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* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-17  5:55 Justin Lecher
  2013-06-17  5:55 ` [gentoo-commits] proj/sci:fixing " Justin Lecher
  2013-06-17  5:55 ` [gentoo-commits] proj/sci:jlec " Justin Lecher
  0 siblings, 2 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-17  5:55 UTC (permalink / raw
  To: gentoo-commits

commit:     574effd9590ac60471bebdc4225aaa87a727b8a5
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 16 16:03:40 2013 +0000
Commit:     Justin Lecher <jlec <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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:vtk commit in: /
@ 2013-07-11 20:26 Justin Lecher
  2013-07-08 11:54 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-07-11 20:26 UTC (permalink / raw
  To: gentoo-commits

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



^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:vtk commit in: /
@ 2013-07-11 20:26 Justin Lecher
  2013-07-08 11:54 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-07-11 20:26 UTC (permalink / raw
  To: gentoo-commits

commit:     f964406968cbe45f9268653af44c2dc6b52baadd
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 26 15:26:34 2013 +0000
Commit:     Justin Lecher <jlec <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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
@ 2013-07-08 11:54 Justin Lecher
  2013-07-08 11:54 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-07-08 11:54 UTC (permalink / raw
  To: gentoo-commits

commit:     e88605269a92bfb4a232752657f59519603709da
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Wed Jun 26 18:32:49 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
@ 2013-07-08 11:54 Justin Lecher
  2013-07-08 11:54 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-07-08 11:54 UTC (permalink / raw
  To: gentoo-commits

commit:     5bdbd20181a8d1c6e88a852b8c869804ebf450d1
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 26 16:53:22 2013 +0000
Commit:     Justin Lecher <jlec <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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-07-08 11:54 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-07-08 11:54 UTC (permalink / raw
  To: gentoo-commits

commit:     3833417300c4a4415fac9efa033c5a11f0bb42d7
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 30 11:39:22 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 30 11:39:22 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=38334173

Merge branch 'master' into ccp4

* master: (46 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
  ...

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

Conflicts:
	sci-chemistry/shiftx/ChangeLog
	sci-chemistry/shiftx/shiftx-1.1.ebuild


 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/shiftx/ChangeLog                     |   5 +-
 sci-chemistry/shiftx/shiftx-1.1.ebuild             |   3 +
 sci-chemistry/ucsf-tools/ChangeLog                 |   3 +
 sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild    |  13 +-
 sci-libs/bigdft-abi/ChangeLog                      |  21 +++
 ...abi-1.0.4.ebuild => bigdft-abi-1.0.4-r1.ebuild} |   9 +-
 .../files/bigdft-abi-1.0.4-CUDA_gethostname.patch  |  22 +++
 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/etsf_io/ChangeLog                         |   4 +
 sci-libs/etsf_io/etsf_io-1.0.3-r2.ebuild           |   6 +-
 sci-libs/fox/ChangeLog                             |   4 +
 .../files/4.1.2-r2-install-customizations.patch    |   4 +-
 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-libs/trilinos/ChangeLog                        |   7 +-
 sci-libs/trilinos/metadata.xml                     |  16 ++
 sci-libs/trilinos/trilinos-11.2.3.ebuild           | 186 +++++++++++++++++++++
 sci-physics/abinit/ChangeLog                       |   4 +
 sci-physics/abinit/files/6.12.3-gui-makefiles.tbz  | Bin 0 -> 14600 bytes
 sci-physics/bigdft/ChangeLog                       |   8 +
 sci-physics/bigdft/bigdft-1.7_pre24.ebuild         |   2 +
 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 ++++
 92 files changed, 1091 insertions(+), 786 deletions(-)

diff --cc sci-chemistry/shiftx/ChangeLog
index 85e5049,f656301..2efad58
--- a/sci-chemistry/shiftx/ChangeLog
+++ b/sci-chemistry/shiftx/ChangeLog
@@@ -5,8 -8,8 +8,8 @@@
    20 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx-1.1.ebuild,
    files/1.1-Makefile.patch, +files/1.1-bfr-overflow.patch, metadata.xml:
    Fix patch and add patch for buffer overflow fix
--
    16 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx-1.1.ebuild, metadata.xml:
++
    Bump to EAPI=5 and fix license
  
  *shiftx-1.1 (14 Jun 2009)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-07-08 11:54 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-07-08 11:54 UTC (permalink / raw
  To: gentoo-commits

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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
@ 2013-06-26  7:09 Justin Lecher
  2013-06-19  6:53 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-26  7:09 UTC (permalink / raw
  To: gentoo-commits

commit:     43ae215b3409c36d8f51402580ead76fc6624763
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Tue Jun 18 13:55:47 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-19  6:53 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-19  6:53 UTC (permalink / raw
  To: gentoo-commits

commit:     7deb8b2f53280b43e75b7bbe369a64ce85eac123
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 19 06:53:31 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 19 06:53:31 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7deb8b2f

Merge branch 'master' into ccp4

* master:
  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
  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-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-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/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/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/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/metadata.xml                  |   5 +-
 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                     |   6 +
 ...ebuild => talosn-4.01.2013.148.15.55-r2.ebuild} |  13 +-
 sci-chemistry/ucsf-tools/metadata.xml              |   2 +-
 sci-chemistry/unio/metadata.xml                    |   5 +-
 sci-libs/Cgraph/metadata.xml                       |   5 +-
 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/bigdft/metadata.xml                       |  19 +--
 sci-libs/cnsface-scripts/metadata.xml              |   3 -
 sci-libs/driftwood/metadata.xml                    |   5 +-
 sci-libs/etsf_io/metadata.xml                      |   5 +-
 sci-libs/fox/metadata.xml                          |  19 +--
 sci-libs/libxc/Manifest                            |   2 +-
 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/pagmo/metadata.xml                        |  13 +-
 sci-libs/starparse/metadata.xml                    |   5 +-
 sci-libs/wannier90/metadata.xml                    |   5 +-
 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                       |   3 +
 sci-physics/abinit/Manifest                        |   3 +-
 sci-physics/abinit/abinit-7.2.2.ebuild             |   2 +-
 sci-physics/atompaw/metadata.xml                   |  11 +-
 sci-physics/atompaw2abinit/metadata.xml            |   5 +-
 sci-physics/bigdft/ChangeLog                       |   5 +
 sci-physics/bigdft/Manifest                        |   1 +
 sci-physics/bigdft/bigdft-1.7_pre24.ebuild         |   2 +-
 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 -
 109 files changed, 482 insertions(+), 463 deletions(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-19  6:53 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-19  6:53 UTC (permalink / raw
  To: gentoo-commits

commit:     83a6f8e906f3701f214c034c05285f7106cc5413
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Tue Jun 18 13:54:29 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
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 )


