typo
++  * Update cluster patches to support XRC on mlx4 devices
++  * Add new cluster sources
++  * Update init.d
++  * Make use of external locking optional
++  * Update deps
++  * Update patches
++  * Update ocfs2
++  * Update ocfs2
++  * [infiniband] Add ib support for dhcp
++  * [sci-chemistry/gromacs] only USE=fkernels needs fortran
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Added fortran-2.eclass support
++  * Tweak the ebuild
++  * commit
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Added fortran-2.eclass support
++  * Moved to tree
++  * commit
++  * commit
++  * Added fortran-2.eclass support
++  * Make cvxopt use pkg-config to set BLAS/LAPACK, add glpk useflag description in metadata.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Final changes before move to the main tree.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-chemistry/gromacs] switch to cmake
++  * media-gfx/librecad: version bump to 1.0.0rc1
++  * Mikes suggestions
++  * Version BUmp, added missing die
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/scilab-5.3.2.ebuild: ebuild fixes
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci into guillaume
++  * new version of paraview (3.10.1)
++  * Last changes before review.
++  * fortran-2.eclass nearly finished for review.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Updated to current HEAD
++  * fortan-2.eclass in progress
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * move to pkg_pretend for EAPI=4
++  * [fortran-2.eclass] remove unnecessary quotes
++  * fix typos
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Fix pkg-config files, #369263
++  * [fortran-2.eclass] FCOPENMP -> FC_NEED_OPENMP
++  * [fortran-2.eclass] add pathscale compiler to get_fcomp, fix tabs
++  * Also export F90=$FC
++  * fortran-2.eclass, added mpif* cpabilities and get_fcomp function
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * fortran-2 some cosmetic changes
++  * [fortran-2.eclass] tc-has-fortran -> have-valid-fortran, remove some quotes, add checks for openmp support for other compilers
++  * [fortran-2.eclass] Fix openmp check to be F77 compliant
++  * fortran-2.eclass added
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * media-gfx/librecad: fix manifest
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-mathematics/scilab] version bump to 5.3.2
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge remote-tracking branch 'origin/master'
++  * [sci-mathematics/scilab] version bump
++  * sci-biology/sra_sdk-2.0.1: quote properly
++  * sci-biology/sra_sdk-2.0.1: fix install for amd64
++  * sci-biology/sra_sdk-2.0.1: a new package to access NCBI Short Read Archive
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * media-gfx/librecad: clean up unused files folder
++  * media-gfx/librecad: added tagged version
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [dev-java/jlatexmath-fop] Fix broken manifest
++  * [dev-java/jlatexmath-fop] version bump
++  * [dev-java/jlatexmath] version bump
++  * [dev-java/jlatexmath] version bump
++  * sci-visualization/v_sim: added maintainer email
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-visualization/v_sim: version bump to 3.6.0
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [dev-java/hdf-java] version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-chemistry/ambertools: Version bump to 1.5
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-chemistry/votca-csg] use default instead of tip
++  * [sci-libs/votca-tools] use default instead of tip
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/cadabra: version bump to 1.29
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-libs/votca-tools] added sqlite3 support
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Fix collision with dev-python/webpy, #368947
++  * Fixes for latest HEAD
++  * idb bump
++  * [sci-misc/boinc-bin] Remove obsolete package version.
++  * ipp bump
++  * ipp bump
++  * [sci-visualization/gnuplot] sync with tree
++  * [sci-visualization/gnuplot] 4.4.3-r1 InCVS
++  * [sci-chemistry/votca-csg] added boost use flag
++  * Version Bump
++  * Version Bump
++  * Version Bump
++  * Cleaned for current HEAD
++  * Sandbox fix
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * media-gfx/librecad: switch from svn to git
++  * sci-biology/mira: revbump to force inclusion on dev-util/google-perftools deps
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * xdsstat-bin: bump to latest.
++  * Version Bump
++  * Correct for double prfix
++  * Fix license dir to  /opt/intel/composerxe-2011.2.137/licenses/
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Add missing path to LDPATH, #367959
++  * fix intel-sdp.eclass for prefix
++  * sci-biology/mira-3.2.1.17-r1: maks the devel. version until it can be compiled (due autoreconf issues)
++  * sci-biology/mira-3.2.1-r1: added an extra patch for traceinfo off-by-one error
++  * sci-biology/consed-20-r1: improve message on die()
++  * sci-biology/consed-20-r1: improve message on die()
++  * moved ipp from my overlay
++  * move icc,idb,ifc from my overlay
++  * added casacore
++  * sci-mathematics/giac: QA fixes
++  * sci-mathematics/giac: fix manifest
++  * [sys-fs/zfs] Patch merged upstream
++  * [sys-fs/zfs] Update patch
++  * [sys-fs/zfs] Fix typo
++  * [sys-fs/zfs] Fix gentoo detection
++  * [sys-fs/zfs] Update to recent version
++  * [sys-devel/spl] Update to recent version
++  * sci-mathematics/giac: fix when no fltk
++  * sci-mathematics/giac: new ebuild
++  * sci-mathematics/frama-c: manifest for typo
++  * sci-mathematics/frama-c: fix ebuild typo
++  * sci-mathematics/why: version bump
++  * sci-mathematics/frama-c: version bump
++  * sci-mathematics/flocq: version bump
++  * sci-mathematics/apron: fix doc building
++  * dev-ml/ocamlgraph: version bump
++  * sci-physics/abinit: fixed configure error for fftw3
++  * sci-biology/gbrowse-2.26: fixed sanbox violation but webap-config bug pops up afterwards (happens later during install)
++  * sci-mathematics/gambit: deleted from old category sci-misc
++  * Correct fix for #293665
++  * Another quick version bump. Minor cleanup, smp removed until usable. Bizzare 6.6.2 ebuild mostly ignored, but not deleted until discussed. In the list?
++  * Version bump.
++  * Version bump.
++  * Version bump.
++  * Version bu,p
++  * Remove file with missing download.
++  * Version bump
++  * Remove old ebuilds since the sources have disappeared
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * manifest fix
++  * Manifest fix
++  * tiff -> tiff-compat
++  * Moved from media-libs/tiff to media-libs/tiff-compat
++  * Moved from media-libs/tiff to media-libs/tiff-compat
++  * [sci-visualization/gnuplot] sync with tree and bug #366129#c11
++  * [media-libs/tiff] Undo the bump (see bug #364181)
++  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci
++  * media-gfx/librecad: fix for gcc-4.6
++  * Version bump to avoid conflict with tree
++  * sci-biology/Gambit: BAM file viewer
++  * Re-enable some tests
++  * Enable debugging as recommended by upstream (#362655)
++  * disable parallel install
++  * add hppa keyword, fix herd
++  * Sync with main tree.   Add ~hppa, fix comments, fix #293665 fix.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/tablet-bin: added missing die call
++  * [sci-physics/phun] removed: unsupported software
++  * sci-biology/tablet-bin: version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * merging
++  * sci-biology/tablet-bin: removed references to my /scratch filesystem
++  * [sci-libs/spr] moved to main tree
++  * [dev-python/idlsave] included in scipy-0.9.0
++  * [dev-python/cosmolopy] now in main tree
++  * Version Bump, notified by euscan
++  * Version Bump, notified by euscan
++  * Version Bump, notified by euscan
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * small fixes for spl
++  * Small fixes for zfs
++  * Fix x11-libs/goocanvas SLOT
++  * Version bump. Use system hwloc. Switch to hydra instead of mpd for pm. Disable more tests as suggested by upstream. #362655.
++  * add ppc and ppc64
++  * Fix hardened test failure (#360185) and cleanup.
++  * [sci-chemistry/gromacs] sync with tree
++  * More zfs updates
++  * more zfs stuff
++  * updates to zfs
++  * [sys-fs/zfs] Add init.d from bug #365435
++  * media-gfx/librecad: initial port, #344791
++  * sci-biology/tablet-bin-1.11.02.18: fixed ebuild for the package and version bump
++  * Version BUmp
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Fix include path  for zfs and spl
++  * Fixed underlinking problems
++  * Cleaned old patches
++  * Fixed patches for current HEAD
++  * Version Bump, Minor corrects to fullfil repoman QA
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/consed-20-r1: added nLine.h patch from upstream to fix negative line numbers in phd files wrapped in phd.ball.1
++  * Make zfs install to / not to /usr
++  * sci-physics/abinit: Removed old versions
++  * Fix broken manifest
++  * [sci-physics/espresso] live ebuild update
++  * sci-physics/abinit: version bump to 6.6.2
++  * [sci-physics/espresso] live ebuild update
++  * [sci-physics/espresso] added live ebuild
++  * updated package.mask
++  * update for petsc-3.1_p8 from bug 53386
++  * [media-gfx/brlcad] Moved to tree, updated metadata
++  * [sys-cluster/scalasca] accept flags
++  * sci-libs/vtk moved to tree and unmasked.
++  * sci-mathematics/gambit: new category, moved from sci-misc
++  * [sys-cluster/scalasca] updated homepage
++  * Moved to tree
++  * Made ebuild tree ready
++  * sci-misc/gambit: Initial port. #47670
++  * media-gfx/brlcad: Added dev-tcltk/tkpng to RDEPEND, #363251
++  * [sys-fs/zfs] Initial import from sping overlay
++  * [sys-devel/spl] Initial import
++  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/acl2: have to build books in place
++  * Fix ups
++  * Version Bump
++  * Fix for python ABI stuff
++  * Fix for python ABI stuff
++  * Fix for python ABI stuff
++  * Fix for python ABI stuff
++  * Fix for python ABI stuff
++  * media-gfx/brlcad: version bump to 7.18.4
++  * sci-mathematics/acl2: fixed certificate dir
++  * Slightly streamlined ebuild
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Make working with py-2.7
++  * Added missing RDEPEND
++  * Fixed for latest upstream release
++  * Merge branch 'master' of ssh://git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/acl2: industrial strength theorem prover, #49316
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * Updated to latest upstream tarball, #363283
++  * sci-mathematics/cadabra: version bump to 1.28. Fixed dev-cpp/pangomm slot to 1.4
++  * [app-doc/gromacs-manual] updated
++  * [sci-chemistry/gromacs] remove 4.0.* (EOM)
++  * v_sim: version bump to 3.5.2
++  * Fix FFTW3 lib path on amd64. Need more work to get C/Fortran bindings
++  * version bump; bug #248372. Restrict netcdf deps to current stable in tree
++  * sci-geosciences/seawater: Version bump
++  * sci-geosciences/swmm: Correcting 'Manifest'
++  * sci-geosciences/pydap: Version bump.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Corrected Slot of fltk to 1
++  * Corrected Slot of fltk to 1, thanks Jan M. Simons noticing this
++  * [sys-cluster/scalasca] version bump
++  * Fixed typo in emboss.eclass
++  * Useless blank line on line: 13
++  * Fix to latest head
++  * Missing script dirs included
++  * Adding keywords for testing by wider audience.
++  * Last fix for 64bitness
++  * Corrected slot of fltk, #360641
++  * Move sci-chemistry/stdinchi to sci-libs/inchi
++  * Add updates for sci-chemistry/inchi
++  * sci-libs/inchi moved to tree
++  * sci-chemistry/openbabel* moved to tree
++  * Install into vendor dir
++  * Moved swig to DEPEND
++  * Do not in gzipped libs, thanks rei4dan noticing me
++  * sci-chemistry/stdinchi removed. Duplication
++  * openbabel-perl: Fix install in sandbox
++  * openbabel-python: Add Python3 iterator and wrap OBInternalCoord patches
++  * Semi broken perl support for openbael
++  * Cleaned ebuild
++  * keyworded for ~x86
++  * moved inchi from sci-chemistry to sci-libs
++  * Removed python again
++  * Cleaned ebuild
++  * Cleaned ebuild, moved from sci-chemistry to sci-libs
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Fix compile correctly against postgresql, #359959
++  * Remove libtool if it was installed by USE=vt, bug #359917.
++  * Make the USE=vt blockers conditional on being an unclasssed merge.
++  * mpi.eclass:  Improve handling of unclassed dep strings
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Last cleanup to emboss.eclass
++  * Remove commented RESTRICT
++  * Bump #349076
++  * Implicit decs fix, thanks bicatali for help
++  * added nco for testing
++  * bumped to dev-python/pyamg-2.0.0
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Updates from review
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * Fixed for reviewed eclass
++  * added petsc-3.1_p8 ebuild
++  * added hypre-2.7.0b
++  * [sci-chemistry/gromacs] Update ebuild for using pkg-config and blas
++  * [sci-physics/root] now in main tree
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Straighten ENV
++  * Fixed doc installation path
++  * Fix malformated Header
++  * Remove fortran.eclass
++  * Ignore fatal patch size
++  * Manifest fixed
++  * New emboss_src_install used
++  * Fixed Manifest
++  * Last writing corrections
++  * Naming of eclass changed
++  * Naming of eclass changed
++  * Naming of eclass changed
++  * Naming of eclass changed
++  * Naming of eclass changed
++  * Naming of eclass changed
++  * Naming of eclass changed
++  * Naming of eclass changed
++  * Naming of eclass changed
++  * Naming of eclass changed
++  * Naming of eclass changed
++  * Naming of eclass changed
++  * Naming of eclass changed
++  * renamed embassy-ng -> emboss.eclass
++  * Naming of eclass changed
++  * Naming of eclass changed
++  * Naming of eclass changed
++  * Naming of eclass changed
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [dev-python/cosmolopy]: bump
++  * Version bump.  Use system sys-app/hwloc.
++  * Moved media-libs/jpeg -> virtual/jpeg
++  * Moved media-libs/jpeg -> virtual/jpeg
++  * Moved media-libs/jpeg -> virtual/jpeg
++  * Moved media-libs/jpeg -> virtual/jpeg
++  * Moved media-libs/jpeg -> virtual/jpeg
++  * Moved media-libs/jpeg -> virtual/jpeg
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * dev-python/pythonocc: Manifest commit
++  * dev-python/pythonocc: restrict to opencascade-6.3 dependency
++  * EOV not needed to be set anymore
++  * EOV not needed to be set anymore
++  * EOV not needed to be set anymore
++  * sci-visualization/vtkPOFFReader: changed SRC_URI top ESVN_REPO_URI due to problems with md5sum's
++  * EOV not needed to be set anymore
++  * EOV not needed to be set anymore
++  * EOV not needed to be set anymore
++  * EOV not needed to be set anymore
++  * EOV not needed to be set anymore
++  * EOV not needed to be set anymore
++  * EOV not needed to be set anymore
++  * EOV not needed to be set anymore
++  * EOV not needed to be set anymore
++  * EOV not needed to be set anymore
++  * EOV not needed to be set anymore
++  * EOV not needed to be set anymore
++  * EOV not needed to be set anymore
++  * Ebov not needed to be set anymore
++  * Last cleanings before review
++  * Version Bump
++  * Rev bump, to ahead of the tree ebuild
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sys-cluster/scalasca] cleanup + url updates
++  * [app-doc/gromacs-manual] updated
++  * updated package.mask
++  * [app-doc/votca-manual] moved to votca-csg-manual
++  * [app-doc/votca-csg-manual] move + update
++  * [sci-chemistry/votca-csg] updated deps
++  * [app-doc/votca-manual] renamed to votca-csg-manual
++  * Unset DOCS as we do not have any
++  * embassy-ng.eclass respects DOCS
++  * Correct naming of patch
++  * Move away from embass-ng_src_install
++  * Move away from embass-ng_src_install
++  * Move to new embassy-ng.eclass
++  * embassy-ng.eclass progressing
++  * Move to new embassy-ng.eclass
++  * Move to new embassy-ng.eclass
++  * Move to new embassy-ng.eclass
++  * Move to new embassy-ng.eclass
++  * Move to new embassy-ng.eclass
++  * Move to new embassy-ng.eclass
++  * Move to new embassy-ng.eclass
++  * Move to new embassy-ng.eclass
++  * Move to new embassy-ng.eclass
++  * Move to new embassy-ng.eclass
++  * Move to new embassy-ng.eclass
++  * Move to new embassy-ng.eclass
++  * Move to new embassy-ng.eclass
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Move to new embassy-ng.eclass
++  * Version Bump, Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * Version Bump, Move to new embassy-ng.eclass
++  * Move to new embassy-ng.eclass
++  * Move to new embassy-ng.eclass
++  * Move to new embassy-ng.eclass
++  * Version Bump, Move to new embassy-ng.eclass
++  * Removed largefile from local USE description
++  * Move to new embassy-ng.eclass
++  * Version Bump, Move to new embassy-ng.eclass
++  * defualt for largefile support
++  * Emboss-6.3.1 imported from tree
++  * [sci-mathematics/octave-epstk] in the main tree
++  * sci-visualization/paraview: removed OFF patch as this is now an external plugin
++  * sci-visualization/vtkPOFFReader: New ebuild for bug 358077
++  * sci-libs/geom: New ebuild from bug 358061
++  * sci-libs/gmsh: Added sci-mathematics/petsc support
++  * [sci-libs/votca-tools] 1.1.1 InCVS
++  * [sci-chemistry/votca-csg] 1.1.1 InCVS
++  * [sci-chemistry/gromacs] added fixes from 4.5.3-r4
++  * [ambertools] apply upstream bugfixes
++  * Fix another typo with symlinks
++  * Fix another typo with symlinks
++  * Fix another typo
++  * [sci-chemistry/ambertools] Fix typo
++  * [sci-chemistry/ambertools] Fix issues with path
++  * A quick bump to sci-physics/abinit-6.6.1. Some cleanup, some mess. Switched from fftw2 to fftw3. OpenMP still broken.
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * QA things
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * QA STUFF
++  * Correct Slots for gtk 3 introduction to tree
++  * QA STUFF
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * QA things
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * Correct Slots for gtk 3 introduction to tree
++  * Fix typo
++  * [sci-chemistry/ambertools] now it should work
++  * [sci-chemistry/ambertools] Now it compiles =D
++  * More updates and fixes
++  * Initial import =) may not work
++  * sci-biology/staden-2.0.0_beta8: provide LDPATH=/usr/lib/staden through /etc/env.d/99staden to /etc/ld.so.conf
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/gap2caf-2.1.0: ebuild cleanup
++  * [sci-libs/armadillo] move to the main tree
++  * healpix not yet ready
++  * [sci-libs/spooles] in main tree
++  * [media-gfx/freecad] Moved to main portage tree
++  * [media-gfx/freecad] Added comment about nature of parallel make failures
++  * sci-biology/amos-short: new package
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/smalt-bin-0.5.1: version bump
++  * [media-gfx/freecad] Add -DBOOST_FILESYSTEM_VERSION=2 workaround for boost-1.45
++  * [media-gfx/freecad] Circumvent parallel make issues :(
++  * [media-gfx/freecad] Version bump; added required RESTRICT with comments; many cleanups and enhancements
++  * [media-gfx/freecad] pkgmove from sci-misc to media-gfx category
++  * [dev-python/pivy] Moved to main tree
++  * [sci-chemistry/votca-csg] switched to cmake
++  * [sci-libs/votca-tools] switched to cmake
++  * [sci-chemistry/votca-csg] version bump
++  * [sci-libs/votca-tools] version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Adding noarch ebuild - work in progress.
++  * Adding noarch ebuild - work in progress.
++  * os-mpi moved to tree as native-mpi
++  * [os-mpi] update os-mpi for prefix
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [mpi] Add os-mpi for prefix support
++  * Coot live fixes
++  * sci-biology/smalt-bin: an alternative to ssaha2 for even shorter reads
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/bambus: added goBambus.pl script and perl/python dependencies
++  * [sci-libs/opencascade] Moved to main tree.
++  * sci-biology/ssaha2-bin: new package, the GRL license text extracted from the saha2-manual.pdf seems kind of ... not like a real License text
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/ssaha2: new package, the GRL license text extracted from the saha2-manual.pdf seems kind of ... not like a real License text
++  * Add epatch_user back for gromacs live ebuilds
++  * sci-mathematics/frama-c: fix install doc
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Cleaned ChangeLog
++  * Version Bump
++  * Version Bump
++  * Live ebuild updated
++  * [sci-physics] Fix manifests
++  * [sci-electronics/tnt] Assigned to sci-electronics herd
++  * [sci-electronics/tnt] New application
++  * A supporting utility of sci-physics/abinit to convert the data generated by sci-physics/atompaw for the use with abinit
++  * A program to generate atomic data for the Projector Augmented Wave method of DFT calculations. Added to support sci-physics/abinit
++  * sci-biology/est2uni: current Manifest file
++  * sci-biology/est2uni: working EST annotation package
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/est2uni: env.d/ file
++  * [sci-visualization/gnuplot] updated deps
++  * sci-mathematics/frama-c: temporary retro-compatibility patch
++  * sci-mathematics/frama-c: keep previous version for now
++  * [sci-visualization/gnuplot] removed pdf use flag + bump to EAPI=3
++  * moved to g-x86
++  * moved to g-x86
++  * sci-biology/tgicl: make sure we call perl and not perl-5.15.2 directly
++  * [sci-chemistry/votca-csg] fixed a typo
++  * [app-doc/votca-manual] fixed install location
++  * [app-doc/votca-manual] initial commit
++  * updated package.mask
++  * [sci-chemistry/votca-csg] version bump
++  * [sci-libs/votca-tools] version bump
++  * [sci-chemistry/gromacs] 4.5.3-r3 InCVS
++  * sci-biology/OBO-Edit: added license file
++  * sci-biology/OBO-Edit: added license file
++  * sci-biology/est2uni: EST assembly+annotation: a perl-based analysis pipeline including php-based web interface
++  * sci-biology/picard-tools: Java-based command-line utilities manipulating SAM/BAM files with Java API (SAM-JDK)
++  * sci-biology/OBO-Edit: Java-based editor optimized for the OBO biological ontology file format
++  * sci-biology/swissknife: fixed Gentoo Copyright text
++  * sci-biology/swissknife: Perl library of modules to manipulate SwissProt flatfiles
++  * sci-biology/go-db-perl: Gene Ontology Database perl API
++  * sci-biology/ONTO-PERL: tools to manipulate OWL- and OBO-formatted files
++  * [sci-chemistry/gromacs] version bump
++  * sci-biology/tgicl: metadata checksum fix in Manifest
++  * sci-biology/clview: metadata checksum fix in Manifest
++  * sci-biology/zmsort: metadata checksum fix in Manifest
++  * sci-biology/nrcl: metadata checksum fix in Manifest
++  * sci-biology/cdbfasta: metadata checksum fix in Manifest
++  * sci-biology/tclust: metadata checksum fix in Manifest
++  * sci-biology/psx: metadata checksum fix in Manifest
++  * sci-biology/sclust: metadata checksum fix in Manifest
++  * sci-biology/seqclean: description line cleanup
++  * sci-mathematics/gappalib-coq: sci-mathematics/flocq added as a dependency
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/gappa: bogus manifest fixed
++  * sci-biology/lucy: a sequencing masking tool
++  * sci-biology/staden-2.0.0_beta8: new release
++  * [sci-chemistry/gromacs] fixes bug #339837
++  * sci-biology/estscan: added missing EAPI line
++  * sci-biology/: fixing 3 of my Manifest files
++  * sci-biology/align_to_scf: fix sed trickery
++  * sci-biology/estscan: added the license text
++  * sci-biology/tablet-bin: version bump
++  * sci-biology/estscan: new package, something wrong with IUSE?
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/jalview: version bump
++  * sci-mathematics/why: version bump
++  * sci-biology/gbrowse: version bump, more DEPS added, tiny webappconfig improvement
++  * sci-mathematics/frama-c: previous beta compatible why
++  * sci-mathematics/frama-c: clean-up
++  * sci-mathematics/frama-c: version bump
++  * dev-libs/simclist: version bump
++  * dev-ml/ocamlgraph: version bump
++  * sci-mathematics/gappalib-coq: version bump
++  * sci-mathematics/flocq: new package
++  * [sci-chemistry/votca-csg] version bump
++  * [sci-libs/votca-tools] version bump
++  * [sci-chemistry/gromacs] qa fixes
++  * sci-mathematics/gappa: version bump
++  * sci-mathematics/apron: doc generation for cxx fixed using dev-tex/rubber
++  * [sci-chemistry/votca-csg] 1.0.1 moved to the main tree
++  * [sci-libs/votca-tools] 1.0.1 moved to the main tree
++  * [sci-chemistry/votca-csg] version bump
++  * [sci-libs/votca-tools] version bump
++  * Moved sci-math/jags to main tree per bug 317741
++  * moved to g-x86
++  * sys-cluster/heartbeat moved to main tree
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Version Bump
++  * sys-cluster/keepalived and pacemaker-gui bumps
++  * A simple version bump. An unsolved problem with fortran flags when USE="+netcdf -mpi" circumvented. Minor changes to reports and logs when testing
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [ocfs2] another small update to make it works
++  * Update deps for ocfs2
++  * [ocfs2] add new ebuild
++  * mpi.eclass:  support EAPI 3 and 4.
++  * Bump EAPI thanks to scarabeus.
++  * Fix SRC_URI and general cleanup
++  * Bump, #349076.  Re-enable tests with mpi-threads.  Add prefix stuff.
++  * solve file collision in paraview
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Changes in vtk's handling of python-2.7
++  * Improvements to paraview-3.8.1
++  * Fix up ebuild per bug #344721. Thanks to Joel Berendzen.
++  * [sys-block/tgt] Moved to tree
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * housekeeping in vtk
++  * New addition, written by me
++  * USE mask sse in sci-chemistry/almost, works only on 32bit
++  * [sci-chemistry/votca-csg] added doxygen docu
++  * [sci-libs/votca-tools] added doxygen docu
++  * sci-biology/tablet-bin: updated ebuild
++  * sys-block/tgt version bump
++  * [sci-physics/espresso] updated homepage
++  * [sys-cluster/nullmpi] added live ebuild
++  * updated package.mask
++  * [sys-cluster/nullmpi] added support for shared libs
++  * [virtual/mpi] initial version with sys-cluster/nullmpi support
++  * [sci-chemistry/votca-csg] fixes build with =gromacs-9999
++  * [sci-chemistry/gromacs] added back gsl/xml useflag
++  * [sci-chemistry/gromacs] fixed some typos
++  * Added missing env stuff
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Manifest fix
++  * [sci-chemistry/gromacs] add back live manual
++  * Just a forgotten update of Manifest
++  * The typo of getFC corrected to . By Jérôme Borme <jerome.borme@gmail.com>
++  * The typo of getFC corrected to . By Jérôme Borme <jerome.borme@gmail.com>
++  * [sys-cluster/ceph] Moved to tree
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Added missing variable installation in revbump
++  * Fix tests
++  * sys-cluster/ceph-0.24.1 version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * The conditional use of several configure options tweaked to actually work even if a USE flag is unset. Reported by Jérôme Borme <jerome.borme@gmail.com>
++  * Fixing categories, #351818
++  * Corrected the sources location. Thanks to jerome.borme@laposte.net from bug 329429.
++  * [sci-chemistry/gromacs] qa fixes
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * A libxc ebuild for sci-physics/abinit
++  * A FoX ebuild for sci-physics/abinit
++  * An ETSF IO ebuild for sci-physics/abinit
++  * A bigDFT ebuild for sci-physics/abinit; not the latest version but the abinit compatible one.
++  * An ebuild for abinit-6.4.2 using external dependencies as proper Gentoo packages. Based on bug 249493, still work in progress. With USE="smp" compiles, but crashes.
++  * A wannier90 ebuild for sci-physics/abinit
++  * An ebuild for abinit-6.4.2 using external dependencies as proper Gentoo packages. Based on bug 249493, still work in progress. With USE="smp" compiles, but crashes.
++  * [sys-cluster/pacemaker] cib needs to build before pengine
++  * [sys-cluster/pacemaker] further fixes
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Also get rid of valpha.tar during installation
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Update manifest
++  * [sys-cluster/pacemaker] add bits missed in previous commit
++  * [sys-cluster/pacemaker] fix lib ordering wrt #351329. Thanks to Rafał Mużyło <galtgendo@o2.pl> for suggestion.
++  * [sys-cluster/pacemaker] fix autotools issues, patch send upstream
++  * [dev-vcs/mercurial-server] InCVS
++  * Unmask icm-3.7
++  * Correctly manage openmp and otehr linking
++  * sys-cluster/pacemaker dependency bump and LIBADD patch
++  * sys-cluster/pacemaker-gui bump
++  * sys-cluster/pacemaker-gui upstream revision bump
++  * Fix repoman warnings and missing manifest
++  * synchronize polybori with s-o-g overlay
++  * Remove singular - now in tree
++  * sci-libs/cgnsfoam: Version bump
++  * sci-libs/libcgnsoo: Version bump
++  * sci-visualization/paraview: Added 2nd python path
++  * sci-libs/gmsh: delete old version, added some USE-flags
++  * sci-libs:/cgnslib: delete old version, made hdf5 really apply again
++  * moved to g-x86
++  * more cleaning
++  * more removing
++  * removed badly committed files
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-chemistry/gromacs] suffix fix
++  * [sci-chemistry/gromacs] 9999 version uses cmake-utils eclass
++  * [sci-chemistry/votca-csg] does not build with gromacs-9999 anymore
++  * [sci-chemistry/gromacs] 4.5.9999 now uses autotools-utils eclass
++  * [sci-libs/lpsolve] fixed manifest
++  * [dev-python/pymvpa] added manifest
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/consed-20: new ebuild, see bugs #346801 (fixed), #351133 (fixed), #351152 (still affects amd64)
++  * scikits now in in main tree
++  * sci-biology/staden: again dropping arches from live ebuild ;-)
++  * sci-biology/staden: fixed my email address in metadata.xml
++  * mask root svn
++  * condor bump
++  * root fixes
++  * masked root svn
++  * ÿorick bump
++  * maxima gone in tree
++  * sci-biology/consed-bin: fixing a typo and '' expansion, see bug #312893
++  * sci-biology/consed-bin: resurrecting an ebuild for binary package, was bug #253451
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Some QA on ebuild style
++  * Moving www-apps/SwishE to www-apps/py-swish-e
++  * Moving www-apps/SwishE to www-apps/py-swish-e part II
++  * Moving www-apps/SwishE to www-apps/py-swish-e
++  * Some QA on ebuild style
++  * moved to g-x86
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Version Bump
++  * sci-biology/tablet-bin: added licence file
++  * sci-biology/tablet-bin: some QA fixes, still broken ebuild
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * fixed my email in affected metadata.xml files
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/align_to_scf: QA fix, changed pkgdescr and created a README file
++  * updated to latest petsc patchset
++  * Fix manifest and ebuild syntax
++  * Mask sci-biology/tablet-bin #348029
++  * sci-biology/roche454ace2caf: improved description and polished deps
++  * sci-biology/roche454ace2caf: added ksh dependency
++  * sci-biology/align_to_scf: tools needed by roche454ace2caf
++  * license file for align_to_scf, roche454ace2caf, sff_dump
++  * sci-biology/roche454ace2caf: convert ace files to gap4 (part of staden v1)
++  * sci-biology/align_to_scf: new package
++  * sci-biology/sff_dump: convert sff files into fasta/qual formats
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Added missing env
++  * [sys-cluster/keepalived] version bump
++  * [sys-cluster/corosync] version bump
++  * Version Bump
++  * Moved to main tree.
++  * Moved to tree.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Fix typo in metadata.xml
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * synchronize cvxopt with the sage-on-gentoo overlay
++  * Patch vtk for python-2.7
++  * Several fix for paraview, drop old.
++  * [sys-cluster/heartbeat] version 3.0.4 bump
++  * fix bug #348783 about libnet dep on sys-cluster/cluster-glue and sys-cluster/resource-agents
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/bamtools: two current ebuilds
++  * bamtools/bamtools-0.7.47: removed old version
++  * To main tree
++  * [sci-physics/root] bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Fix for fortran detection, thanks Arfrever pointing on it
++  * [sci-libs/exodusii] build shared libs, added test USE flag
++  * Fixing for current HEAD
++  * [dev-vcs/mercurial-server] version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-mathematics/dolfin] Initial import.
++  * moved to main tree
++  * [sci-chemistry/votca-csg] now using autotools-utils eclass
++  * [sci-libs/votca-csg] removed link to live ebuild
++  * [sci-libs/votca-tools] using autotools-utils eclass
++  * [sci-libs/votca-tools] removed link to live ebuild
++  * Fortran detection fixes
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/bamtools: new package
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * fortran.eclass fixes
++  * fortran.eclass fixes
++  * fortran.eclass fixes
++  * Correct handling of OpenMp support
++  * sci-biology/apollo: added dep on java vm
++  * Fix for fortran.eclass removal
++  * Removal of fortran.eclass, #348851
++  * Removal of fortran.eclass, #348851
++  * Removal of fortran.eclass, #348851
++  * Removal of fortran.eclass, #348851
++  * Removal of fortran.eclass, #348851
++  * Removal of fortran.eclass, #348851
++  * again
++  * Update mask
++  * Mask new icm
++  * Update ebuild
++  * fix typo
++  * Add new icm
++  * Make tiff sloted for binary compatibility
++  * [sci-libs/exodusii] Initial import.
++  * Update openmm stuff
++  * [dev-python/viper] Initial import.
++  * [dev-python/instant] Initial import.
++  * [dev-python/ffc] Initial import.
++  * [dev-python/fiat] Initial import.
++  * [dev-python/ufl] Initial import.
++  * Fix maniifest
++  * Some QA, src_configure not needed
++  * [sci-mathematics/armadillo] update license, make BLAS, LAPACK, Boost hard dependencies
++  * [sci-libs/gmsh] Manifest update
++  * [dev-python/pyamg] added ChangeLog, QA fixes
++  * [dev-python/meshpy] added ChangeLog, QA fixes
++  * [sci-mathematics/ufc] added ChangeLog, QA fixes
++  * [sci-libs/armadillo] added ChangeLog
++  * QA fixes
++  * [sci-libs/gmsh] bump to 2.5.0
++  * [sci-mathematics/ufc] Initial commit for UFC 1.4.2
++  * [dev-python/cvxopt] Initial commit for CVXOPT 1.1.3
++  * [sci-libs/armadillo] Initial commit for Armadillo 1.0.0
++  * [dev-python/meshpy]: Initial commit for MeshPy 0.91.2
++  * added ebuild for PyAMG 1.0.0
++  * [sys-cluster/scalasca] version bump
++  * [sys-cluster/cluster-glue] moved to gx86
++  * [sys-cluster/cluster-glue] 1.0.7 version bump
++  * sci-biology/wcd: sequence clustering tool
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/apollo: added java classes to inherit
++  * sci-biology/argo-bin: new package, current 1.0.31 bin-only version
++  * sci-biology/argo: new package, an old 1.0.24 src version
++  * sci-biology/apollo: dropped keywords from live ebuild
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/apollo: dropped actually the whole keywords line from the live ebuild
++  * sci-biology/apollo: dropped actually the whole keywords line from the live ebuild
++  * sci-biology/apollo: dropped keywords from the live ebuild
++  * sci-biology/apollo: new package
++  * update digest
++  * Remove keywords for live ebuild
++  * sci-biology/tgicl: updated package description
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/amos: live ebuild
++  * Moved to tree
++  * [sci-chemistry/gamessq] Moved to tree
++  * Move changelog
++  * Import dev-java/vecmath with history and remanifest
++  * Remove old. (Portage version: 2.2_rc48/svn/Linux x86_64)
++  * Add ~x86.
++  * bump to vecmath-1.5.1
++  * Create repo_name in java-overlay and get rid of Manifest1 digest files.
++  * Changes to overlays according to http://overlays.gentoo.org/proj/java/wiki/March_2007_Summary#Changesinoverlays.
++  * sci-biology/tgicl: einfo additions
++  * sci-biology/tgi-tools: dropped altogether, use tgicl and its deps instead
++  * sci-biology/tgicl: add quotes
++  * sci-biology/tgicl: TIGR tgicl clustering tools
++  * sci-biology/zmsort: TIGR tgi-tools package
++  * sci-biology/seqclean: TIGR tgi-tools package
++  * sci-biology/tclust: TIGR tgi-tools package
++  * sci-biology/sclust: TIGR tgi-tools package
++  * sci-biology/psx: TIGR tgi-tools package
++  * sci-biology/nrcl: TIGR tgi-tools package
++  * sci-biology/clview: an assembly .ace file viewer from TIGR Gene Indices project tools
++  * sci-biology/cdbfasta: part of TIGR tgi-tools
++  * sci-biology/cap3-bin: EST assembler (no sources ever available)
++  * sci-biology/jalview: version bump
++  * sci-biology/staden: removed unused patches
++  * sci-biology/staden: removed unused patches
++  * sci-biology/staden: live SVN and one for upcoming 2.0.0b8
++  * sci-biology/caftools-2.0.2: newer version but lacking manpages and caf_find_misassemblies
++  * sci-biology/caftools: added einfo() line
++  * sci-biology/caftools: new package, bug #259842
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/autoeditor: automatiucally correct basecalling errors using multiple sequence alignments of the Sanger-based reads
++  * sci-biology/bambus: assembly scaffolder
++  * sci-biology/tigr-foundation-libs: TIGR C++ files used by bambus and autoEditor
++  * Bumped in Cvs
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-chemistry/votca-csg] version bump + clean up
++  * [sci-libs/votca-tools] version bump + clean up
++  * depends on scikits
++  * depends on scikits
++  * depends on scikits
++  * depends on scikits
++  * depends on scikits
++  * bump learn
