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 0A6E21381F3 for ; Thu, 11 Jul 2013 20:26:58 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 59C6EE0A8E; Thu, 11 Jul 2013 20:26:57 +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 D299AE0A8D for ; Thu, 11 Jul 2013 20:26:56 +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 BD66233E91F for ; Thu, 11 Jul 2013 20:26:55 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 61899E5458 for ; Thu, 11 Jul 2013 20:26:54 +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: <1371811471.e2667d72a9cda457057fc4531574c2634dc92387.jlec@gentoo> Subject: [gentoo-commits] proj/sci:vtk commit in: / X-VCS-Repository: proj/sci X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: e2667d72a9cda457057fc4531574c2634dc92387 X-VCS-Branch: vtk Date: Thu, 11 Jul 2013 20:26:54 +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: d9cf61b2-c272-4d2b-b319-7b7fd8c6e2d2 X-Archives-Hash: 9638aa2f316e978540cc80ce1239ec30 commit: e2667d72a9cda457057fc4531574c2634dc92387 Author: Justin Lecher gentoo org> AuthorDate: Fri Jun 21 10:44:31 2013 +0000 Commit: Justin Lecher gentoo org> CommitDate: Fri Jun 21 10:44:31 2013 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e2667d72 Merge branch 'master' into jlec * master: (29 commits) sci-chemistry/shiftx: Block shiftx2 at runtime sci-chemistry/shiftx: Fix patch and add patch for buffer overflow fix The announced, but forgotten, change in sci-libs/fox-4.1.2-r2 actually done. The announced, but forgotten, change in sci-libs/etsf_io-1.0.3-r2 actually done. sci-physics/abinit/files/6.12.3-gui-makefiles.tbz put back, its deletion was a mistake. sci-libs/trilinos: Version bump and rewrite sci-libs/coinor-clp: Version bump and patch for mpi For sci-libs/bigdft-abi and sci-physics/bigdft, filter LDFLAGS for cuda use not to break nvcc. To sci-libs/bigdft-abi and sci-physics/bigdft added dev-util/gdbus-codegen among dependencies. Spaces in the testing snippet of fortran code in sci-libs/bigdft-abi-1.0.4.ebuild protected from reformatting. fixed qt4 build fixing manifests big fixes of metadata and package sub-herd re-distribution sci-physics/openmx upgraded to 3.7.3 with some openMP and MPI C/F90 juggling, previous sci-physics/openmx-3.6 preserved for the time being. sci-chemistry/talosn: drop upstream path in favour of our sci-chemistry/modeller: Fix broken symlink, #473680 sci-chemistry/mics: New package sci-chemistry/talosn: New package Abinit & friends upgraded to sci-physics/abinit-7.2.2. BigDFT moved from sci-libs to sci-physics, sci-physics/abinit uses sci-libs/bigdft-abi instead. Usage of LIBDIR/finclude abandoned in favour of /usr/include, as mostly used upstream. Old files cleaned up. Version of bigdft bumped to 1.7_pre24, moved from sci-libs to sci-physics. No longer used as a library by sci-physics/abinit. Usage of LIBDIR/finclude abandoned in favour of /usr/include, as used upstream. ... app-text/dgs/metadata.xml | 3 - app-text/jabref/ChangeLog | 10 + ...jabref-2.10b.ebuild => jabref-2.10_beta.ebuild} | 8 +- app-vim/freefem++-syntax/metadata.xml | 7 +- app-vim/vim-gromacs/metadata.xml | 5 +- dev-db/cppdb/metadata.xml | 19 +- dev-libs/simclist/metadata.xml | 17 +- dev-ml/mlgmpidl/metadata.xml | 23 +- dev-ml/ocamlgraph/metadata.xml | 47 ++- dev-ml/zarith/metadata.xml | 20 +- dev-perl/opal-client/metadata.xml | 3 - dev-python/opal-client/metadata.xml | 5 +- dev-tcltk/img_rotate/metadata.xml | 5 +- dev-tcltk/togl/metadata.xml | 3 - media-gfx/librecad/ChangeLog | 6 + media-gfx/librecad/Manifest | 4 +- media-gfx/librecad/files/1.0.0_rc2-gcc4.6.patch | 38 --- .../files/librecad-1.0.0_rc2-version.patch | 11 - media-gfx/librecad/librecad-1.0.2.ebuild | 45 --- media-gfx/librecad/librecad-2.0.0_beta5.ebuild | 48 --- media-gfx/librecad/librecad-2.0.0_rc1.ebuild | 27 +- media-gfx/librecad/metadata.xml | 23 +- media-libs/OpenMOIV/metadata.xml | 3 - media-libs/libgfx/metadata.xml | 3 - profiles/package.mask | 6 + sci-biology/perlprimer/metadata.xml | 3 - sci-chemistry/GromacsWrapper/metadata.xml | 2 +- sci-chemistry/ball/metadata.xml | 2 +- sci-chemistry/burrow-owl/metadata.xml | 5 +- sci-chemistry/camshift/metadata.xml | 5 +- sci-chemistry/chemBuild/metadata.xml | 2 +- sci-chemistry/chimera-bin/metadata.xml | 2 +- sci-chemistry/chooch/metadata.xml | 5 +- sci-chemistry/cnsface/metadata.xml | 5 +- sci-chemistry/concoord/metadata.xml | 2 +- sci-chemistry/coot/metadata.xml | 3 - sci-chemistry/cs-rosetta/metadata.xml | 2 +- sci-chemistry/curvefit/metadata.xml | 2 +- sci-chemistry/direx/metadata.xml | 3 - sci-chemistry/dssp2pdb/metadata.xml | 3 - sci-chemistry/freeon/ChangeLog | 9 + ...ch => freeon-2012.05.03-no_internal_hdf5.patch} | 32 +- .../files/freeon-9999-no_internal_hdf5.patch | 25 ++ .../files/freeon-9999-no_internal_libs.patch | 47 --- sci-chemistry/freeon/freeon-2012.05.03.ebuild | 7 +- sci-chemistry/freeon/freeon-9999.ebuild | 7 +- sci-chemistry/hydronmr/metadata.xml | 2 +- sci-chemistry/jana2000/metadata.xml | 3 - sci-chemistry/jligand/metadata.xml | 5 +- sci-chemistry/ligplot+/metadata.xml | 2 +- sci-chemistry/mage/metadata.xml | 3 - sci-chemistry/mddnmr/metadata.xml | 5 +- sci-chemistry/mics/ChangeLog | 10 + sci-chemistry/mics/Manifest | 1 + .../{mgltools-autodocktools => mics}/metadata.xml | 0 sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild | 51 +++ sci-chemistry/modelfree/metadata.xml | 2 +- sci-chemistry/modeller/ChangeLog | 6 + ...odeller-9.12.ebuild => modeller-9.12-r1.ebuild} | 2 +- sci-chemistry/mtz2hkl/metadata.xml | 3 - sci-chemistry/mtz2sca/metadata.xml | 3 - sci-chemistry/nMOLDYN/ChangeLog | 12 + sci-chemistry/nMOLDYN/Manifest | 1 + sci-chemistry/{trajng => nMOLDYN}/metadata.xml | 0 sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild | 24 ++ sci-chemistry/phenix-bin/metadata.xml | 2 +- sci-chemistry/polygon/metadata.xml | 5 +- sci-chemistry/pymol-apbs-plugin/metadata.xml | 5 +- sci-chemistry/rosetta-tools/metadata.xml | 3 - sci-chemistry/rosetta/metadata.xml | 23 +- sci-chemistry/shiftx/ChangeLog | 7 + sci-chemistry/shiftx/files/1.1-Makefile.patch | 15 +- sci-chemistry/shiftx/files/1.1-bfr-overflow.patch | 16 + sci-chemistry/shiftx/metadata.xml | 3 - sci-chemistry/shiftx/shiftx-1.1.ebuild | 7 +- sci-chemistry/shiftx2/metadata.xml | 2 +- sci-chemistry/simpson/metadata.xml | 2 +- sci-chemistry/smmp/metadata.xml | 5 +- sci-chemistry/specView/metadata.xml | 2 +- sci-chemistry/ssp/metadata.xml | 2 +- sci-chemistry/talosn/ChangeLog | 16 + sci-chemistry/talosn/Manifest | 1 + .../metadata.xml | 0 .../talosn/talosn-4.01.2013.148.15.55-r2.ebuild | 68 ++++ sci-chemistry/ucsf-tools/metadata.xml | 2 +- sci-chemistry/unio/metadata.xml | 5 +- sci-libs/Cgraph/metadata.xml | 5 +- sci-libs/bigdft-abi/ChangeLog | 29 ++ sci-libs/bigdft-abi/Manifest | 1 + .../bigdft-abi-1.0.4.ebuild} | 78 +++-- .../files/bigdft-abi-1.0.4-tests.tar.bz2 | Bin 0 -> 402968 bytes sci-libs/bigdft/metadata.xml | 19 +- sci-libs/cnsface-scripts/metadata.xml | 3 - sci-libs/coinor-clp/ChangeLog | 6 + sci-libs/coinor-clp/Manifest | 2 +- ...