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-18  9:13 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-18  9:13 UTC (permalink / raw
  To: gentoo-commits

commit:     1c75b2410a7dce9cc1762cb8c434cbabc12fe3ef
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 18 09:12:35 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 18 09:12:35 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1c75b241

Merge branch 'master' into ccp4

* master:
  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.
  Don't let openmpi override malloc, works around sandbox issue in #462602
  Fixed bug in jabref ebuild.
  Renamed ebuild to conform with Gentoo Ebuild Naming Convention (TM).
  media-gfx/librecad: Cleanup and apply patch from bug #473388
  Mangling of the sources of sci-chemistry/freeon reduced, both for 2012.05.03, and for 9999.
  [sci-chemistry/nMOLDYN] Update deps
  [sci-chemistry/nMOLDYN] Add to overlay


 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 +-
 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/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/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/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                      |  12 +
 sci-libs/bigdft-abi/Manifest                       |   3 +
 .../bigdft-abi-1.0.4.ebuild}                       |  79 +++--
 .../files/bigdft-abi-1.0.4-tests.tar.bz2           | Bin 0 -> 402968 bytes
 sci-libs/etsf_io/ChangeLog                         |   9 +-
 ..._io-1.0.3-r1.ebuild => etsf_io-1.0.3-r2.ebuild} |   0
 sci-libs/fox/ChangeLog                             |  10 +-
 ...patch => 4.1.2-r2-install-customizations.patch} |   0
 .../{fox-4.1.2-r1.ebuild => fox-4.1.2-r2.ebuild}   |  10 +-
 sci-libs/libxc/ChangeLog                           |  11 +-
 ...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/mumps/ChangeLog                           |   5 +-
 sci-libs/mumps/mumps-4.10.0-r2.ebuild              |   5 +-
 sci-libs/wannier90/ChangeLog                       |   7 +
 ...annier90-1.2.ebuild => wannier90-1.2-r1.ebuild} |   0
 sci-physics/abinit/ChangeLog                       |   9 +
 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/abinit/files/6.12.3-gui-makefiles.tbz  | Bin 14600 -> 0 bytes
 sci-physics/atompaw/ChangeLog                      |   7 +
 ...aw-3.0.1.9.ebuild => atompaw-3.0.1.9-r1.ebuild} |  11 +-
 {sci-libs => sci-physics}/bigdft/ChangeLog         |  10 +-
 .../bigdft/bigdft-1.7_pre24.ebuild                 |  35 +-
 .../files/bigdft-1.7-dev.24-nolib_mods.patch       |  14 +-
 53 files changed, 497 insertions(+), 797 deletions(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-18  9:13 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-18  9:13 UTC (permalink / raw
  To: gentoo-commits

commit:     bc1068a33cbde9c6324724e313b548ea0ea78e32
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Mon Jun 17 07:14:55 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 17 07:14:55 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bc1068a3

Merge pull request #83 from ercpe/ccp4

Added ebuild for sci-visualization/openastexviewer-3.0


 sci-visualization/openastexviewer/ChangeLog        |  8 +++
 sci-visualization/openastexviewer/Manifest         |  1 +
 .../openastexviewer}/metadata.xml                  |  2 +-
 .../openastexviewer/openastexviewer-3.0.ebuild     | 62 ++++++++++++++++++++++
 4 files changed, 72 insertions(+), 1 deletion(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-18  9:11 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-18  9:11 UTC (permalink / raw
  To: gentoo-commits

commit:     e3125691869347a622c86488f261435ffcd2fbe0
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 18 09:11:43 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 18 09:11:43 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e3125691

Merge branch 'master' into ccp4

* master:
  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.
  Don't let openmpi override malloc, works around sandbox issue in #462602


 sci-libs/mumps/ChangeLog              | 5 ++++-
 sci-libs/mumps/mumps-4.10.0-r2.ebuild | 5 ++++-
 2 files changed, 8 insertions(+), 2 deletions(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-18  8:57 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-18  8:57 UTC (permalink / raw
  To: gentoo-commits

commit:     3a3b096c76d8992f1528113f2d7f974ae02ad522
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 18 08:57:08 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 18 08:57:08 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3a3b096c

Merge branch 'master' into ccp4

* master:
  sci-chemistry/mics: New package
  sci-chemistry/talosn: New package


 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/talosn/ChangeLog                     | 10 ++++
 sci-chemistry/talosn/Manifest                      |  1 +
 .../metadata.xml                                   |  0
 .../talosn/talosn-4.01.2013.148.15.55.ebuild       | 59 ++++++++++++++++++++++
 8 files changed, 132 insertions(+)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:fixing commit in: /
@ 2013-06-18  8:54 Justin Lecher
  2013-06-18  8:54 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  2013-06-19  6:53 ` Justin Lecher
  0 siblings, 2 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-18  8:54 UTC (permalink / raw
  To: gentoo-commits

commit:     4c8b2b623e9305166c334d9c5d3d219cb6b78129
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Mon Jun 17 18:58:38 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-18  8:54 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-18  8:54 UTC (permalink / raw
  To: gentoo-commits

commit:     60dfd44be307c024c87a971398740d48a0d2930c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 18 05:42:32 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 18 05:42:32 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=60dfd44b

Merge branch 'master' into ccp4

* master:
  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.
  Fixed bug in jabref ebuild.
  Renamed ebuild to conform with Gentoo Ebuild Naming Convention (TM).
  media-gfx/librecad: Cleanup and apply patch from bug #473388
  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.
  Mangling of the sources of sci-chemistry/freeon reduced, both for 2012.05.03, and for 9999.
  [sci-chemistry/nMOLDYN] Update deps
  [sci-chemistry/nMOLDYN] Add to overlay


 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 +-
 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/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-libs/bigdft-abi/ChangeLog                      |  12 +
 sci-libs/bigdft-abi/Manifest                       |   3 +
 .../bigdft-abi-1.0.4.ebuild}                       |  79 +++--
 .../files/bigdft-abi-1.0.4-tests.tar.bz2           | Bin 0 -> 402968 bytes
 sci-libs/etsf_io/ChangeLog                         |   9 +-
 ..._io-1.0.3-r1.ebuild => etsf_io-1.0.3-r2.ebuild} |   0
 sci-libs/fox/ChangeLog                             |  10 +-
 ...patch => 4.1.2-r2-install-customizations.patch} |   0
 .../{fox-4.1.2-r1.ebuild => fox-4.1.2-r2.ebuild}   |  10 +-
 sci-libs/libxc/ChangeLog                           |  11 +-
 ...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/wannier90/ChangeLog                       |   7 +
 ...annier90-1.2.ebuild => wannier90-1.2-r1.ebuild} |   0
 sci-physics/abinit/ChangeLog                       |   9 +
 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/abinit/files/6.12.3-gui-makefiles.tbz  | Bin 14600 -> 0 bytes
 sci-physics/atompaw/ChangeLog                      |   7 +
 ...aw-3.0.1.9.ebuild => atompaw-3.0.1.9-r1.ebuild} |  11 +-
 {sci-libs => sci-physics}/bigdft/ChangeLog         |  10 +-
 .../bigdft/bigdft-1.7_pre24.ebuild                 |  35 +-
 .../files/bigdft-1.7-dev.24-nolib_mods.patch       |  14 +-
 43 files changed, 357 insertions(+), 795 deletions(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
@ 2013-06-17  5:55 Justin Lecher
  2013-06-13  7:08 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-17  5:55 UTC (permalink / raw
  To: gentoo-commits

commit:     26e27280f8681d111da0a0e75c5589ce427b0c31
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 12 22:01:16 2013 +0000
Commit:     Justin Lecher <jlec <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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
@ 2013-06-17  5:55 Justin Lecher
  2013-06-13  7:08 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-17  5:55 UTC (permalink / raw
  To: gentoo-commits