++  * added a common scikits package
++  * added jags
++  * [sci-libs/votca-tools] version bump
++  * [sci-chemistry/gabedit] fix Manifest wrt bug 347697
++  * [sci-chemistry/gabedit] Version bump to 2.3.3
++  * sci-visualization/paraview: fixed python path
++  * Fixes for python stuff
++  * New addition
++  * New addition
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Added missing deps on media-fonts/font-sun-misc and x11-apps/xset.
++  * removed stale doc useflag. Fix by Guillaume Horel in bug 301048.
++  * sci-visualization/paraview: added new OpenFOAM patch
++  * sci-libs/mesquite: Initial commit
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-biology/tigr-assembler: fix quoting issues (QA)
++  * sci-biology/tigr-assembler: respect CC from environment, provide run_TA script as a bourne-shell script and not in csh syntax, provide src_test()
++  * added ~amd64
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * dropped erroneous description line
++  * initial and working ebuild
++  * dropped erroneous description line
++  * Version bump and lots of ebuild improvements, it works for me now
++  * Version bump per bug #311857, added description and longdescription to metadata
++  * Update manifest
++  * [sci-chemistry/gromacs] Moved to tree
++  * use original hypre download link
++  * disabled libpetsc.so RPATH
++  * fixed metadata
++  * added petsc parmetis and hdf5 support
++  * fixed petsc hypre support
++  * reworked hypre ebuild
++  * [sci-chemistry/gromacs] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * sci-geosciences:pydap_responses_xls: Version bump and change in numbering.
++  * sci-geosciences/pydap_responses_wms: Version bump.
++  * sci-geosciences/pydap_responses_matlab: Version bump and normalization of version numbering for download.
++  * sci-geosciences/pydap_responses_kml: Version bump.
++  * Version bump.
++  * sci-geosciences/pydap: Version bump.
++  * [sys-cluster/pacameker] 1.0.10 moved to g-x86
++  * [sys-cluster/glusterfs] moved to g-x86 wrt #345427
++  * sci-geosciences/xtide: Version bump.
++  * sci-geosciences/libtcd: Version bump.
++  * sci-geosciences/harmonics-dwf-free-noncomm: Version bump.
++  * sci-geosciences/harmonics-dwf-free: Version bump.
++  * Revert "Sip patch from bgo", fixed upstream
++  * inCvs
++  * QA on quoting
++  * fperms sucks, because it could not handle wildcards
++  * Better goocanvas detection
++  * Added x11-libs/goocanvas as DEPS
++  * Reomove more ifles
++  * Force removal of files
++  * Synchonized with tree ebuild
++  * Fix DEP on x11-libs/guile-gtk
++  * Missing files are executable now
++  * remove nmrproc.com as well
++  * added missfits
++  * sci-astronomy/psfex: Initial import
++  * sci-astronomy/weightwatcher: Initial import
++  * added eye
++  * License and web site changes
++  * License and web site changes
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/pest: Fixed compilation of some of the utilities.
++  * sci-mathematics/pest: Version bump and minor changes.
++  * sci-visualization/ferret-bin: Version bump.
++  * [sys-cluster/glusterfs] better glusterd init script
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sys-cluster/pacemaker] version bump
++  * sci-chemistry/openbabel: Fix testing
++  * sci-chemistry/openbabel: Use system libinchi, add gui USE
++  * New package sci-chemistry/inchi
++  * try to add hypre support to petsc
++  * added hypre version 2.4
++  * removed useless python use flag
++  * added hypre package
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-chemistry/openbabel-python: Version bump to 2.3.0
++  * sci-chemistry/openbabel: Version bump
++  * Bump and cleanup.  Drop keywords until #345231 is fixed.
++  * Macaulay2 back in the main tree. Cleanup
++  * lrslib in main tree
++  * sci-libs/cdd+ moved to main tree
++  * sci-math/gfan in main tree
++  * sci-libs/mpir is in the main tree
++  * [dev-libs/asmjit] Initial import wrt bug 345183
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/Macualay2 bump to 1.4
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-math/topcom -> main tree
++  * virtual/jpeg for paraview
++  * virtual/jpeg for vtk
++  * cleanup for sci-math/singular (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * moved to main tree
++  * [sci-biology/quicktree] Respect CC,CFLAGS,LDFLAGS. Drop empty deps, add missing die. Fix SRC_URI wrt bug 344715. Thanks to Joel Berendzen <joelb@lanl.gov> for the report.
++  * [sci-biology/codonw] Respect CC,CFLAGS,LDFLAGS. Add missing die. Drop empty deps.
++  * [sci-biology/miranda] Version bump wrt bug 144316. Thanks to Joel Berendzen <joelb@lanl.gov> for the report. Drop old.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-misc/flashdot moved to the main tree
++  * deps updated, ebuild QA (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * sci-mathematics/frobby moved to the main tree
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * removed octave-forge.eclass
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * revbump the news item
++  * fixed octave-forge news item
++  * Prefix fix
++  * Install wrapper correctly, bin QA hacks
++  * added news item for octave-forge removal
++  * removed octave-forge packages. please use g-octave instead
++  * I think I got all libsingular headers sorted now. Even so, sage still doesn't seem to build (compilation stall)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-chemistry/gabedit] ebuild for new version 2.3.2 added
++  * libsingular headers are completely broken so more fix
++  * Fix broken libsingular headers
++  * -r1 drops libsingular, -r0 small fixes. (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sys-cluster/ceph] adding reference for bug submitted upstream
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Fix typo in singular-3.1.2
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [dev-python/numpydoc] Add ~x86, restrict python-3.*. Thanks to W. Trevor King <wking@drexel.edu> for the report.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sys-cluster/ceph] Version bump. Thanks to Marcin Mirosław <bug@mejor.pl> for the report. Drop old.
++  * Fix build with as-needed, simplify deps, add new use flags for debug and libatomic-ops, remove logrotate flag, don't build static libs, general cleanup. Drop old
++  * sci-math/polymake added to main tree
++  * sci-math/normaliz in main tree, old versions remain for Macaulay2 (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * sci-math/singular: bump to 3.1.2 (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * InCvs
++  * sci-mathematics/unuran: bump
++  * [sci-chemistry/gromacs] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * sci-mathematics/frama-c: remove no-longer-needed patch
++  * sci-libs/calculix-cgx: Version bump
++  * sci-libs/calculix-ccx: Version bump
++  * Readd patch accidentally deleted.
++  * Restore paraview-3.8.0 while problems with 3.8.1 are sorted out.
++  * adding missing patch (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * Added missing patch (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * New Addition
++  * Version bump to sfst-1.4, add library installation
++  * sci-misc/salome-* bumped to 5.1.4 ebuild by Michael Riss in bug 330303
++  * Moved sci-math/nauty and its license to main tree
++  * Fix installation of internal copies of 3rd party libraries.
++  * bump to paraview 3.8.1
++  * Package.masking vtk-5.6.1
++  * Import new vtk-5.6.1 in the overlay. package asked a there are no stable version.
++  * [sys-cluster/pacemaker-gui] proposed ebuild
++  * [sys-cluster/pacemaker] proposed version bump
++  * glusterfs bump to better handle glusterd and gluster CLI
++  * [sci-chemistry/gromacs] added natural vmd support (bug #340651#c8) (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-libs/dcmtk] Version bump
++  * Keyworded for ~-linux prefix
++  * Merge branch 'master' of ssh://bes.ibi.kfa-juelich.de/opt/scisoft64/data/sci
++  * openmp fix
++  * Added missing Manifest
++  * Added all files
++  * Merge ssh://bes.ibi.kfa-juelich.de/opt/scisoft64/data/sci into HEAD
++  * Real OPENMP fix
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * Sip patch from bgo
++  * InCvs
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-chemistry/molsketch] tiny changes regarding style of metadata.xml and ebuild - thanks to Justin Lecher (jlec) for giving a hint
++  * reworked passing configure options to petsc config script
++  * [sci-chemistry/molsketch] initial import of version 0.2.0; thanks a lot to Kacper Kowalik (Xarthisius) for direction to a proper ebuild.
++  * [sci-chemistry/gromacs] multilib fix (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-chemistry/gromacs] added vmd use flag (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * sci-mathematics/normaliz QA (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * Version Bump
++  * Cleanup and gcc44 patch added, thanks Joel Berendzen
++  * [sci-mathematics/singular] Added symlink needed by prefixed Sage (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
++  * 4ti2 moved to the main tree
++  * bumped to 0.5.2, ebuild by Andrzej Krentosz in bug 266249 (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * sci-mathematics/netgen: Removed old version
++  * sci-mathematics/netgen: Version bump
++  * sci-mathematics/frama-c: various EAPI3 cleanups
++  * sci-chemistry/gabedit: Version bump. Thanks to maxb <max-braeu@gmx.de>. Drop old.
++  * [sci-chemistry/gromacs] renamed manual distfile (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * sci-mathematics/singular: backport fix for bug 341357
++  * sci-mathematics/lrslib: QA fixes (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
++  * Fixing dependencies of sci-mathematics/Macaulay2 (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Initial import
++  * Updated ebuild for ceph
++  * sci-mathematics/rngstreams: Initial import
++  * sci-mathematics/prng: Initial import
++  * sci-physics/root: backport upstream patch to fix build with gmake-3.82
++  * [sci-chemistry/votca-csg] deps update (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-chemistry/gromacs] live ebuild updates (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-chemistry/gromacs] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-libs/openmm] export OPENMM_PLUGIN_DIR (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * added changelog
++  * sci-libs/amdlibm: AMD libm replacement
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-physics/root: root experimental
++  * Remove non-working doins in kayali
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * mering Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-mathematics/singular] Added ~x86-linux keyword and Prefix patch (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
++  * now in main tree
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Fixing boost dependency and moved to qt4-r2 eclass in paraview
++  * sci-math/Macaulay2-1.4 fixed SRC_URI and small updates
++  * added a proposal of agenda for the first sci-electronics meeting
++  * [sys-cluster/ceph] Add initscripts from bug #338008
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Removing package.mask for sci-mathematics/axiom. Bug 336789 resolved by bump and unkeywording
++  * Bump: sci-mathematics/axiom-201009
++  * Macaulay2-1.4_pre SVN from 1.4 branch
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * Another prefix fix
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/frama-c: fixes Manifest
++  * sci-mathematics/frama-c/frama-c-20100401.ebuild: EAPI3 typos
++  * Prefix Fixes
++  * nmrpipe update
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [app-doc/gromacs-manual]: fixed install location (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * coot openmp
++  * Version Bump
++  * Openmp linking patch
++  * Bump jgraphx to 1.4.1.2
++  * petsc-3.1-p5: appending fortran configure flags dependent on fortran use-flag
++  * fixed digest
++  * added petsc ebuild of latest patchset
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/frama-c: EAPI3 cleanups
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Update ceph. init scripts will come soon
++  * [sci-libs/openmm] initial commit (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-libs/openmm] masked
++  * updated use.local.desc
++  * [sci-chemistry/votca-csg] fixed bootstrap for live ebuild (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * ucsf license added
++  * New addition
++  * unio license added
++  * [dev-tex/revtex] Moved to main tree
++  * [dev-tex/natbib] Moved to main tree
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [sci-chemistry/votca-csg] added live ebuild (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-chemistry/votca-csg] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-libs/votca-tools] added live ebuild (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-libs/votca-tools] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * dev-python/numpydoc: Bump
++  * Initial upload of dev-java/jlatexmat-fop Ebuild by Dmitry S. Kulyabov in bug 301048
++  * dev-java/jlatexmath bump due to Dmitry S. Kulyabov in bug #301048
++  * pyglet now in main tree
++  * masked fftw-3.3_alpha1
++  * sci-mathematics/Macaulay2-9999: Upstream fixed a bug
++  * [app-portage/g-octave] moved g-octave-0.4.ebuild to the main tree
++  * [sci-chemistry/gromacs] version 4.5.1 now in tree (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [dev-tex/revtex] Corrected texmf installation directory (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-tex/natbib] Corrected TEXMF installation directory (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [pmask] Mask axiom-201005 temporarily because of bug 338762
++  * Bump
++  * sci-math/axiom: Deps adjusted per bug 336789
++  * sci-mathematics/Macaulay2-9999 with split lrslib
++  * New package: sci-libs/lrslib Corresponding bug: 338685
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * [sci-electronics/gspiceui] Moved to main tree.
++  * coot: Fix build error and MTZ-opening crash.
++  * [sci-chemistry/gromacs] updated manifest (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-electronics/klayout] Moving to tree
++  * sci-math/Macaulay2-9999 fixed
++  * [sci-electronics/magic] Prepare moving this back to the tree.
++  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
++  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
++  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
++  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
++  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
++  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
++  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
++  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
++  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
++  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
++  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
++  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
++  * virtual/glut -> media-libs/freeglut & virtual/glu -> virtual/opengl Correction
++  * Better and more complete fix for parallel make in singular
++  * sci-math/Macaulay2 live ebuild
++  * One more parallel make fix for singular. Hopefully the last one.
++  * [sci-misc/gcam] In main tree now.
++  * New package: sci-mathematics/nauty Corresponding bug 337810
++  * new license: 'nauty' for sci-math/nauty
++  * Deps of Macaulay2 adjusted.
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * Minor prefix corrections
++  * [sci-libs/clapack] Was bumped to tree by bicatali.
++  * [sci-libs/pfft] added --disable-la-files option (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * Remove lam-mpi.
++  * [dev-tex/natbib] Fixed description, made myself maintainer, and removed RESTRICT. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-libs/clapack] Switch to cmake-based build system. Create install target and cmake export file. Build and run tests conditionally. Use f2c symbol prefix. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * fix repoman warnings
++  * Disable support for gforker as it breaks debug builds and is being abandonded upstream, see http://trac.mcs.anl.gov/projects/mpich2/ticket/898.
++  * Due to pvfs2 upstream continuously lagging behind the kernel the useflag is being dropped.
++  * Fix for petsc and adding license
++  * New package: sci-mathematics/petsc Ebuild due to J. M. Gottfried Corresponding Bug: 53386  (Meeh... that's from 2004!)
++  * Respect LDFLAGS, #335590.  Fix metadata.
++  * Respect LDFLAGS #336969.
++  * merge Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * Some scripts are in the wrong place
++  * [sci-libs/fftw] added static-libs useflag (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-libs/pfft] added static-libs useflag (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-libs/nfft] initial commit (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-libs/pfft]: initial commit (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-libs/fftw] Added alpha version to test mpi interface (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [dev-tex/revtex] Upstream bumped the patch level without renaming the file... (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
++  * mpir version bump
++  * Local bump of sci-mathematics/axiom-201005
++  * Version Bump
++  * Moved to the tree. See bug #79082.
++  * [dev-vcs/mercurial-server] updated elog messages (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * sci-mathematics/normaliz bump to 2.5
++  * Add missing factory headers for libsingular.
++  * Imort all my fixes to singular from the sage-on-gentoo overlay.
++  * Import Christopher's version of factory migrated to the autotools-utils eclass from the sage-on-gentoo overlay.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Version Bump
++  * Fixed patch
++  * sci-geosciences/swmm: Version bump.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Version bump.
++  * sci-geosciences/pydap: Version bump.
++  * [sci-chemistry/gromacs] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * moved to the main tree
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * New package: sci-mathematics/Oid Ebuild due to Johannes Rauh
++  * [sci-libs/mpir] Migrate to autotools-utils.eclass (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
++  * [sci-mathematics/4ti2] Use autotools-utils.eclass (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
++  * Fixed SRC_URI
++  * Cleaned ebuild (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Version Bump, removed old (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Keyworded for *-linux prefix (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Version bump, fixed umfpack version to <=0.5.4, reported by Philippe BAUCOUR (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Version Bump (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-chemistry/gromacs] switch to live manual (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [app-doc/gromacs-manual] initial commit (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * updated package.mask
++  * Moved to tree, see bug #135573
++  * [sci-biology/clover] Trivial version bump. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * Version bump, drop non-existent betas
++  * Fixed lib/lib64 troubles properly in modglue (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
++  * [sci-chemistry/bist] Moved from sunrise to sci overlay. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-misc/gcam] Version bump. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * Keyword factory ~ppc - I have the hardware.
++  * Keyword cadabra ~amd64 (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
++  * Keyword lie ~amd64 (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
++  * Fix parallel make in modglue. (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
++  * Keyword modglue ~amd64 and apply a patch for it. (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
++  * MAke xcadabra respect FLAGS in cadabra. (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
++  * Put lie's help system under /usr/share. (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
++  * [sci-libs/m4ri] Version bump (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
++  * sci-geosciences/pydap: Version bump.
++  * sci-geosciences/pydap_responses_matlab: Version bump.
++  * Version bump.
++  * Bump cadabra to 1.25, drop old.
++  * Bump modglue to 1.16, now respect LDFLAGS. (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
++  * [dev-python/pywcs] version bump
++  * update HOMEPAGE of astrolib pkgs
++  * [sci-geosciences/qgis] sync with portage ebuild
++  * [sci-libs/fgsl] Initial import
++  * Fix last QA issues - hopefully that solved parallel make for good. (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
++  * sci-geosciences/pydap_handlers_csv: Version bump.
++  * Migrated lie to EAPI 3 and fixed various QA. (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
++  * [sci-mathematics/normaliz] Fixed SRC_URI (Portage version: 2.1.8.3/git/Linux i686)  (Unsigned Manifest commit)
++  * [sci-chemistry/avogadro] drop patch
++  * [sci-chemistry/avogadro] Add live ebuild for avogadro
++  * Add epatch_user =)
++  * bumped matio
++  * sci-geosciences/pydap_responses_xls: Initial ebuild.
++  * sci-geosciences/pydap_responses_netcdf: Version bump and changed SRC_URI to use mirror://pypi.
++  * sci-geosciences/pydap_responses_wms: Initial ebuild.
++  * sci-geosciences/pydap_responses_matlab: Initial ebuild.
++  * sci-geosciences/pydap_responses_kml: Version bump, changed SRC_URI to use mirror://pypi.
++  * sci-geosciences/pydap_handlers_sql: Initial ebuild.
++  * sci-geosciences/pydap_handlers_netcdf: Version bump.
++  * Deleted file that should have been included in much earlier commit.
++  * Initial ebuild.
++  * sci-geosciences/pydap_handlers_nca: Version bump and change to SRC_URI to use pypi mirror.
++  * sci-geosciences/pydap_handlers_csv: Initial ebuild to serve (handle) CSV files the pydap server.
++  * sci-geosciences/pydap_handlers_cdms: Changed SRC_URI to use pypi mirror.
++  * sci-geosciences/pydap: Version bump.  Minor edits to RDEPEND.
++  * [sci-geo/qgis] remove 1.5.0. Moved to main tree.
++  * scikits_learn bump
++  * Fix python handling, thanks to jlec for noticing. (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix #313045, add missing libs during linking (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * cleanup (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * [app-portage/g-octave] Updated the live ebuild. Added the USE flag 'doc' (Portage version: 2.2_rc67/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [app-portage/g-octave] Version bump (Portage version: 2.2_rc67/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [dev-python/cosmolopy] Version bump
++  * [dev-python/cosmolopy] Initial import
++  * [sci-chemistry/gromacs] Version bump + new manual (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [dev-python/atpy] Version bump
++  * [app-portage/g-octave] Removed the PySVN dependency from the live ebuild (Portage version: 2.2_rc67/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sci-chemistry/gromacs] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * masked gromacs-4.5.9999
++  * Correct SRC_URI in paraview-3.8.0 (Portage version: 2.2_rc67/git/Linux i686)  (Unsigned Manifest commit)
++  * [sci-physics/espresso] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * Keyworded for *-linux (Portage version: 2.2.00.15842-prefix/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
++  * sci-mathematics/singular: Cloning libsingular fixes from sage-overlay, thanks to kiwifb.
++  * [sci-chemistry/gromacs] doc fixes (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-physics/espresso] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-chemistry/gromacs] ffamber now officialy shipped with gromacs =)
++  * [dev-python/pysolar]: Initial import
++  * sci-mathematics/singular: Install missing headers, upstream tarball change.
++  * sci-mathematics/frobby: QA
++  * vo bumped
++  * [sci-geosciences/qgis-1.5.0] keyword unstable
++  * New package: sci-mathematics/cipi Bug: 329169
++  * [sci-geosciences/qgis] add new qgis-1.5.0 version. fix inherit in 9999
++  * added inference
++  * removed doc and examples flags
++  * removed doc and examples flags
++  * added idlsave
++  * sci-mathematics/singular: Bump to 3.1.1.4 and cleanup
++  * [dev-python/numpydoc]: Initial import
++  * InCvs
++  * InCVS
++  * added cosmocalc
++  * [sci-electronics/gspiceui] Version bump. Fix for wrong doc path and missing lib files if USE=examples (Portage version: 2.1.8.3/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sys-cluster/scalasca] version bump (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * initial import of astlib
++  * asciitable added
++  * Keywording g-cran-9999.ebuild
++  * Fix manifest for g-cran
++  * [app-portage/g-octave] Live ebuild updated. Already works with py3k. (Portage version: 2.2_rc67/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-mathematics/gfan: Imported updated ebuild from sage overlay
++  * sci-mathematics/singular: libdir for amd64
++  * runtime text relocations preliminary fix, soname added to libsingular
++  * [package.mask] removed app-portage/g-octave-0.2.1
++  * [app-portage/g-octave] Version bump (Portage version: 2.2_rc67/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-mathematics/singular-3.1.1.3 revbump and QA
++  * [sci-astronomy/stuff]: Fixed typo in HOMEPAGE
++  * [sci-astronomy/kapteyn]: Moved to gentoo-x86
++  * [dev-java/jeuclid-core,sci-biology/jalview] Removed pmask for packages with dependencies in the java overlay. For now.
++  * Version bump. Fixes only bug wrt buffer overflow on long filenames. (Portage version: 2.1.8.3/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Merge branch 'singular'
++  * sci-math/singular: Experimental support for libsingular
++  * [sci-libs/omalloc]: Make shared libs, fix tests, fix install paths
++  * Macaulay2-1.3.1-r4: Various QA, static libfac/factory, respect CFLAGS, optimization USE-Flag
++  * [sci-libs/cgnslib] Made the hdf5 patches apply again. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * In tree
++  * Imported to tree
++  * [sci-visualization/nodemon] Silenced repoman. FIXME: it looks like the pbs switch is not implemented properly. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-visualization/paraview] Silenced repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-mathematics/gfan]: Respect CXX, LDFLAGS, fix build with GCC-4.5
++  * [sci-libs/factory]: fix as-needed issue and parallel build
++  * [sci-mathematics/why] Silenced repoman; dropped ~sparc since dependencies cannot be fulfilled. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-mathematics/frama-c] Dropped ~sparc since dependencies cannot be fulfilled. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-libs/cgnslib] Removed hdf5 functionality in ...3 since the required library versions are not available anymore. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-java/jeuclid-core] Masked for removal since dependencies cannot be fulfilled
++  * [package.mask] Mask sci-biology/jalview for removal
++  * [sci-biology/jalview] Masked for removal (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sys-infiniband/libnes] Silenced repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sys-infiniband/libmlx4] Silenced repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sys-infiniband/libibvpp] Silenced repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sys-infiniband/libibcm] Silenced repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sys-infiniband/openib-srptools] Silenced repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-chemistry/procheck] Silence repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-chemistry/phaser] Silence repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-chemistry/openbabel-ruby] Silence repoman. Drop openbabel-ruby-2.2.0 since dependencies cannot be fulfilled anymore. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-chemistry/openbabel-python] Silence repoman. Drop openbabel-python-2.2.0 since dependencies cannot be fulfilled anymore. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-chemistry/openbabel-perl] Silence repoman. Drop openbabel-perl-2.2.0 since dependencies cannot be fulfilled anymore. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-chemistry/jligand] Silence repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * Fixed handling of long path and filenames (Portage version: 2.1.8.3/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sci-libs/factory]: remove old
++  * [sci-libs/factory]: Make shared libs, fix install paths, QA
++  * [sys-infiniband/libibmad] Shortened description. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sys-cluster/ceph] Shortened description (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-mathematics/octave-forge-communications] Silence repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-mathematics/octave-forge-splines] Added metadata.xml (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-mathematics/octave-forge-octgpr] Added metadata.xml (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * Bump mpir to version 2.1.1.
++  * Import an enhanced vtk-5.6.0 with support for database and ffmpeg.
++  * Import gl2ps with automagic dependencies fix.
++  * [sci-chemistry/gromacs] fix for bug #301854 (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * sci-mathematics/why: Version bump
++  * sci-mathematics/frama-c: Version bump
++  * dev-ml/ocamlgraph: some RDEPEND clean-ups
++  * sci-mathematics/*: some ChangeLog clean-ups
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * trivial fixes, keyword x86
++  * sci-mathematics/singular: Even better readline support and QA
++  * sci-mathematics/singular: readline support fixed
++  * [sci-geosciences/qgis-9999] add live ebuild to test version 1.5 (to be released soon)
++  * Bump sci-libs/libfac-3.1.1
++  * Bump sci-libs/factory-3.1.1
++  * dev-ml/ocamlgraph: depend fixes
++  * [sys-infiniband/openib-drivers]: no /sbin/lsmod symlink for >sys-apps/module-init-tools-3.6
++  * [app-portage/g-octave] masked version 0.2.1, due to broken SRC_URI
++  * [app-portage/g-octave] live ebuild now using the git repository (Portage version: 2.2_rc67/git/Linux i686)  (Signed Manifest commit)
++  * [sci-libs/omalloc]: Cleanup
++  * new package: sci-libs/omalloc
++  * [sci-chemistry/gromacs]: fortran fix (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [dev-tex/revtex] Needs a newer natbib than in texlive 2009... (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-tex/natbib] Added RESTRICT=primaryuri (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-tex/natbib] New package, updated natbib version required by revtex-4.1 (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-chemistry/gromacs] Fixes for Bug #326331 (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [dev-tex/revtex] Version bump to enforce reinstallation (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-tex/revtex] Added installation of the required rtx files (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-misc/finomaton] ChangeLog update
++  * [sci-misc/finomaton] Silence repoman; fix metapost dependency (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-misc/nltk] Silence repoman; drop ~amd64 since dependencies cannot be fulfilled. No keywords left. :( (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-misc/stanford-tagger] Silence repoman (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-misc/stanford-parser] Silence repoman (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-mathematics/ltl2ba] Silence repoman. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [licenses] Added CeCILL-2.0 as referenced by sci-mathematics/gappa
++  * [sci-mathematics/gappa] Silence repoman; improve license description; move doc generation dependencies to RDEPEND (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-mathematics/apron] Silence repoman; drop ~sparc since dependencies cannot be fulfilled; move doc generation dependencies to RDEPEND (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * dev-ml/ocamlgraph: version bump 1.5
++  * Local bump of sci-math/singular
++  * sci-mathematics/pff: QA fixes
++  * sci-mathematics/gappalib-coq: Version bump 0.13
++  * sci-mathematics/gappa: Version bump 0.13.0
++  * sci-mathematics/gappalib-coq: QA fixes
++  * sci-mathematics/gappa: QA fixes
++  * sci-mathematics/apron: building process fixed for the latest sources
++  * Added longdescription to metadata.xml (Portage version: 2.1.8.3/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Initial ebuild (see bug #316807) (Portage version: 2.1.8.3/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Dropped Lucas from maintainership on his request. Taking it over (Portage version: 2.1.8.3/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Dropped Lucas from maintainership on his request (Portage version: 2.1.8.3/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sci-chemistry/gamessq] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [licenses] Added missing license of sci-physics/phun
++  * [sci-electronics/gsmc] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-python/numexpr]: Moved to gentoo-x86
++  * [dev-python/pytables]: Moved to gentoo-x86
++  * [dev-python/numexpr]: Cleanup. Thanks to Arfrever
++  * [dev-python/pytables]: Cleanup. Thanks to Arfrever
++  * [dev-python/pytables]: Tests fail only with hdf5[debug]. Removing patch.
++  * sci-mathematics/apron: QA fixes
++  * dev-ml/mlgmpid: mpfr-3.0.0 compatibility
++  * Remove debug code (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Update python handling (#316937). Cleanup deps. Automatically turn on threads if mpi-threads are requested. (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * [app-portage/g-octave] Version bump with cleanup (Portage version: 2.2_rc67/git/Linux i686)  (Signed Manifest commit)
++  * [sci-electronics/magic] Make it use LDFLAGS, improve tutorial file location (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * dev-libs/simclist: simclist-1.4.4_rc3 version bump
++  * dev-libs/libanomaly dropped
++  * [dev-python/pytables]: Version bump
++  * [app-portage/g-octave] Version bump and cleanup. (Portage version: 2.2_rc67/git/Linux i686)  (Signed Manifest commit)
++  * Updated the app-portage/g-octave live ebuild (Portage version: 2.2_rc67/git/Linux i686)  (Signed Manifest commit)
++  * [sci-electronics/magic] Version bump with cleanups, also fixing bug 299476 (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-electronics/magic] Cleanup: removed versions without keywords. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-electronics/magic] Copied from main tree
++  * New ebuild for sci-electronics/xnec2c. Based on the work of Dominique Michel <dominique.michel@vtxnet.ch> in bug #138770
++  * [sci-visualization/v_sim] New application, see bug 109547. Ebuild submitted by Jérôme Borme.
++  * added myself to docs/proj/index.html
++  * Fix manifest
++  * Adding self to docs/proj/index.xml
++  * Adding myself to project page
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Version bump
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [docs/index.xml] Added myself.
++  * Added myself to docs/proj/index.xml
++  * added app-portage/g-octave-0.2_rc1. URL fixes (Portage version: 2.2_rc67/git/Linux i686)  (Signed Manifest commit)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * added app-portage/g-octave (Portage version: 2.2_rc67/git/Linux i686)  (Signed Manifest commit)
++  * octave-forge-image bump
++  * Version Bump, EAPI bump, drop patch included upstream (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * cleanup (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Moving g-cran from sys-apps to app-portage
++  * Remove empty lines (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Remove empty lines (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * removed old (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * removed old (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * removed old (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * removed old (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes, implicit declaration fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Borken with current stuff (numpy, etc)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Clean ancient version (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * gone
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Import a version of maxima-5.20.1 that solve bug #255673
++  * sci-libs/calculix-cgx: Version bump
++  * sci-libs/calculix-ccx: Version bump
++  * [sci-chemistry/gromacs]: added missing patch (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * removed gentoo_prefix again
++  * renamed patch (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Added prefix to masters
++  * Version BUmp (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for Python ABIs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes and fixes for implicit declarations (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes II (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * No support for current stuf like py >2.5 and numpy
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Removed old (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Respecting LDFLAGS (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Version Bump, Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * InCvs
++  * [licenses] Added tmhmm license as referenced in sci-biology/tmhmm