-clp-1.15.0.ebuild => coinor-clp-1.15.1.ebuild} | 4 +- .../files/coinor-clp-1.15.1-mpi-header.patch | 12 + sci-libs/driftwood/metadata.xml | 5 +- sci-libs/etsf_io/ChangeLog | 13 +- ..._io-1.0.3-r1.ebuild => etsf_io-1.0.3-r2.ebuild} | 6 +- sci-libs/etsf_io/metadata.xml | 5 +- sci-libs/fox/ChangeLog | 14 +- ...patch => 4.1.2-r2-install-customizations.patch} | 4 +- .../{fox-4.1.2-r1.ebuild => fox-4.1.2-r2.ebuild} | 10 +- sci-libs/fox/metadata.xml | 19 +- sci-libs/libxc/ChangeLog | 11 +- sci-libs/libxc/Manifest | 2 +- ...libxc-1.1.0-r1.ebuild => libxc-1.2.0-r1.ebuild} | 26 +- .../{libxc-1.2.0.ebuild => libxc-2.0.1.ebuild} | 27 +- sci-libs/libxc/libxc-9999.ebuild | 27 +- sci-libs/libxc/metadata.xml | 5 +- sci-libs/med/metadata.xml | 5 +- sci-libs/msms/metadata.xml | 5 +- sci-libs/mumps/ChangeLog | 5 +- sci-libs/mumps/mumps-4.10.0-r2.ebuild | 5 +- sci-libs/pagmo/metadata.xml | 13 +- sci-libs/starparse/metadata.xml | 5 +- sci-libs/trilinos/ChangeLog | 7 +- sci-libs/trilinos/metadata.xml | 16 + sci-libs/trilinos/trilinos-11.2.3.ebuild | 186 +++++++++++ sci-libs/wannier90/ChangeLog | 7 + sci-libs/wannier90/metadata.xml | 5 +- ...annier90-1.2.ebuild => wannier90-1.2-r1.ebuild} | 0 sci-mathematics/alt-ergo/metadata.xml | 23 +- sci-mathematics/apron/metadata.xml | 31 +- sci-mathematics/flocq/metadata.xml | 17 +- sci-mathematics/frama-c/metadata.xml | 28 +- sci-mathematics/gap-guava/metadata.xml | 5 +- sci-mathematics/gappa/metadata.xml | 22 +- sci-mathematics/gappalib-coq/metadata.xml | 15 +- sci-mathematics/giac/metadata.xml | 24 +- sci-mathematics/ltl2ba/metadata.xml | 3 - sci-mathematics/pff/metadata.xml | 17 +- sci-mathematics/why/metadata.xml | 32 +- sci-physics/LoopTools/metadata.xml | 2 +- sci-physics/abinit/ChangeLog | 16 + sci-physics/abinit/Manifest | 3 +- sci-physics/abinit/abinit-7.0.5.ebuild | 356 --------------------- .../{abinit-7.0.4.ebuild => abinit-7.2.2.ebuild} | 75 +++-- sci-physics/abinit/files/6.0.3-fftw.patch | 14 - .../abinit/files/6.12.1-libabinit_options.patch | 57 ---- sci-physics/atompaw/ChangeLog | 7 + ...aw-3.0.1.9.ebuild => atompaw-3.0.1.9-r1.ebuild} | 11 +- sci-physics/atompaw/metadata.xml | 11 +- sci-physics/atompaw2abinit/metadata.xml | 5 +- {sci-libs => sci-physics}/bigdft/ChangeLog | 23 +- sci-physics/bigdft/Manifest | 1 + .../bigdft/bigdft-1.7_pre24.ebuild | 37 +-- .../files/bigdft-1.7-dev.24-nolib_mods.patch | 14 +- sci-physics/elk/ChangeLog | 4 + sci-physics/elk/elk-1.4.22.ebuild | 2 +- sci-physics/herwig++/metadata.xml | 2 +- sci-physics/openmx/ChangeLog | 7 + sci-physics/openmx/Manifest | 2 + sci-physics/openmx/files/3.7-fortran_objects.patch | 15 + sci-physics/openmx/metadata.xml | 2 +- sci-physics/openmx/openmx-3.7.3.ebuild | 161 ++++++++++ sci-physics/thepeg/metadata.xml | 2 +- sci-visualization/gnuplot/ChangeLog | 3 + sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild | 2 +- sci-visualization/v_sim/metadata.xml | 3 - www-apps/py-swish-e/metadata.xml | 5 +- x11-libs/tr/metadata.xml | 3 - 163 files changed, 1278 insertions(+), 1264 deletions(-) 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 A145B1381F3 for ; Wed, 26 Jun 2013 07:10:01 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id C13ABE0A76; Wed, 26 Jun 2013 07:09:57 +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 48B99E0A76 for ; Wed, 26 Jun 2013 07:09:57 +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 3334833E742 for ; Wed, 26 Jun 2013 07:09:56 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 92A59E5462 for ; Wed, 26 Jun 2013 07:09:53 +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: <1371811471.e2667d72a9cda457057fc4531574c2634dc92387.jlec@gentoo> Subject: [gentoo-commits] proj/sci:jlec commit in: / X-VCS-Repository: proj/sci X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: e2667d72a9cda457057fc4531574c2634dc92387 