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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
@ 2013-06-17  5:55 Justin Lecher
  2013-06-13  7:08 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-17  5:55 UTC (permalink / raw
  To: gentoo-commits

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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
@ 2013-06-17  5:55 Justin Lecher
  2013-06-13  7:08 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-17  5:55 UTC (permalink / raw
  To: gentoo-commits

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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:fixing commit in: /
@ 2013-06-17  5:55 Justin Lecher
  2013-06-17  5:55 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-17  5:55 UTC (permalink / raw
  To: gentoo-commits

commit:     945c34bebc2ff7e4d3c1769c0c4320ee9a0a13dd
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 16 20:57:33 2013 +0000
Commit:     Justin Lecher <jlec <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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:fixing commit in: /
@ 2013-06-17  5:55 Justin Lecher
  2013-06-17  5:55 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-17  5:55 UTC (permalink / raw
  To: gentoo-commits

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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-17  5:55 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-17  5:55 UTC (permalink / raw
  To: gentoo-commits

commit:     b26366da352ed3bf258da85228b0844317178372
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 17 05:54:44 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 17 05:54:44 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b26366da

Merge branch 'master' into ccp4

* master:
  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.
  broken ebuild for java fixing Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
  sci-astronomy/astrometry: Added extra use flag to plot
  sci-astronomy/astrometry: Added python bindings. Fixed more gsl bundling


 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-python/healpy/ChangeLog                        |   9 +
 dev-python/healpy/Manifest                         |   1 +
 dev-python/healpy/healpy-1.6.2.ebuild              |  34 ++++
 dev-python/healpy/metadata.xml                     |  10 +
 profiles/package.mask                              |   5 +
 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/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 ++++++++++
 64 files changed, 1127 insertions(+), 323 deletions(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-17  5:55 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-17  5:55 UTC (permalink / raw
  To: gentoo-commits

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(+)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:master commit in: /
@ 2013-06-16 17:23 Justin Lecher
  2013-06-17  5:55 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-16 17:23 UTC (permalink / raw
  To: gentoo-commits

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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-16 15:53 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-16 15:53 UTC (permalink / raw
  To: gentoo-commits

commit:     b9353507412d6956fb46781c7b44713829b128d8
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 16 15:46:14 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 16 15:46:14 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b9353507

Merge branch 'fixing' into ccp4

* fixing:
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
sci-chemistry/pymol-apbs-plugin: Drop KEYWORDS from live ebuild
sci-chemistry/pymol-apbs-plugin: Bump to EAPI=5 and bump to
python-r1.eclass
broken Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-chemistry/nmrpipe: Bump to EAPI=5 and fix license
sci-chemistry/nwchem: Drop old; drop virtual/fortran as the eclass
depends on it
sci-chemistry/ssp: Bump to EAPI=5 and fix license
sci-chemistry/shiftx: Bump to EAPI=5 and fix license
sci-chemistry/pymol-plugins-ezviz: Bump to EAPI=5 and bump to
python-r1.eclass
sci-chemistry/polygon: Version BUmp; fixed license
sci-chemistry/nmrview: Bump to EAPI=5 and fix license

Conflicts:
	sci-chemistry/phaser/phaser-2.5.0.ebuild


 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/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 +-
 37 files changed, 211 insertions(+), 358 deletions(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:fixing commit in: /
@ 2013-06-16 14:23 Justin Lecher
  2013-06-16 14:23 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-16 14:23 UTC (permalink / raw
  To: gentoo-commits

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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-16 14:23 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-16 14:23 UTC (permalink / raw
  To: gentoo-commits

commit:     23df69597a2cfcc76d8369e2d8bf66e865f66edd
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 16 11:31:58 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 16 11:31:58 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=23df6959

Merge branch 'master' into ccp4

* master: (35 commits)
  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
  x11-misc/envytools: Fix license
  sci-astronomy/astrometry: Fix unquoted variable
  sci-physics/espresso: Bump to EAPI=5 and drop KEYWORDS of live ebuilds; bump to new python eclasses
  sci-physics/espresso++: Bump to EAPI=5 and drop KEYWORDS of live ebuilds; bump to new python eclasses
  sci-visualization/gnuplot: Drop KEYWORDS of live ebuilds
  sys-cluster/nullmpi: Drop KEYWORDS of live ebuilds
  sci-astronomy/scamp: Drop KEYWORDS of live ebuilds
  ...


 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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-14 11:21 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-14 11:21 UTC (permalink / raw
  To: gentoo-commits

commit:     3c71e81e85316ad2d2bcaf502153541cb9e6c865
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 14 06:07:53 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 14 06:07:53 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3c71e81e

Merge branch 'master' into ccp4

* master:
  sci-astronomy/astrometry: Version bump. Rewrote the patches
  manifests fixes
  mpe2: main tree more up to date
  dev-python/go-parser: Bump to EAPI=5 and distutils-r1.eclass
  dev-python/fiat: Version Bump; Bump to EAPI=5 and distutils-r1.eclass
  dev-python/coords: Bump to EAPI=5 and distutils-r1.eclass
  dev-python/ffc: Version Bump; Bump to EAPI=5 and distutils-r1.eclass
  dev-python/emcee: Version Bump; Bump to EAPI=5 and distutils-r1.eclass
  Obsolete package Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
  dev-python/dimensionful: Bump to EAPI=5 and distutils-r1.eclass
  dev-python/cosmocalc: Bump to EAPI=5 and distutils-r1.eclass
  dev-python/coards: VersionBump; Bump to EAPI=5 and distutils-r1.eclass; fix license
  dev-python/astropy: Bump to EAPI=5 and distutils-r1.eclass
  dev-python/GOGrapher: Bump to EAPI=5 and distutils-r1.eclass
  dev-python/GOGrapher: Bump to EAPI=5 and distutils-r1.eclass
  dev-python/GOGrapher: Bump to EAPI=5 and distutils-r1.eclass
  app-benchmarks/numbench: Bump to EAPI=5 and distutils-r1.eclass
  dev-python/astropysics: Bump to EAPI=5 and distutils-r1.eclass