++  * [sci-biology/twinscan] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-biology/tmhmm] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-biology/tgi-tools] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-biology/signalp] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-biology/samtools] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [package.mask] Mask sci-biology/newbler for removal (no download source)
++  * [sci-biology/mrbayes] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * Update manifests
++  * Add prefix support and drop old versions
++  * Add development ebuild for G-CRAN
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Python ABI fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix PYTHON ABI Stuff (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix PYTHON ABI Stuff (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix PYTHON ABI Stuff (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Another little fix (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix PYTHON ABI Stuff (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix PYTHON ABI Stuff (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * email changed
++  * Fixed octave dep, #285236 (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fixed my mail in metadata.xml (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fixed my mail in metadata.xml (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-libs/xdrfile] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-libs/symmetrica] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-libs/oasa] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-libs/msms] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-libs/med] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * Revert "[sci-libs/factory] QA fixes, removed useflag singular which had no effect" because of side effects
++  * [sci-libs/gmsh] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-libs/factory] QA fixes, removed useflag singular which had no effect (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-libs/csrosetta-pdbh] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-libs/csrosetta-cs] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-libs/csrosetta-angless] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-libs/cddlib] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-libs/calculix-cgx] QA fixes: ghostscript dependency, built_with_use replaced (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-libs/calculix-ccx] QA fixes: ghostscript dependency (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sys-cluster/ceph] Version bump
++  * [sci-chemistry/gromacs] fixed prefix (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * [sci-biology/cluster] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-biology/clover] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [net-misc/bbscp] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [net-ftp/bbftp-server] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [net-ftp/bbftp-client] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-tex/picins] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [licenses] Added AURA license as referenced in dev-python/pywcs
++  * [dev-python/omniorbpy] QA fixes: removed ~ia64 keyword, bad dependencies (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-python/ffnet] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-ml/mlgmpidl] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-libs/simclist] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-libs/libunzip] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [package.mask] Mask dev-lang/aldor for removal (no sources available anymore)
++  * [dev-cpp/growler-thread] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-cpp/growler-math] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-cpp/growler-link] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-cpp/growler-core] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-cpp/growler-arch] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [app-vim/freefem++-syntax] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [app-text/dgs] Added note: upstream is dead (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [app-text/dgs] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-chemistry/rosetta] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-cpp/growler] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-mathematics/frama-c] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-ml/ocamlgraph] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-libs/simclist] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [dev-libs/libanomaly] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-misc/jwnl] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-mathematics/lattE-macchiato] QA fixes (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/gromacs: added stable patch + prefix (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * condor: more config fixes
++  * fixed sed line
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * condor: more initd fixes, now local config will reside in /var/lib
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * [dev-perl] Imported packages Lab::VISA, Lab::Instrument, and Lab::Tools (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [perl-core/encoding-warnings] Imported package. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-libs/ni-visa] Added dummy ebuild...
++  * sys-infiniband/librdmacm: adding pc file
++  * sys-infiniband/libibverbs: adding pc file
++  * Imported changes from tree (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Upstream already included this patch (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fixed my mail in metadata.xml (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fixed my mail in metadata.xml (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fixed my mail in metadata.xml (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fixed my mail in metadata.xml (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fixed my mail in metadata.xml (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * changed my mail adress
++  * Fixed metadata (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * remanifesting
++  * condor version bump
++  * Trying a fix for paraview-3.8.0 with mpi.
++  * Undelete Jmol
++  * InCvs
++  * Added missing dep on dev-libs/popt (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fixing compilation with gcc4, repecting CXXFLAGS/LDFLAGS, reMANIFEST (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Rename 1.4.1 as 1.4.1-r1 so users can easily get stable version from main tree. (Portage version: 2.2_rc67/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * dev-python/pytables: Adding dropped ~x86 keyword
++  * dev-python/numexpr: add ~x86 and src_test
++  * Bump to EAPI=2, temporarily drop ~ppc, ~x86
++  * dev-python/pytables: adding last rc for testing
++  * Adding support for multiple python abis
++  * Need qt4 ruby bindings which aren't available
++  * [dev-tex/revtex] New package (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix for compilation with gcc4.4, #271017 (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * InCvs as sci-libs/punc
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * dev-java/jgrapx is not available
++  * InCvs
++  * InCvs
++  * InCvs
++  * removed masks
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * inCvs
++  * [sci-misc/gcam] Moved from sunrise to sci overlay. (Portage version: 2.1.8.3/git/Linux x86_64)  (Signed Manifest commit)
++  * inCvs
++  * Version Bump, Prefixify, keyworeded for ~-linux (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * modeller bump
++  * [sci-electronics/gspiceui] Imported from sunrise. (Portage version: 2.1.8.3/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sci-electronics/klayout] Fixed manifest. (See bug 321871...)
++  * [sci-electronics/klayout] Trivial version bump. Still needs proper rubyfication.
++  * [sci-electronics/klayout] Imported from sunrise.
++  * classads bump
++  * [sci-geosciences/grass] remove the grass version. better one available in portage now
++  * dev-tex/atexmk-416a now in portage
++  * Importing new version of paraview in the overlay for testing
++  * Fixes for envs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * added missing envs (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fixed patch (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * nrpie patch fixed
++  * Version Bump (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-biology/foldingathome] move files (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-biology/foldingathome] Version bump (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * dev-ml/ocamlgsl now in portage
++  * Fixing SRC_URI wrt to bug 322383
++  * dev-tex/latexmk: version bump + bash completion (Portage version: 2.1.8.3/git/Linux i686)  (Signed Manifest commit)
++  * removed gasgano, cpl, esorex, now in main tree
++  * remove old
++  * remove old
++  * octave-forge-optim bump
++  * qcl fixes for gcc and deps
++  * coot missing link lib patch
++  * sci-mathematics/mdp: fixed manifest
++  * sci-mathematics/mdp: Version bump to 2.6
++  * Fixed HOMEPAGE (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * mpir revbump and clean.
++  * sci-libs/cgnstools: Fixed gcc-4.4 compile problems
++  * InCvs
++  * coot updated to fit with current head (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * in tree
++  * libf2c removed agauibn
++  * HEAD fixes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Added pysparse
++  * libf2c added temporarly
++  * New Addition (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * New package, ebuild written by me
++  * [sys-cluster/ceph] Version bump (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * inherit prefix (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * keyword ~amd64-linux ~x86-linux (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Fixing procheck (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Version bump, now using a patch from the Fedora project to honor FHS.
++  * dev-python/astropysics: Adding proper
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * InCvs
++  * fixing ChangeLog
++  * dev-python/astropysics: initial import wrt bug 317655
++  * dev-python/vo: Skipping failing tests, fixing assertions.
++  * dev-python/vo: removing docs, updating deps and Python style
++  * dev-python/pywcs-1.8.1: updating dependencies and Python style
++  * New package, ebuild written by me
++  * sci-astronomy/kapteyn: vesion bump
++  * renamed patch (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * dev-python/coords: initial import wrt bug #317365
++  * dev-python/pywcs-1.8.1: version bump
++  * sci-geosciences/pydap*: Updated to latest python ebuild standards.
++  * sci-geosciences/cdat-lite: Updated to latest style for Python ebuilds.
++  * dev-python/coards: Updated to latest style for Python ebuilds.
++  * dev-python/numexpr: Updated to latest style for Python ebuilds.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * version Bump (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Corrected Manifest file
++  * Initial commit for bug 315801
++  * sci-mathematics/polymake bump
++  * [sys-cluster/ceph] Version bump (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Manifest fixed (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-visualization/ferret-bin: Version bump
++  * sci-libs/gmsh-9999: added sci-libs/taucs support
++  * Imported from tree (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-misc/salome-*: changed fetch URL + cleaning (thanks Oliver), new patch + modifs to (partially) solve med_int issues on amd64
++  * Importet tree changes (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Changed DEPEND of media-libs/SoQt from 1.4.2_alpha4181 to 1.4.2_alpha1841 (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Update and clean cadabra.
++  * Added scikits_statsmodels
++  * Added scikits_image
++  * Added scikits_learn
++  * Added test suite
++  * Added scikits_optimization
++  * Now really installing docs
++  * Cleanup, added x86
++  * sys-cluster/nullmpi: initial commit (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * sys-cluster/scalasca: version bump (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * sci-physics/espresso: fixed a typo (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * Remanifesting
++  * sci-physics/espresso: version bump (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * bump
++  * new: dev-libs/simclist
++  * app-admin/syscall_anomaly dropped
++  * [sys-cluster] Add ceph - distributed petascale fs
++  * Corrected removing of valpha tarball (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * Corrected behaviour in EAPI>1 (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * removed old prefix support behaviour (Portage version: 2.2_rc67/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-misc/salome-*: make egencache work again
++  * sci-chemistry/votca-csg: added dev use flag (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/votca-tools: added dev use flag (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/votca-csg: update (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/votca-tools: update (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * sci-visualization/gnuplot: Sync with tree and clean up (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * [sci-chemistry/votca-csg] Fix small typo (Portage version: 2.2_rc65/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-chemistry/votca-csg: gcc-4.4 fix (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/votca-csg: added support for gromacs double-precision (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * New version with additional USE-flag source
++  * Fixing final QA issue on sci-mathematics/Macaulay2
++  * QA for sci-mathematics/Macaulay2
++  * sci-chemistry/votca-csg: version bump (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/votca-tools: version bump (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * New upstream version, cleanup new ebuild
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Added examples USE-flag; replaced all installation paths with variable
++  * sci-mathematics/topcom overhaul and ~amd64
++  * updated 6.3 to eapi=2 and make repoman happy; removed old
++  * libfac URI updated
++  * sci-misc/salome-* : Version bump (5.1.3) + removed broken 3.2.6
++  * Add hydra pm.  #309353 (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * Bump and fix #293665 (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * dev-vcs/mercurial-server: fixed bug #286695#c8 (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * Added doc generation to burrtools
++  * InCvs
++  * nmrview readded (Portage version: 2.2_rc65/git/Linux x86_64)  (Signed Manifest commit)
++  * Keyworded for ~amd64-linux ~x86-linux (Portage version: 2.2_rc65/git/Linux x86_64)  (Signed Manifest commit)
++  * Keyworded for ~amd64 ~x86 (Portage version: 2.2_rc65/git/Linux x86_64)  (Signed Manifest commit)
++  * rm valpha*.tar (Portage version: 2.2_rc65/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * app-admin/eselect-gnuplot: useless, dropped gnuplot mulitslot useflag
++  * dev-vcs/mercurial-server: dev-util -> dev-vcs (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * dev-vcs/mercurial-server: dev-util -> dev-vcs
++  * dev-util/mercurial-server: clean up (Portage version: 2.1.7.17/git/Linux i686, RepoMan options: --force)  (Signed Manifest commit)
++  * sci-visualization/gnuplot removed multislot use flag (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * sci-visualization/gnuplot-4.5.9999: checkout right branch (Portage version: 2.1.7.17/git/Linux i686)  (Signed Manifest commit)
++  * sys-libs/libtermcap-compat not needed anymore (Portage version: 2.2_rc65/git/Linux x86_64)  (Signed Manifest commit)
++  * Added flexdock
++  * sci-mathematics/normaliz QA
++  * QA for sci-mathematics/gfan
++  * sci-mathematics/frobby QA/ebuild improvements
++  * sci-mathematics/4ti2: Ebuild improvements
++  * sci-mathematics/Macaulay2 ebuild improvements
++  * QA: respecting FLAGS, metadata.xml fixed (Portage version: 2.2_rc63/git/Linux x86_64)  (Signed Manifest commit)
++  * InCvs
++  * Update uri for ffamber (Portage version: 2.2_rc63/git/Linux x86_64)  (Signed Manifest commit)
++  * InCvs
++  * Remanifesting
++  * [sci-chemistry/gromacs] Fix typo (Portage version: 2.2_rc63/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sci-chemistry/gromacs] Fix typo (Portage version: 2.2_rc63/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sci-chemistry/gromacs] Fix typo (Portage version: 2.2_rc63/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sci-chemistry/gromacs] Add missing patch (Portage version: 2.2_rc63/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sci-chemistry/gromacs] Add ffamber port to gromacs (Portage version: 2.2_rc63/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-mathematics/Macaulay2-1.3.1-r3 since upstream changed source files
++  * Cleaning scilab
++  * Masked >=jgraphx1.3, unmasked scilab for wider exposure
++  * Version bumps for jgraphx
++  * More fixes introduced by Guillaume Horel. Disabling blind Debian patches until further recommandation
++  * [sci-mathematics/scilab] regenerate manifest (Portage version: 2.2_rc63/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * InCvs
++  * inCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * scilab version bump
++  * Removed brlcad, now in main tree
++  * Removed tnt and jama, now in main tree
++  * Moved to tree
++  * sci-visualization/gnuplot-4.4.9999 added stable cvs-gnuplot (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
++  * package.mask: added =sci-visualization/gnuplot-4.4.9999
++  * sci-visualization/gnuplot-4.5.9999 patch went upstream (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
++  * Fix minorsyn errors
++  * Version bump.
++  * touch mpir to enable testing on non-x86/amd64 archs. Remove old mpir.
++  * InCvs
++  * Removed old versions of Macaulay2 and updated deps
++  * move mpir in sci-libs and adjust Macaulay2-1.3.* dependencies accordingly.
++  * [sci-chemistry/gromacs] patch appliyed upstream (Portage version: 2.2_rc62/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sci-chemistry/gromacs] Update dirent.h patch (Portage version: 2.2_rc62/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sci-chemistry/gromacs] Dropped unneded patches. They all were applied to git master (Portage version: 2.2_rc62/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sci-chemistry/gromacs] Add dirent detection patch (Portage version: 2.2_rc62/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-mathmatics/topcom-0.16.2 added Kudos to Johannes Rauh
++  * [sci-chemistry/gromacs] threads now on by default and they works fine with mpi (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-visualization/gnuplot-4.5.9999: clean up (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
++  * condor bump
++  * InCvs
++  * more scilab love
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * more scilab love
++  * Bump
++  * Bump
++  * Bump
++  * Added comments in ChangeLog
++  * New patches for scilab
++  * mpi goodness to hdf-java
++  * scripts dir cleaned
++  * InCvs
++  * sci-chemistry/gromacs-9999: added as-needed fix (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
++  * InCvs
++  * sci-chemistry/votca-csg: fixed as-neeeded bug (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/votca-csg: Version bump (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/votca-tools: Version bump (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
++  * sci-visualization/gnuplot: app-default patch went upstream (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
++  * added missing RDEP (Portage version: 2.2_rc62/git/Linux i686)  (Signed Manifest commit)
++  * added RDEP sci-chemistry/mgltools-mglutil (Portage version: 2.2_rc62/git/Linux i686)  (Signed Manifest commit)
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * InCvs
++  * InCvs
++  * InCvs
++  * sci-chemistry/gromacs-4.0.7-r1: InCvs (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/gromacs: docdir patch went upstream (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
++  * [media-gfx/tachyon] Fix sed line sequence (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * revbumped mpir to 1.3.1, changed nocxx to +cxx
++  * Added lattE-macchiato Bug 303653
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs
++  * Remove Safe-World from DEPEND per bug 303589
++  * Remove Safe-World from DEPEND per bug 303589
++  * Version bump
++  * Fixed wrong description for cdd+
++  * added myself to index.xml
++  * Add myself to index.xml
++  * added myself in the doc
++  * mpi and libc fixes
++  * added mpi support for hdf-java
++  * Fixed conflict man dir for brlcad
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Remanifest
++  * add vina_license
++  * [sci-chemistry/autodock_vina] Initial import per bug #282682 (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccpn-2.1.2.1_p100204 -- Added todays python fixes (Portage version: 2.2_rc62/git/Linux i686)  (Signed Manifest commit)
++  * sci-visualization/gnuplot: some fixes went upstream (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
++  * Add upstream fix for wrapper flag ordering
++  * InCvs
++  * InCvs
++  * InCvs
++  * InCvs (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * brlcad version bump (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * Version bump (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * removed old versions Upstream proper tarball added (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * Initial commit of fitscut (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * [media-gfx/tachyon] Now tachyon compiles with gentoo cflags (Portage version: 2.2_rc62/git/Linux x86_64)  (Unsigned Manifest commit)
++  * apbs plugin support now depends on sci-chemistry/pymol-apbs-plugin (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * InCvs (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/gromacs: live ebuild update (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
++  * removed octave fixes, now in main tree
++  * some syntax fixes
++  * inCvs
++  * inCvs
++  * sci-geosciences/seawater: Removed the earlier setting for S which with the new upstream numbering isn'g needed.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-geosciences/seawater: Upstream change numbering conventions.
++  * sci-chemistry/oasis -- RDEPEND changed sci-chemistry/ccp4 -> sci-chemistry/ccp4-apps, thanks alexxy for reporting (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccp4-apps -- Fix for 301762, thanks Johan Hattne for the patch (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/oasis -- remove forced RDEPEND on arp-warp (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * littel update to tachyon ebuild (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * [media-gfx/tachyon] Initial import. thanks to Christopher Schwan (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-visualization/ferret-bin: Removed old ebuilds. Reformatted to removed duplicate blank lines.
++  * sci-mathematics/pest: Removed unnecesary line.
++  * sci-mathematics/mdp: Removed unnecessary blank lines and fixed copyright years.
++  * sci-libs/scikits_timeseries: Removed unnecessary blank line at end of ebuild.
++  * dev-python/numexpr: Removed ending blank line.
++  * dev-python/coards: Removed useless blank lines.
++  * sys-cluster/pyslice: Removed unnecessary ending blank line. (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sys-cluster/blcr: Repoman sweep (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-geosciences/tcd-utils: Removed useless blank lines (leaving the useful lines alone) and fixed copyright years. (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-geosciences/tcd-editor: Removed useless blank lines. (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-geosciences/tappy: Useless blank line at end and fixed copyright years. (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-geosciences/seawater: Useless ending line. (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-geosciences/swmm: Useless blank lines and copyright fix (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-geosciences/congen: Useless blank line. (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-geosciences/cdat-lite: Blank line fixes from repoman. (Portage version: 2.1.7.16/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-geosciences/pydap*: Minor repoman fixes (removed ending blank lines)
++  * sci-chemistry/imosflm -- Version Bump (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-chemistry/coot -- Version Bump (Portage version: 2.2_rc62/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/ccp4-apps -- Bad upstream, changed tarball w/o bumping (Portage version: 2.2_rc62/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/ccp4-apps -- Bad upstream, changed tarball w/o bumping (Portage version: 2.2_rc62/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/ccp4-apps -- Bad upstream, changed tarball w/o bumping (Portage version: 2.2_rc62/git/Linux i686)  (Signed Manifest commit)
++  * sci-geosciences/pydap*: Corrected the license.
++  * sci-libs/votca-tools: version bump (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/votca-csg: version bump (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/votca-csg: completion file was moved (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/monomer-db -- version bump (Portage version: 2.2_rc62/git/Linux x86_64)  (Signed Manifest commit)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/superlu -- fixed bug #302763 (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * bumped mpir to 1.3.0, remove old rc, adjust copyright in 1.2.2
++  * sci-chemistry/pymol-apbs-plugin -- fixes for some file locations (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-chemistry/ccpn-2.1.2.1_p100129 -- Added todays python fixes (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/pymol-apbs-plugin -- Initial addition by me (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/pymol-apbs-plugin masked
++  * sci-visualization/gnuplot: Added ~amd64 keyword (bug #232363) (Portage version: 2.1.7.16/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/refmac -- Version bump (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/refmac -- Version bump (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/refmac -- Version bump (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-geosciences/pydap*: Corrected license.
++  * sci-geosciences/seawater: Corrected license. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
++  * dev-python/numexpr: Initial ebuild. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-geosciences/seawater: Initial ebuild (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sci-geosciences/grass-6.4.0_rc5] sync with portage version and add a missing patch
++  * sci-visualization/ferret-bin: Changed ebuild to correctly install according to x86 and amd64 architectures. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-visualization/ferret-bin: Version bump. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Added ffnet
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * fixed superlu for newer tar ball
++  * sci-misc/simpy: Deleted old ebuild. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sys-cluster/pyslice: Removed old ebuild. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sys-cluster/blcr: Removed old ebuild and updated copyright years on 0.8.2. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-mathematics/pest: Version bump, plus new download file naming convention.  Removed old non-working ebuilds. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-geosciences/xtide: Included 'non-commercial' use flag in metadata.xml.  Fixed dependencies. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-geosciences/libtcd: Included use flag 'non-commercial' in metadata.xml. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-geosciences/tcd-editor: Updated copyright years. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-geosciences/tappy: Updated manifest and removed old ebuild. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Fixed copyright year. (Portage version: 2.1.6.13/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sci-geosciences/qgis-9999] add gps useflag again and make QWT optional
++  * Removed qgis-1.4 now in main tree
++  * sci-geosciences/pydap_handlers_cdms: Initial ebuild.
++  * sci-geosciences/cdat-lite: Initial ebuild.
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-chemistry/votca-csg: dep fix (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/gromacs: Fixes bug #302048 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/ccpn -- updated patches and corrected versioning (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-geosciences/pydap_responses_kml: Initial ebuild.
++  * sci-geosciences/pydap_handlers_nca: Corrected RDEPEND.
++  * sci-geosciences/pydap_handlers_netcdf: Forgot the ChangeLog
++  * sci-geosciences/pydap_handlers_nca: Initial ebuild.
++  * sci-geosciences/pydap_handlers_netcdf: Initial ebuild.
++  * sci-geosciences/pydap_responses_netcdf: Updated Manifest
++  * sci-geosciences/pydap_responses_netcdf: Initial ebuild.
++  * sci-geosciences/pydap: Initial ebuild.
++  * dev-python/coards: Initial ebuild.  Converts from COARDS time (days since X) into python datetime.
++  * sci-visualization/gnuplot: some fixes went upstream (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/votca-csg: live ebuild added (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/votca-tools: live ebuild added (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * added masks for votca live ebuilds
++  * sci-chemistry/votca-csg: added ~amd64 keyword (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/votca-tools: added ~amd64 keyword (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/gromacs: fixed --as-needed confusion (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-biology/samtools: Fixed manifest (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * Version bump
++  * Added open-axiom
++  * Fixed octave dep to libX11
++  * Masked scilab
++  * Import of newer scilab
++  * Initial import of jlatexmath
++  * Import of jgraphx
++  * Import of jeuclid-core
++  * Initial import of hdf-java
++  * move EGIT stuff up before inherit
++  * sci-chemistry/scala -- Version bump (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/pointless -- Version bump -- thanks Johan Hattne for reporting (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci/sci-chemistry/gromacs: sync with tree and removed old versions (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * cleanup (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * Stable x86 and amd64 (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * Version bump with fixes to env.d files. (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * Cleanup (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * Remove older hdf5
++  * revbump to avoid conflicts with portage tree. (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/cyana added (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/scikits_timeseries: fixed Manifest (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/scikits_timeseries: Version bump, fixed licenses, and added pytables to RDEPEND.
++  * New Package sci-libs/cdd+
++  * Move include files into a subdirectory
++  * Remove paraview as it has been revbumped in the main tree by Markus Dittrich
++  * Only mask the paraview version in the science overlay
++  * sci-visualization/gnuplot: multislot fixes (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/ccpn -- todays patches added (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/refmac -- version bump (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-libs/monomer-db -- version bump (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * dev-util/smartgit -- version bump (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-libs/clipper -- Version Bump, nuking the as-needed patch (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ksdssp added (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/libpdb missed header wrong place (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/libpdb++ missed header wrong place (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/libpdb missed header installation (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/libpdb++ missed header installation (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/libpdb added (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/libpdb++ added (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/dssp2pdb added (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * dev-util/mercurial-server: Added ~am64 keyword (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * Bump sys-cluster/openmpi-1.4.1
++  * [sci-geosciences/qgis] version 1.4.0 released. remove live ebuild for this version
++  * [sci-chemistry/pyquante] Initial version bump (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * Initial import of burrtools
++  * Bump. Now based on Debian modifications
++  * There is now blast-db anymore, use ncbi-tools++ instead
++  * sci-biology/psipred -- Fixed dep another time (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-biology/blast-db -- missing perl DEPS added (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/mars --  RDEPEND on sci-biology/psipred (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-biology/psipred -- exprefixed (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-biology/psipred --  adopted to new blast-db (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/nmrpipe -- EPREFIXed (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-biology/blast-db --  We do not install the complete db anymore (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/nmrpipe -- EPREFIXed (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/nmrpipe -- missing patch moved (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/nmrpipe -- Version Bump 5.0.2010.008.16.00 (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/scala -- Version Bump 3.3.16 (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/mars -- EPREFIXed (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/mars -- final fixes part 2 (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/mars -- final fixes (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/mars -- more fixes part 2 (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/mars -- more fixes (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/mars -- fixed ebuild (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/mars -- New Ebuild Added (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/ccp4-apps-6.1.2* is blocking sci-chemistry/sfcheck (Portage version: 2.2_rc61/git/Linux i686)  (Signed Manifest commit)
++  * sci-visualization/gnuplot added multislot support (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * app-admin/eselect-gnuplot: needed for gnuplot[multislot] (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * New package sci-misc/flashdot Bug 300384
++  * Adding ocamlgsl(Bug 280939) from sunrise to science.
++  * [sci-geosciences/qgis] added new 1.4 live version until the release happens, fixed deps of qgis-9999 (gps no longer optional)
++  * added patch to fix missing definitions
++  * added patch to fix missing definitions
++  * Add mpi.eclass enabled sci-libs/hdf5
++  * new ebuild: app-admin/syscall_anomaly and dev-libs/libanomaly
++  * sci-visualization/qtiplot is bumped in the tree
++  * cforms is in tree now
++  * sci-chemistry/refmac -- version bump (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * dev-util/mercurial-server: version bump (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * x11-libs/xforms -- version bump (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/rasmol PREFIX ready (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-libs/neartree -- PREFIX ready (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/cbflib -- PREFIX ready (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/cbflib -- PREFIX ready (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-libs/cbflib -- PREFIX ready (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-libs/cbflib prefix ready (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/talos+ -- depending on rasmol (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/talos+ PREFIX ready (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/mddnmr Initial commit (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  *  sci-chemistry/arp-warp-bin -- needs specific revision of ccp4 (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * update license
++  * mddnmr license added
++  *  sci-chemistry/ccpn -- fixed some python stuff (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/pymol-1.2.2 is in the tree (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/sparky -- Fixed usage of python.eclass (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * app-arch/lbzip2 -- added symlink USE, to link lbzip to /usr/bin/bzip2 (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/pointless -- Version Bump PREFIX whitelist ready (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/sparky -- Version bump 3.115 complete rewrite: multilib aware, not using crappy buildsystem for installation, fixing locations, as-needed respecting, no fixed python version (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/sparky imported from tree
++  * sci-chemistry/pymol -- QA work (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * dev-tex/qtexengine x11-libs/gl2ps are in the tree now
