From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1S5EmN-0003X0-BT for garchives@archives.gentoo.org; Wed, 07 Mar 2012 11:11:35 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id CEFB9E071C; Wed, 7 Mar 2012 11:10:52 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 8CF1FE0716 for ; Wed, 7 Mar 2012 11:10:52 +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 CBDEC1B402E for ; Wed, 7 Mar 2012 11:10:51 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 94A8FE5428 for ; Wed, 7 Mar 2012 11:10:50 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1330932927.b1a4da34a7aba6ff9286adf75eb2871b85331ce1.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: / X-VCS-Repository: proj/sci X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: b1a4da34a7aba6ff9286adf75eb2871b85331ce1 X-VCS-Branch: master Date: Wed, 7 Mar 2012 11:10:50 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: e28a5ffc-0f26-4bf4-aa26-46d2b3cedcfe X-Archives-Hash: 42a4f5833447d95ca6fb964b1f6ee67b commit: b1a4da34a7aba6ff9286adf75eb2871b85331ce1 Author: Justin Lecher gentoo org> AuthorDate: Mon Mar 5 07:35:27 2012 +0000 Commit: Justin Lecher gentoo org> CommitDate: Mon Mar 5 07:35:27 2012 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3Db1a4da34 Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci; gith= ub.com:gentoo-science/sci * 'master' of git+ssh://git.overlays.gentoo.org/proj/sci: (28 commits) added superlu on activated hypre flag got sparse flag working disabled non-working dependencies Moved to tree moved to tree fixed undefined reference when using afterimage Moved to tree Block pypy usage Added sci-libs/libsufr-0.3.2 removed obsolete call to env-update reworked fortran and openmp support sci-chemistry/ambertools: Add another buffer overflow patch fixed disable X option and use deps sci-chemistry/ambertools: Add bugfixes 22-27 sci-libs/lemon: added a note how to eventually create a shared library added optional boost and afterimage dep Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github= .com:gentoo-science/sci sci-libs/inchi: Version bump, new licence further simplification, added more optional deps fixed banned dosed, added more comments ... * github.com:gentoo-science/sci: (28 commits) added superlu on activated hypre flag got sparse flag working disabled non-working dependencies Moved to tree moved to tree fixed undefined reference when using afterimage Moved to tree Block pypy usage Added sci-libs/libsufr-0.3.2 removed obsolete call to env-update reworked fortran and openmp support sci-chemistry/ambertools: Add another buffer overflow patch fixed disable X option and use deps sci-chemistry/ambertools: Add bugfixes 22-27 sci-libs/lemon: added a note how to eventually create a shared library added optional boost and afterimage dep Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci; github= .com:gentoo-science/sci sci-libs/inchi: Version bump, new licence further simplification, added more optional deps fixed banned dosed, added more comments ... media-gfx/PhiloGL/Manifest | 2 +- .../{PhiloGL-1.4.2.ebuild =3D> PhiloGL-1.4.3.ebuild} | 0 sci-biology/cufflinks/ChangeLog | 10 + sci-biology/cufflinks/Manifest | 1 + sci-biology/cufflinks/cufflinks-1.3.0.ebuild | 20 + .../cufflinks}/metadata.xml | 0 sci-biology/cutadapt/ChangeLog | 10 + sci-biology/cutadapt/Manifest | 1 + sci-biology/cutadapt/cutadapt-1.0.ebuild | 21 + .../cutadapt}/metadata.xml | 0 sci-biology/phylobayes/ChangeLog | 10 + sci-biology/phylobayes/Manifest | 2 + .../phylobayes}/metadata.xml | 0 sci-biology/phylobayes/phylobayes-3.3b.ebuild | 37 + sci-chemistry/ambertools/ChangeLog | 12 +- ...ools-1.5-r2.ebuild =3D> ambertools-1.5-r3.ebuild} | 6 +- .../files/ambertools-1.5-bugfix_22-27.patch | 3343 ++++++++++++++= ++++++ .../ambertools/files/ambertools-1.5-overflow.patch | 30 + sci-chemistry/gromacs/ChangeLog | 10 + sci-chemistry/gromacs/gromacs-4.5.9999.ebuild | 3 +- sci-chemistry/gromacs/gromacs-4.6.9999.ebuild | 88 +- sci-chemistry/gromacs/gromacs-9999.ebuild | 3 +- sci-chemistry/openbabel-perl/ChangeLog | 10 - sci-chemistry/openbabel-perl/Manifest | 1 - .../files/openbabel-perl-2.3.1-makefile.patch | 9 - sci-chemistry/openbabel-perl/metadata.xml | 12 - .../openbabel-perl/openbabel-perl-2.3.1.ebuild | 69 - sci-chemistry/openbabel-python/ChangeLog | 10 - sci-chemistry/openbabel-python/Manifest | 1 - .../openbabel-python-2.3.1-system_openbabel.patch | 15 - sci-chemistry/openbabel-python/metadata.xml | 12 - .../openbabel-python/openbabel-python-2.3.1.ebuild | 53 - sci-chemistry/openbabel/ChangeLog | 11 - sci-chemistry/openbabel/Manifest | 1 - .../files/openbabel-2.3.0-test_lib_path.patch | 12 - sci-chemistry/openbabel/metadata.xml | 14 - sci-chemistry/openbabel/openbabel-2.3.1.ebuild | 69 - sci-chemistry/pymol/ChangeLog | 3 + sci-chemistry/pymol/pymol-9999.ebuild | 2 +- sci-libs/lemon/ChangeLog | 13 + sci-libs/lemon/Manifest | 1 + sci-libs/lemon/lemon-1.2.3.ebuild | 32 + .../Bio-BigFile =3D> sci-libs/lemon}/metadata.xml | 0 sci-libs/libsufr/ChangeLog | 5 + sci-libs/libsufr/Manifest | 1 + .../{libsufr-0.3.1.ebuild =3D> libsufr-0.3.2.ebuild} | 0 .../petsc/files/petsc-disable-env-warnings.patch | 13 + .../petsc/files/petsc-fix-afterimage.patch | 71 + sci-mathematics/petsc/files/petsc-fix-xops.patch | 21 + sci-mathematics/petsc/metadata.xml | 7 +- sci-mathematics/petsc/petsc-3.2_p6.ebuild | 211 +- 51 files changed, 3811 insertions(+), 477 deletions(-)