 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/joda-convert/Manifest                     |   2 +-
 dev-java/vecmath/Manifest                          |   4 +-
 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/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/instant/Manifest                        |   2 +-
 dev-python/meshpy/Manifest                         |   2 +-
 dev-python/numpydoc/Manifest                       |   2 +-
 dev-python/omniorbpy/Manifest                      |   2 +-
 dev-python/opal-client/Manifest                    |   2 +-
 dev-python/pyhdf/Manifest                          |   2 +-
 dev-python/pythoncgns/Manifest                     |   2 +-
 dev-python/ufl/Manifest                            |   2 +-
 dev-python/viper/Manifest                          |   2 +-
 dev-tcltk/togl/Manifest                            |   2 +-
 dev-util/smartgit/Manifest                         |   2 +-
 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 +-
 sci-astronomy/astrometry/ChangeLog                 |  12 +-
 sci-astronomy/astrometry/Manifest                  |   2 +-
 sci-astronomy/astrometry/astrometry-0.38.ebuild    |  57 --
 sci-astronomy/astrometry/astrometry-0.43.ebuild    |  71 +++
 .../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        | 704 +++++++++++++++++++++
 sci-astronomy/astrometry/metadata.xml              |   4 +-
 sci-biology/ONTO-PERL/Manifest                     |   2 +-
 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/Manifest                      |   4 +-
 sci-biology/cap3-bin/Manifest                      |   4 +-
 sci-biology/cdbfasta/Manifest                      |   2 +-
 sci-biology/clover/Manifest                        |   4 +-
 sci-biology/clview/Manifest                        |   4 +-
 sci-biology/codonw/Manifest                        |   2 +-
 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/Manifest                         |   4 +-
 sci-biology/est2uni/Manifest                       |  10 +-
 sci-biology/fastdnaml/Manifest                     |   4 +-
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 sci-biology/jalview/Manifest                       |   2 +-
 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 +-
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 sci-biology/nrcl/Manifest                          |   4 +-
 sci-biology/perlprimer/Manifest                    |   2 +-
 sci-biology/proda/Manifest                         |   2 +-
 sci-biology/psx/Manifest                           |   2 +-
 sci-biology/quicktree/Manifest                     |   2 +-
 sci-biology/rnaplex/Manifest                       |   2 +-
 sci-biology/roche454ace2caf/Manifest               |   2 +-
 sci-biology/sclust/Manifest                        |   4 +-
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 sci-biology/signalp/Manifest                       |   2 +-
 sci-biology/smalt-bin/Manifest                     |   2 +-
 sci-biology/ssaha2-bin/Manifest                    |  10 +-
 sci-biology/swissknife/Manifest                    |   2 +-
 sci-biology/tablet-bin/Manifest                    |   2 +-
 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/Manifest                      |   2 +-
 sci-biology/zmsort/Manifest                        |   4 +-
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 sci-chemistry/pyquante/Manifest                    |   2 +-
 sci-chemistry/rosetta-tools/Manifest               |   2 +-
 sci-chemistry/shiftx/Manifest                      |   2 +-
 sci-chemistry/smmp/Manifest                        |   2 +-
 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/calculix-cgx/Manifest                     |   4 +-
 sci-libs/cgnsfoam/Manifest                         |   2 +-
 sci-libs/cgnslib/Manifest                          |   2 +-
 sci-libs/cnsface-scripts/Manifest                  |   2 +-
 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/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/Manifest                         |   1 +
 sci-libs/trilinos/metadata.xml                     |  56 +-
 sci-mathematics/Oid/Manifest                       |   4 +-
 sci-mathematics/acl2/Manifest                      |   2 +-
 sci-mathematics/apron/Manifest                     |   5 +-
 sci-mathematics/aribas/Manifest                    |   2 +-
 sci-mathematics/axiom/Manifest                     |   2 +-
 sci-mathematics/burrtools/Manifest                 |   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/qcl/Manifest                           |   8 +-
 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/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/Manifest                       |   2 +-
 sys-cluster/pyslice/Manifest                       |   2 +-
 sys-devel/gdebugger/Manifest                       |   4 +-
 sys-infiniband/librxe/Manifest                     |   2 +-
 x11-libs/tr/Manifest                               |   2 +-
 298 files changed, 1674 insertions(+), 5428 deletions(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-13  7:08 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-13  7:08 UTC (permalink / raw
  To: gentoo-commits

commit:     0944dd9ae2211da33b30cfb52496b342575640ed
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun 13 07:07:55 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun 13 07:07:55 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0944dd9a

Merge branch 'master' into ccp4

* master: (34 commits)
  Package dropped Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
  sci-astronomy/galfit-bin: Fix license
  sci-astronomy/eazy: Fix license
  sci-astronomy/bpz: Bump to EAPI=5 and python-single-r1; restrict license
  dev-tcltk/img_rotate: Bump to EAPI=5 and fix license
  dev-python/inference: Bump to EAPI=5 and distutils-r1.eclass; make license more restrictive as we cannot check it right now
  sci-libs/blastdb: Add missing build dep; fix license
  x11-libs/xview-bin: Drop all keywords
  sci-biology/pybrain: Bump to EAPI=5 and distutils-r1.eclass
  sys-cluster/lustre: Move virtual/linux-sources to build deps
  sci-mathematics/cadabra: Drop old, move doxygen to build deps
  sci-libs/ipopt: Fix local USE description
  sci-libs/ipopt: Version bump
  fixed as-needed
  sci-chemistry/hydronmr: Drop empty last line
  sci-biology/ncbi-tools++: Drop empty line
  sci-chemistry/ball: Bump EAPI and python eclass
  sci-libs/trilinos: Drop old, fix handling of qt support
  Merge live ebuilds on top drop unversioned "mask for testing" drop obsolete Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
  sci-libs/coinhsl: Initial import
  ...