++  * sci-chemistry/pynmr -- imported to save (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * app-arch/lbzip2-0.20 -- Version bump and cleanup of old versions (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/xds-bin -- version bump (Portage version: 2.2_rc61/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/sfcheck -- nano sfcheck-7.03.16.ebuild <ccp4-apps-6.1.3 (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/sfcheck -- blocking <ccp4-apps-6.1.3 (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccp4-apps -- don't build sfchack, but depend on it (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/sfcheck -- Initial commit (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-libs/balbes-db -- Version bump (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccp4-apps -- Version bump (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccp4i -- Version bump (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-libs/ccp4-libs -- Version bump (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccp4 -- Version bump (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccpn -- inclusion of todays patchset (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccpn -- fixes for doc installation (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/poitnless -- version bug (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/xia2 -- version bug, fixes bug 297238 (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
++  * media-libs/soqt removed
++  * dev-util/smartgit --  version bump to 1.0.1 (Portage version: 2.2_rc60/git/Linux x86_64)  (Signed Manifest commit)
++  * Update dev-libs/mpir-1.2 branch. Using portage yasm now.
++  * sci-mathematics/frobby QA: Respect users -O setting and no pre-stripping
++  * media-libs/SoQt -- little QA (Portage version: 2.2_rc59/git/Linux x86_64)  (Signed Manifest commit)
++  * media-libs/SoQt -- is maintainer-needed (Portage version: 2.2_rc59/git/Linux x86_64)  (Signed Manifest commit)
++  * media-libs/SoQt -- renamed correctly soqt -> SoQt (Portage version: 2.2_rc59/git/Linux x86_64)  (Signed Manifest commit)
++  * we don't need .svn
++  * sci-chemistry/votca-csg: Version bump (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/votca-tools: Version bump (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-mathematics/polymake revbump
++  * Repairing some depencies of freecad
++  * Initial import of Pivy
++  * Soqt back in science , because it's still not in main tree
++  * paraview ebuild improvements.
++  * [sci-geosciences/qgis-9999] adapt ebuild to portage changes plus some extras
++  * sci-chemistry/coot -- clean up (Portage version: 2.2_rc58/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-mathematics/octave-forge-meta -- dep of sci-mathematics/octave-forge-quaternion added, thanks by Emil Karlsson (Portage version: 2.2_rc58/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-mathematics/octave-forge-quaternion -- Initial commit, written by Emil Karlsson (Portage version: 2.2_rc58/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/votca-csg: added googlecode mirror (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/votca-tools: added googlecode mirror (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * >=sci-visualization/paraview-3.6.1-r2: HARDMASKED as this is an experimental ebuild
++  * Import "improved" paraview ebuild
++  * [sci-geosciences/swmm] Update manifest and remove stale ebuild
++  * Version bump.  Removed documentation since upstream changes without changing name so manifest could not be kept up to date.
++  * dev-util/mercurial-server: version bump to 1.0 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/votca-csg: corrected description (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-visualization/gnuplot: added version 4.4.0_rc1 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/votca-csg initial add - bug #296707 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/votca-tools initial add - bug #296707 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * Deleted because it's in the main tree
++  * sci-chemistry/coot -- some fixes towards the gtk-2 migration from upstream (Portage version: 2.2_rc58/git/Linux x86_64)  (Signed Manifest commit)
++  * Deleted coin because it's has reached main tree
++  * Version bump to version 4.1.2 revision 4181
++  * sci-libs/framewave: Add ~amd64 keyword and fix deps
++  * sci-mathematics/frama-c/files/frama-c-20090901-always_init.patch
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/frama-c/files/frama-c-20090901-always_init.patch
++  * Added patch to fix incorrectly declared variable (#293905).
++  * dev-scheme/guile-gnome-platform: Deleted since it's already in main tree
++  * Changed error in MY_P
++  * In main tree
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * dev-util/smartgit -- SRC_URI fixed (Portage version: 2.2_rc56/git/Linux i686)  (Signed Manifest commit)
++  * dev-util/smartgit -- version bump the release 1 (Portage version: 2.2_rc56/git/Linux i686)  (Signed Manifest commit)
++  * Added ~x86. Thanks to Derk W. te Bokkel
++  * Fully commit the openmpi-1.4 bump.
++  * Bump openmpi-1.4.
++  * sci-chemistry/openbabel-python: Block openbabel[python], #288199
++  * [sci-libs/coin] Fix b0rked manifest (Portage version: 2.2_rc55/git/Linux x86_64)  (Signed Manifest commit)
++  * Version bump of Coin to 3.1.2
++  * sci-chemistry/burrow-owl fixed starparse dpe to >=1.0 (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
++  * workaround for parallel installation added, fixes bug 288235 (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/nmrpipe fixed missing lip.patch (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
++  * dev-scheme/guile-gnome-platform correctly assigned contributer -- thanks Rafael G. Martins (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
++  * dev-scheme/guile-gnome-platform added to fix bug 293655 (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-libs/starparse unkeyworded te live ebuild again (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-libs/starparse release 1.0 added (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/mrbump don't use /usr/lib64/ccp4/ccp4i (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
++  * nmrpipe version bump (Portage version: 2.2_rc56/git/Linux x86_64)  (Signed Manifest commit)
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * To main tree
++  * deleted freecad in wrong directory
++  * Change user from root to Roelof Wobben
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Change user from root to Roelof Wobben
++  * Add sci-libs/framewave-1.3.1
++  * x11-libs/guile-gtk: Removed because it was commited to main tree
++  *  Initial import of freecad
++  * add mpi_pkg_set_ld_library_path()
++  * Fix eselect-mpi config file.
++  * Fix eselect-mpi config file.
++  * Add MPI_PKG_USE_ROMIO to mpi.eclass.
++  * Note revisions of patches in upstream repo.
++  * sci-chemistry/coot -- version bump to 0.6 and cleanup of old versions (Portage version: 2.2_rc55/git/Linux i686)  (Signed Manifest commit)
++  * app-arch/lbzip2 -- version bump to 0.1.9 (Portage version: 2.2_rc55/git/Linux i686)  (Signed Manifest commit)
++  * pdb-extract-3.004 has been merged into portage tree.
++  * sci-chemistry/mage Everything fixed (Portage version: 2.2_rc54/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/mage Imported fron dberkholz overlay (Portage version: 2.2_rc54/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/probe Everything fixed (Portage version: 2.2_rc54/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/probe Imported fron dberkholz overlay (Portage version: 2.2_rc54/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/neartree -- version bump to 2.1.4 (Portage version: 2.2_rc54/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/gromacs docdir->htmldir (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/gromacs: htmldoc was installed in the wrong path (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/factory Manifest
++  * sci-visualization/gnuplot: fixed bug #294467 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-mathematics/frama-c20090901: always_init.patch -> fix ptr init
++  * Repomans QA issues in sci-libs
++  * Added use flag descriptions for 'singular' used in sci-libs/factory and sci-libs/libfac
++  * sci-mathematics/Macaulay2 updated dependencies
++  * Repomans QA fixes in my sci-mathematics packages
++  * drop dapl support, seems not needed if you use infiniband
++  * Re-manifest
++  * Added patches to octave
++  * sci-mathematics/octave-forge-meta -- sci-mathematics/octave-forge-video added as dep (Portage version: 2.2_rc52/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-mathematics/octave-forge-video -- Written by Emil Karlson (Portage version: 2.2_rc51/git/Linux i686)  (Signed Manifest commit)
++  * add infiniband and dapl support via extrenal libs to openmpi
++  * sci-chemistry/ccp4-apps -- nesseccary fix to work together with Arp/Warp (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-mathematics/frama-c-20090901: always_init.patch
++  * Added to tree
++  * sci-chemistry/drawxtl -- SRC_URI fix, thanks to Hannes Krueger (Portage version: 2.2_rc51/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/ccp4i -- Manifest fixed (Portage version: 2.2_rc51/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/arp-warp-bin -- Fixed instruction when python is bumped (Portage version: 2.2_rc51/git/Linux i686)  (Signed Manifest commit)
++  * Macaulay2-1.3.1-r2 completely split ebuild
++  * Frobby, now installing missing header
++  * New package sci-mathematics/frobby Final dep for Split Macaulay :) Bug #294503
++  * Update homepage at request of upstream. (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccp4-apps -- masked bad version (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/pointless-1.4.5 -- version bump (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccp4-apps -- missing $ and pisa/sbase installation fix (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccp4i -- typo corrected
++  * sci-libs/balbes-db -- set env BALBES_ROOT (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * ccp4-apps start to fix usage of ccp4.setup.*
++  * New package: sci-libs/factory Dependency of sci-libs/libfac
++  * New package sci-libs/libfac A dependency of sci-mathematics/Macaulay2 and sci-mathematics/Singular
++  * Remove older versions of sys-cluster/mpich2 (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * bump sys-cluster/mpich2-1.2.1 (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * qgis-9999: add sqlite use dep to python. needed for the OSG plugin to work.
++  * sci-mathematics/frama-c-20090901: always_define.patch
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * Added an experimental octave
++  * sci-mathematics/frama-c-20090901: init_locals_defined.patch
++  * New package, ebuild written by me
++  * sci-chemistry/ccpn -- Bad mistake in setting compile options --> leads to opengl crashes (Portage version: 2.2_rc51/git/Linux i686)  (Signed Manifest commit)
++  * Needs octave > 3.2, bug #293814
++  * Normaliz Manifest. Upstream did change that file!!!
++  * Filesize for mpir-1.2.2 Did upstream change that .tar.gz??
++  * Importing iml-1.0.3
++  * Fix openib.init.d and env.d (Portage version: 2.2_rc51/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * sci-chemistry/gromacs build mpi and non-mpi libs in 4.0.5-r1 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-visualization/qtiplot -- Fixed sip patch to work with <sip-4.9 (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix openib.conf for modprobe (Portage version: 2.2_rc51/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Import polybori
++  * Add a patch and a use flag to dev-libs/mpir
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * qgis-9999: fix the subdir paths so that extensions work again. Still getting QA reports from portage. maybe someone else can look at that?
++  * Fix manifest (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * missing dep (Portage version: 2.2_rc50/git/Linux i686)  (Unsigned Manifest commit)
++  * [sci-geosciences/qgis-9999]: remove unneeded patch
++  * qwt removed again
++  * sci-visualization/qtiplot version bump to 0.9.7.10 (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * x11-libs/gl2ps -- Version bump & ported to cmake buildsystem (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * x11-libs/gl2ps imported from tree
++  * media-libs/emfengine missing dep added (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * media-libs/emfengine added (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * dev-tex/qtexengine -- add missing deps and compile dynamic lib (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * dev-tex/qtexengine -- use it right (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * dev-tex/qtexengine -- use of PATCHES from qt4.eclass (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * x11-libs/qwt -- version bump to latest commit in svn, needed for qtiplot (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * dev-tex/qtexengine added (Portage version: 2.2_rc51/git/Linux x86_64)  (Signed Manifest commit)
++  * qtiplot imported
++  * refetching qgis samples
++  * qgis now in main tree, adapted svn qgis
++  * mpir 1.2 branch updated. Sage people will care for 1.3
++  * Updated deps of Macaualay
++  * Revert "sci-geosciences/swmm: Version bump and upstream now includes version in"
++  * sci-geosciences/swmm: Version bump and upstream now includes version in download file.
++  * Manifest fix for mpir
++  * sci-mathematics/4ti2 good to go on amd64
++  * sci-mathematics/Macaulay2-1.3.1-r1 with doc fixes. Removed old versions
++  * gredata Manifest fix
++  * sci-chemistry/solve-resolve-bin -- Manifest fix (Portage version: 2.2_rc50/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/ccp4 -- oasis4 USE removed again (Portage version: 2.2_rc50/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/oasis4 -- oasis4 USE removed again (Portage version: 2.2_rc50/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccp4-apps -- oasis4 USE removed again (Portage version: 2.2_rc50/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccp4i -- oasis4 use removed again (Portage version: 2.2_rc50/git/Linux x86_64)  (Signed Manifest commit)
++  * BUGS is not in distribution
++  * add emake install and dodoc to src_install
++  * Initial ebuild of HFST package
++  * Manifest for gfan
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Initial condor ebuild
++  * sci-chemistry/oasis -- Initial commit Written by me fixes bug 290588 (Portage version: 2.2_rc50/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccp4i commiting all fixes for oasis support (Portage version: 2.2_rc50/git/Linux x86_64)  (Signed Manifest commit)
++  * last fix for oasis support in ccp4-apps (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
++  * mv SCIAPPS in ccp4-apps to PEDEPEND (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
++  * fixed oasis USE dep to ccp4-apps (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/solve-resolve-bin added to overlay (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
++  * add solve license
++  * oasis license added
++  * sci-mathematics/Macaulay2-1.3.1 revbump
++  * New Package: dev-libs/mpir (integer arithmetics, drop-in replacement for gmp) Bug #293383
++  * New package sci-mathematics/gfan (Computations in tropical and toric algebra) Bug #293381
++  * sci-chemistry/xia2 -- added missing fixes for bytecompiling (Portage version: 2.2_rc50/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/xia2 -- SRC_URI fix (Portage version: 2.2_rc50/git/Linux i686)  (Signed Manifest commit)
++  * dev-python/omniorbpy: copied last version from portage
++  * dev-util/mercurial-server version bump to 0.9 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/coot -- greg-data digest fixed (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/refmac -- Upstream did a change to the tarball (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/xia2 -- version bump (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
++  * app-text/txt2tags-2.5 added to fix bug #278317 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/gromacs fix for bug #284431 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/ccpn -- fixes for internal help and opengl usage (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/coot -- dev-scheme/goosh dep removed (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
++  * dev-util/smartgit version bump (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccpn version bump (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
++  * fixed inherit, stupid me (Portage version: 2.2_rc49/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/smmp ifrst checkin (Portage version: 2.2_rc49/git/Linux i686)  (Signed Manifest commit)
++  * removed ntl, in main tree
++  * fixes patching for sci-chemistry/ccpn (Portage version: 2.2_rc49/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/nmrpipe -- corrected patch name (Portage version: 2.2_rc49/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/ccpn -- version bump (Portage version: 2.2_rc49/git/Linux i686)  (Signed Manifest commit)
++  * version bump (Portage version: 2.2_rc49/git/Linux i686)  (Signed Manifest commit)
++  * fasta version bump and fix of chatastrophic ebuild, src_test is still broken (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
++  * [sys-block/tgt] Version bump (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
++  * Added acknowledgement (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-libs/clapack -- fixed SRC_URI to upstreams (Portage version: 2.2_rc49/git/Linux x86_64)  (Signed Manifest commit)
++  * givaro bump
++  * sci-libs/cctbx version bump fixes boost <-> python-2.6.4 issues (Portage version: 2.2_rc48/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-chemistry/coot bumped to bills latest stable release (Portage version: 2.2_rc48/git/Linux x86_64)  (Unsigned Manifest commit)
++  * greg-data Manifest fix (Portage version: 2.2_rc48/git/Linux x86_64)  (Signed Manifest commit)
++  * Fixed sprintf bug (fixes #290373).
++  * Merged Justin's fix into portage.
++  * Moved to tree
++  * Add ICM License
++  * icm-browser version bump (Portage version: 2.2_rc46/git/Linux x86_64)  (Unsigned Manifest commit)
++  * icm version bump (Portage version: 2.2_rc46/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-chemistry/coot bumped to latested release from fink (Portage version: 2.2_rc48/git/Linux x86_64)  (Signed Manifest commit)
++  * m4ri version bump
++  * give some gcc-4.4 love to modglue
++  * more parallel make fixes for lie
++  * cadabra version bump
++  * sci-chemistry/ccp4i fix for f2mtz bug 289379
++  * sci-visualization/gnuplot: version bump to 4.5.9999 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * update package.mask for gnuplot-4.5.9999
++  * sci-libs/opencascade fix for java include, reported via IRC by roelof
++  * fix bug 291597
++  * small fix (Portage version: 2.2_rc48/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/libcmatrix version bump to 3.2.1 (Portage version: 2.2_rc48/git/Linux i686)  (Signed Manifest commit)
++  * Add GamessQ (Portage version: 2.2_rc48/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-chemistry/wxmacmolplt] Moved to tree
++  * ccp4-libs -- fixed the 64bit fix (Portage version: 2.2_rc48/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccp4-apps: PYTONPATH patch added -- thanks Donnie for pointing this out (Portage version: 2.2_rc47/git/Linux i686)  (Signed Manifest commit)
++  * sci-libs/cgnstools: Fixed problems with 2D meshes and cgns_to_vtk.
++  * dev-python/pythoncgns: Initial release for bug 291221
++  * apbs version bump (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sys-cluster/scalasca missing dep bug #290560 (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * 64bit fix (Portage version: 2.2_rc46/git/Linux i686)  (Signed Manifest commit)
++  * app-arch/lbzip2 version bump (Portage version: 2.2_rc46/git/Linux i686)  (Signed Manifest commit)
++  * apbs version bump (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * fix for bug 289032 (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * fix for bug 290754 (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * import from stride
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * In main tree
++  * renamed patch which was missing
++  * nedit is fixed in tree
++  * smartgit version bump
++  * app-arch/lbzip2 version bump to 0.16 (Portage version: 2.2_rc46/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/ccpn python update (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/talos+  version bump fixes bug 289651
++  * sci-chemistry/nmrpipe version bump (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * talos missing RDEPEND added
++  * nmrpiep fixes (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/nmrpipe various fixes (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/tinker version bump fixes bug 290459 Thanks Ivan Fedyanin for providing a updated ebuild (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * app-editors/nedit missing die (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * dev-ml/mlgmpidl-1.1: fix depend variable
++  * wrong CAT name
++  * update gre-test digest (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * app-editors/nedit fix for bug 290337 (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * nedit import from portage
++  * New package, bug 155780. Ebuild written by me and dawe <daweonline@gmail.com>
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * more eapi2 updates
++  * various eapi2 updates
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/sage-bin: I stopped trying to make sage-bin work some time ago.  Upstream made it very difficult.  Ebuild not updated since then and now trying to work out an ebuild to compile sage rather than install the binaries.
++  * New package, bug 155780. Ebuild written by me and dawe <daweonline@gmail.com>
++  * version bump fix for upstream typo
++  * sci-electronics/linsmith version bump patch created by TomJBE (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * Added gcb
++  * Added classads
++  * sci-chemistry/polygon initial commit written by me (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * needed die added
++  * sci-libs/gmsh-9999: moved sources to svn repesitory
++  * app-arch/lbzip2 version bump to 0.16_rc1 Maintainer wrote me a mail. (Portage version: 2.2_rc46/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/refmac version bump (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * [sci-biology/sequin] Please dont brake metadata. Run repoman full before you commit something. Or use repoman commit it works with git too (Portage version: 2.2_rc46/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Add desktop shortcut
++  * Fix manifest
++  * New package, ebuild written by me
++  * sci-chemistry/molrep tests enhanced (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * version bump of pointless (Portage version: 2.2_rc46/git/Linux i686)  (Signed Manifest commit)
++  * molrep version bump (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * refmac version bump to 5.5.108 (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-libs/med-2.3.5 needs >=sci-libs/hdf5-2.6.4
++  * removed numeric dep (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-mathematics/apron/apron: fix ppl install on x86
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/gappa(lib-coq): bump version to 0.12(.1)
++  * sci-libs/gmsh-9999: removed keywords
++  * Manifest fix again (Portage version: 2.2_rc46/git/Linux i686)  (Signed Manifest commit)
++  * Cleaning and much QA, tested on amd64
++  * Manifest (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * tried to fix coot test
++  * qa
++  * sci-mathematics/why: fix search with pvs binary
++  * dropping sci-mathematics/pvs: unmaintained mainstream and PITA to maintain in portage
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/pvs: fix sbcl-patch on i*86
++  * sci-libs/gmsh: small corrections + version bump + nightly version
++  * sci-libs/cgnslib: fixed DEPEND and RDEPEND confusion
++  * sci-libs/med: Version bump + corrections, doc and examples USE flags added
++  * [sys-infiniband/ibutils] Fix bug 289037. thanks to Kacper Kowalik (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * Version bump to blcr-0.8.2.  Minor edits to remove unused vmadump module and unneeded sandbox warning.
++  * refmac version bump to 5.5.0107
++  * fix Manifest and remove old versions (Portage version: 2.2_rc46/git/Linux i686)  (Signed Manifest commit)
++  * manifest fix
++  * [sci-chemistry/ccpn] Fix manifest (Portage version: 2.2_rc46/git/Linux x86_64)  (Signed Manifest commit)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * new version needs testing
++  * ccpn update
++  * cctbx version bump
++  * refmac bump to 5.5.106
++  * coot libcurl dep added
++  * ccpn version bump to 2.1.1
++  * sci-mathematics/frama-c: varinfo_export patch dev-ml/ocamlgraph: eapi2 fix
++  * octave-epstk-2.1.ebuild -- fix for bug 288586 Some QA, rest is commented in the ebuild
++  * Bump ICC 10 series per bug 284801
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * Version bump, rewrite and rename to gbrowse
++  * ccpn update
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * New package, ebuild written by me
++  * Import of lwpr
++  * ccpn now includes updates from upstream which are not provided in the releases
++  * pointless tarball mirrored
++  * [eclass] Update openib eclass per bgreen mail
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * opendx changes now in main tree
++  * Bump sys-cluster/mpich2-1.2
++  * Added working docs from old gentooscience repo
++  * aplpy version bump
++  * vo version bump
++  * atpy bump
++  * sci-chemistry/mgltools-autodocktools Needs python[tk]
++  * sci-chemistry/autodock Qa and respect flags
++  * sci-chemistry/mgltools-autodocktools -- Added sci-chemistry/mgltools-support to RDEPEND
++  * removed icc idb ifc ipp now in main tree
++  * Some QA on coot
++  * fixed ChangeLog and Manifest
++  * coot fixes as-needed patch not needed anymore Same for reduce sed rappermc patch added
++  * molrep version bump to 10.2.34
++  * refmac version bump to 5.5.105
++  * [sci-biology/foldingathome] Version bump (Portage version: 2.2_rc43/git/Linux x86_64)  (Signed Manifest commit)
++  * Merge remote branch 'origin/master'
++  * Fixed bug in octave-forge eclass.
++  * Bumped remaining octave-forge ebuilds.
++  * [sci-biology/fasta] Fix manifest (Portage version: 2.2_rc42/git/Linux x86_64)  (Signed Manifest commit)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-visualization/ferret-bin:  Version bump to 6.3.
++  * In main tree
++  * Bumped additional octave-forge ebuilds.
++  * Manifest
++  * Fixing shaders patch
++  * Fixing pymol shaders patch.
++  * Bumped some of the octave-forge packages.
++  * In main tree
++  * pymol bump to 1.2.2
++  * sci-mathematics/netgen: fixed Manifest hopefully
++  * sci-mathematics/netgen: fixed Manifest and Changelog
++  * sci-mathematics/netgen: fixed libTogl location as it changed; removed old 4.4er patches
++  * sci-mathematics/netgen: Changed opencascade path to /opt/opencascade-6.3/ros 4.9.11; removed old 4.4er versions
++  * dev-tcltk/togl: Fixed install paths for togl-1.7; removed 2.0 as this is now in portage
++  * MANIFEST
++  * ccp4i should have been bumped before
++  * Merge git+ssh://kancheli/data/local/science into refmac
++  * refmac bump and cleanup
++  * version bump
++  * Add dep on sys-cluster/empi to mpi.eclass for classed packages.
++  * [dev-util/mercurial-server] Homepage updated (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * Remove incorrect blocker.
++  * clustalw-1.83-r3 is in the tree
++  * [dev-util/mercurial-server] Initial commit (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * In main tree
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * New package, ebuild written by me
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/frama-c: varinfo patch only to fix export
++  * [sys-block/tgt] Add missing rdepend (Portage version: 2.2_rc41/git/Linux x86_64)  (Unsigned Manifest commit)
++  * net-fs/glusterfs moved to tree as sys-cluster/glusterfs
++  * Another bunch of updates related to Frama-C
++  * Various updates related to Frama-C.
++  * removed h5py now in main tree
++  * removed h5py now in main tree
++  * coot -- upstream fixes COOT_TEST_DATA_DIR and included our patch for tests
++  * smartgit version bump
++  * dev-python/h5py: Version bump to 1.2.1.
++  * app-text/dgs: fix + modifs thanks to Olivier Huber
++  * New package: sci-mathematics/topcom-0.16.0 Bug #285619
++  * manifest
++  * manifest
++  * Manifest fix
++  * ccpn update
++  * smartgit versio bump
++  * smart-git version bump
++  * ccpn versionbump
++  * test
++  * ccpn minor fixes
++  * sci-chemistry/pymol-plugins-bni-tools added
++  * ccpn version bump and rewrittings
++  * sci-libs/gmsh: Reworked ebuild from Etienne Lorriaux
++  * sci-mathematics/netgen: Version bump
++  * tablelist: bump to 4.12.
++  * Bump mpich2-1.1.1_p1
++  * fixed env files for ifc and icc
++  * Replaced the broken opencascade-6.3 by opencascade-6.3-r1
++  * First import in science overlay as an opencascade dependency
++  * Cleaning  Committer: Etienne Lorriaux <etienne.lorriaux@gmail.com>  Changes to be committed: 	deleted:    Changelog 	modified:   Manifest 	modified:   med-2.3.1.ebuild 	modified:   med-2.3.4.ebuild
++  * Added correct manifest  Changes to be committed: 	modified:   Manifest  Changed but not updated: 	deleted:    Changelog
++  * Version bump + trivial changes for QA check  Committer: Etienne Lorriaux <etienne.lorriaux@gmail.com>  Changes to be committed: 	new file:   ChangeLog 	new file:   files/med-2.3.4-gcc-4.3.patch 	new file:   med-2.3.4.ebuild 	new file:   metadata.xml  Changed but not updated: 	deleted:    Changelog 	modified:   Manifest 	modified:   med-2.3.1.ebuild 	modified:   med-2.3.4.ebuild
++  * New package, thanks to Philippe Veber for the ebuild
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * New package, thanks to Philippe Veber for the ebuild
++  * HOMEPAGE corrected bug 285068 bumped prerelease to r2312 which will be the version of the second prerelease Included src_test in prerelease
++  * fix for bug 285068
++  * Gentoo is UNIX isn't it?
++  * sci-visualization/ferret-bin-6.2: Version bump plus much simpler because upstream generously changed download names.  Fixed some environment variables that didn't work in files/99ferret.
++  * coot working test revision to log added
++  * test-data was updated
++  * coot src_test cleanup
++  * src_test is working on coot
++  * prelimary src_test fix
++  * New package, ebuild written by me
++  * sci-mathematics/freefem++: version bump and cleanup.
++  * coot -- typo fixed
++  * coot -- use test condition missing for unpack
++  * coot -- src_test is working
++  * greg-1.5 added
++  * [dev-lang/ifc] Fix manifest; Please\! Dont commit ebuild with broken manifests\! (Portage version: 2.2_rc40/git/Linux x86_64)  (Signed Manifest commit)
++  * fix license
++  * fix license
++  * fix license
++  * missing quotations
++  * pointless -- version bump
++  * dev-scheme/greg added
++  * dev-util/smartgit version bump
++  * removed the env-update from pkg_postinstall
++  * Various updates related to sci-mathematics/frama-c
++  * New package, ebuild written by me
++  * Version bump
++  * Fixed closing quotations
++  * Modified env files for icc and ifc
++  * [dev-lang/ifc] Fix manifest (Portage version: 2.2_rc40/git/Linux x86_64)  (Signed Manifest commit)
++  * Fixed collision files among Intel packages
++  * fixed tagged source script
++  * Added numscons
++  * New ebuild for icc gathering all components
++  * New package: sci-mathematics/normaliz Bug #283676
++  * [sci-geosciencies/josm] New version
++  * sci-mathematics/netgen: Changed to slotted togl-1.7, minor changes for opencascade
++  * dev-tcltk/togl: Slotted ebuild for version 1.7
++  * readded togl
++  * coot Upstream fixed the check maketarget
++  * togl is fixed in the tree
++  * [sci-geosciences/qgis] Version bump. Ebuild fixed. Dropped postgis from dependencies. Delete gdal from overlay
++  * sci-mathematics/netgen: fixed netgen.desktop
++  * sci-mathematics/netgen: Version bump, make repoman happy; Thanks to Christoph Lehrenfeld, Adam Zdunek and Daniel Tourde
++  * dev-tcltk/togl: Reintroduced togl-1.7 as dependency for >netgen-4.9*
++  * sci-libs/cgnslib: Reintroduced cgnslib-2.5.3, as it needs <sci-libs/hdf5-1.8
++  * sci-libs/cgnslib: Needs now >=sci-libs/hdf5-1.8
++  * sci-libs/cgnstools: Corrected checksums, as upstream changed tarball.
++  * sci-libs/cgnslib: Corrected checksums, as upstream changed tarball.
++  * coot -- src_test developed
++  * version bump
++  * smartgit version bump
++  * ccp4i added crank_shelxd.tcl.patch QA removed WINDOWS and UNIX binary dirs cleaned up old versions
++  * talos+ version bump
++  * prelimary src_test support for coot
++  * sci-libs/driftwood written by me
++  * probcons ldflags and collision fix
++  * sci-chemistry/mosflm parallel cbf make patch
++  * QA on lbzip
++  * QA on my sci-libs packages
++  * superlu version bump
++  * fetch url fixed
++  * smartgit added
++  * lincense smartgit added
++  * sci-libs/calculix-cgx: Version bump.
++  * sci-libs/calculix-ccx: Version bump.
++  * sci-libs/cgnstools: Version bump
++  * sci-libs/cgnslib: Version bump, restricted to <sci-libs/hdf5-1.8
++  * [sci-chemistry/almost] Fix manifest (Portage version: 2.2_rc40/git/Linux x86_64)  (Signed Manifest commit)
++  * Bug #282174 was fixed. Removed workarounds from ebuild.
++  * Manifest
++  * sci-chemistry/mrbump superpose fix
++  * [eclass] Update openib.eclass
++  * [sys-block/tgt] we need to wait for 1 second to setup tgtd (Portage version: 2.2_rc38/git/Linux i686)  (Unsigned Manifest commit)
++  * [sys-block/tgt] update tgtd init.d (Portage version: 2.2_rc38/git/Linux i686)  (Unsigned Manifest commit)
++  * [sys-block/tgt] make ebuild eapi=2 (Portage version: 2.2_rc38/git/Linux i686)  (Unsigned Manifest commit)
++  * [sys-block/tgt] Update patch (Portage version: 2.2_rc38/git/Linux i686)  (Unsigned Manifest commit)
++  * sci-mathematics/pest-11.3: Updated copyright line in header
++  * sci-mathematics/pest-11.11: Version bump.  New web site and download.
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * [qgis-9999] when enabled, depend on python with sqlite support (needed for OSM plugin)
++  * fix for bug 282503
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * sci-libs/cbflib QA rpath and soname fixed
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * fixed bug 238300
++  * New package, ebuild written by me
++  * New package, ebuild written by me
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * [sys-infiniband] Update rds-tools
++  * [eclass] Update openib eclass
++  * [eclass] Update openib eclass
++  * [eclass] Update openib eclass
++  * [eclass] Update openib eclass
++  * [sys-infiniband] Add rds-tools
++  * [sys-infiniband] Add missing dep to ibutils
++  * [sys-infiniband] Add ibutils
++  * [sys-infiniband] Add ibutils
++  * [sys-infiniband] Add patch for OSM
++  * [sys-infiniband] Add patch for OSM
++  * [sys-infiniband] Update to OFED 1.4.1
++  * [sys-block/tgt] Version Bump to 0.9.8 (Portage version: 2.2_rc38/git/Linux i686)  (Unsigned Manifest commit)
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Rewritten version of sci-mathematics/Macaulay2 to fix QA issues.
++  * removed hdf5 now in main tree
++  * Add blocker against app-text/lcdf-typetools when vt is enabled. #281318
++  * Add blocker against app-text/lcdf-typetools when vt is enabled. #281318
++  * Remove -I hack for fortran
++  * manifest
++  * PYTHONPYTH fix and configure cut
++  * collision ccp4i and mrbump
++  * right clustalw added to overlay
++  * x11-libs/libjwc_f add patch until ccp4 6.1.2
++  * x11-libs/libjwc_cfixed the fix
++  * libjwc update to 6.1.2 and as-needed fix
++  * another blocker
++  * fix for bug 281734
++  * sci-chemistry/mrbump -- typo fixed in RDEPEND
++  * sci-chemistry/mrbump dependency added
++  * mrbump dependency fixed
++  * fixes mrbump collision fixes some variables
++  * [sys-infiniband/librdmacm] Add libibverbs to depend (Portage version: 2.2_rc38/git/Linux i686)  (Unsigned Manifest commit)
++  * sci-mathematics/freefem++: version bump.
++  * sci-chemistry/imosflm -- IMOSFLM_VERSION is set by sci-chemistry/imosflm
++  * sci-chemistry/ccp4-apps -- IMOSFLM_VERSION is set by sci-chemistry/imosflm
++  * Another git add . block for <sci-chemistry/ccp4-6.1.2
++  * sci-chemistry/imosflm rewritten compile phase
++  * ccp4 USE db renamed to balbesdb as suggested by Donnie and Afrever
++  * mmdb blocks !! ccp4-libs
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * ccp4-apps Manifest renewel due to merge
++  * ccp4i -- fixes to remove imosflm
++  * ccp4 setup.sh part 2
++  * imosflm bump and lib fix
++  * sci-chemistry/ccp4-apps fix for bash/sh compatibility
++  * .
++  * fix manifest
++  * keyworded ~amd64 after testing
++  * remove keywords. live version should not be installed by accident
++  * ingleborough is released
++  * balbes-db PDEPEND handled by sci-chemistry/ccp4
++  * ccp4 -- balbes is now optionall
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * sys-cluster/scalasca DOCDIR fix (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sys-cluster/scalasca version bump (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * trry to build libmmdb seperatly
++  * libmmdb build seperatly
++  * coot gcc-4.4 compatibility is fix by upstream
