* [gentoo-commits] proj/sci:master commit in: /
2013-06-16 14:23 [gentoo-commits] proj/sci:fixing commit in: / Justin Lecher
@ 2013-06-16 11:31 ` Justin Lecher
2013-06-16 14:23 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-17 5:55 ` [gentoo-commits] proj/sci:jlec " Justin Lecher
2 siblings, 0 replies; 13+ messages in thread
From: Justin Lecher @ 2013-06-16 11:31 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] 13+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: /
2013-06-16 14:23 [gentoo-commits] proj/sci:fixing commit in: / Justin Lecher
2013-06-16 11:31 ` [gentoo-commits] proj/sci:master " Justin Lecher
@ 2013-06-16 14:23 ` Justin Lecher
2013-06-17 5:55 ` [gentoo-commits] proj/sci:jlec " Justin Lecher
2 siblings, 0 replies; 13+ 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] 13+ messages in thread
* [gentoo-commits] proj/sci:fixing commit in: /
@ 2013-06-16 14:23 Justin Lecher
2013-06-16 11:31 ` [gentoo-commits] proj/sci:master " Justin Lecher
` (2 more replies)
0 siblings, 3 replies; 13+ 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] 13+ messages in thread
* [gentoo-commits] proj/sci:fixing commit in: /
2013-06-17 5:55 [gentoo-commits] proj/sci:ccp4 " Justin Lecher
@ 2013-06-17 5:55 ` Justin Lecher
0 siblings, 0 replies; 13+ 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] 13+ messages in thread
* [gentoo-commits] proj/sci:fixing commit in: /
2013-06-16 17:23 [gentoo-commits] proj/sci:master " Justin Lecher
@ 2013-06-17 5:55 ` Justin Lecher
0 siblings, 0 replies; 13+ messages in thread
From: Justin Lecher @ 2013-06-17 5:55 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] 13+ messages in thread
* [gentoo-commits] proj/sci:fixing commit in: /
@ 2013-06-17 5:55 Justin Lecher
0 siblings, 0 replies; 13+ 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] 13+ messages in thread
* [gentoo-commits] proj/sci:fixing commit in: /
2013-06-17 5:55 [gentoo-commits] proj/sci:ccp4 " Justin Lecher
@ 2013-06-17 5:55 ` Justin Lecher
0 siblings, 0 replies; 13+ 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] 13+ messages in thread
* [gentoo-commits] proj/sci:fixing commit in: /
@ 2013-06-17 5:55 Justin Lecher
0 siblings, 0 replies; 13+ 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] 13+ messages in thread
* [gentoo-commits] proj/sci:jlec commit in: /
2013-06-16 14:23 [gentoo-commits] proj/sci:fixing commit in: / Justin Lecher
2013-06-16 11:31 ` [gentoo-commits] proj/sci:master " Justin Lecher
2013-06-16 14:23 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
@ 2013-06-17 5:55 ` Justin Lecher
2 siblings, 0 replies; 13+ messages in thread
From: Justin Lecher @ 2013-06-17 5:55 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] 13+ messages in thread
* [gentoo-commits] proj/sci:fixing commit in: /
@ 2013-06-18 8:54 Justin Lecher
0 siblings, 0 replies; 13+ 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] 13+ messages in thread
* [gentoo-commits] proj/sci:fixing commit in: /
2013-06-19 6:53 [gentoo-commits] proj/sci:ccp4 " Justin Lecher
@ 2013-06-22 10:49 ` Justin Lecher
0 siblings, 0 replies; 13+ messages in thread
From: Justin Lecher @ 2013-06-22 10:49 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] 13+ messages in thread
* [gentoo-commits] proj/sci:fixing commit in: /
2013-06-26 7:09 [gentoo-commits] proj/sci:jlec " Justin Lecher
@ 2013-06-22 10:49 ` Justin Lecher
0 siblings, 0 replies; 13+ messages in thread
From: Justin Lecher @ 2013-06-22 10:49 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] 13+ messages in thread
* [gentoo-commits] proj/sci:fixing commit in: /
@ 2013-06-22 10:49 Justin Lecher
0 siblings, 0 replies; 13+ messages in thread
From: Justin Lecher @ 2013-06-22 10:49 UTC (permalink / raw
To: gentoo-commits
commit: cce50ebf51440b0d0b894465e42b13f88f4f0072
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 22 10:49:00 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun 22 10:49:00 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cce50ebf
Merge branch 'master' into fixing
* master: (22 commits)
Added new package: charmdebug.
sci-chemistry/shiftx: Block shiftx2 at runtime
sci-chemistry/shiftx: Fix patch and add patch for buffer overflow fix
The announced, but forgotten, change in sci-libs/fox-4.1.2-r2 actually done.
The announced, but forgotten, change in sci-libs/etsf_io-1.0.3-r2 actually done.
sci-physics/abinit/files/6.12.3-gui-makefiles.tbz put back, its deletion was a mistake.
sci-libs/trilinos: Version bump and rewrite
sci-libs/coinor-clp: Version bump and patch for mpi
For sci-libs/bigdft-abi and sci-physics/bigdft, filter LDFLAGS for cuda use not to break nvcc.
To sci-libs/bigdft-abi and sci-physics/bigdft added dev-util/gdbus-codegen among dependencies.