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

Conflicts:
	sci-chemistry/sfcheck/metadata.xml


 dev-python/inference/ChangeLog                     |   7 +-
 dev-python/inference/inference-0.4.ebuild          |  31 +--
 dev-python/inference/metadata.xml                  |   4 +-
 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 +-
 licenses/HSL                                       | 222 +++++++++++++++++++++
 profiles/package.mask                              | 113 +++--------
 sci-astronomy/bpz/ChangeLog                        |   5 +-
 sci-astronomy/bpz/bpz-1.99.3.ebuild                |  57 +++---
 sci-astronomy/bpz/metadata.xml                     |   4 +-
 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-biology/ncbi-tools++/ChangeLog                 |   6 +
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |   3 +-
 sci-biology/pybrain/ChangeLog                      |   6 +-
 sci-biology/pybrain/metadata.xml                   |   2 +-
 sci-biology/pybrain/pybrain-9999.ebuild            |  25 ++-
 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/blastdb/ChangeLog                         |   8 +
 sci-libs/blastdb/blastdb-9999.ebuild               |   8 +-
 sci-libs/blastdb/metadata.xml                      |  31 +--
 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/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/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 +-
 sci-mathematics/algae/files/unbundle.patch         |  41 ----
 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 +-
 sys-cluster/lustre/ChangeLog                       |   4 +
 sys-cluster/lustre/lustre-9999.ebuild              |   6 +-
 sys-cluster/lustre/metadata.xml                    |  20 +-
 x11-libs/xview-bin/ChangeLog                       |   3 +
 x11-libs/xview-bin/xview-bin-3.2_p1428.ebuild      |   2 +-
 55 files changed, 540 insertions(+), 684 deletions(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-13  7:08 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-13  7:08 UTC (permalink / raw
  To: gentoo-commits

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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
@ 2013-06-12  8:13 Justin Lecher
  2013-06-04 11:59 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-12  8:13 UTC (permalink / raw
  To: gentoo-commits

commit:     ddc3495e1874a534526ab006232b9453d05a58d5
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Mon Jun  3 23:33:21 2013 +0000
Commit:     Justin Lecher <jlec <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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
@ 2013-06-12  8:13 Justin Lecher
  2013-06-04 11:59 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-12  8:13 UTC (permalink / raw
  To: gentoo-commits

commit:     37c670d2b2023da28771040ed39a12bcb8e2fb70
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Mon Jun  3 08:36:50 2013 +0000
Commit:     Justin Lecher <jlec <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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
@ 2013-06-12  8:13 Justin Lecher
  2013-06-01 17:24 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-12  8:13 UTC (permalink / raw
  To: gentoo-commits

commit:     9c925b3b9c8753ba4f3cf41bb304c0870b4027fc
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Fri May 31 15:31:31 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
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(+)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
@ 2013-06-12  8:13 Justin Lecher
  2013-06-01 17:24 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-12  8:13 UTC (permalink / raw
  To: gentoo-commits

commit:     5829b50ce4ea2442bc66e5f5773ea393ad6c1217
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Fri May 31 13:10:20 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
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(+)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
@ 2013-06-12  8:13 Justin Lecher
  2013-05-30 10:31 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-12  8:13 UTC (permalink / raw
  To: gentoo-commits

commit:     b81fff6dcf24a0ab91f631a42e9996b556a05439
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Thu May 16 06:33:04 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
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 file changed, 3 insertions(+)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
@ 2013-06-12  8:13 Justin Lecher
  2013-05-30 10:31 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-12  8:13 UTC (permalink / raw
  To: gentoo-commits

commit:     622626fb55bac4fc611c9f41148e634d426efa20
Author:     Christoph Junghans <christoph.junghans <AT> googlemail <DOT> com>
AuthorDate: Wed May 15 19:48:11 2013 +0000
Commit:     Justin Lecher <jlec <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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
@ 2013-06-12  8:13 Justin Lecher
  2013-05-30 10:31 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-12  8:13 UTC (permalink / raw
  To: gentoo-commits

commit:     00c58fa25bbf4f532f15d305b12b8cbb1a922fbb
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Wed May 15 11:30:37 2013 +0000
Commit:     Justin Lecher <jlec <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(+)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
@ 2013-06-12  8:13 Justin Lecher
  2013-05-30 10:31 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-12  8:13 UTC (permalink / raw
  To: gentoo-commits

commit:     e2ebd47001ac3f20d9f10b3fea8091dacdfa757b
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed May 15 08:09:29 2013 +0000
Commit:     Justin Lecher <jlec <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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
@ 2013-06-12  8:13 Justin Lecher
  2013-05-30 10:31 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-12  8:13 UTC (permalink / raw
  To: gentoo-commits

commit:     6ca1acbed7e02eeb48b39f436f2e22452c6d5e77
Author:     Kacper Kowalik (Xarthisius) <xarthisius <AT> gentoo <DOT> org>
AuthorDate: Wed May  1 20:09:09 2013 +0000
Commit:     Justin Lecher <jlec <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 file changed, 5 insertions(+), 1 deletion(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-10 12:01 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-10 12:01 UTC (permalink / raw
  To: gentoo-commits

commit:     d16a962a0cf74a66345e4a528395811573a7689e
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 10 12:00:33 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 10 12:00:33 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d16a962a

Merge branch 'master' into ccp4

* master: (46 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
  ...

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

Conflicts:
	sci-chemistry/mgltools/ChangeLog
	sci-chemistry/mgltools/mgltools-1.5.6.ebuild
	sci-physics/root/ChangeLog
	sci-physics/root/root-5.34.08.ebuild


 app-doc/root-docs/ChangeLog                        |  6 ++
 app-doc/root-docs/Manifest                         |  7 +-
 ...ocs-5.34.07.ebuild => root-docs-5.34.08.ebuild} |  2 +-
 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-astronomy/stilts/ChangeLog                     |  9 ++-
 sci-astronomy/stilts/Manifest                      |  2 +-
 .../{stilts-2.4.ebuild => stilts-2.5.ebuild}       |  4 +-
 sci-astronomy/topcat/ChangeLog                     |  8 ++-
 sci-astronomy/topcat/Manifest                      |  2 +
 .../{topcat-3.9.ebuild => topcat-4.0b.ebuild}      |  4 +-
 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                   | 10 +++
 sci-chemistry/mgltools/Manifest                    |  1 -
 sci-chemistry/mgltools/mgltools-1.5.4.ebuild       | 42 ------------
 sci-chemistry/mgltools/mgltools-1.5.6.ebuild       |  4 +-
 sci-physics/geant-vmc/ChangeLog                    |  7 ++
 sci-physics/geant-vmc/Manifest                     |  4 +-
 ...-vmc-3.1.14.ebuild => geant-vmc-3.1.15a.ebuild} |  0
 ...-vmc-4.2.14.ebuild => geant-vmc-4.2.14a.ebuild} |  2 +-
 sci-physics/root/ChangeLog                         |  6 ++
 sci-physics/root/Manifest                          |  4 +-
 .../{root-5.34.07.ebuild => root-5.34.08.ebuild}   |  4 +-
 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 +
 ...ules-3.2.9c-r1.ebuild => modules-3.2.10.ebuild} |  8 +--
 142 files changed, 334 insertions(+), 1812 deletions(-)

diff --cc sci-chemistry/mgltools/ChangeLog
index ec9cc14,0806cda..34f728b
--- a/sci-chemistry/mgltools/ChangeLog
+++ b/sci-chemistry/mgltools/ChangeLog
@@@ -2,6 -2,13 +2,16 @@@
  # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
  # $Header: $
  