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * sync openmpi-1.3.3 with portage.
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * mmdb version bump added, needed for coot
++  * ccp4-6.1.2 tarball changes -- Manifest update
++  * pointless masked
++  * pointless version bump
++  * burrow-owl has some fixes from upstream now
++  * Adjusted DEPEND and RDEPEND.
++  * burrow-owl added from donnies overlay
++  * =sci-chemistry/burrow-owl-9999_pre15 masked
++  * ccp4-libs -- libccif.so gets build correctly on amd64
++  * reduce firxes for bug 280857 & 280858
++  * starparse keyworded for ~x86
++  * coot -- fixes for gcc4.4 and glibc-2.10
++  * where does  *.seave come from
++  * scale for 6.1.2!
++  * sci-libs/balbes-db ready for 6.1.2
++  * nmrpipe ver bump 5.0.2009.203.18.54
++  * repoman told about additional lines
++  * ccp4-apps imosflm excluded
++  * ccp4 cleanup and transmission to ccp4-6.1.2
++  * molrep version bump
++  * xia bump for ccp4-6.1.2
++  * ccp4-apps which I broke somehow are fixed now
++  * pointless bump
++  * guile-www bump
++  * ccp4-6.1.2 deps masked
++  * ccp4-apps transmission ccp4 --> ccp4-apps and ccp4 as meta package
++  * dev-tcltk/tablelist version bump
++  * sci-libs/med: Just updated SRC_URI; repoman is not yet happy :-S
++  * sci-libs/cgnsfoam: Initial import to science overlay
++  * sci-libs/libcgnsoo: Initial import to science overlay
++  * [sci-biology/wgs-assembler] Update manifest (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
++  * pymol-1.2.1 is in tree, lets remove it from Manifest
++  * Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci
++  * Added to portage tree.
++  * removed keywords
++  * Version bump
++  * re-manifest
++  * Modified stuff and skymaker licenses
++  * the new ccp4-apps package masked
++  * ccp4i adapted to ccp4-apps
++  * ccp4 -- ccp4-apps
++  * RDEPEND fixed
++  * ccp4 --> ccp4-apps
++  * starparse Manifest fix and tree version removed
++  * netcdf removed and bug 279817 filed
++  * scala masked
++  * scala added -- to be excluded from ccp4
++  * pymol cleanup to move to the tree as requested by fauli in bug 269119
++  * [sys-infiniband] Deps cleanup
++  * version bump netcdf to 4.0.1 hdf5 support and any new features is not included yet
++  * molrep bump to 10.2.33
++  * ccp4-libs bumped to 6.1.2
++  * ccp4i bump to 6.1.2
++  * masked ccp4i-6.1.2
++  * here we can sort and store patches which are used by multiple packages to create tarballs out of them which can be mirrored
++  * update-monomers-db fixed --> sha256sum ouput
++  * automatic bump
++  * tinker now builds
++  * [sci-astronomy/skymaker] Update Manifest (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
++  * gabedit version bump requested by Maximilian Bräutigam bug 279438
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * suff initial import
++  * skymaker: version bump
++  * RASLIC license added
++  * balbes-db files permission QA
++  * Jligand has some internal wierdness
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * In main tree
++  * tinker bump to 5.0
++  * sci-chemistry/jligand -- written by me
++  * Version bump
++  * In main tree
++  * Revert "In main tree"
++  * In main tree
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * In main tree
++  * sci-chemmistry/rasmol version bump 2.7.5
++  * cbflib fix for fortran compatibility
++  * sci-libs/neartree written by me
++  * sci-libs/neartree written by me
++  * dev-libs/cvector written by me
++  * Merge branch 'freefem++-3.4'
++  * sci-mathematics/freefem++: fix dependencies for document building, cleanup  old files for freefem++-3.2.
++  * jana200 for Hannes Krüger
++  * changed sys-cluster to sys-infiniband in DEPEND
++  * updated Manifest
++  * changed "sys-cluster" to "sys-infiniband" in dependency spec.
++  * nmrpipe version bump
++  * remanifesting
++  * removed old cpl
++  * esorex version bump
++  * gasgano version bump
++  * added prroper license
++  * Initial import of kapteyn
++  * sci-libs/oasa: Version bump to 0.13.1
++  * sci-chemistry/wxmacmolplt: Version bump to 7.3
++  * sci-libs/cgnslib: executable rights for adf2hdf/hdf2adf
++  * [sys-infiniband] Move Infiniband Here
++  * [eclass] Update OpenIB eclass
++  * atpy initial import
++  * vo initial import
++  * add romio to mpi dep
++  * aplpy version bump
++  * pywcs version bump
++  * sci-libs/gmsh: Version bump; del hdf5 patch; dep fixes; EAPI=2
++  * Links now directly against libcgns; Changed to EAPI=2
++  * Installs ADF.h even without hdf5 USE-flag
++  * Added patches from debian; changed to EAPI=2
++  * version bump for cforms
++  * cbflib bump to 0.8.1
++  * Merge branch 'master' of ssh+git://134.94.85.9//data/local/science
++  * cbflib version bump
++  * sci-chemistry/openbabel-ruby: Version bump to 2.2.2
++  * sci-chemistry/openbabel-python: Version bump to 2.2.2
++  * sci-chemistry/openbabel-perl: Version bump to 2.2.2
++  * remove old version of cadabra
++  * update to cadabra 1.14
++  * Deleted old ebuild.
++  * Version bump.
++  * change Grass to wxwidgets USE flag
++  * add qgis libe ebuild for SVN trunk
++  * Fix up patch to apply to rc1
++  * Modified patch
++  * anifest
++  * add a copy of pymol-1.2_rc1-shaders.patch too...
++  * Changelog
++  * fix Manifest
++  * copy pymol-1.2_rc0-data-path.patch pymol-1.2_rc1-data-path.patch
++  * clipper bump
++  * mtz2sca DESCRITPION fixed
++  * mtz2sca added
++  * Initial add mtz2hkl Thanks to jlec for writting this ebuild pending bug is 278048
++  * fix manifests after merge conflict and wrong choice :-/
++  * change the postgres dep for qgis and grass
++  * now cns Manifest is fixed
++  * cns manifest fix
++  * fixed bug 277829
++  * clipper depends on fftw
++  * readded the j1 in ccp4
++  * Fix attribution
++  * New package, bug 119636
++  * live ebuilds are live ebuilds and do not have reviesions
++  * ccpn -- QA typo fixed and old patch removed
++  * clipper LDADD -> LIBADD
++  * ccp4 --disable-mosflm
++  * aria added to overlay
++  * fixed src-tarball name for aria
++  * cns -- aria support, ixes for bug 247579 and 276308, LDFLALGS are respected now, some QA
++  * ccpn -- python[ssl]
++  * fixed drawxtl dep to fltk:1,1
++  * pymol -- media-video/mpeg-tools dep added
++  * remove keywords
++  * make sure gdal does not compile against grass and make qgis depend on this fixed gdal version
++  * make sqlite optional for qgis-1.1.0 and clean up some issues
++  * sci-geosciences/qgis - remove unneeded patch, add development version
++  * update deps - in java overlay
++  * update deps - in java overlay
++  * initial import of new versions of Grass, QGIS, gdal and gdal-grass. The gdal-grass lib will resolve the current situation of circular dependencies between gdal and grass in portage and make depending on gdal-grass support easier.
++  * coor clipper dependency fixed
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * treectrl bump
++  * mpi.eclass:  mpi_doman fixes.
++  * Version bump. Changed dependency and added test (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
++  * pymol -- vmd and numpy support added
++  * mosflm CFLAGS fix -- Thanks Donnie for pointing that out
++  * In main tree
++  * pymol bump to secaond release candidate for 1.2
++  * drawxtl fix -- upstream ships objects
++  * drawxtl version bump thanks Hannes Krüger for the ebuild
++  * refmac version bump and test QA
++  * pymol has two buildsstems. We use the distutils one.
++  * rci ebuildlayout fixed
++  * resort dependencies in ccp4
++  * ccp4i depends on media-gfx/graphviz
++  * ccp4i baubles fix
++  * cctbx is depending on shelx for amd64
++  * pointless bump
++  * Donnie says pointless works for him
++  * xia doesn't use specific pointless version
++  * xdsi kpdf -> xpdf fix
++  * In gentoo-x86
++  * In gentoo-x86
++  * xdsi dep fix
++  * another syntax fix
++  * reverted
++  * CCP4_SCR fixed
++  * ccp4i -- superpose renamed to superpose-ccp4
++  * missing dep of xia2 added
++  * ccp4-libs aadditional bin installation
++  * xia license changed to BSD
++  * xia depends on right ccp4 version
++  * ccü4 needed for xia
++  * xia version bump
++  * balbes-db now in right place
++  * ccp4 userpriv and usersandbox fixed
++  * ccp4 upstream ctruncate patch included next version added
++  * caver bump
++  * cealign QA
++  * masked ccp4 6.1.2
++  * molrep bump
++  * sys-cluster/pyslice: Forgot to commit the ChangeLog.
++  * sys-cluster/pyslice: Version bump.  Fixed DEPEND and RDEPEND.
++  * sci-mathematics/mdp: Version bump.  Fixed DEPEND and RDEPEND.
++  * sci-geosciences/tappy: Version bump. Fixed DEPEND and RDEPEND.
++  * sci-geosciences/tappy: Version bump.  Fixed DEPEND and RDEPEND.
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * sci-mathematics/mdp: Version bump to 2.5.  Fixed DEPEND and RDEPEND.
++  * newbin > exeinto+newexe.  Thanks jlec
++  * refmac bump, test still broken
++  * Fix empi install location.
++  * pymol 1.2 rc0
++  * pymol nosplash fix for Je_fro
++  * refmac test.log patch fix
++  * metadata.xml fixed
++  * refmac test improved
++  * xdsi added
++  * xdsstat-bin added
++  * pymol src_unpack fix (thanks to Rene Meier)
++  * refmac bump
++  * empi:  Fix the location of the changelog.
++  * Bump mpi.eclass.  See sys-cluster/empi-0.6 ChangeLog for details.
++  * Remove app-admin/eselect-mpi, included in sys-cluster/empi.
++  * Bump empi-0.6, see included changelog for details.
++  * Version bump (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
++  * Initial import pywcs
++  * Initial import of aplpy
++  * Added dependency on libtool-2 and szip-2
++  * another pymol splash fix
++  * coot live fix
++  * refmac fixes and version bumps
++  * monomer fix
++  * refmac version bump hosting of apbs patch
++  * refmac -- make download of test sets conditionally
++  * test version of hdf5-1.8.x import
++  * test version of hdf5-1.8.x import
++  * refmac test case added
++  * monomer-db crap fixed
++  * refmac experimental version bump
++  * final fix for update-monomers-db
++  * automatic bump
++  * automatic bump
++  * automatic bump
++  * automatic bump
++  * automatic bump
++  * automatic bump
++  * automatic bump
++  * fix of update-monomers-db
++  * automatic bump
++  * talos+ QA
++  * refmac bump
++  * [metadata] add metadata layout.conf and git ingore for users who wants to use cache generated by layman
++  * refmac bump
++  * masked gromacs live ebuilds
++  * sci-chemistry/gromacs: added live ebuilds for old, stable, experimental branch (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * sci-chemistry/gromacs-4.0.4: Fixed some repoman errors (Portage version: 2.1.6.13/git/Linux i686)  (Signed Manifest commit)
++  * in portage
++  * masked new monomer-db
++  * monomer-db reversioning and addition of "maybe" unstable monomer-db This has to be involved
++  * refmac unstable bump and dep to new monomer-db added
++  * dev-python/h5py-1.1.0:  Fix SRC_URI and digest.
++  * [sci-chemistry/icm] Add new ebuild (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
++  * keyworded coot-9999.ebuild and added new coot-data as dependency
++  * simplify apbs patch for pamol -- Donnie told to go the most easy way for the maintainer
++  * cara rdepend fixed
++  * sci-visualization/ferret-bin: Forgot to commit the Changelog.
++  * sci-geosciences/xtide: Fixed copyright years. Removed '~x86' from keywords because repoman complained.
++  * sci-libs/scikits_timeseries-0.91.1: Fixed DEPEND, RDEPEND, and metadata.xml.
++  * sci-visualization/ferret-bin-6.1: Fixed RDEPEND.
++  * sci-libs/scikits_timeseries-0.91.1.ebuild:  Initial ebuild.  Please file bugs at http://bugs.gentoo.org/show_bug.cgi?id=274430
++  * sci-visualization/ferret-bin-6.1.ebuild:  Initial ebuild.  Report bugs at http://bugs.gentoo.org/show_bug.cgi?id=274425
++  * pymol bump to beta7
++  * >=dev-lisp/cmucl-19e : needed by sci-mathematics/pvs
++  * Hopefully last patch to opendx for a while
++  * shiftx added
++  * digest
++  * Manifest
++  * fix patch
++  * Add fix from Christian Becke in bug #237634. Hopefully this doesn't break things for anyone else :)
++  * Remove old sys-cluster/hpl version.
++  * Sync sys-cluster/hpl with gentoo-cvs
++  * Remove old openmpi versions.
++  * Openmpi to EAPI=2, Sync ebuild with gentoo-cvs. Fix install location of vt include files when using empi.
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * Merge branch 'freefem++-3.3'
++  * sci-mathematics/freefem++: Version bump, now FHS comliant.
++  * ccp4 -- molref not installed anymore -> linked against libs we don't want to depend on
++  * frama-c: more clean ups.
++  * clean ups.
++  * sci-geosciences/tcd-utils: Correct bug in 20080820 ebuild, no longer needs $S specified.
++  * sci-geosciences/tcd-utils: Version bump to 20080820.  Updated copyright year.
++  * sci-geosciences/swmm: Missed the Manifest file.
++  * sci-geosciences/harmonics-dwf-free-noncomm: Fixed header copyright date.
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * sci-geosciences/harmonics-dwf-free: Version bump to 20081228.
++  * sci-geosciences/harmonics-dwf-free-noncomm: Version bump to 20081228.
++  * sci-geosciences/libtcd: Version bump to 2.2.4.  Add 'non-commercial' use flag to use.local.desc.
++  * ccp4libs cleanup
++  * pointless fix dependency
++  * ccp4-libs another linking problem fixed
++  * ccp4 examples are now optional
++  * another linking thing in ccp4-libs
++  * working pointless for Donnie
++  * pymol rekeyworded
++  * talos+ written
++  * [sys-block/tgt] Update deps (Portage version: 2.2_rc33/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sys-block/tgt] Update patch (Portage version: 2.2_rc33/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sys-block/tgt] Fix Makefile (Portage version: 2.2_rc33/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sys-block/tgt] Fix install (Portage version: 2.2_rc33/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sys-block/tgt] Fix install (Portage version: 2.2_rc33/git/Linux x86_64)  (Unsigned Manifest commit)
++  * [sys-block/tgt] Initial import (Portage version: 2.2_rc33/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-geosciences/swmm Version bump + minor change to edit Makefile
++  * dev-python/h5py: Version bump to 1.1.0
++  * masked pointless
++  * cctbx should be linkable now
++  * pointless added
++  * talos+ added
++  * nmrpipe is on the way to be fixed
++  * cctbx fixes
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * xds-bin: bump to 20090327.
++  * fixed coot KEYWORD
++  * mask live ebuilds
++  * live coot added
++  * pymol live ebuild added
++  * refmac bump and fix the eclass usage
++  * coot: fix as-needed build.
++  * Fix mrbayes building with mpi but without empi.
++  * coot fixed
++  * coot QA fixes and EAPI="2" for Donnie
++  * refmac qa
++  * Add a mpi.eclass version of mrbayes.
++  * rasmol QA
++  * cleaner glibc-2.10 fix in ccp4
++  * updated version of coot -- upstream includes our patches
++  * ccp4-libs version cleanup
++  * coot prereleases added
++  * ccp4-lins fix for glbic-2.10 (getline problem) bug 270615
++  * ccp4 glibc-2.10 getline fix bug 270617
++  * refmac experimental version bumped
++  * Fixing Manifest and EAPI location in LiE, modglue and cadabra
++  * mama manifest fixed
++  * opencascade now implictly rely on X when USE="opengl"
++  * phaser should work now
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * missing phaser patch added
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * phaser added thanks to Johan Hattne
++  * phaser licenses added
++  * old cctbx version removed
++  * refmac experimental version bump
++  * refmac bump to refmac-5.5.0095
++  * mmtk: set PYTHON_MODNAME.
++  * gabedit: new ebuild for a computational chemistry GUI.
++  * patch fixed
++  * mgltools manifest fixation
++  * nmrpipe version bump to 5.0.2009.103.20.08
++  * nmrpipe
++  * Manifest fix
++  * last fix of nmrpipe env, now it works
++  * another fix in the nmrpipe env file
++  * new nmrpipe env
++  * mmtk: fix location of .so modules, and dep on Scientific >=2.6.
++  * mmtk: bump to 2.6.0.
++  * manifest fix
++  * version bump of refmac A problem related with TLS has been fixed. The problem was that not in all cycle TLS contributions were added to B values and that could make refinement unstable.
++  * mgltools-webservices dependency fix
++  * zsi removed -- in tree
++  * clipper version bump
++  * sci-mathematics/freefem++: New ebuild for freefem++-3
++  * in tree
++  * Moving definition of INSPATH
++  * Add arches for testing
++  * Fix dying
++  * [sci-chemistry/pdb2pqr] Drop accidently added keywords and add gcc-4.4 patch (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
++  * masked nmrpipe-9.27.2009.120.14.28 for tsting
++  * prelimary ebuild of nmrpipe
++  * masked nmrpipe
++  * clipper version bump
++  * refmac version bump
++  * fixed a typo
++  * mask gnuplot-cvs
++  * added gnuplot-cvs ebuild (Portage version: 2.1.6.11/git/Linux i686)  (Signed Manifest commit)
++  * added dev-tex/picins (Portage version: 2.1.6.11/git/Linux i686)  (Signed Manifest commit)
++  * ccpn added missing dep and fixed python > 2.4 incompatibility
++  * added sci-libs/xdrfile-1.1b (Portage version: 2.1.6.11/git/Linux i686)  (Signed Manifest commit)
++  * Manifest fix
++  * fixed a typo in clipper-config and migrated frem sed to patch
++  * clipper-config changes included
++  * Add ~amd64 keyword and gcc-4.4 patch (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
++  * clipper-config fixed
++  * dev-tcltk/img_rotate added
++  * anigif update
++  * correct versioning of zsi in dev-python/opal-client
++  * sci-chemistry/mgltools fix USEdep
++  * sci-chemistry/mgltools-stride missing license added
++  * sci-chemistry/mgltools-utpackages missing license added
++  * UTPackages license added
++  * mgltools unmasked
++  * old togl removed
++  * sci-chemistry/mgltools-opengltk cannot depend on external togl
++  * dev-tcltk/togl-1.7 added, needed by mgltools
++  * dev-python/zsi upstream released the alpha
++  * mgltools-webservices another fix
++  * mgltools-volume another fix
++  * mgltools-visionlib another fix
++  * mgltools-vision another fix
++  * mgltools-viewer-framework another fix
++  * mgltools-utpackages another fix
++  * mgltools-symserv another fix
++  * mgltools-support another fix
++  * mgltools-stride another fix
++  * mgltools-sff another fix
++  * mgltools-scenario another fix
++  * mgltools-qslimlib another fix
++  * mgltools-pyglf another fix
++  * mgltools-pybabel another fix
++  * mgltools-pyautodock another fix
++  * mgltools-pmv another fix
++  * mgltools-opengltk another fix
++  * mgltools-networkeditor another fix
++  * mgltools-molkit another fix
++  * mgltools-mglutil another fix
++  * mgltools-gle another fix
++  * mgltools-geomutils another fix
++  * mgltools-dejavu another fix
++  * mgltools-cmolkit another fix
++  * mgltools-bhtree another fix
++  * mgltools-autodocktools another fix
++  * sci-chemistry/mgltools fixup
++  * sci-chemistry/mgltools-autodocktools fixup
++  * sci-chemistry/mgltools-bhtree fixup
++  * sci-chemistry/mgltools-cmolkit fixup
++  * sci-chemistry/mgltools-dejavu fixup
++  * sci-chemistry/mgltools-geomutils fixup
++  * sci-chemistry/mgltools-gle fixup
++  * sci-chemistry/mgltools-mglutil fixup
++  * sci-chemistry/mgltools-molkit fixup
++  * sci-chemistry/mgltools-networkeditor fixup
++  * sci-chemistry/mgltools-opengltk fixup
++  * sci-chemistry/mgltools-pmv fixup
++  * sci-chemistry/mgltools-pyautodock fixup
++  * sci-chemistry/mgltools-pybabel fixup
++  * sci-chemistry/mgltools-pyglf fixup
++  * sci-chemistry/mgltools-qslimlib fixup
++  * sci-chemistry/mgltools-scenario
++  * sci-chemistry/mgltools-sff fixup
++  * sci-chemistry/mgltools-stride fixup
++  * sci-chemistry/mgltools-support fixup
++  * sci-chemistry/mgltools-symserv fixups
++  * sci-chemistry/mgltools-utpackages fixups
++  * sci-chemistry/mgltools-viewer-framework fixup
++  * sci-chemistry/mgltools-vision misses file to install
++  * sci-chemistry/mgltools-vision fixup
++  * sci-chemistry/mgltools-visionlib fixup
++  * sci-chemistry/mgltools-volume fixup
++  * sci-chemistry/mgltools-webservices fix little typo
++  * sci-chemistry/mgltools-webservices fixup
++  * sci-chemistry/mgltools little fix
++  * sci-chemistry/mgltools masked for testing
++  * sci-chemistry/mgltools added
++  * manifest fix
++  * sci-chemistry/mgltools-autodocktools added
++  * sci-chemistry/mgltools-dejavu added
++  * sci-chemistry/mgltools-molkit added
++  * sci-chemistry/mgltools-networkeditor
++  * sci-chemistry/mgltools-pmv added
++  * sci-chemistry/mgltools-pyautodock added
++  * sci-chemistry/mgltools-pybabel added
++  * mgltools-qslimlib added
++  * mv libgfx from media-gfx to media-libs
++  * media-gfx/libgfx added
++  * sci-chemistry/mgltools-support added
++  * sci-chemistry/mgltools-utpackages aadded
++  * sci-chemistry/mgltools-viewer-framework added
++  * sci-chemistry/mgltools-vision added
++  * sci-chemistry/mgltools-visionlib added
++  * sci-chemistry/mgltools-volume added
++  * sci-chemistry/mgltools-WebServices added
++  * sci-chemistry/mgltools-bhtree added
++  * Manifest fix
++  * sci-chemistry/mgltools-cmolkit added
++  * sci-chemistry/mgltools-geomutils added
++  * sci-chemistry/mgltools-gle added
++  * mgltools-mglutil added
++  * Manifest fix
++  * sci-chemistry/mgltools-opengltk added
++  * togl updated
++  * Togl license removed as it is BSD
++  * sci-chemistry/mgltools-pyglf added
++  * sci-chemistry/mgltools-scenario added
++  * simpy version bump
++  * sff small change
++  * sci-chemistry/mgltools-sff added
++  * mgltools-samserv added
++  * little fix in mgltools-stride
++  * mgltools-stride added
++  * Update scalasca ebuild (Portage version: 2.1.6.11/git/Linux i686)  (Signed Manifest commit)
++  * refmac fix
++  * ccp4i manifest fix
++  * Added to portage
++  * fixed a bug in scalasca (Portage version: 2.1.6.11/git/Linux i686)  (Signed Manifest commit)
++  * sci-mathematics/freefem++: cleanup, fix copyright notice and Manifest
++  * app-vim/freefem++-syntax: cleanup, fix copyright notice and Manifest
++  * added scalasca licence
++  * added sys-cluster/scalasca ebuild (Portage version: 2.1.6.11/git/Linux i686)  (Signed Manifest commit)
++  * Added sci-physics/espresso ebuild (Portage version: 2.1.6.11/git/Linux i686)  (Signed Manifest commit)
++  * fix typo (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
++  * add mounting facility support for initscript in case of using nufa (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
++  * Update ebuild (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
++  * Update ebuild (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
++  * Update ebuild (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
++  * Update ebuild (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
++  * Add glusterfs. big #167955 (Portage version: 2.2_rc33/git/Linux x86_64)  (Signed Manifest commit)
++  * QA review of dssp
++  * sci-chemistry/dssp added
++  * ccp4i clean up
++  * dssp license added
++  * Manifest fixed for updated patches
++  * ccp4 upstream patch included -- bug 269504
++  * ccp4 upstream patch included -- bug 269504
++  * ccp4 upstream patch included -- bug 269504
++  * ccp4i QA
++  * sci-chemistry/chooch autotools based build system fixed
++  * moved sci-libs/chooch to sci-chemistry/chooch part two
++  * moved sci-libs/chooch to sci-chemistry/chooch
++  * sci-libs/chooch unmasked
++  * chooch working verion ready
++  * fix opendx manifest before pushing to the overlay
++  * small fix to an opendx patch.
++  * Nothing in overlay should be executable
++  * patches should not be executable
++  * Licenses should not be executable
++  * secong typo fixed
++  * Manifest fixation (Portage version: 2.2_rc33/git/Linux x86_64)  (Unsigned Manifest commit)
++  * New package: sci-mathematics/4ti2 Corresponding bug is #269472
++  * fixed typo
++  * bump almost to adept to boost 1.3.6
++  * new revision of opendx and import of a new version of opendx-samples to cope with it.
++  * fixed bug 266470
++  * zsi SRC_URI fixed.
++  * direx unmasked
++  * direx license added
++  * direx ebuild completed
++  * thanks alexxy for breaking my push
++  * sorry for segf with eix
++  * Rename wrong ebuild (Portage version: 2.2_rc33/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * mask direx
++  * direx added but masked
++  * refmac Manifest fix
++  * refmac experimantel version bump
++  * Fix for bug #268064
++  * Updated a dependency
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * Fixes an issue with docs improved ebuild
++  * litlle QA
++  * updated digest. sorry.
++  * Proper patch for frama-c
++  * I've separated two patches for consistency.
++  * DESCRIPTION corrected
++  * DESCRIPTION corrected
++  * Fixed typos in Changelog
++  * New package sci-mathematics/polymake
++  * Latest added to portage, thanks!
++  * csrosetta-pdbh added
++  * csrosetta-angless cp section gives response now
++  * csrosetta-cs added
++  * csrosetta-angless added
++  * blast-db can include one db more
++  * RCI added
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * ntl --  bumped the ebuild to 5.5. Fixed error if LDFLAGS have "--" inside.
++  * Fix license
++  * New package sci-biology/newbler
++  * moving to portage
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * Moved to portage
++  * Moved exonerate to portage.
++  * perlprimer updated ~x86 added and one dep fixed
++  * cleand up
++  * adopted balbes-db to new monomers-db package
++  * Another fix of coot-data PATHs
++  * New package
++  * sci-biology/ncbi-tools++ fixed libdir (Portage version: 2.2_rc31/git/Linux i686)  (Unsigned Manifest commit)
++  * zsi SRC_URI changed
++  * update of update-monomer-db
++  * opal-python blocks sci-chemistry/apbs-1.1.0
++  * fix ccp4 data dir path in coot-data
++  * fix ccp4 data dir path in monomer-db
++  * fixed data dir path in ccp4-libs
++  * New package
++  * aloow tcl/tk-8.5 with imosflm
++  * rewind the mask of imosflm as it totally broken with tcl 8.5
++  * mask sci-chemistry/imosflm-1.0.0-r1.ebuild test version for tcl/tk-8.5
++  * refmac bump
++  * coot-data fix
++  * monomer-db install path corrected dudes be carefull when setting such things
++  * coot-data bumped to reflect the existence of sci-libs/monomer-db
++  * bumped experimental refmac and adopted patch
++  * cleaned molrep and added src_test
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * fix epatch (Portage version: 2.2_rc31/git/Linux x86_64)  (Signed Manifest commit)
++  * add block to apbs (Portage version: 2.2_rc31/git/Linux x86_64)  (Signed Manifest commit)
++  * needed apbs bump
++  * more molrep fixes
++  * molrep version bump and some fixes
++  * update-monomers-db added
++  * sci-libs/monomer-db added
++  * imosflm HOMEPAGE fixed
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * ccp4-libs: moved momoner-db to seprate ebuild
++  * refmac 5.6 masked
++  * refamc bumped to experimental version
++  * Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci
++  * moved scripts from Documentation to scripts part 2
++  * moved scripts from Documentation to scripts
++  * New Package: sci-mathematics/Macaulay2 (Bug #246095)
++  * first version of automatic bump script for blast-dbs checked in
++  * fixed install phase (Portage version: 2.2_rc31/git/Linux x86_64)  (Unsigned Manifest commit)
++  * New package
++  * removed bundled opal and ZSI from apbs (Portage version: 2.2_rc31/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-chemistry/tinker ~amd64 added see bug 263006 (Portage version: 2.2_rc31/git/Linux x86_64)  (Unsigned Manifest commit)
++  * fix cadabra's manifest
++  * sci-chemistry/jmol update to 11.6
++  * sci-chemistry/tinker LDFLAGS respect added and X support removed because jav3d-bin is totaly broken but there is a src package in java-overlay dev-java/j3d-core
++  * bug 262905 digest thing fixed
++  * Manifest fix
++  * apbs checkin
++  * version bump of pdb2pqr
++  * dev-python/opal-client fix DEST PATH
++  * Manifest fix
++  * dev-perl/opelclient added
++  * ChnageLog entry added
++  * zsi version bump
++  * opal license added
++  * cleanup
++  * New package, bug 121921
++  * removed guile-gui as it is keyworded in the tree now
++  * Fix DEPEND line
++  * cleaning of the cadabra related ebuilds.
++  * continuing opendx renovation
++  * Important bump of ccpn which fixes the 1D bug
++  * Removed herwig and cernlib-montecarlo, changed applied to the tree
++  * New package
++  * Bump
++  * importing opend from the main tree
++  * fix coot license to GPL-3 which has been changed since 	 Jul 02, 2007
++  * Added zarja
++  * another qa for pymol Thanks bicatali
++  * QA on pymol
++  * removed flexdock as it is already in java-experimental
++  * app-arch/lbzip2 fixed src_test according to the suggestions of Daniel Lin
++  * Manifest fix
++  * fixes things from lbzip2
++  * removed additional patchs
++  * dev-java/flexdock-0.5.1 added It is a dep of the new scilab version
++  * removed use description from old packages
++  * lbzip2 version bump and src_test fix
++  * fix missing files in install
++  * app-arch/lbzip2 added
++  * rosetta USE="doc" is broken --> removed. See online docs instead https://www.rosettacommons.org/software/academic/3.0/rosetta3_user_guide/
++  *  "sci-chemistry/rosetta-tools added"
++  * refmac version bump to ...90
++  * sci-chemistry/rosetta added
++  * dev-libs/libunzip added
++  * renamed:    generate_tarball.sh -> generate_boinc-src_tarball.sh fixed:		libboinc_zip.a can now be build 			uses system libzip.a and libunzip.a
++  * To main tree
++  * sci-mathematics/freefem++: fix building the documentation with >=app-text/texlive-2008 app-vim/freefem++-syntax: moved download location to omploader
++  * pymol version bump to beta 6
++  * blast-db added
++  * rosetta-fragments added
++  * psipred added
++  * license psipred added
++  * rosetta-db DESCRIPTION changed
++  * fix some zip things in generate_tarball.sh
++  * Edited generate-tarball.sh so that only the bundled zip stuff is kicked out but the libboinc_zip.a could still be build
++  * cleaned the sci-libs/symmetrica ebuild by porting it to EAPI2
++  * changed the homepage for sci-libs/modglue
++  * Removed udav now in main tree
++  * Removed scidavis now in main tree
++  * rosetta licenses added
++  * sci-chemistry/ccpn version bump to 2.0.7
++  * removed libf2c, now in main tree
++  * phun-5.28.ebuild
++  * sci-chemistry/ambertools removed as I gave up getting chimera in
++  * added a patch for cadabra solving the --as-needed problem
++  * To main tree
++  * frama-c and why + dependencies new ebuilds
++  * To main tree
++  * New package sci-biology/mauve
++  * libmems, libmuscle, libgenome - deps of sci-biology/muscle
++  * updating manifest related to cadabra
++  * Importing cadabra and its dependencies modglue and lie
++  * Fix license
++  * New package sci-biology/shrimp
++  * New package sci-biology/mpiblast
++  * Removed mathgl, in main tree
++  * tnt version bump
++  * pyglet version bump
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * Fix manifest, again
++  * Remove envd file from ebuild and manifest as well.
++  * Remove envd file, no longer necessary.
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * sys-cluster/mpich2 Manifest fix
++  * sys-cluster/mpich2:  fix #259805 by backing out the site-packages fix.  It'll be better off just sent directly to upstream.
++  * Fix undeclared local variable.
++  * Phun version bump
++  * New package sci-biology/signalp
++  * New license signalp for package sci-biology/signalp
++  * pymol version cleanup and patch fix
++  * USE lua added to cara
++  * !media-libs/raptor removed from ccp4
++  * sci-chemistry/ccp4 unmacked
++  * sci-chemistry/ccp4i bump due to change in recmac5.tcl
++  * sci-chemistry/ambertools update but still problems
++  * reviewed version of clapack
++  * sci-libs/clapack RDEPEND missing
++  * sci-libs/clapack added
++  * removed .svn and added ChengeLog entry
++  * dev-libs/libf2c version bump
++  * sci-chemistry/ambertools added
++  * sci-chemistry/ambertools masked
++  * www-apps/SwishE added
++  * dev-scheme/guile-gui added for testing on ~amd64 pending bug is 259599
++  * tr src_install fixed
++  * sys-devel/ucpp added
++  * x11-libs/tr added
++  * mmtk Chnagelog added
++  * sci-libs/mmtk add with version bump and ~amd64
++  * Merge branch 'sci-libs/mmtk-import'
++  * sorry duplicated package to tree package
++  * sci-chmistry/mdtools added
++  * media-libs/freejpeg initial checkin
++  * sci-libs/msms added -> bug 209161
++  * dev-tcltk/togl added
++  * Removed ggobi, now in main tree
++  * apbs docs installation to the right place
++  * apbs: Ugly automagic removed make --> emake
++  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * add support for OFED-1.4.1-rc2
++  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
++  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
++  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
++  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
++  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
++  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
++  * Drop old versions (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
++  * fix openib-diags (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
++  * fix typo (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
++  * fix opensm (Portage version: 2.2_rc26/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-libs/libcmatrix license fixed
++  * sci-chemistry/gsim die added
++  * sci-chemistry/gsim added
++  * sci-libs/libcmatrix include destination fixed
++  * Fix digests for openmpi.
++  * sci-libs/libcmatrix added
++  * Bump openmpi-1.3.1
++  * apbs fix of doc installation dir
++  * tinker fix see bug 241180
++  * fix for apbs
++  * sci-chemistry/pymol APBS_PSIZE fix
++  * use deps fix in apbs
++  * sci-chemistry/apbs update Bug 262905
++  * dev-libs/punc created
++  * sci-libs/superlu update to 3.1
++  * sci-libs/libssm added (Portage version: 2.2_rc25/git/Linux x86_64)  (Unsigned Manifest commit)
++  * In main tree
++  * sci-chemistry/openbabel-python: Fix S
++  * Made some changes to the ebuild, do not configure in the src_unpack phase.
++  * sci-chemistry/pymol-plugins-cealign added
++  * sci-libs/balbes-db RESTRICT="binchecks strip" to save time
++  * sci-chemistry/refmac version bump to 5.5.0089 \n older versions removed (Portage version: 2.2_rc25/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Manifest fixed (Portage version: 2.2_rc25/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-chemistry/ccp4i conflict of rapper with media-libs/raptor (Portage version: 2.2_rc25/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-chemistry/ccp4 repper --> rappermc renaming
++  * sci-libs/cctbx another step to the end moved installdir from pothonsitedir to ${CCP4}/ (Portage version: 2.2_rc24/git/Linux x86_64)  (Unsigned Manifest commit)
++  * pdb-extract file collision conflict solved
++  * sci-visualization/xds-viewer uses new features from cmake-utils.eclass (Portage version: 2.2_rc24/git/Linux x86_64)  (Unsigned Manifest commit)
++  * cctbx fixing sinstalltion of some shell scripts
++  * xds input templat compression changed (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-libs/cctbx total rewrite of src_install (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * cctbx-2009.02.15.2320-r2 masked
++  * Change versioning to match internal package versioning
++  * New package sci-biology/miranda
++  * New package sci-biology/miranda
++  * sci-chemistry/xds-bin EPAI2fied (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-chemistry/pymol version bump to 1.2b5 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * sci-chemistry/phaser masked until all tests are passed
++  * New package sci-biology/infernal
++  * xds-viewer version bump to 0.6
++  * sci-chemistry/ccpn now respects LDFLAGS and is as-needed ready
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * cctbx scons fixes ASRP license added
++  * sci-libs/pycifrw initial checkin
++  * In gentoo-x86
++  * coot: update ccp4-libs/clipper deps to current versions.
++  * Remove -static
++  * Add metadata
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * cctbx now depends on system scons
++  * Remove webcheck option by default
++  * Fix changelog
++  * New package sci-biology/plink, bug 224017
++  * sci-libs/cctbx fixed and initial push Have fun and don't complain: THE BUILDSYSTEM IS CRAPPY!
++  * Merged sci-libs/cctbx from my overlay into sci overlay sci-chemistry/cbflib fixing LDFLAGS respect
++  * revert messed up commits
++  * sci-chemistry/xia version bump to 0.2.7.2 and fixing fperms --> chmod
++  * corrected linking gcc-config -X --> gcc-config -L
++  * ccp4i first patch set included
++  * sci-libs/balbes wierd code fixes
++  * sci-libs/clipper added as RDEPEND because it sin't build anymore
++  * New package sci-biology/mothur
++  * New package sci-biology/dotur
++  * New package sci-biology/dotur
++  * New package sci-biology/dotur
++  * sci-chemistry/openbabel-ruby: Version bump to 2.2.1
++  * sci-chemistry/openbabel-python: Version bump to 2.2.1
++  * sci-chemistry/openbabel-perl: Version bump to 2.2.1
++  * ccp4i: fixes for finding smartie.
++  * ccp4: try to get PYTHONPATH right.
++  * ccp4,ccp4i: rename truncate to ftruncate, build clipper progs, cleanup.
++  * clipper: bump, and stop installing examples.
++  * last cctbx changes
++  * libxdl_view: fix with --as-needed by linking libX11/libXt & adding deps.
++  * ccp4: reindent deps.
++  * ccp4: clean up cruft in weird places (files/delete/, *.bak).
++  * coot: pull in newly split clipper.
++  * ccp4-libs: make it suck less.
++  * clipper: bump to 20081201
++  * sci-chemistry/rasmol dep fix (x11-libs/vte)
++  * sci-libs/cbflib total cleanup include dir permissions fixed
