From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 2A1B31381F3 for ; Mon, 8 Jul 2013 11:54:29 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id A4913E0A53; Mon, 8 Jul 2013 11:54:18 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 2E662E0A53 for ; Mon, 8 Jul 2013 11:54:18 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 125BA33E8BA for ; Mon, 8 Jul 2013 11:54:17 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id A6F0FE5458 for ; Mon, 8 Jul 2013 11:54:15 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1372592362.3833417300c4a4415fac9efa033c5a11f0bb42d7.jlec@gentoo> Subject: [gentoo-commits] proj/sci:ccp4 commit in: / X-VCS-Repository: proj/sci X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 3833417300c4a4415fac9efa033c5a11f0bb42d7 X-VCS-Branch: ccp4 Date: Mon, 8 Jul 2013 11:54:15 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 2f01b2bb-5653-48e0-9e35-6595494e5392 X-Archives-Hash: b2004ee63c51be9cbc93ea06f0cf720e commit: 3833417300c4a4415fac9efa033c5a11f0bb42d7 Author: Justin Lecher gentoo org> AuthorDate: Sun Jun 30 11:39:22 2013 +0000 Commit: Justin Lecher gentoo 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 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 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 shiftx-1.1.ebuild, metadata.xml: ++ Bump to EAPI=5 and fix license *shiftx-1.1 (14 Jun 2009)