++<<<<<<< HEAD
++=======
+   10 Jun 2013; Justin Lecher <jlec@gentoo.org> mgltools-1.5.6.ebuild:
+   move to virtual/python-imaging
+ 
+   10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-1.5.4.ebuild,
+   mgltools-1.5.6.ebuild:
+   Drop odl and drop py2.5
+ 
++>>>>>>> master
    04 Jun 2013; Justin Lecher <jlec@gentoo.org> mgltools-1.5.6.ebuild:
    Fix for correct usage of new python eclasses
  


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-10 12:01 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-10 12:01 UTC (permalink / raw
  To: gentoo-commits

commit:     2e117aae2ef793064afeb2676ca1e1f243d007e4
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Fri Jun  7 23:42:39 2013 +0000
Commit:     Justin Lecher <jlec <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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:master commit in: /
@ 2013-06-10 11:57 Justin Lecher
  2013-06-10 12:01 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-06-10 11:57 UTC (permalink / raw
  To: gentoo-commits

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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-04 11:59 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-04 11:59 UTC (permalink / raw
  To: gentoo-commits

commit:     4a0cd7b7880db8bceb9a2c757d2dbce678822e6a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jun  4 10:16:53 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun  4 10:16:53 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4a0cd7b7

Merge branch 'master' into ccp4

* master:
  added ~amd64-linux + clean up
  update minimal versions of some dependencies for scilab
  replacing patch with epatch
  using versioned patch for sys-cluster/modules, too
  now using versioned patches
  Fixed SRC_URI.
  implemented clean fix for changed errorline API in TCL
  relaced custom CURL with stock version
  minor fixes to comply with Gentoo coding style
  initial commit
  sync with gx86
  sci-chemistry/coot: Update pc patches
  sci-chemistry/coot: Fix PYTHON() -> ${EPYTHON} for new eclasses
  added fix for recent glibc with PGI
  added PGI ebuild
  added updated Manifest
  fixed compilation of modules with recent tcl

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

Conflicts:
	sci-chemistry/coot/ChangeLog
	sci-chemistry/coot/coot-9999.ebuild


 dev-java/jcip-annotations/ChangeLog                |    3 +
 .../jcip-annotations-1.0-r1.ebuild                 |    2 +-
 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-chemistry/coot/ChangeLog                       |    5 +
 sci-chemistry/coot/Manifest                        |    2 +-
 sci-chemistry/coot/coot-9999.ebuild                |   20 +-
 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             | 1040 ++++++++++++++++++++
 sci-chemistry/coot/files/9999-ssm.patch            |   56 --
 sci-chemistry/gromacs/ChangeLog                    |    3 +
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild      |    7 +-
 sci-chemistry/mdsctk/ChangeLog                     |   13 +
 sci-chemistry/mdsctk/Manifest                      |    1 +
 sci-chemistry/mdsctk/mdsctk-1.0.0.ebuild           |   51 +
 .../mdsctk}/metadata.xml                           |    3 +
 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 +-
 26 files changed, 1609 insertions(+), 141 deletions(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-04 11:59 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-04 11:59 UTC (permalink / raw
  To: gentoo-commits

commit:     20d1eb3e5708da1f9ce3e9ea54df28962e4ac2e6
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Mon Jun  3 14:35:50 2013 +0000
Commit:     Justin Lecher <jlec <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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-06-01 17:24 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-06-01 17:24 UTC (permalink / raw
  To: gentoo-commits

commit:     2e5282927d502d2b1d688c6b0c86fb569d60b970
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun  1 08:38:20 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun  1 08:38:20 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2e528292

Merge branch 'master' into ccp4

* master:
  sync with gx86
  Added die to test.
  added cuda toolkit 5.5
  Added src_test().
  The "-DALLOCA_H" compiler flag appears to be unnecessary...
  More cleanup. Beautify!
  Added examples use flag.
  Version bump to sys-cluster/charm-6.5.0.
  sci-chemistry/freeon improved, the ebuild of the latest snapshot added. sci-chemistry/nwchem bumped to 6.3, building docs allowed.

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

Conflicts:
	dev-util/nvidia-cuda-toolkit/ChangeLog
	dev-util/nvidia-cuda-toolkit/metadata.xml
	dev-util/nvidia-cuda-toolkit/nvidia-cuda-toolkit-5.5.11.ebuild
	sys-cluster/charm/ChangeLog
	sys-cluster/charm/charm-6.5.0.ebuild


 dev-lang/ispc/ChangeLog              |  3 +++
 dev-lang/ispc/ispc-9999.ebuild       | 13 ++++---------
 sys-cluster/charm/ChangeLog          |  3 +++
 sys-cluster/charm/charm-6.5.0.ebuild |  2 +-
 4 files changed, 11 insertions(+), 10 deletions(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

commit:     cd7d9ba38de3df2079f68c53db8ae4fa6fb3dab3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu May 30 10:29:38 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu May 30 10:29:38 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cd7d9ba3

Merge branch 'master' into ccp4

* master: (776 commits)
Moved to tree Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-chemistry/coot: Move to new python eclasses
sci-chemistry/coot: Drop version from clipper
root-docs: fix sandbox access violation
root: fix build with postgres
Moved html documentation one folder up.
Version bump.
Added html documentation.
sci-libs/blas-reference: proper versioning for live ebuild
sci-libs/coinor-flopcpp: Initial import
Switch to EAPI5
sci-libs/coinor-sample: Version bump
sci-libs/coinor-symphony: Version bump
sci-libs/coinor-cppad: Version bump
sci-libs/coinor-cbc: Version bump
sci-libs/coinor-cgl: Fixed missing header
sci-libs/coinor-buildtools: Initial import
sci-libs/coinor-alps: Version bump
removed in source builds
sci-libs/coinor-cgl: Version bump
...