++  * ccp4-libs nearly good linking
++  * rasmol fixed dep --> x11-libs/vte bug 238302
++  * sci-libs/cbflib cleanup
++  * coot: keyword ~amd64.
++  * sci-libs/chooch has automagic deps which aren't fixed --> masked
++  * Nessecary fixes in src. Should be fine now.
++  * cgraph.h installation fixed linking fixed
++  * sci-chemistry/Cgraph submitt
++  * sci-chemistry/ccp4 patch cleanup sci-chemiszty/chooch added sci-libs/cgraph added
++  * sci-chemistry/molrep added
++  * libjwc* docs not installed
++  * changed mosflm dep to build w/o ccp4
++  * x11-libs/libjwc_c/f added
++  * x11-libs/xdl_view added
++  * sci-chemistry/openbabel-ruby: Remove untested arches
++  * sci-chemistry/openbabel-perl: Remove untested arches
++  * sci-chemistry/openbabel-python: Add RDEPEND for OASA and PIL
++  * keyword amd64
++  * New package sci-biology/codonw
++  * sci-chemistry/openbabel-python: Fix ChangeLog
++  * sci-chemistry/openbabel-ruby: Fix ChangeLog
++  * sci-chemistry/openbabel-perl: Fix ChangeLog
++  * sci-chemistry/bkchem: Fix ChangeLog
++  * sci-chemistry/bkchem: Split out OASA library (now in sci-libs/oasa)
++  * New package sci-libs/oasa (split from BKChem)
++  * fix Manifest
++  * New package sci-biology/bowtie
++  * sci-libs/bables-db Changelog added
++  * Merged sci-libs/balbes-db in from dberkholz overlay
++  * Removed scamp, now in main tree
++  * masked ccp4
++  * Merge sci-chemistry/ccp4 from dberkholz overlay to sci fixed missing files in mrbump fixed msflm deps
++  * balbes-db clean up for merge
++  * sci-chemistry/xia2 metadata.xml added
++  * Merged sci-chemistry/xia2 from dberkholz overlay to sci
++  * sci-visualization/xds-viewer Good that no one tests my packages so typos won't harm. Typo in SRC_URI fixed
++  * Fixing dependencies of xds-viewer
++  * In gentoo-x86
++  * In gentoo-x86
++  * sci-biology/phred in gentoo-x86
++  * New package sci-biology/samtools
++  * sci-chemistry/refmac version bump to 5.5.0088
++  * QA and doc building
++  * QA and doc building
++  * sci-chemistry/xds version bump at 30 Jan 2009 and handling X changed
++  * sci-visulization/xds-viewer added
++  * sci-chemistry/chemtool: Fix ChangeLog
++  * sci-chemistry/chemtool: Remove unneeded files
++  * Manifest fixed
++  * sci-chemistry/cara keyworded for ~amd64
++  * Version bump (Portage version: 2.2_rc23/git/Linux i686)  (Unsigned Manifest commit)
++  * sci-chemistry/easychem: Fix strip, bug #252034
++  * sci-chemistry/chemtool: Add ebuilds from tree, bug #219528
++  * manifest fixed
++  * sci-chemistry/pymol version bump to 1.2beta4
++  * sci-chemistry/bkchem: Version bump to 0.13.0
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * fixed revision for pymol-1.2_beta3
++  * Adjusted Manifest
++  * Verion bump
++  * remove sed patch
++  * sci-libs/gmsh Version bump
++  * Push Vampir Trace includes to a subdir.  #257086
++  * sci-chemistry/stdinchi: Add doc use, fix prestriped files, make honor CFLAGS
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * Add 'append-ldflags' to facilitate building for users with --as-needed.
++  * New package sci-chemistry/stdinchi
++  * sci-chemistry/wxmacmolplt: Put -lGLU back in configure
++  * sci-chemistry/wxmacmolplt: Fix DEPEND vs RDEPEND
++  * sci-chemistry/wxmacmolplt: Set wxGTK opengl use dependency, flash use
++  * sci-chemistry/bkchem: Version bump to 0.12.6
++  * sci-chemistry/openbabel-ruby: Use EAPI=2, fix swig use
++  * sci-chemistry/openbabel-python: Use EAPI=2, fix swig use
++  * sci-chemistry/openbabel-perl: Use EAPI=2, fix swig use
++  * imosflm deps fixed and unmasked
++  * New package sci-chemistry/openbabel-ruby, #212212
++  * New package sci-chemistry/openbabel-python, #212212
++  * New package sci-chemistry/openbabel-perl, #212212
++  * dev-tcltk/anigif added
++  * dev-tcltk/combobox added to sci overlay
++  * sci-chemistry/openbabel-2.2.0-r1: New ebuild with doxyfile patch, #212212
++  * New package sci-chemistry/bkchem, #95178 (Thanks to Beda Kosata)
++  * Merge branch 'master' of ../asd
++  * dev-tcltk/tablelist added
++  * tktreectrl MANIFEST and Changelog fix
++  * Merged dev-tcltk/tktreectrl into sci overlay
++  * sci-chemistry/ghemical: Added ghemical package
++  * Imosflm checked in but masked because deps are missing or tbw
++  * mosflm Changelog and manifest fised
++  * Merged sci-chemistry/mosflm from dberkholz overlay to sci overlay
++  * mosflm cleaned for merge
++  * sci-chemistry/rasmol ChangeLog
++  * sci-chemistry/rasmol intial checkin
++  * sci-libs/cbflib added
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * Remove unused local use flag from metadata for sys-cluster/openmpi.
++  * Bump sys-cluster/openmpi-1.2.9.
++  * Version bump\! (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * fixed totaly messed up mrbump src_install
++  * Make libgmxmopac7.a -fpic library (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
++  * Fix typo (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * sci-chemistry/mrbump added to overlay
++  * Cleaned sci-chemistry/mrbump
++  * Add support for qm/mm with mopac7 for gromacs (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Add mopac7 with support library for gromacs (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/ccp4i  moved from Dberkholz overlayy to sci Thanks Donnie
++  * Manifest fixing
++  * New package sci-biology/phred
++  * sci-chemistry/ccp4i made ready for merge
++  * removed old versions of ccpn as they use hardcoded things and latest is okey
++  * Make tk verion not hardcodded (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
++  * Add ~amd64 kyword to ccpn; make python not hardocded (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
++  * Moved to tree
++  * sci-chemistry/pymol bumped to 1.2 beta 3
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * Version bump.
++  * fix manifests
++  * version bump
++  * version bump
++  * New packages sci-biology/pals, piler, pilercr
++  * New package sci-biology/mreps
++  * New package sci-biology/lagan
++  * New package sci-biology/lagan
++  * new package sci-biology/trf
++  * GAMESS - Version bump (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
++  * Forgot to block the ccp4-6.0* series
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * Merged sci-chemistry/coot from dberkholz-overlay to sci-overlay version bump to 0.5.2 We now build against ccp4-libs
++  * Missing line continuation, #259209.
++  * Merged dev-scheme/guile-lib-0.1.6 from dberkholz overlay to sci overlay We need this for coot
++  * Merged sci-chemistry/coot updates from my overlay into dberkholz-overlay
++  * Merged x11-libs/guile-gtk from my overlay into sci-overlay This is an updated version of the tree ebuild Bug is 251793
++  * Merged sci-libs/ccp4-libs from dberkholz-overlay to sci overlay Thanks Donnie for your work on this
++  * sci-libs/ccp4-libs bumped to 6.1.1 and cleaned for merge into sci-overlay
++  * Update HOMEPAGE for icm (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
++  * Update deps for icm (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/refmac merged from dberkholz-overlay to sci-overlay
++  * Fix syntax (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
++  * Update icon for icm-broser (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * sci-chemistry/refamc bumped to latest version (5.5.0085) and polished to submitt into sci overlay
++  * Update deps for icm-broser (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Update deps for icm-broser (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
++  * Add block to icm-broser (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Add icm-broser (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Add menuentry for icm (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Added herwig flag to cernlib, see bug #257732
++  * Added herwig
++  * removing, now in main tree
++  * Various QA fixes
++  * fix compilation of wxmacmolplt (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
++  * sci-chemistry/almost missed to install to headers which are needed to build sci-chemistry/aqva against it.
++  * sci-chemistry/azara Typo fix so that LDFLAGS are respected
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * sci-chemistry/ccpn version bump to 2.0.6.1
++  * Add patch for gcc 4.3 (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
++  * Add wxmacmolplt bug #197131 (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
++  * add MolSoft licence
++  * Add icm-pro (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Signed Manifest commit)
++  * Fix manifest for mpich2 (Portage version: 2.2_rc23/git/Linux x86_64)  (Signed Manifest commit)
++  * Added the skel files from tree so that  we can use tools like echangelog.
++  * Fix the mpich2 pkgconfig file, #257921.  Mark patchses to be sent upstream.
++  * aria and cns changes
++  * Update boinc generator script. now server should build.
++  * sci-chemistry/procheck moved from Donnies overlay to sci overlay
++  * cctbx openmp depency fixed
++  * sci-chemistry/pymol-1.2_beta added. I will maintain all beta versions in sci overlay.
++  * cctbx fixes with donnie
++  * [QA]: Add missing diags USE flag to IUSE
++  * [QA]: Remove redundant src_compile, fix SRC_URI for new location
++  * [QA]: We need EAPI=1 for SLOT dependencies
++  * [QA]: Remove redundant src_compile
++  * [QA]: Remove redundant src_compile
++  * [QA]: Remove redundant src_compile
++  * [QA]: change RESTRICT=nomirror to RESTRICT=mirror
++  * [QA]: Remove redundant src_compile
++  * Fix Manifest.
++  * [QA]: Add test to IUSE
++  * [QA]: Order categories file
++  * some things added, nothing to mention
++  * x11-libs/xview bump and sci-chemistry/nmrpipe
++  * Revert "Revert "sci-chemistry/ccpn numpy USE flag removed""
++  * Revert "sci-chemistry/ccpn numpy USE flag removed"
++  * sci-chemistry/ccpn numpy USE flag removed (Portage version: 2.2_rc23/git/Linux i686)  (Unsigned Manifest commit)
++  * Add patch to fix crash on startup with tcl8.5 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Re-manifest
++  * Added gasgano
++  * cpl: added wcs and gasgano support
++  * sci-electronics/stage: add SLOT
++  * sci-electronics/player: add SLOT
++  * cdsclient: version bump
++  * cdsclient: version bump
++  * Added bug ref
++  * pyglet version bump
++  * Clean up
++  * Clean up
++  * move boinc to the tree.
++  * One more CUDA fix (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
++  * fix cuda support (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
++  * Same as previous commit but this time for normal boinc.
++  * Add things noted by bicatali
++  * Added ggobi
++  * sys-cluster/openmpi-1.3:  Don't build Vampir Trace on sparc, #256529.
++  * cuda++
++  * Add our bundled init script.
++  * Remove bundled init scripts
++  * Bit cleanup in boinc.
++  * sci-chemistry/ccpn version bump  to 2.0.6
++  * sci-chemistry/almost added to sci overlay, bug 248455 (Portage version: 2.2_rc23/git/Linux i686)  (Unsigned Manifest commit)
++  * sci-chemistry/pdb-extract-3.004.ebuild added for testing pending bug is 249933
++  * sci-chemistry/azara and sci-chemistry/ccpn added to overlay
++  * uncommited files
++  * Patch to fix when using libtool-2.2+, #228183.  Also remove sweep to avoid file conflict with media-libs/sweep, #245439 c2.
++  * First pass for boinc, NOTE: install is not done yet :]
++  * Update comments.
++  * Add some empty depend :]
++  * More boinc updates.
++  * Fix cuda stuff a bit :P
++  * Forget to add correct groups :P Now should cuda really work :]
++  * Update deps.
++  * Update generating script to hopefuly final version.
++  * matio-1.3.3 version bump
++  * Ups forgot one dep.
++  * Working cuda :]
++  * Update script.
++  * Umm. Fix breakage.
++  * Remove prerelease. We wont bother.
++  * More updates.
++  * Moar init fixups. (Portage version: 2.2_rc20/git/Linux 2.6.27-gentoo x86_64)  (Unsigned Manifest commit)
++  * Update boinc-bin a bit, fixup initscript severly. (Portage version: 2.2_rc20/git/Linux 2.6.27-gentoo x86_64)  (Unsigned Manifest commit)
++  * Update profiles/categories/ and add generate_tarball.sh for boinc (that script is heavy WIP)
++  * Update openib-osm ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Update openib-osm ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Update openib-osm ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Update openib-osm ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Update openib ebuild (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
++  * Update openib ebuild (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
++  * Update openib ebuild (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
++  * Update openib ebuild (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
++  * Update openib-files (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
++  * update eclass
++  * Update openib-files ebuild (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
++  * eclass update
++  * update
++  * Add metapackage for openib (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
++  * Add new openib-perf (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
++  * Add new openib-files (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
++  * Update ebuilds (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Add new diags (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Add new opensm (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * updaet eclass
++  * update ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * update ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * update ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * add libnes (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * update ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * add  driver for mlx4 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * update ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * update ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * updaet ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * update ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * update ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Add new libiubmad-1.2.3_p20081118 (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
++  * Add new libibmad-1.2.3_p20081118 (Portage version: 2.2_rc23/git/Linux x86_64, RepoMan options: --force)  (Unsigned Manifest commit)
++  * Update libibcommon ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Add new libibcommon-1.1.2_20082010 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * update eclass
++  * Add new libibcm-1.0.4 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Add new libehca-1.2.1 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Update dapl ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Update librdmacm ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Update libibverbs ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Unmask for testing
++  * Update libibverbs ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Update librdmacm ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Update compat-dapl ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Update dapl ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Add librdmacm metapackage (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Update dapl ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Add libibverbs metapackage (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Add libibverbs metapackage (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * update dapl ebuild (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * add to pmask
++  * Add dapl compatibility layer (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * fix headers and ebuild to work with eclass (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Update ebuild according to eclass (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * update eclass a bit
++  * fix openib eclass
++  * add p.mask entry
++  * add experimental ebuild for dapl-2.0.15 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci
++  * sys-cluster/mpich-1.0.8 bugfixes, no revbump.  Fix some doc file locations (#255748).  Fix sandbox errors (254167).
++  * fix typo
++  * add new openib eclass
++  * Add empty package.mask, for use by broken/in-development/9999 packages.
++  * Slightly update the previous commit.
++  * Fix bug 243194. Update init so it uses CFS. Hope it wont harm kittens looks fine now.
++  * Whitespacie notes.
++  * Update slightly initscript. Note: it (as whole) needs review
++  * Fix bug 137224. Wrong attach usage. Note: i will close it and when this boinc versions are passed to the tree it will be just updated.
++  * add boinc-bin. Cuda not created there is library ${S}/libcudart.so which needs to be placed somewhere. So somebody with nvidia, tweak yourself up :P
++  * Drop smp use flag since its defautl for openmpi (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * fix syntax
++  * initial version bump to 1.3 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Make it work with current libtool (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * We dont want static gromacs by default (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Fix headers (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Fix headers (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Fix syntax issues (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Fix syntax issues (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * Bump gromacs to 4.0.3 (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * fix keywords and hader for gtk-gamess (Portage version: 2.2_rc23/git/Linux x86_64)  (Unsigned Manifest commit)
++  * fix manifests
++  * dev-python/h5py - Bumped version to 1.0.0.
++  * gap:version bump
++  * Version bump
++  * Added ekee
++  * Update mpi.eclass.  Major changes include simplyfing use and allowing non empi builds to still get some information.  Also updated all related packages using this eclass.
++  * Header change w/o getting the 1000s commit
++  * Header change w/o getting the 1000s commit
++  * Header change in ./sci-libs/cctbx/cctbx-2008.05.19.2030.ebuild
++  * Header change in ./sci-libs/mmdb/mmdb-1.0.10.ebuild
++  * Finite state toolkit foma. Initial ebuild.
++  * Bump to OpenCascade 6.3 Needs testing...
++  * version bump
++  * In CVS
++  * In CVS
++  * http://bugs.gentoo.org/show_bug.cgi?id=251793 (Portage version: 2.2_rc17/svn/Linux 2.6.26-gentoo-r4-cdrom i686)
++  * phun: version bump
++  * cctbx update -- rosetta++ added from bug 250401
++  * intial checkin version bump which results in broken digest of ebuild in tree (bug 247788) (Portage version: 2.2_rc17/svn/Linux 2.6.26-gentoo-r4-noata i686)
++  * removing old version
++  * spr: fixed data files and added use flag description
++  * spr: initial import for testing
++  * sci-chemistry/cara-bin Initial checking in (Portage version: 2.2_rc17/svn/Linux 2.6.26-gentoo-r4 i686)
++  * CARA license added
++  * esorex: version bump
++  * cpl: version bump
++  * sci-mathematics/freefem++: fix a P1 FE bug and examples++-load
++  * Removed spooles USE-flag for sci-libs/calculix-ccx
++  * sci-libs/calculix-ccx: Removed spooles USE-flag, spooles is no longer optional
++  * sci-libs/gmsh: Version bump
++  * rasmol: bump to latest. also added new dep, cbflib. (#238302).
++  * rasmol: bump to latest. also added new dep, cbflib. (#238302).
++  * Force serial build of mpich2... Ironically.  #248456
++  * new USE-flag 'chaco' for sci-libs/gmsh
++  * sci-libs/gmsh: Fixed metis compilation problem and added chaco USE-flag
++  * app-vim/freefem++-syntax: version bump.
++  * sci-libs/gmsh: Improved typo
++  * sci-libs/gmsh: Version bump
++  * removed speedcrunch now in main tree
++  * sci-geosciences/tappy-0.8.1.ebuild - Version bump
++  * mosflm: bump to 7.0.4; parallel build is broken.
++  * Version bump.
++  * Fix 242180, comment 5 by just allocating a buffer for the string instead of trying to use PATH_MAX.
++  * sci-mathematics/sage-bin: Updated Manifest
++  * sci-mathematics/sage-bin: Version 3.1.2 no longer available for download.  Minor change in SRC.  Explicit installation of sage-* and explicit creation of /usr/bin/sage symlink.
++  * Updated mpi.eclass to handle packages with blockers and mpich2
++  * dev-python/h5py-0.3.1.ebuild Python interface to HDF5 files.  Initial ebuild.
++  * sys-cluster/mpe2 needs to handle building without empi.
++  * Integrate Joel's fixes for #220877 into mpich2 (fpic ->fPIC)
++  * Add empi-capable mpe2, tests pass with mpich2, some issues with openmpi
++  * Add empi-capable mpich2
++  * sci-misc/salome-med: Reordered dependencies
++  * sci-mathematics/freefem++: gcc-4.3 and no-X11R6 symlink fixes
++  * removed cgal, now in main tree
++  * removed cgal-python, now in main tree
++  * sci-misc/salome-kernel: Reordered dependencies
++  * deleted USE-flag 'corba' for sci-misc/salome-kernel
++  * sci-mathematics/mdp - Even though I couldn't reproduce the error, I updated the Manifest, per http://bugs.gentoo.org/show_bug.cgi?id=146976#c6
++  * Added patch to support hdf5-1.6.7
++  * Added support to VTK 5.2
++  * Added support to VTK 5.2
++  * Added support to VTK 5.2
++  * sci-mathematics/mdp-2.4.ebuild : A Python data processing framework. Bumped to version 2.4, updated DEPEND.
++  * removed plplot, now in main tree
++  * removed lasi, now in main tree
++  * ipython now in tree
++  * Fix bug #242574, version bump and gcc-4.3 patch.
++  * bump sys-cluster/openmpi-1.2.8 and clean up old version.
++  * new USE flags 'arpack' and 'spooles' for sci-libs/calculix-ccx
++  * sci-libs/calculix-cgx: Reworked ebuild for bug 125775, thanks to pva
++  * sci-libs/calculix-ccx: Reworked ebuild for bug 125773, thanks to pva
++  * sci-libs/spooles: Reworked ebuild for bug 125772, thanks to abraxxas and pva
++  * sci-geosciences/swmm Initial ebuild for SWMM - Storm Water Management Model, developed by the U.S. Environmental Protection Agency and Camp, Dresser, McKee (CDM).
++  * sci-mathematics/sage-bin This is the Sage binary package.  Sage is very difficult to tease out the sources to build separately and so I gritted my teeth and created this binary package ebuild.  See http://bugs.gentoo.org/show_bug.cgi?id=201321 for information on the conventional source based ebuild.
++  * Added Manifest for ipython
++  * Added ipython-0.9.1 for testing
++  * Automated script commit
++  * Automated script commit
++  * Probably the last fix. Fixing of path in right place' (Portage version: 2.2_rc11/svn/Linux 2.6.25-gentoo-r8 i686)
++  * Automated script commit
++  * aribas-1.63
++  * Automated script commit
++  * Removed superfluous files.
++  * Automated script commit
++  * Added second set of octave-forge updates.
++  * latest version
++  * Nearly ready
++  * Nearly ready
++  * Automated script commit
++  * Automated script commit
++  * Automated script commit
++  * Bump first batch of octave-forge packages to new revision.
++  * Removed octave since octave-3 has been merged to the main tree.
++  * Automated script commit
++  * cdsclient: bump to 3.01
++  * removed root, now in main tree
++  * sci-misc/salome-kernel: fixed dependency
++  * sci-misc/salome-kernel: Fixed typo in dependency
++  * gmpy-1.03 is now in the tree
++  * Bring in latest openmpi-1.2.7 with empi support.  Remove old 1.2.5, cleanup repoman warnings.
++  * upstream patched; redigest
++  * Version bump. Patch for gcc-4.3.
++  * Version bump; ensure python has tkinter
++  * manifest update
++  * In gentoo-x86
++  * New package, bug 236954
++  * sci-misc/salome-med: Added patch for >=dev-libs/boost-1.35.0
++  * sci-misc/salome-kernel: Fixed version dependency
++  * sci-misc/salome-kernel: Fixed version dependency
++  * sci-misc/salome-superv: Fixed typo in patch file
++  * sci-misc/salome-pycalculator: removed omniorb* dependencies, as they are already in salome-kernel
++  * sci-misc/salome-visu: removed omniorb* dependencies, as they are already in salome-kernel
++  * sci-misc/salome-superv: removed omniorb* dependencies, as they are already in salome-kernel; added omniorb_4.1.patch
++  * sci-misc/salome-component: removed omniorb* and med dependencies, as they are already in salome-kernel and salome-med
++  * sci-misc/salome-smesh: removed omniorb* dependencies, as they are already in salome-kernel
++  * sci-misc/salome-med: removed omniorb* dependencies, as they are already in salome-kernel
++  * sci-misc/salome-geom: removed omniorb* dependencies, as they are already in salome-kernel
++  * sci-misc/salome-gui: Most USE-flags doesn't seem to be optional, changed default settings; added pyobject.patch
++  * sci-misc/salome-kernel: Reworked USE-flags, changed default behaviour, added omniorb_4.1.patch
++  * pyglet-1.1.1.ebuild: version bump
++  * The GIS Django branch was merged into the trunk.
++  * +Manifest
++  * Initial commit for bug 221965, thanks to Marek Miller <mlm@ngc17.pl>
++  * root: added better emacs support
++  * dev-python/sympy is now in the main tree
++  * jama: cleaning
++  * tnt: version bump and fixes
++  * pythia now in main tree
++  * added root for test on extra patches
++  * pythia6: rev bump
++  * pythia6: added additional declarations for root
++  * sympy-0.6.2: with docs (using sphinx), mpmath and pyglet are internal so far
++  * Added USE-flags for the sci-misc/salome-* ebuilds
++  * sci-misc/salome-smesh: Now really removed fetch restriction
++  * sci-misc/salome-visu: Removed fetch restriction, removed hardcode
++  * sci-misc/salome-superv: Removed fetch restriction, removed hardcode
++  * sci-misc/salome-smesh: Removed fetch restriction, removed hardcode
++  * sci-misc/salome-pycalculator: Removed fetch restriction, removed hardcode
++  * sci-misc/salome-meta: Fixed repoman errors, removed hardcode
++  * sci-misc/salome-med: Removed fetch restriction, removed hardcode
++  * sci-misc/salome-gui: Removed fetch restriction, removed hardcode
++  * sci-misc/salome-geom: Removed fetch restriction, removed hardcode
++  * sci-misc/salome-component: Removed fetch restriction, removed hardcode
++  * sci-mathematics/netgen: Fixed dependency for opencascade
++  * Added corba and openpbs USE-flags for sci-misc/salome-kernel
++  * sci-misc/salome-kernel: Removed fetch restriction, added python-2.5 support, removed hardcode
++  * Added cgns, metis and opencascade USE-flags for sci-libs/gmsh
++  * sci-libs/cgnstools: New Ebuild for bug 176455
++  * sci-libs/cgnslib: New Ebuild for bug 176455
++  * sci-libs/gmsh: New Ebuild for bug 195980
++  * gmpy-1.03: an update to the package in the main tree
++  * pyglet-1.1: version bump
++  * avbin-bin-6: version bump
++  * sci-libs/mathgl-1.7.ebuild *1.7 version based on 1.6.2. *Removed unneeded patches and 'sed' commands, updated SRC_URI, added append-flags for CPPFLAGS and LDFLAGS.
++  * pythia-8: install data files
++  * sci-visualization/scidavis-0.1.3.ebuild - Changed two lines indented with spaces to indented with tabs.
++  * sci-visualization/nodemon-0.3.5.ebuild - Changed description to < 100 characters and updated copyright date.
++  * sci-misc/brlcad-7.10.4.ebuild - Removed BSD license which was for the BRLCAD wiki content and updated copyright year.
++  * sci-misc/simpy-1.9.1.ebuild - Initial ebuild for simpy, a process and event simulation system for Python.
++  * sci-geosciences/congen-1.6.ebuild - Congen calculates astronomic parameters necessary to analyse tides.
++  * ccp4: split out ccp4i into separate package.
++  * ccp4: split out ccp4i into separate package.
++  * coot: require librsvg (reported by Hari Jarayam).
++  * coot: also needs imlib.m4 or it fails on systems without imlib-1.
++  * app-office/texmacs is in the main tree
++  * Moved to portage
++  * Remove sys-cluster/ganglia as it's in the main tree.
++  * Fixed Manifests
++  * ccp4: pull in balbes-db.
++  * Add balbes-db, split out from ccp4.
++  * ccp4: pull in standalone xia2.
++  * Add split-out xia2 ebuild.
++  * refmac: install refmac5 symlink.
++  * ccp4: more fixes.
++  * ccp4: pull in standalone refmac.
++  * Add standalone refmac.
++  * ccp4: pull in imosflm.
++  * ccp4: pull in standalone mosflm.
++  * New package: standalone mosflm.
++  * ccp4: initial version that depends on ccp4-libs.
++  * Move ccp4-libs to sci-libs.
++  * ccp4: add imosflm deps. fix quoting syntax error.
++  * tktreectrl: dep for new ccp4, from bug #217706.
++  * Use category in has_version, thanks to filko on #-science for pointing it out.
++  * Add ganglia-3.1.0.  Python is not fully working yet, but everything else checks out.
++  * ccp4: bump to 6.0.99e, alpha ebuild.
++  * added ~x86
++  * minor fixes to symmetrica and cddlib
++  * Added givaro
++  * Added Symmetrica
++  * Added dev-libs/ntl-5.4.2
++  * minor change to gdmodule
++  * added fplll
++  * added m4ri
++  * added gdmodule
++  * added cddlib
++  * sci-mathematics/mdp * Added ~x86 per http://bugs.gentoo.org/show_bug.cgi?id=146976
++  * sci-mathematics/mdp * Initial ebuild
++  * coot: bump to 0.5_pre1-r1272.
++  * coot: Bump to 0.5_pre1-r1212, drop 0.4.1.
++  * Added pythia (6 and 8)
++  * gap-4.4.10: sysinfo.gap now installed
++  * removed libsdp-1.1.ebuild added libsdp-1.1.99.ebuild
++  * added libehca-1.2.ebuild removed libehca-1.1.ebuild
++  * manifest
++  * taking patch away
++  * svn housekeeping
++  * fix patch name
++  * Added surfer
++  * In the portage tree
++  * pyglet-1.1_beta2
++  * sci-mathematics/pest * Added '-j1' to MAKEOPTS to force correct compile order.
++  * bump as openmpi-1.2.6-r1 just hit the tree.
++  * sci-geosciences/pyslice * Added ~x86
++  * sci-geosciences/tappy * Added ~x86 as per https://bugs.gentoo.org/show_bug.cgi?id=138005#c8
++  * sci-geosciences/geodjango-svn * Added ~x86 per https://bugs.gentoo.org/show_bug.cgi?id=230880#c4
++  * Version bump
++  * fix digest
++  * version bump
++  * New package, bug 207250
++  * New license for sci-biology/mavid
++  * New package, bug 114089
++  * sys-cluster/hpl * Minor repoman edits.
++  * sys-cluster/pyslice * Initial ebuild entry.
++  * sci-geosciences/tappy * Added correct header.
++  * sys-cluster/blcr * Minor repoman edits.
++  * sci-geosciences/tappy * Initial ebuild.
++  * sci-geosciences/geodjango-svn * Initial import of GeoDjango branch.
++  * sci-geosciences/xtide * Added ~x86 per https://bugs.gentoo.org/show_bug.cgi?id=214868#c9
++  * manifest
++  * compressing the patch
++  * Updated the gcc-4.3 patch for salome-kernel (Thanks Bart K.)
++  * sci-geosciences/libtcd * Added ~x86 per http://bugs.gentoo.org/show_bug.cgi?id=214867#c4
++  * sci-geosciences/harmonics-dwf-free-noncomm * Added ~x86 per http://bugs.gentoo.org/show_bug.cgi?id=214873#c4
++  * sci-geosciences/tcd-utils * Added ~x86 per http://bugs.gentoo.org/show_bug.cgi?id=214875#c4
++  * sci-geosciences/xtide * Added required dependencies to fix   http://bugs.gentoo.org/show_bug.cgi?id=214868#c4
++  * patches
++  * Import for testing
++  * add metadata.xml
++  * Add changelog, and thanks to Jose Maria Fernandez Gonzalez
++  * Initial import.
++  * adding local variables myconf_s and myconf_d to keep track of flags
++  * fixing cases when all you want is double-precision, thanks to Shvetsov Alexey on bug #193532
++  * guile-lib: bump to 0.1.6.
++  * scamp:version bump and fixes
++  * coot: Bump to 0.5_pre1-r1192.
++  * openmotif, not motif
++  * openmotif, not motif
++  * openmotif, not motif
++  * switch virtual/motif to x11-libs/openmotif for bug #204249.
++  * switch virtual/motif to x11-libs/openmotif for bug #204249.
++  * switch virtual/motif to x11-libs/openmotif for bug #204249.
++  * new cluster, make license file
++  * note in license file this is for sci-biology/cluster
++  * License for sci-biology/cluster
++  * Remove opencv from overlay, it's now in gentoo-x86
++  * Made media-libs/lasi ebuild adhere to multilib-strict.
++  * sci-chemistry/drawxtl:  * Added metadata.xml
++  * sci-calculators/speedcrunch:  * Added metadata.xml
++  * sci-astronomy/scamp: Simple repoman inspired edit  * Changed copyright date
++  * dev-lang/aldor: Simple repoman inspired edits  * Updated copyright dates  * Removed unneeded 'cd "${S}"'
++  * dev-cpp/growler: Simple repoman inspired edits  * Changed copyright dates  * Shortened long DESCRIPTIONs to under 100 characters  * Fixed svn Headers
++  * app-office/texmacs: Simple repoman edit  * Added trailing semicolon in files/TeXmacs.desktop
++  * eselect-mpi: Simple repoman guided edits.  * Deleted trailing spaces  * Quote variables  * Added metadata.xml
++  * Update description
++  * add manifest
++  * New package
++  * In gentoo-x86
++  * Final fixes before eclass goes out for review.
++  * Latest gromacs for testing
++  * fix Manifest
++  * fix headers and utf
++  * added libsfmt and libdsfmt
++  * Remove unnecessary RESTRICT, keyword for x86 since pchrist tested it
++  * Bump eselect-mpi-0.0.4.  Adds /etc/profile.d support.  Thanks to Bryan Green for suggesting this.
++  * Fix step 6 in the README, paths were wrong.  Thanks again to Bryan Green.
++  * Fix a couple of bad csh environment var settings.  Thanks to Bryan Green for pointing this out, #226105
++  * Actually bump empi correctly.
++  * And add a missing patch, forgot to 'svn add'
++  * Fix ffmpeg linking with sws_getContext by adding -lswscale to FFMPEGLIBS, and fix up ffmpeg's configure checks as well
++  * Add demos USE flag for sample opencv applications, change to a better format(unified) for the cvcapffmpeg patch
++  * Add demos local USE flag description for opencv
++  * Fixxor AC_CONFIG_MACRO_DIR conflicts with ACLOCAL_AMFLAGS
++  * repoman fixups
++  * git-svn-id: svn+ssh://svn.j-schmitz.net/svn/portage-overlay/ebuilds@413 848b6a78-a7b0-4e08-a36b-699b422dbac5
++  * Initial import, bug #70506
++  * removed clhep, now in main tree
++  * removed geant, now in main tree
++  * removed dawn, now in main tree
++  * added openib.env per bug #223955 comment #17
++  * updates to several openib packages
++  * Final cleanup.
++  * added ebuilds for OFED/openib 1.2.5.5
++  * fixed doc install
++  * added speedcrunch
++  * Added patch to fix stdout problem in chi2rnd function.
++  * esorex: bump to 3.6.8
++  * cpl: version bump to 4.1
++  * geant: patch bump
++  * More cleanups.
++  * Added Gcc-4.3 support. Thanks to Bert K. for his patches!
++  * Added Gcc-4.3 support. Thanks to Bert K. for his patches!
++  * Added Gcc-4.3 support. Thanks to Bert K. for his patches!
++  * Added Gcc-4.3 support. Thanks to Bert K. for his patches!
++  * Added Gcc-4.3 support. Thanks to Bert K. for his patches!
++  * Corrected a minor bug
++  * Added Gcc-4.3 support. Thanks to Bert K. for his patches!
++  * Added Gcc-4.3 support. Thanks to Bert K. for his patches!
++  * Added the license file for OpenCascade. Corrected issues with the configuration of OpenCascade (Thanks Richard W.!)
++  * More manifest fixing
++  * fixing manifests and ebuild name
++  * new package: libibvpp
++  * Major ebuild cleanup. Disabled failing tests and added patched from debian svn.
++  * pyglet-1.1_beta1
++  * avbin-bin-3 (needed by pyglet)
++  * added openib-mvapich2-1.0.1-r1 to MPI_EMPI_COMPAT
++  * minor fix, added use of ${mpi_conf_args}
++  * added openib-mvapich2 to MPI_ALL_IMPS
++  * added ~x86 keyword, updated copyright dates
++  * added openib-mvapich2-1.0.1-r1.ebuild, added ~x86 keyword
++  * Initial import, thanks to Jan Marten Simons, Hannes Kruger, and Srebrodolskite.
++  * add menu entry
++  * Remove quotes
++  * Cleanup and add ApE license file.
++  * Initial import.
++  * In gentoo-x86
++  * Compilation and installation now properly takes place in src_compile and src_install. Also, make the compile and install phases more verbose.
++  * git-svn-id: svn+ssh://svn.j-schmitz.net/svn/portage-overlay/ebuilds@406 848b6a78-a7b0-4e08-a36b-699b422dbac5
++  * asciidata: version bump
++  * visual-4_beta26 now in main tree
++  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
++  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
++  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
++  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
++  * Modified a minor bug regarding the location of some python/salome shared directory
++  * gle is in the main tree now
++  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
++  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
++  * scidavis-0.1.3: translations are now handled correctly
++  * Added new octave-forge packages.
++  * Heavy rework of the ebuild and the associated epatches. WARNING: At the moment, OpenCascade support is broken (at least on amd64)
++  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
++  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
++  * Corrected a minor issue (the icon reference)
++  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
++  * Initial update. There is still some work to do but it starts to get shape! ;) See bug #155974
++  * Added ~x86 in the KEYWORDS list. I tested it, it seems to work correctly.
++  * Initial import. See bug #130502 for more info
++  * Bug correction. Thank you Dewald for testing and showing me how to solve it.
++  * scidavis-0.1.3
++  * qtiplot-0.9.6 is now in the main tree
++  * Initial import of xtide.  A tidal prediction program that has graphical interfaces and a web server.
++  * Utilities for the creation and restoration of Tidal Constituent Database files.
++  * Initial import of an ebuild for and graphical editor of Tidal Constituent Database files.
++  * Initial import of libtcd, a library for the editing of Tidal Constituent Database files.
++  * Initial import of Tidal Constituent Database. Dependency of other tide related programs (libtcd, tcd-editor, tcd-utils, xtide).
++  * Initial import of Tide Constituent Database ebuilds. Dependency of several tide related programs (libtcd, tcd-editor, tcd-utils, and xtide).
++  * Added sci-geosciences to add new ebuilds.