Spaces in the testing snippet of fortran code in sci-libs/bigdft-abi-1.0.4.ebuild protected from reformatting.
fixed qt4 build
fixing manifests
big fixes of metadata and package sub-herd re-distribution
sci-physics/openmx upgraded to 3.7.3 with some openMP and MPI C/F90 juggling, previous sci-physics/openmx-3.6 preserved for the time being.
sci-chemistry/talosn: drop upstream path in favour of our
sci-chemistry/modeller: Fix broken symlink, #473680
sci-chemistry/mics: New package
sci-chemistry/talosn: New package
Abinit & friends upgraded to sci-physics/abinit-7.2.2. BigDFT moved from sci-libs to sci-physics, sci-physics/abinit uses sci-libs/bigdft-abi instead. Usage of LIBDIR/finclude abandoned in favour of /usr/include, as mostly used upstream. Old files cleaned up.
...
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
Conflicts:
sci-chemistry/talosn/ChangeLog
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/ChangeLog | 7 +
sci-chemistry/shiftx/files/1.1-Makefile.patch | 15 +-
sci-chemistry/shiftx/files/1.1-bfr-overflow.patch | 16 ++
sci-chemistry/shiftx/metadata.xml | 3 -
sci-chemistry/shiftx/shiftx-1.1.ebuild | 7 +-
sci-chemistry/shiftx2/metadata.xml | 2 +-
sci-chemistry/simpson/metadata.xml | 2 +-
sci-chemistry/smmp/metadata.xml | 5 +-
sci-chemistry/specView/metadata.xml | 2 +-
sci-chemistry/ssp/metadata.xml | 2 +-
sci-chemistry/talosn/ChangeLog | 7 +-
...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 | 17 ++
sci-libs/bigdft-abi/Manifest | 2 -
sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild | 11 +-
sci-libs/bigdft/metadata.xml | 19 +--
sci-libs/cnsface-scripts/metadata.xml | 3 -
sci-libs/coinor-clp/ChangeLog | 6 +
sci-libs/coinor-clp/Manifest | 2 +-
...-clp-1.15.0.ebuild => coinor-clp-1.15.1.ebuild} | 4 +-
.../files/coinor-clp-1.15.1-mpi-header.patch | 12 ++
sci-libs/driftwood/metadata.xml | 5 +-
sci-libs/etsf_io/ChangeLog | 4 +
sci-libs/etsf_io/etsf_io-1.0.3-r2.ebuild | 6 +-
sci-libs/etsf_io/metadata.xml | 5 +-
sci-libs/fox/ChangeLog | 4 +
.../files/4.1.2-r2-install-customizations.patch | 4 +-
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/mumps/ChangeLog | 5 +-
sci-libs/mumps/mumps-4.10.0-r2.ebuild | 5 +-
sci-libs/pagmo/metadata.xml | 13 +-
sci-libs/starparse/metadata.xml | 5 +-
sci-libs/trilinos/ChangeLog | 7 +-
sci-libs/trilinos/metadata.xml | 16 ++
sci-libs/trilinos/trilinos-11.2.3.ebuild | 186 +++++++++++++++++++++
sci-libs/wannier90/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 | 7 +
sci-physics/abinit/Manifest | 3 +-
sci-physics/abinit/abinit-7.2.2.ebuild | 2 +-
sci-physics/abinit/files/6.12.3-gui-makefiles.tbz | Bin 0 -> 14600 bytes
sci-physics/atompaw/metadata.xml | 11 +-
sci-physics/atompaw2abinit/metadata.xml | 5 +-
sci-physics/bigdft/ChangeLog | 13 ++
sci-physics/bigdft/Manifest | 1 +
sci-physics/bigdft/bigdft-1.7_pre24.ebuild | 4 +-
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 -
sys-cluster/charmdebug/ChangeLog | 9 +
sys-cluster/charmdebug/Manifest | 1 +
sys-cluster/charmdebug/charmdebug-6.2.0.ebuild | 29 ++++
.../charmdebug}/metadata.xml | 0
www-apps/py-swish-e/metadata.xml | 5 +-
x11-libs/tr/metadata.xml | 3 -
131 files changed, 840 insertions(+), 482 deletions(-)
diff --cc sci-chemistry/talosn/ChangeLog
index dea3c84,9d358bf..93eccf6
--- a/sci-chemistry/talosn/ChangeLog
+++ b/sci-chemistry/talosn/ChangeLog
@@@ -7,4 -13,4 +13,3 @@@
18 Jun 2013; Justin Lecher <jlec@gentoo.org>
+talosn-4.01.2013.148.15.55.ebuild, +metadata.xml:
New package
--
^ permalink raw reply [flat|nested] 13+ messages in thread
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2013-06-16 14:23 [gentoo-commits] proj/sci:fixing commit in: / Justin Lecher
2013-06-16 11:31 ` [gentoo-commits] proj/sci:master " Justin Lecher
2013-06-16 14:23 ` [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-17 5:55 ` [gentoo-commits] proj/sci:jlec " Justin Lecher
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2013-06-16 17:23 [gentoo-commits] proj/sci:master " 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 ` [gentoo-commits] proj/sci:fixing " Justin Lecher
2013-06-17 5:55 Justin Lecher
2013-06-17 5:55 Justin Lecher
2013-06-18 8:54 Justin Lecher
2013-06-19 6:53 [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-06-22 10:49 ` [gentoo-commits] proj/sci:fixing " Justin Lecher
2013-06-22 10:49 Justin Lecher
2013-06-26 7:09 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-06-22 10:49 ` [gentoo-commits] proj/sci:fixing " Justin Lecher
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