Conflicts:
	sci-chemistry/jligand/ChangeLog
	sci-chemistry/jligand/Manifest
	sci-chemistry/jligand/jligand-1.0.37.ebuild


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 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 +
 1409 files changed, 29080 insertions(+), 27064 deletions(-)

diff --cc sci-chemistry/jligand/ChangeLog
index b555231,79845c4..9e2c106
--- a/sci-chemistry/jligand/ChangeLog
+++ b/sci-chemistry/jligand/ChangeLog
@@@ -1,17 -1,11 +1,17 @@@
  # ChangeLog for sci-chemistry/jligand
- # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
  # $Header: $
  
-   10 Dec 2012; Justin Lecher <jlec@gentoo.org> -jligand-1.0.19.ebuild,
-   +jligand-1.0.37.ebuild:
-   Version Bump
+   03 Mar 2013; Justin Lecher <jlec@gentoo.org> jligand-1.0.19.ebuild,
+   metadata.xml:
+   Fix version of refmac dep
  
 +*jligand-1.0.37 (10 Dec 2012)
 +
 +  10 Dec 2012; Justin Lecher <jlec@gentoo.org> -jligand-1.0.19.ebuild,
 +  +jligand-1.0.37.ebuild:
 +  Version Bump
 +
  *jligand-1.0.19 (25 Jun 2011)
  
    25 Jun 2011; Justin Lecher <jlec@gentoo.org> -jligand-0.1.ebuild,


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

commit:     09bde6b122936401cd0f27bafa2c565c1d29a9e1
Author:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
AuthorDate: Tue May 28 20:27:32 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

commit:     d6c6e1c2e0344384f91edf1416824713ef207142
Author:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
AuthorDate: Thu May 16 21:22:58 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
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 file changed, 3 insertions(+)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

commit:     d0e84807421952d08fa33651bca8034dd8d9ef66
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed May 15 10:59:54 2013 +0000
Commit:     Justin Lecher <jlec <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 file changed, 9 insertions(+), 11 deletions(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

commit:     dbf1d3a5ed02ce670672682a4bdc6fec652edd92
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed May 15 07:04:28 2013 +0000
Commit:     Justin Lecher <jlec <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 +
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 dev-java/jlatexmath-fop/Manifest                   |     3 +-
 .../files/jlatexmath-fop-1.0.2-fixpaths.patch      |    13 +
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 .../jlatexmath-fop/jlatexmath-fop-1.0.2.ebuild     |    45 +
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 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 +
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 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 +
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 ...keley_upc_translator-2.16.0-stackoverflow.patch |    18 +
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 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 +-
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 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
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 dev-libs/libpfm/ChangeLog                          |    12 +
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 dev-libs/libpfm/libpfm-4.3.0.ebuild                |    35 +
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 {x11-misc/envytools => dev-libs/papi}/metadata.xml |     0
 dev-libs/papi/papi-5.1.0.2.ebuild                  |    30 +
 dev-ml/lacaml/ChangeLog                            |     6 +-
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 dev-python/astlib/metadata.xml                     |     3 +-
 dev-python/pymvpa/ChangeLog                        |     6 +-
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 dev-python/pymvpa/pymvpa-0.4.4.ebuild              |    30 +-
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 .../{pythonocc-0.4.ebuild => pythonocc-0.5.ebuild} |    19 +-
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 dev-util/VampirTrace/metadata.xml                  |    13 +
 licenses/ECL-2.0                                   |    97 +
 licenses/blasr                                     |    65 +
 licenses/mgltools                                  |    42 +
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 media-gfx/PhiloGL/ChangeLog                        |     6 +-
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 profiles/arch.list                                 |    44 +
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 ...ld-make-AC-check-for-linux-arch-sandbox-f.patch |    95 +
 ...rnel-3.0-SuSE-and-3.6-FC18-server-patches.patch | 21302 +++++++++++++++++++
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 ...6-kernel-Kernel-update-for-3.7.2-201.fc18.patch |   184 +
 ...pat-posix_acl_-to-from-_xattr-take-user_n.patch |   159 +
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 923 files changed, 36037 insertions(+), 9438 deletions(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

commit:     0d7bd5b0a5573db70afe91a91985ea501de5990b
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed May  1 18:30:38 2013 +0000
Commit:     Justin Lecher <jlec <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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

commit:     d557b6f923a63df5cd78512561ec0f59ebf23369
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed May  1 18:29:34 2013 +0000
Commit:     Justin Lecher <jlec <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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
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From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

commit:     e334b4c9480ce3caa26dfe0f22d51d9fad528a5c
Author:     Kacper Kowalik <xarthisius.kk <AT> gmail <DOT> com>
AuthorDate: Wed May  1 20:07:14 2013 +0000
Commit:     Justin Lecher <jlec <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 file changed, 5 insertions(+), 1 deletion(-)


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* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

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(-)


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* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
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From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

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(-)


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* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

commit:     92f5fe738767b83d6b5633fa9b2a1a14c4e68721
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 29 16:21:49 2013 +0000
Commit:     Justin Lecher <jlec <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(-)


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* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
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From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

commit:     52856f2bdf0d60884389fb5362340c64e693f6e6
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Mon Apr 29 06:32:16 2013 +0000
Commit:     Justin Lecher <jlec <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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
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From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

commit:     4873ee2bc60d04d34ab4a70d7b4e19dfeee51b83
Author:     Sébastien Fabbro <bicatali <AT> gentoo <DOT> org>
AuthorDate: Wed Apr 24 15:29:10 2013 +0000
Commit:     Justin Lecher <jlec <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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
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From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

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(-)


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* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2013-05-30 10:31 Justin Lecher
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From: Justin Lecher @ 2013-05-30 10:31 UTC (permalink / raw
  To: gentoo-commits

commit:     6d23e13180fb3099af32a680e3a94a26d53a7160
Author:     Andreas Schäfer <gentryx <AT> gmx <DOT> de>
AuthorDate: Wed Apr 24 11:49:52 2013 +0000
Commit:     Justin Lecher <jlec <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 +
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 sci-misc/sfst/sfst-1.4.2.ebuild                    |     4 +-
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 sci-physics/abinit/abinit-7.0.4.ebuild             |    27 +-
 ...abinit-6.12.3-r2.ebuild => abinit-7.0.5.ebuild} |    63 +-
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 sci-physics/elk/elk-1.4.22.ebuild                  |    92 +-
 sci-physics/elk/metadata.xml                       |    10 +-
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 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 +-
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 .../phenix-bin => sci-physics/openmx}/metadata.xml |     0
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 .../root/files/root-5.34.05-nobyte-compile.patch   |   137 +
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 .../{root-5.34.03.ebuild => root-5.34.05.ebuild}   |    19 +-
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 ...eg-1.8.2-java.patch => thepeg-1.8.3-java.patch} |     0
 .../{thepeg-1.8.2.ebuild => thepeg-1.8.3.ebuild}   |     2 +-
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 sci-visualization/v_sim/Manifest                   |     4 +-
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 sci-visualization/v_sim/v_sim-3.5.1.ebuild         |    80 -
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 skel.ChangeLog                                     |  8022 +++++++
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 .../empi/{empi-0.7.ebuild => empi-0.8.ebuild}      |     2 +-
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 .../files/{eselect.mpi-0.7 => eselect.mpi-0.8}     |     2 +-
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 ...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 +-
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 .../{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 +-
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 .../{scalapack-1.8.ebuild => scalapack-2.0.ebuild} |     6 +-
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 .../{xview-3.2-r7.ebuild => xview-3.2-r8.ebuild}   |     8 +-
 894 files changed, 42959 insertions(+), 9213 deletions(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:master commit in: /
@ 2013-05-15  6:19 Justin Lecher
  2013-05-30 10:31 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-05-15  6:19 UTC (permalink / raw
  To: gentoo-commits