++  * Initial ebuild for the PEST model calibration, Parameter ESTimation, and uncertainty analysis tool.
++  * qwt-5.1.0: in the main tree
++  * qtiplot-0.9.6: dependencies corrected
++  * Committed new versions for octave-forge packages.
++  * bump to empi-0.4 fixing issue with directories in portage_confdir, reported by Radice David
++  * qtiplot-0.9.6
++  * qwt-5.1.0
++  * Added librdmacm-1.0.7.ebuild
++  * Fixed recursive dohtml (see bug #221905) in sci-libs/lapackpp.
++  * mmtk: bump to 2.5.23.
++  * Updated to netgen-4.4-r1
++  * Bump to opencascade-6.2-r1
++  * OpenCascade belongs to sci-libs, not sci-misc. OpenCascade being fundamentally a library....
++  * OpenCascade belongs to sci-libs, not sci-misc. OpenCascade being fundamentally a library....
++  * My first contrib on the science overlay is a library for DICOM files (Digital Imaging and COmmunications in Medecine)
++  * mathgl-1.6.2, udav-0.3.2: ~ppc added
++  * udav-0.3.2: several improvements
++  * mathgl-1.6.2: several improvements
++  * Bump to new versions.
++  * Added compatibility with new imagemagick to octave-forge-image.
++  * added libibverbs-1.2.2.ebuild
++  * keyworded amd64
++  * keyworded amd64
++  * freefem++ version bump, added freefem++-syntax
++  * Upstream changed tarballs again
++  * coot: bump to 0.5_pre1-r87, add gcc 4.3 patch.
++  * extrema is now in the main tree
++  * maxima-5.15.0 and wxmaxima-0.7.5 are in the main tree
++  * udav-0.3.2: cleanup
++  * mathgl-1.6.2 cleanup and improvements
++  * Don't spit out errors if people aren't using empi
++  * udav-0.3.2: Universal Data Array Visualization
++  * mathgl-1.6.2: Math Graphics Library
++  * maxima-5.15.0 and related stuff
++  * Call eautoreconf in every required directory by hand as AC_CONFIG_SUBDIRS isn't uses and autotools.eclass can't find everything.
++  *  Fix for gcc-4.3.0.  Change 'char * argv[]' to 'char **argv' in configure scripts.  Thanks to Peter Alfredsen (peter.alfredsen at gmail) for the fix.
++  * Version bump.
++  * added phun
++  * plplot: more use flags dep checking
++  * empi, add x86.  Thanks to Shvetsov Alexey (alexxyum at gmail) for testing.
++  * eselect-mpi, add x86.  Thanks to Shvetsov Alexey (alexxyum at gmail) for testing.
++  * bump openmpi to 1.2.6.  Thanks to    Shvetsov Alexey (alexxyum at gmail) for the note.
++  * Fixed incorrect package descriptions.
++  * geant4: fixed a wrong sed command
++  * checksum change
++  * geant4: fixed syntax
++  * geant4: new ebuild with exports
++  * point {do,new}bin to correct functions
++  * add missing mpi.eselect-0.0.3
++  * removed skycat now in main tree
++  * removed tkimg, now in main tree
++  * added slotted geant-3, data dir is now /usr/share/geant-4/data for geant-4
++  * geant4: fix a bad env name and removed and extra fi in the no-source patch
++  * Changelog
++  * fixing license
++  * Add license for sci-chemistry/modeller
++  * Initial import, added MY_PV, thanks to the prolific Justin Schmitz
++  * readded geant
++  * removed geant4
++  * geant-4: fixed data installation
++  * added geant-4
++  * added dawn
++  * plplot: more fixes on use flags and fortran
++  * plplot: add missing use, more fortran fixes
++  * Initial import, openFST finite state transducer toolkit
++  * Bump eselect-mpi.  Fix mpi.eclass so it correctly reports the mpi_dir when building implementations via empi.
++  * removed mkl, now in main tree
++  * cdsclient: bump
++  * removed parmetis, now in main tree
++  * imported lasi
++  * Add digest for blcr changelog too.
++  * Initial import of blcr.  Thanks to kuffs (Aaron Tygart) for the ebuild.
++  * bump empi-0.3.  See ChangeLog for details.
++  * visual-4_beta26
++  * Don't use eselect-mpi in get_mpi_dir if empi is not being used
++  * octave-forge.eclass now uses octave's pkg.m for compiling packages.
++  * coot: bump to 0.5_pre1-r875.
++  * gle-4.1.2b
++  * yorick-2.1.05: DEPEND corrected
++  * texmacs-1.0.6.14
++  * breqn-0.97a
++  * mkl: more polishing
++  * yorick-2.1.05
++  * Added patch to have 'pkg install' exit with error code if it can't find the source tarball.
++  * moved overlay to new directory
++  * coot: keyword ~amd64
++  * mmtk: Bump to 2.5.22
++  * ccp4: revbump with new upstream patches and Gentoo build fixes.
++  * Update coot to 0.4.1.
++  * Drop unneeded packages and packages that exist in other repos.
++  * move stuff to root
++  * deleted ifc and icc, now in main tree
++  * qtiplot-0.9 Depends on x11-libs/qwtplot3d built with qt-4 (bug #184652)!!!
++  * freemat in main tree
++  * harminv: fixed autotools
++  * freemat-3.5
++  * octave-2.9.14 (seems to work fine on my x86 without any patches)
++  * metis: fixed autotools patch and license
++  * fixed cxsparse autotools patch
++  * added cholmod and metis
++  * revert acml
++  * revert acml
++  * acml manifest fix
++  * extrema-4.2.8
++  * added: colamd ccolamd cxsparse camd
++  * removed blas-goto, updated in main tree
++  * added gsl-1.10 with cblas support
++  * *-atlas: set default fortran flags
++  * cleaning license and use flag
++  * removed cmt, now in main tree
++  * sci-mathematics/gretl: Fixed for lapack settings, removed tetex.
++  * removed maxima, now in main tree
++  * boa-constructor-0.6.1
++  * lapack-atlas: fixed clapack error
++  * sci-biology/sibsim4: version bump
++  * sci-biology/gmap: version bump
++  * removed cfitsio, now in main tree
++  * texmacs-1.0.6.11
++  * icc/ifc: few fixes with envd files
++  * delete numeric, now in main tree
++  * numeric: fix for 2.5
++  * ifc/icc: added rootpath in env files
++  * mkl: swap restrict fetch and mirror
++  * icc: added emul-linux-compat-x86
++  * maxima-5.13.0 and texmacs-1.0.6.10-r1 with a patch to run maxima-5.13.0
++  * added icc-10
++  * added ifc-10
++  * cleaning
++  * Added ipp
++  * cleaning
++  * removed root, geant, cernlib, cernlib-montecarlo, paw, now in main tree
++  * cleaning
++  * cleaning
++  * removed xbae, now in main tree
++  * removed numdisplay, now in main tree
++  * extrema-4.2.7: added ~amd64
++  * removed gdl, now in main tree
++  * extrema-4.2.7: data analysis and visualization
++  * removed gsl, now in main tree
++  * removed blas,cblas,lapack-reference, now in main tree
++  * lapackpp update
++  * lapackpp cleanup
++  * lapackpp: initial import
++  * {blas,lapack}-atlas: updated patch
++  * mkl: re-fix access violation and a comment
++  * mkl: lapack.pc fix
++  * mkl update
++  * updated virtual with deps
++  * atlas: fixed bug
++  * mkl update
++  * blas/lapack pkg-config file update
++  * fixed *.pc.in to work on x86
++  * added many updates to blas/lapack packages
++  * added new virtual blas, cblas and lapack
++  * cernlib.eclass: cleanup
++  * removed libctl, now in main tree
++  * removed pygsl, now in main tree
++  * removed muParser update, now in main tree
++  * Whoops! inherit autotools
++  * Fix typos
++  * Remove LICENSE until I have time to fix it.
++  * Initial import of cluster-1.36 thanks to Favero Francesco
++  * sci-physics/root: root: fixed Manifest
++  * Merged many things to gentoo-x86, mostly coot-related
++  * sci-astronomy/sextractor: filter optim flags
++  * removed ds9, now in main tree
++  * dev-lang/gdl: gdl: fftw>=3
++  * sci-astronomy/scamp: cleaning
++  * sci-astronomy/scamp: Version bump
++  * removed freemat, now in main tree
++  * dev-cpp/muParser: Version bump
++  * sci-astronomy/ds9: Version bump
++  * sci-astronomy/swarp: swarp: version bump
++  * dev-lang/gdl: added ChangeLog
++  * dev-lang/gdl: gdl: version update
++  * dev-python/pygsl: pygsl: version bump
++  * sci-physics/bullet: bullet version bump
++  * sci-physics/root: root:added patch release
++  * sci-physics/root: root: fixed CC -> CXX
++  * sci-physics/root: root: added truetype option, fixed intel and fortran compilers support
++  * cernlib.eclass cleanup
++  * sci-physics/cernlib: cernlib: fixed an ifc problem
++  * sci-physics/cernlib: cernlib:updated patch
++  * sci-physics/root: Version bump
++  * added makedepend dep on cernlib.eclass
++  * Making gtk-gamess ~amd64 only until I can fix up gamess to include the amd64 arch.
++  * Removing, as ghemical is now in the main tree.
++  * Removing as it's now in the tree.
++  * Removed apbs, as it made it into portage and was causing confusion.
++  * coot: pull guile 1.8 patch from upstream instead of our custom one.
++  * coot: fix build with guile 1.8 / gmp 4.2.1
++  * Changed to use markusle's octave ebuild.
++  * Deleted jmol as it's now in the tree.
++  * Replacing octave-2.9.12.ebuild with markusle's ebuild.
++  * Removing keywords.
++  * Fixing manifest.
++  * Bumping to octave-2.9.12
++  * add bullet
++  * Removed pymol as it's now in the main tree.
++  * Testing pymol-0.99_rc10.
++  * Coot: delete old snapshot, newer version's in portage.
++  * Add burrow-owl NMR package, and its new guile deps, bumps and patches.
++  * Fixed a typo in jmol.
++  * paw: version bump
++  * added root digest
++  * root: version bump
++  * Fix jmol digest
++  * sci-chemistry/jmol: changed to use sci-libs/jmol-acme
++  * More java cleanup thanks to nichoj.
++  * Depend on saxon-6.5 to generate documentation.
++  * sci-biology/gmap: upstream re-rolled tarball due to single bug, updating digests
++  * sci-biology/gmap: version bump
++  * sci-physics/root: root: mit-krb5 -> virtual/krb5
++  * sci-mathematics/gretl: gretl:initial import
++  * dev-python/numeric: dev-python/numeric: various new patches to work with python 2.5
++  * More cleanup...
++  * Cleanup and get ready for portage migration.
++  * Removing from overlay as it's now it portage. Getting ready to introduce JMol.
++  * Removing from here as it's in portage. Getting ready to introduce JMol.
++  * geant: debian patches update
++  * paw: fixed back to older debian cernlib
++  * sci-astronomy/scamp: scamp: version bump
++  * More appropriate file name for vecmath-objectclub.
++  * Took out the symlink to plugin.jar.
++  * Emptied KEYWORDS temporarily.
++  * Fixed all jars except for netscape.jar. Ugly hack used. :(
++  * Initial import.
++  * Initial import...comments welcome :D
++  * Adjusted $ARCH
++  * Moved jmol-acme as it fits better in sci-libs.
++  * Argh!
++  * Re-adding jmol-acme.
++  * Moving from sci-chemistry to sci-libs,
++  * More cleanup
++  * Fixing DEPEND
++  * Adding KEYWORDS
++  * Tidy up a bit.
++  * Improved the 11.0 build and removed 10.2
++  * Adding -sourcepath "" as per Caster's suggestion.
++  * Initial import.
++  * The patch has been applied upstream (without changing the version number)
++  * texmacs-1.0.6.10
++  * Manifest corrected
++  * sci-physics/root: bumped root from main tree with cernlib compatibility
++  * an attempt to solve the problem that /usr/share/maxima/5.12.0/doc/html/ is created twice on some systems
++  * added use local flag hdf5 for meep
++  * sci-physics/meep: added meep
++  * sci-physics/harminv: harminv: enabled shared library
++  * sci-libs/libctl: added libctl
++  * sci-physics/harminv: added harminv
++  * git-svn-id: http://overlays.gentoo.org/svn/proj/science/overlay@597 32389bae-6d03-0410-99cf-db05cde120eb
++  * sci-libs/cfitsio: Version bump
++  * Added a check that, if guile is 1.8, it is emerged with +deprecated
++  * Please don't leave inconsistent Manifest files in the tree!
++  * fixed for new debian directory structure
++  * texmacs-1.0.6.9-r1: support for maxima-5.12.0
++  * maxima-5.12.0
++  * Moved ebuild to portage.
++  * Getting rid of pymol since it's in the tree now...
++  * cernlib: version bump+cleaning
++  * qcl version bump and added amd64 for testing
++  * pygsl version bump. added src_test
++  * added muparser
++  * sci-biology/blat: version bump!
++  * Updated ChangeLog.
++  * Added ~amd64.
++  * Add changelog thanking hodak at ncsu.
++  * Importing pymol-0.99_rc8.
++  * Adding svn pymol build.
++  * add metatadata.xmls for all these poor souls
++  * Mass import from sunrise
++  * new use flag for sci-biology import
++  * new licenses for sci-biology
++  * new license gmap for sci-biology/gmap
++  * rkward now in main tree
++  * qwt was moved in main tree
++  * Manifest update.
++  * removed paraview, now in main tree
++  * vtk now in main tree
++  * mayavi-1.5 now in main tree
++  * minor cleanup
++  * jdk dep for vtk
++  * added mayavi
++  * added paraview
++  * vtk suite
++  * added new vtk
++  * liborigin now in main tree
++  * sci-astronomy/sextractor: sextractor: cleanup
++  * sci-astronomy/ds9: ds9: version bump
++  * aldor-1.1.0_rc
++  * sci-astronomy/skymaker: Initial import of skymaker
++  * sci-mathematics/rkward: rkward: version bump
++  * sci-mathematics/freemat: freemat: added post_install function
++  * sci-mathematics/freemat: freemat version bump
++  * maxima changes now in main tree
++  * removed obsolete itpp
++  * dev-util/cmt: Version bump
++  * final cernlib cleaning
++  * fixed keywording for cernlib eclass
++  * fixed keywording for cernlib packages
++  * cernlib now uses the cernlib.eclass
++  * added cernlib eclass
++  * fixed for type -P/which
++  * deleted geant321
++  * sci-physics/geant: geant: version cleaning and update
++  * sci-physics/cernlib: cleaning cernlib
++  * sci-physics/cernlib-montecarlo: cleaning cernlib-montecarlo
++  * sci-physics/paw: version adapted for cernlib-2006 paw new revision for cernlib-2006
++  * x11-libs/xbae: initial import
++  * sci-physics/cernlib-montecarlo: cleaning
++  * sci-physics/cernlib-montecarlo: version bump version bump
++  * sci-physics/cernlib: changelog commit
++  * sci-physics/cernlib: version bump
++  * cleaning old versions of cernlib packages
++  * sci-mathematics/maxima: maxima: added latex stuff from bug #169178.
++  * dev-tcltk/tkimg: cleaning tkimg
++  * sci-astronomy/swarp: cleaning swarp
++  * sci-astronomy/skycat: cleaning skycat
++  * sci-astronomy/stiff: cleaning
++  * sci-astronomy/sextractor: cleaning
++  * sci-astronomy/esorex: cleaning esorex
++  * sci-astronomy/scamp: scamp version bump
++  * esorex version bump
++  * cpl version bump
++  * bumped cdsclient
++  * cleaning
++  * removed arpack, now in main tree
++  * rkward: fixed rdeopend
++  * kayali version bump
++  * rkward version bump
++  * cleaning
++  * removed pspp from overlay, now in main tree
++  * Changed ARCH for jmol temporarily.
++  * removed pgplot, now in main tree
++  * Initial import of gromacs.
++  * Initial import...jmol-11.0.ebuild is NOT working yet...
++  * cleaning maxima, a few fixes
++  * Fix guile dep as per b.g.o bug 169488.
++  * removed root, now in main tree
++  * freemat-3.0
++  * cleanup
++  * fixed cfitsio
++  * root-5.14 fixes
++  * removed basemap, now in main tree
++  * added an updated version of root
++  * finalize apbs-0.5.0 cleanup
++  * cleaning Manifest and digests
++  * removed minuit, now in main tree
++  * removed root, now in portage
++  * removed hippodraw, now in portage
++  * Fixing apbs-0.5.0
++  * Fixing apbs-0.5.0
++  * removed wxmaxima, now in main tree
++  * removed imaxima, now in main tree
++  * removed qfits, now in main tree
++  * cleanup bogus patches
++  * removing umfpack now in main tree
++  * removing scipy, now in main tree
++  * asymptote is now in the main portage tree
++  * aldor-1.0.3 (binary, x86 only)
++  * aldor-1.0.3 (binary, x86 only)
++  * TeXmacs-1.0.6.9
++  * removed matplotlib (now in main tree)
++  * cleaning scipy
++  * removed numeric, now in main tree
++  * removed cfortran, now in main tree
++  * removed blas-docs and lapack-docs, now in main tree
++  * cleaned matplotlib
++  * removed pyfits (in main tree)
++  * removed numarray (in main tree)
++  * Initial apbs import.
++  * removed numpy (in main tree)
++  * removed libafterimage, now in main tree
++  * removed wcstools (in main tree)
++  * removed celestia (in main tree)
++  * TeXmacs-1.0.6.8-src.tar.gz has silently changed at ftp.texmacs.org
++  * asymptote-1.20: a fix in DEPEND
++  * maxima-5.11.0-r1: now depends on x11-misc/xdg-utils, sbcl-disable-debugger.patch dropped
++  * asymptote-1.20
++  * TeXmacs-1.0.6.8
++  * Use science for repo_name
++  * Adding categories and repo_name to profiles following glep 42 and reminded by dev-zero
++  * Whoops, putting mopac7 back :)
++  * Remove mopac7 from IUSE.
++  * Removed mopac7 USE flag.
++  * Add gtk-gamess to RDEPEND.
++  * Changed help browser to allow seamonkey or firefox.
++  * add ~amd64 to texmacs-1.0.6.7
++  * Fix for bug 162154.
++  * Corrected SRC_URI.
++  * Adding the forgotten metadata file.
++  * Initial cgal-python import
++  * initial import of the CGAL library
++  * Add dependency to RDEPEND.
++  * Initial import of ghemical-2.10 into sci overlay.
++  * Initial import of gtk-gamess.
++  * Bump coot to latest prerelease.
++  * added basemap
++  * agg removed, now in main tree
++  * hippodraw version 1.19.1 update
++  * hippodraw version 1.19.1 update
++  * removed scigraphica, now in main tree
++  * root-5.14.00 version update
++  * pspp cleaning
++  * wxmaxima version bump
++  * umfpack version update
++  * qfits manifest
++  * minuit version bump
++  * cleaning skycat
++  * cleaning swarp
++  * cleaning stiff
++  * cleaning scamp
++  * cleaning ds9
++  * cleaning esorex
++  * cleaning cpl
++  * cleaning sextractor
++  * wcstools-3.6.6 version bump
++  * removed icc flag, too buggy
++  * tclx now in main tree
++  * fixed some changelogs
++  * added asciidata
++  * cfortran: minor patch update
++  * imaxima version bump
++  * maxima-5.11.0: version bump
++  * texmacs-1.0.6.7: version bump
++  * cfitsio-3.030 update
++  * Add dev version of mmtk. PyMol plugins for it are available on the homepage.
++  * Add coot snapshots.
++  * fixed numpy changelog
++  * scipy version bump
++  * numpy version bump
++  * numpy: fixed lapack flag
++  * gle-4.0.12 with lots of new stuff (Qt4 GUI, etc.)
++  * dev-utils/cmt version bump to 1.19
++  * sci-libs/cfitsio version bump and cleaning
++  * asymptote-1.18: imported from bug 82871, with a fix for sandbox violation
++  * freemat-2.0: now builds with recent umfpack ebuilds
++  * qtiplot-0.8.8 depends on liborigin and qwt-5 (with USE=qt3); for now, emerge it with USE=-python
++  * qwt5: USE=qt3 builds a qt3-version needed for qtiplot
++  * muParser ebuild removed - now in the mainline tree
++  * a fix for muParser
++  * moving muParser, part 2
++  * moving muParser to dev-cpp
++  * Comment about rlwrap corrected
++  * matplotlib-0.87.7: version update
++  * added numpy-1.0
++  * cfortran: some cleanup
++  * imaxima: removed version in tree
++  * tclx-8.4: minor fixes
++  * remove SLOT and made sed statement more readable.
++  * misc cleanup and beautification
++  * fixed metadata.xml
++  * misc cleanup and beautification
++  * Fixes per bug #138619
++  * Initial import of jmol.
++  * Minor fix to comment.
++  * git-svn-id: http://overlays.gentoo.org/svn/proj/science/overlay@394 32389bae-6d03-0410-99cf-db05cde120eb
++  * OPJFile.h is now installed
++  * An improved liborigin ebuild by George Shapovalov
++  * added OpenIB-related USE-flags
++  * Initial import for OpenIB-/OFED-1.1
++  * Updated for 1.1 release of openib/OFED
++  * root-5.12: only use fortran when cern is selected
++  * hippodraw-1.19.0 version bump
++  * removed scientificpython, now in main tree
++  * removed orsa, now in main tree
++  * coot: merged to gentoo-x86
++  * ds9: fixed a typo and cflags
++  * tree cleaning: manifest, metadata, old versions.
++  * added esorex
++  * added cpl
++  * added qfits
++  * scamp, sextractor, stiff, swarp: removed flag filtering + cleaning
++  * root-5.12.00e-r1: fixes for asimage, xrootd and qt3
++  * hippodraw: cleanup
++  * hippodraw-1.18.6 version bump. updated license.
++  * geant321: removed ifc support for now
++  * paw-2.14.04-r1.ebuild: updated patches
++  * cernlib-montecarlo-2005-r1: updated patches
++  * cernlib-2005-r1: updated patches
++  * added umfpack use flag
++  * celestia: added cairo flag + fixes
++  * fixed deps for x11 modular
++  * oops
++  * wxmaxima-0.70a: version bump
++  * pspp: updated plotutils flag
++  * scipy: removed ppc (because of umfpack)
++  * arpack: clean up
++  * deleted mkl (now in main tree)
++  * cfitsio: depends on cfortran (better between arches)
++  * ds9-4.0_beta10: updated version and patches.
++  * git-svn-id: http://overlays.gentoo.org/svn/proj/science/overlay@360 32389bae-6d03-0410-99cf-db05cde120eb
++  * git-svn-id: http://overlays.gentoo.org/svn/proj/science/overlay@359 32389bae-6d03-0410-99cf-db05cde120eb
++  * git-svn-id: http://overlays.gentoo.org/svn/proj/science/overlay@358 32389bae-6d03-0410-99cf-db05cde120eb
++  * git-svn-id: http://overlays.gentoo.org/svn/proj/science/overlay@357 32389bae-6d03-0410-99cf-db05cde120eb
++  * scamp-1.2.11: added eselect deps.
++  * scamp-1.2.11: added warning if atlas is not selected
++  * orsa: added metadata.xml
++  * added wcstools-3.6.5
++  * imaxima-0.95 version bump
++  * cmt-1.18.20061003: version bump
++  * tclx-8.4: removed amd64 bad bit
++  * scientificpython: bumped stable 2.6
++  * matplotlib-0.87.6: proper commit this time
++  * numeric-24.2-r2: fixed lapack, added a math patch
++  * numarray-1.5.2-r1: fixed lapack stuff
++  * pygsl: updated gsl min version
++  * matplotlib-0.87.6: version bump
++  * added: liborigin-20060616
++  * added: muparser-1.25
++  * matio: minor cleanup
++  * wxmaxima/Manifest fixed
++  * Updated ChangeLog
++  * -libibverbs-1.0.9999.ebuild, -libibverbs-1.1.9999.ebuild
++  * Initial import
++  * hippodraw-1.18.3: added an addwrite for qt settings
++  * scipy-0.5.1-r1: fix a PIC for non-x86 arches
++  * umfpack-5.0.1: fixed an missing include file
++  * sync scipy with main tree, add one with umfpack
++  * redigesting
++  * added use flags for hippodraw
++  * deleted packages bumped in main tree
++  * added hippodraw-1.18.3
++  * readded minuit + version update to 5.12.00
++  * wxmaxima-0.7.0 is for the new maxima-5.10.0
++  * maxima-5.10.0: a major new version
++  * added cern use flag
++  * added numpy-1.0_rc1.ebuild
++  * matplotlib-0.87.5: removed ppc keywods (agg untested)
++  * scientificpython, cmt: changed license to CeCill-2
++  * Changed CeCiLL license, added agg use flag
++  * numarray-1.5.2.ebuild: fixed lapack and fortran deps
++  * umfpack: added a warning about upgrading. Is there a better solution??
++  * matio-1.3.1: version bump
++  * qcl ebuild now honours the user's $CXXFLAGS
++  * added a working celestia-1.4.1-r1
++  * added plplot use flag
++  * added sci-astronomy/scamp
++  * added sci-astronomy/cdsclient
++  * added sci-astronomy/stiff
++  * removed swarp-2.15.7, cleaning
++  * some cleaning
++  * updated metadata.xml
++  * added tclx-8.4 and tkimg-1.3
++  * added skycat-3.0.1
++  * orsa-0.7-r1: ebuild update
++  * orsa-0.7-r1: qt -> qt3 use flag
++  * deleted minuit (now in >=root-5)
++  * new ebuild for libafterimage
++  * major root-5.12.00e ebuild update, removed old one.
++  * scientificpython-2.5.11 update
++  * cleaning white spaces, digest and others.
++  * some cleaning
++  * version bump for openmpi+pg fortran compiler
++  * added new fortran eclass
++  * added matplotlib-0.87.5, removed old (buggy) 0.87.4-r1
++  * updated root to 5.12a and moved to sci-physics
++  * added geant321-3-21.14
++  * added cernlib-montecarlo-2005
++  * added paw-2.14.04
++  * split cernlib, updated ebuild and put it in sci-physics
++  * added scientificpython-2.4.11 and scientificpython-2.5.10
++  * added torque-2.1.2
++  * added scipy-0.5.1
++  * fixed a test in umfpack-5.0.1
++  * added umfpack-5.0.1
++  * added swarp-2.16.0
++  * added sextractor-2.5.0
++  * added cmt-1.18.20060606, removed old versions
++  * added numpy-1.0_beta5, removed old versions
++  * numarray-1.5.2: version update and clean
++  * added matplotlib-0.87.4-r1
++  * more flexibility to change versions of AMD and UFconfig
++  * coot: bump to 0.1.2
++  * added a forgotten file
++  * changed download url for UFconfig to a fixed version instead of current
++  * changed amd download url to a fixed version (1.2) instead of current
++  * matplotlib: updated to 0.87.4-r1, removed 0.87.3 and various cleanups
++  * agg: updated Manifest, removed agg-2.3
++  * fixed sandbox violation with USE flag doc
++  * matio-1.3.0 download url fixed
++  * matio-1.3.0 (version bump); freemat-2.0 (patch for building with matio-1.3.0)
++  * added texmacs-1.0.6.6
++  * Corrected herd in metadata.xml
++  * added qcl-0.6.2
++  * new version: texmacs-1.0.6.5
++  * new version: texmacs-1.0.6.5
++  * Added xspice and X use flag. See bug 140402
++  * New ebuild for gerbv-1.0.2
++  * removed old files
++  * Version bump to 0.99.1
++  * Version bump to 0.99.1
++  * Making repoman happy.
++  * Version bump. Removed old version
++  * Removed some ebuilds older than the ones in the tree
++  * added: freemat-2.0
++  * new version: texmacs-1.0.6.4
++  * Added initial ebuild for rkward
++  * Minor fixes to kayali in order to please repoman
++  * minor cleanups
++  * new version: texmacs-1.0.6.3
++  * Adding kayali ebuild
++  * Merged ccp4, coot and deps to gentoo-x86
++  * Merged ccp4, coot and deps to gentoo-x86
++  * bug fix in matio-1.1.4
++  * added matio-1.1.4, removed matio-1.0 (this last ebuild was unsatisfactory)
++  * There's a new coot 0.1.2-pre1 with fixed hydrogen hiding.
++  * added USE flags for texmacs
++  * added matio-1.0
++  * matplotlib: cleanup
++  * matplotlib-0.87.3-r1: fixed wxpython versioning, added patch for tcltk
++  * imaxima: changed ChangeLog
++  * imaxima-0.94b: added patch
++  * maxima-5.9.3-r1: fixed linguas, added new patches
++  * ccp4 double-defines gerror_ in library_f.c on ppc/gcc4
++  * pyfits-1.0.1: version bump
++  * numpy-0.9.8: fixed some typos
++  * Add missing patch
++  * Make coot prereleases work.
++  * ccp4: install everything formerly in /usr/lib/ccp4/ to /usr/share/ccp4/ with the exception of ccp4i, because it contains binaries and scripts. Fix installation of some html docs that tried going to /usr/html/. Fix generation of symlinks in /usr/lib/ccp4/ so ccp4i documentation works. Also sed MOLREPLIB in the setup scripts, so programs using it work.
++  * Minimal changes to get ccp4 6.0.1 working.
++  * Initial bump of coot to 0.1.2-pre1
++  * arpack: fixed typo
++  * added imaxima-0.94b
++  * added maxima-5.9.3-r1
++  * cfitsio: fix $PF to $ for docs
++  * Bump ccp4 to 6.0.1
++  * Instead of a hackish check for whether our rpaths will kills us, just add stricter to RESTRICT.
++  * agg-2.4: redigesting
++  * scigraphica: fixed ALL_LINGUAS
++  * libscigraphica: fixed ALL_LINGUAS
++  * matplotlib-0.87.3: version bump
++  * scigraphica & libscigraphica: major update
++  * sci-astronomy: cleanup
++  * umfpack: fixed a typo in libtool tag
++  * scipy-0.4.9: added swig dependency for umfpack bindings
++  * numeric-24.2-r1: cleaned, updated changelog.
++  * numpy-0.9.8: blocks f2py. tested with gcc-4.1
++  * added algae-4.3.6
++  * scipy-0.4.9: version bump + fixes
++  * dev-python: cleanup
++  * added numeric-24.2-r1: various fixes
++  * arpack96-r1: autotoolization
++  * Moved the the portage tree.
++  * Minor updates.
++  * cernlib-2005-r1: fixed cernlib script, added imake dep.
++  * added pgplot-5.2.2-r1
++  * Bump coot.
++  * Pull in coot-data, also add missing guile-gui dep
++  * cfitsio-3.006-r1: proper libtoolization
++  * numpy-0.9.8: version bump
++  * agg-2.4: updated for X modular
++  * orsa-0.7.0-r1: added patch to compile with for gcc-4.1
++  * added texmacs-1.0.6.2
++  * matplotlib-0.87.2-r2.ebuild: swap numeric/numpy
++  * wxmaxima: fixed for wxwidget versioning
++  * Moved to the main portage tree.
++  * added yorick-1.5.22
++  * added qtiplot-0.8.5
++  * added keyword -amd64
++  * Stop patching in gfortran 4.0 tarball and remove the associated patch. Bill Scott suggests the stuff's already in 6.0.
++  * numarray-1.5.1-r2: fixed for gcc-4.1, lapack and headers
++  * Add ccp4 patches from prerelease/ section. Pass --tmpdir so imake doesn't attempt to write to /imakeXXXXXX
++  * Forgot to add the ccp4 patch to fix builds w/ gcc 4.1
++  * added scigraphica-2.1.0 and libscigraphica-2.1.1
++  * torque: version bump to 2.1.0
++  * added blas-docs and lapack-docs
++  * agg-2.4: fixed virtual/x11
++  * agg: updated to 2.4
++  * wxmaxima: version bump to 0.6.5
++  * cmt-1.18: version bump and fixed emacs USE flag
++  * openmpi: fixed use fortran
++  * Update sauerbraten version. Add RMD160 and SHA256 digests to ccp4.
++  * cmt-1.18.20060301.ebuild: fixed CMTDIR
++  * Add gfortran to allowed compilers.
++  * Don't mirror this stuff.
++  * Since we install with insecure RPATH settings, add a check to see whether portage has been edited to allow it.
++  * Apply upstream patches.
++  * Set CCP4_LIB to try and get the X programs linking with libxdl_view.
++  * Try einstall instead of make install to see whether it improves rpath issues.
++  * Do a more generic sed to change CCP4_MASTER.
++  * Fix up some formatting.
++  * Add a ccp_patch() wrapper that makes it look like we're bulk patching.
++  * Minimal changes to get it working.
++  * Copy 5.99.5 to new version.
++  * added cmt-1.18.20060301
++  * minuit: fixed ChangeLog
++  * root-5.10.00: fixed CXXFLAGS, doc
++  * general cleaning
++  * root-5.10.00: added doc keyword and install
++  * cernlib-2005: fixed cfortran to use installed one.
++  * cernlib: fixed doc targets
++  * cfortran-4.4: updated debian patch
++  * root-5.10.00: fixed EXTRA_ECONF and some cleaning
++  * added root-5.10.00 (major version bump)
++  * cernlib-2005: fixed a doc installation
++  * added cernlib-2005
++  * added agg-2.3 (for matplotlib)
++  * matplotlib-0.87.2-r2: added agg support
++  * openmpi: fixed digest
++  * Removed src_compile
++  * removed useless src_compile
++  * Adding ebuild for generecon
++  * Merge in comet overlay.
++  * Initial commit of portage overlay.
++  * Initial commit of portage overlay.
++  * arpack cleaning
++  * openmpi-1.0.2: version bump
++  * major update for umfpack-4.6
++  * arpack: fixed a bunch of things, new blas flag, libtoolization.
++  * added mkl-8.0.2.004.ebuild (simple version bump)
++  * Moved to the main portage tree.
++  * Added ebuild for magic-7.4.2
++  * Adding new ebuild for octave-epstk
++  * added mkl-8.1.014 (working experimental version)
++  * Fixed documentation issue
++  * Moved to the main portage tree.
++  * Cleaning up as they are now in the main portage tree.
++  * cleaned to sync with portage
++  * added gle-4.0.11
++  * Fixed IUSE line
++  * Various small cleanups of the ebuild, added examples USE flag and marked ~amd64.
++  * Version bump
++  * maxima-5.9.3: removed unicode patch
++  * various ebuild cleaning
++  * swarp-2.15.7 version bump
++  * cleaned numdisplay
++  * added numpy-0.9.6-r1
++  * pruned old numpy and added numpy-0.9.6-r1
++  * cleaned cfortran and pruned R
++  * Removed previous linsmith versions
++  * Version bump for linsmith-0.9.4
++  * Version bump for linsmith-0.9.4
++  * Version bump for linsmith-0.9.4
++  * maxima-5.9.3: version bump, fixes + removed 5.9.2
++  * matplotlib/Manifest: fixed
++  * added an ATLAS check. corrected some path in site.cfg
++  * mkl-8.0.1.006.ebuild: added env.d and a few cleaning
++  * openmpi-1.0.1.ebuild: fixed links added noexecstack and
++  * numarray-1.5.1-r1.ebuild: put lapack sed in src_unpack
++  * openmpi-1.0.1.ebuild: fix USE flags, links
++  * cleaning
++  * torque-2.0.0_p8.ebuild: now pic only for libpbs with a patch
++  * torque-2.0.0_p8.ebuild: forced fPIC and added PBS_SERVER_NAME
++  * openmpi-1.0.1.ebuild: removed warning if not pic
++  * arpack-96.ebuild: fortran and mpi fixes
++  * numpy-0.9.6.ebuild: fix atlas/lapack again
++  * removed src_test
++  * added scipy-0.4.8.ebuild with proper fftw and atlas treatment
++  * added matplotlib-0.87.2.ebuild, also with wxpython flag
++  * scipy-0.4.6.ebuild: removed ifc flag
++  * torque-2.0.0_p8.ebuild: changed pic and tcltk behaviour, added netkit-rsh
++  * openmpi-1.0.1.ebuild: slight more info on pic behaviour
++  * scipy-0.4.6.ebuild: removed eselect dependencies
++  * fixed pic behaviour for openmpi and torque
++  * added openpbs-common-1.1.1
++  * deleted torque-2.0.0_p7.ebuild and changed DEPENDS for torque-2.0.0_p8.ebuild
++  * white space cleaning for torque-2.0.0_p8.ebuild
++  * added torque-2.0.0_p8.ebuild and patches
++  * openmpi-1.0.1.ebuild: removed pic flag, forced -fPIC for amd64
++  * scipy-0.4.6.ebuild: fixed threaded-ATLAS directory
++  * scipy-0.4.6.ebuild: eselect corrections
++  * openmpi-1.0.1.ebuild: added pic use flag and corrected fortran stuff
++  * bumped numpy-0.9.6
++  * added matplotlib-0.87.1 patches
++  * added sys-cluster/{torque,openmpi} very experimental ebuilds
++  * matplotlib-0.87.1 version bump and doc clean
++  * added numpy/ChangeLog
++  * changed lapack config: added use flag. removed test for now.
++  * added numarray-1.5.1-r1
++  * added matplotlib-0.87
++  * added cfitsio-3.006
++  * forgot scipy-0.4.6 digest
++  * added numpy-0.9.5
++  * scipy-0.4.6 version bump
++  * general cleaning (licenses, USE flags descriptions, headers)
++  * orsa-0.7.0.ebuild: removed useless USE flags
++  * cfortran-4.4.ebuild: fixed error in license
++  * scipy-0.4.4: lapack-atlas instead of virtual/lapack
++  * mkl: added blas/lapack routines files for shared libs
++  * Adding new freehdl from bug 122790
++  * mkl-8.0.1.006.ebuild: make shared libs, removed cpu detection, threading by default
++  * mkl: removing threaded scripts and c-lapack
++  * local USE flags description file added
++  * updated license and metadata.xml
++  * scipy/scipy-0.4.4.ebuild: changed fortran
++  * added scipy-0.4.4
++  * mkl-8.0.1.006.ebuild: improved cpu detection
++  * mkl-8.0.1.006: config scripts, license stuff
++  * added licenses directory and AURA, mkl licenses
++  * mkl: reworked ebuild: +fortran95, rpm work and install, not yet operational
++  * mkl-8.0.1.006.ebuild: reworked lib install + tests
++  * mkl/mkl-8.0.1.006.ebuild: corrected some installation bugs
++  * added experimental mkl-8.0.1.006
++  * Version bump
++  * maxima-5.9.2.ebuild: changed gnuplot category for sci-visualisation
++  * maxima-5.9.2.ebuild: changed gnuplot dep for sci-visualisation
++  * maxima-5.9.2: final fixes for ebuild and updated metadata.xml
++  * maxima-5.9.2.ebuild: some cleaning
++  * maxima-5.9.2.ebuild: gcl use flag is back.
++  * maxima-5.9.2: added patches (browser+emaxima) + cleaning
++  * gdl in portage
++  * maxima-5.9.2.ebuild: forced >=sbcl-0.9.4, and rlwrap change
++  * maxima-5.9.2.ebuild: put back the eautoreconf to build on x86
++  * Adding geos-2.2.1 Bug 120479
++  * Adding geos-2.2.1 Bug 120479
++  * Adding a new patch to configure.ac
++  * ebuild cleaning
++  * added maxima-5.9.2
++  * added wxmaxima package
++  * Adding a missing digest
++  * pspp-0.4.0.ebuild: emacs now uses elisp-common stuff
++  * added package dev-python/numdisplay
++  * Adding the path posted in the bug modified to work with 7.6.6. It does not solve the TK problem
++  * orsa-0.7.ebuild: change MPI stuff
++  * umfpack/umfpack-4.4.ebuild: changed doc behaviour and removed harcoded -j1
++  * sci-astronomy/orsa/orsa-0.7.0.ebuild: restored lam-mpi
++  * added sci-astronomy/orsa-0.7.0
++  * Very initial import of brlcad, from bug 77197. Does not compile here yet - needs work.
++  * fixed for USE=examples
++  * removed celestia (in portage)
++  * added package arpack (version -96)
++  * celestia/celestia-1.4.0.ebuild: fixed USE=kde deps.
++  * cleaning metadata and ebuild
++  * ebuild cleaning
++  * ebuild cleaning
++  * ebuild cleaning
++  * In the main portage tree.
++  * Moved to the main portage tree.
++  * Several minor corrections and enhancements.
++  * added package pygsl
++  * pyfits/pyfits-1.0.ebuild: license info
++  * Moved veusz to the main repo - thanks.
++  * Cleaned up some white space issues.
++  * Corrected a few whitespace issues, added doc to IUSE.
++  * sci-astronomy/celestia/celestia-1.4.0.ebuild: dependencies cleaning
++  * ds9-4.0_beta7.ebuild: added () for dohtml
++  * added celestia-1.4.0.ebuild
++  * added veusz-0.8.ebuild
++  * Added pspp-0.4.0.ebuild
++  * minuit-1.7.9 version bump
++  * minuit-1.7.9 version bump
++  * minuit-1.7.9.ebuild version bump
++  * minuit-1.7.6.ebuild: added insinto for doc, cfortran-4.4.ebuild added a link for cfortran.h
++  * New ebuild added: cfortran
++  * Small fix to header too...
++  * Tweaking dep.
++  * Initial import from bug 50565.
++  * IDL_STARTUP + cosmetics
++  * added umfpack-4.4.ebuild
++  * change gdl category to dev-lang + slight ebuild update
++  * minuit: pdf doc with DISTDIR
++  * cosmetics + RDEPEND without icc
++  * Added new ebuild for swarp-2.15.6
++  * Added new ebuild for ds9-4.0_beta7
++  * Adding ebuild for kseg
++  * added pyfits-1.0.ebuild
++  * added examples to test even without doc flag
++  * USE flags cleaning (ncurses, imagemagick and python)
++  * Adding linsmith patch
++  * Added new ebuild for minuit-1.7.6
++  * Added new ebuild for gdl-0.8.11
++  * Added new ebuild for sextractor-2.4.4
++  * Adding linsmith-0.9.2.ebuild
++  * Adding emu-1.10 form bug #98051
++  * Added new ebuild for linsmith-0.9.2
++  * Adding R-2.2.0 ebuild from bug 112022
++  * Adding kst-1.1.1
++  * New ebuild for linsmith-0.9.1
++  * Removed boinc -> moved to main tree.
++  * Cleaned up deps on X and modular X, bug 110606.
++  * Add experimental boinc ebuild to the overlay for testing.
++  * Moved to portage main tree.
++  * Small cleanup.
++  * Forgot to add the revbumped kst ebuild...
++  * Clean up old ebuilds not changed in overlay, revision bump, reset keywords and a few small ebuild cleanups.
++  * new ebuild for another smith chart calculation program
++  * New patch to really fix bug 104617
++  * Added media-gfx/kst with patch to fix bug #104617
++  * Fixed some errors in the ebuild and in the ChangeLog
++  * Adding new ebuild for gsmc-1.0
++  * Created initial directory structure.
  # ChangeLog for <CATEGORY>/<PACKAGE_NAME>
  # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
  # $Header: $

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6c5e261b0f3571c0831bf816772a9e0f34ec9573
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Sat Apr  6 09:57:16 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Apr  6 09:57:16 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6c5e261b

Merge pull request #60 from lilrc/master

Inclusion of gnome-chemistry-utils


 sci-chemistry/gnome-chemistry-utils/ChangeLog      |   20 +++++++++
 sci-chemistry/gnome-chemistry-utils/Manifest       |    1 +
 .../gnome-chemistry-utils-0.14.2.ebuild            |   44 ++++++++++++++++++++
 sci-chemistry/gnome-chemistry-utils/metadata.xml   |   11 +++++
 4 files changed, 76 insertions(+), 0 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     cda0f4cd87b1eae49441fc8c6c7cae23cb4167a8
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Apr  8 08:47:27 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Apr  8 08:47:27 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cda0f4cd

Merge branch 'master' of github.com:gentoo-science/sci

# By Karl Lindén
# Via Justin (1) and Karl Lindén (1)
* 'master' of github.com:gentoo-science/sci:
  sci-chemistry/gnome-chemistry-utils: Migrate to gnome2 eclass. Sort inherits. Add slots where suitable.
  Fix missing inherit.
  sci-chemistry/gnome-chemistry-utils: initial ebuild


 sci-chemistry/gnome-chemistry-utils/ChangeLog      |   20 +++++++++
 sci-chemistry/gnome-chemistry-utils/Manifest       |    1 +
 .../gnome-chemistry-utils-0.14.2.ebuild            |   44 ++++++++++++++++++++
 sci-chemistry/gnome-chemistry-utils/metadata.xml   |   11 +++++
 4 files changed, 76 insertions(+), 0 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     6f484cb3721e2ac6ab3506540c80ad7634b6f480
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Apr  1 13:26:39 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Apr  1 13:26:39 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6f484cb3

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  Add patches for gcc-4.8 and linux-3.9
  Enable more options
  Add patch to fix as-needed issue
  Fix autogen
  build was renamed to config
  Update rebased patches
  sci-mathematics/cadabra-1.31: new line fixes, thanks to jlec
  sci-mathemtics/cadabra-1.31: different fixes, thanks to jlec
  sci-mathematics-cadabra-1.31: bump to EAPI-5
  sci-mathematics/cadabra: version bump


 sci-mathematics/cadabra/ChangeLog                  |    8 ++-
 sci-mathematics/cadabra/Manifest                   |    1 +
 .../{cadabra-1.28.ebuild => cadabra-1.31.ebuild}   |   40 ++++-----
 sys-cluster/lustre/ChangeLog                       |   53 +++++++++++++
 ...d-make-AC-check-for-linux-arch-sandbox-f.patch} |   22 +++---
 ...fs-use-sock_alloc_file-instead-of-sock_m.patch} |    8 +-
 ...at-posix_acl_-to-from-_xattr-take-user_n.patch} |   10 +-
 ...04-LU-2800-llite-introduce-local-getname.patch} |    4 +-
 ...d-check-header-files-in-generated-uapi-d.patch} |   24 +++---
 ...0-kernel-3.8-upstream-removes-vmtruncate.patch} |    4 +-
 ...2850-kernel-3.8-upstream-kills-daemonize.patch} |   42 +++++-----
 ...tch => 0008-LU-2987-llite-rcu-free-inode.patch} |    4 +-
 ...ubuntu-Fix-build-failures-on-Ubuntu-12.04.patch |   58 ++++++++++++++
 ...3077-build-fix-warnings-in-client-modules.patch |   34 ++++++++
 ...nel-3.9-hlist_for_each_entry-uses-3-args.patch} |   54 ++++++++++---
 ...50-kernel-f_vfsmnt-replaced-by-f_path.mnt.patch |   82 ++++++++++++++++++++
 sys-cluster/lustre/lustre-9999.ebuild              |   36 ++++++---
 sys-cluster/lustre/metadata.xml                    |    3 +
 18 files changed, 380 insertions(+), 107 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Alexey Shvetsov]

commit:     a1d83fa05e456d2d7491ec061f90b015fb059eed
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 31 11:15:37 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Sun Mar 31 11:15:37 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a1d83fa0

Merge remote-tracking branch 'github/master'


 sci-mathematics/cadabra/ChangeLog                  |    8 +++-
 sci-mathematics/cadabra/Manifest                   |    1 +
 .../{cadabra-1.28.ebuild => cadabra-1.31.ebuild}   |   40 +++++++++-----------
 3 files changed, 26 insertions(+), 23 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Alexey Shvetsov]

commit:     2d2fc9706532b0e9f490dafbe19e6eb84e394524
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Thu Mar 28 13:14:27 2013 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu Mar 28 13:14:27 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2d2fc970

Merge pull request #58 from jauhien/cadabra-1.31

sci-mathematics/cadabra: version bump


 sci-mathematics/cadabra/ChangeLog                  |    8 +++-
 sci-mathematics/cadabra/Manifest                   |    1 +
 .../{cadabra-1.28.ebuild => cadabra-1.31.ebuild}   |   40 +++++++++-----------
 3 files changed, 26 insertions(+), 23 deletions(-)

[gentoo-commits] proj/sci:master commit in: /

[Justin Lecher]

commit:     61bbc1f4fd6066aa1c15b23e8c298617e1f11ef8
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 26 07:51:09 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 26 07:51:09 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=61bbc1f4

Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  Update deps


 dev-python/RecSQL/ChangeLog           |    4 ++++
 dev-python/RecSQL/Manifest            |    1 -
 dev-python/RecSQL/RecSQL-0.7.8.ebuild |   31 -------------------------------
 dev-python/RecSQL/RecSQL-9999.ebuild  |    4 +++-
 4 files changed, 7 insertions(+), 33 deletions(-)