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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:master commit in: /
@ 2013-05-15  6:19 Justin Lecher
  2013-05-30 10:31 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-05-15  6:19 UTC (permalink / raw
  To: gentoo-commits

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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:master commit in: /
@ 2013-05-06  8:26 Justin Lecher
  2013-05-30 10:31 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2013-05-06  8:26 UTC (permalink / raw
  To: gentoo-commits

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(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2012-12-12  9:23 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2012-12-12  9:23 UTC (permalink / raw
  To: gentoo-commits

commit:     87b28664cc5e4dfee010012bafca333f580a0b99
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Dec 10 14:48:36 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec 10 14:48:36 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=87b28664

Merge branch 'master' into ccp4

* master:
  sci-biology/pybrain: Drop comments from metadata.xml; drop keywords from live ebuild
  ran repoman -vdx fix as per jlec'S recommendation
  Added live ebuild for pybrain


 sci-biology/pybrain/ChangeLog                      |    8 ++++++
 .../omniorbpy => sci-biology/pybrain}/metadata.xml |    0
 sci-biology/pybrain/pybrain-9999.ebuild            |   25 ++++++++++++++++++++
 3 files changed, 33 insertions(+), 0 deletions(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
@ 2012-12-12  9:23 Justin Lecher
  0 siblings, 0 replies; 72+ messages in thread
From: Justin Lecher @ 2012-12-12  9:23 UTC (permalink / raw
  To: gentoo-commits

commit:     37e60011545e1c93774198df085dc88a5dcdfcc3
Author:     Justin <jlec <AT> j-schmitz <DOT> net>
AuthorDate: Mon Dec 10 14:43:58 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec 10 14:43:58 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=37e60011

Merge pull request #36 from TheChymera/master

Live ebuild for pybrain


 .../pybrain/metadata.xml                           |    0
 sci-biology/pybrain/pybrain-9999.ebuild            |   25 ++++++++++++++++++++
 2 files changed, 25 insertions(+), 0 deletions(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
* [gentoo-commits] proj/sci:master commit in: /
@ 2012-12-10 14:47 Justin Lecher
  2012-12-12  9:23 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
  0 siblings, 1 reply; 72+ messages in thread
From: Justin Lecher @ 2012-12-10 14:47 UTC (permalink / raw
  To: gentoo-commits

commit:     abec81ec27eb8b7a07dba4c8772c85804cf5b1f9
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Dec 10 14:45:48 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec 10 14:45:48 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=abec81ec

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

# By TheChymera
# Via Justin (1) and TheChymera (1)
* 'master' of github.com:gentoo-science/sci:
  ran repoman -vdx fix as per jlec'S recommendation
  Added live ebuild for pybrain


 .../pybrain/metadata.xml                           |    0
 sci-biology/pybrain/pybrain-9999.ebuild            |   25 ++++++++++++++++++++
 2 files changed, 25 insertions(+), 0 deletions(-)


^ permalink raw reply	[flat|nested] 72+ messages in thread
end of thread, other threads:[~2013-07-08 11:54 UTC | newest]

Thread overview: 72+ messages (download: mbox.gz follow: Atom feed
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2013-06-17  5:55 [gentoo-commits] proj/sci:ccp4 commit in: / Justin Lecher
2013-06-17  5:55 ` [gentoo-commits] proj/sci:fixing " Justin Lecher
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2013-07-11 20:26 [gentoo-commits] proj/sci:vtk " Justin Lecher
2013-07-08 11:54 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-07-11 20:26 [gentoo-commits] proj/sci:vtk " Justin Lecher
2013-07-08 11:54 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-07-08 11:54 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-07-08 11:54 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-07-08 11:54 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-07-08 11:54 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-07-08 11:54 Justin Lecher
2013-07-08 11:54 Justin Lecher
2013-06-26  7:09 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-06-19  6:53 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-19  6:53 Justin Lecher
2013-06-19  6:53 Justin Lecher
2013-06-18  9:13 Justin Lecher
2013-06-18  9:13 Justin Lecher
2013-06-18  9:11 Justin Lecher
2013-06-18  8:57 Justin Lecher
2013-06-18  8:54 [gentoo-commits] proj/sci:fixing " Justin Lecher
2013-06-18  8:54 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-19  6:53 ` Justin Lecher
2013-06-18  8:54 Justin Lecher
2013-06-17  5:55 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-06-13  7:08 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-17  5:55 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-06-13  7:08 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-17  5:55 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-06-13  7:08 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-17  5:55 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-06-13  7:08 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-17  5:55 [gentoo-commits] proj/sci:fixing " Justin Lecher
2013-06-17  5:55 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-17  5:55 [gentoo-commits] proj/sci:fixing " Justin Lecher
2013-06-17  5:55 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-17  5:55 Justin Lecher
2013-06-17  5:55 Justin Lecher
2013-06-16 17:23 [gentoo-commits] proj/sci:master " Justin Lecher
2013-06-17  5:55 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-16 15:53 Justin Lecher
2013-06-16 14:23 [gentoo-commits] proj/sci:fixing " Justin Lecher
2013-06-16 14:23 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-16 14:23 Justin Lecher
2013-06-14 11:21 Justin Lecher
2013-06-13  7:08 Justin Lecher
2013-06-13  7:08 Justin Lecher
2013-06-12  8:13 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-06-04 11:59 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-12  8:13 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-06-04 11:59 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-12  8:13 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-06-01 17:24 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-12  8:13 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-06-01 17:24 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-12  8:13 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-05-30 10:31 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-12  8:13 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-05-30 10:31 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-12  8:13 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-05-30 10:31 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-12  8:13 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-05-30 10:31 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-12  8:13 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-05-30 10:31 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-10 12:01 Justin Lecher
2013-06-10 12:01 Justin Lecher
2013-06-10 11:57 [gentoo-commits] proj/sci:master " Justin Lecher
2013-06-10 12:01 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-04 11:59 Justin Lecher
2013-06-04 11:59 Justin Lecher
2013-06-01 17:24 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-30 10:31 Justin Lecher
2013-05-15  6:19 [gentoo-commits] proj/sci:master " Justin Lecher
2013-05-30 10:31 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-05-15  6:19 [gentoo-commits] proj/sci:master " Justin Lecher
2013-05-30 10:31 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-05-06  8:26 [gentoo-commits] proj/sci:master " Justin Lecher
2013-05-30 10:31 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2012-12-12  9:23 Justin Lecher
2012-12-12  9:23 Justin Lecher
2012-12-10 14:47 [gentoo-commits] proj/sci:master " Justin Lecher
2012-12-12  9:23 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher

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