X-VCS-Branch: jlec Date: Wed, 26 Jun 2013 07:09:53 +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: 270ff5f3-752f-4f0e-a572-fdf9f355c038 X-Archives-Hash: 3a8181a607f82c31a929806f8f8bc763 Message-ID: <20130626070953.04HhQ6fEwDKPTzQdy3YLU6ZUjjkWLaeOaVbldBO-f9I@z> commit: e2667d72a9cda457057fc4531574c2634dc92387 Author: Justin Lecher gentoo org> AuthorDate: Fri Jun 21 10:44:31 2013 +0000 Commit: Justin Lecher gentoo org> CommitDate: Fri Jun 21 10:44:31 2013 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e2667d72 Merge branch 'master' into jlec * master: (29 commits) sci-chemistry/shiftx: Block shiftx2 at runtime sci-chemistry/shiftx: Fix patch and add patch for buffer overflow fix The announced, but forgotten, change in sci-libs/fox-4.1.2-r2 actually done. The announced, but forgotten, change in sci-libs/etsf_io-1.0.3-r2 actually done. sci-physics/abinit/files/6.12.3-gui-makefiles.tbz put back, its deletion was a mistake. sci-libs/trilinos: Version bump and rewrite sci-libs/coinor-clp: Version bump and patch for mpi For sci-libs/bigdft-abi and sci-physics/bigdft, filter LDFLAGS for cuda use not to break nvcc. To sci-libs/bigdft-abi and sci-physics/bigdft added dev-util/gdbus-codegen among dependencies. Spaces in the testing snippet of fortran code in sci-libs/bigdft-abi-1.0.4.ebuild protected from reformatting. fixed qt4 build fixing manifests big fixes of metadata and package sub-herd re-distribution sci-physics/openmx upgraded to 3.7.3 with some openMP and MPI C/F90 juggling, previous sci-physics/openmx-3.6 preserved for the time being. sci-chemistry/talosn: drop upstream path in favour of our sci-chemistry/modeller: Fix broken symlink, #473680 sci-chemistry/mics: New package sci-chemistry/talosn: New package Abinit & friends upgraded to sci-physics/abinit-7.2.2. BigDFT moved from sci-libs to sci-physics, sci-physics/abinit uses sci-libs/bigdft-abi instead. Usage of LIBDIR/finclude abandoned in favour of /usr/include, as mostly used upstream. Old files cleaned up. Version of bigdft bumped to 1.7_pre24, moved from sci-libs to sci-physics. No longer used as a library by sci-physics/abinit. Usage of LIBDIR/finclude abandoned in favour of /usr/include, as used upstream. ... app-text/dgs/metadata.xml | 3 - app-text/jabref/ChangeLog | 10 + ...jabref-2.10b.ebuild => jabref-2.10_beta.ebuild} | 8 +- app-vim/freefem++-syntax/metadata.xml | 7 +- app-vim/vim-gromacs/metadata.xml | 5 +- dev-db/cppdb/metadata.xml | 19 +- dev-libs/simclist/metadata.xml | 17 +- dev-ml/mlgmpidl/metadata.xml | 23 +- dev-ml/ocamlgraph/metadata.xml | 47 ++- dev-ml/zarith/metadata.xml | 20 +- dev-perl/opal-client/metadata.xml | 3 - dev-python/opal-client/metadata.xml | 5 +- dev-tcltk/img_rotate/metadata.xml | 5 +- dev-tcltk/togl/metadata.xml | 3 - media-gfx/librecad/ChangeLog | 6 + media-gfx/librecad/Manifest | 4 +- media-gfx/librecad/files/1.0.0_rc2-gcc4.6.patch | 38 --- .../files/librecad-1.0.0_rc2-version.patch | 11 - media-gfx/librecad/librecad-1.0.2.ebuild | 45 --- media-gfx/librecad/librecad-2.0.0_beta5.ebuild | 48 --- media-gfx/librecad/librecad-2.0.0_rc1.ebuild | 27 +- media-gfx/librecad/metadata.xml | 23 +- media-libs/OpenMOIV/metadata.xml | 3 - media-libs/libgfx/metadata.xml | 3 - profiles/package.mask | 6 + sci-biology/perlprimer/metadata.xml | 3 - sci-chemistry/GromacsWrapper/metadata.xml | 2 +- sci-chemistry/ball/metadata.xml | 2 +- sci-chemistry/burrow-owl/metadata.xml | 5 +- sci-chemistry/camshift/metadata.xml | 5 +- sci-chemistry/chemBuild/metadata.xml | 2 +- sci-chemistry/chimera-bin/metadata.xml | 2 +- sci-chemistry/chooch/metadata.xml | 5 +- sci-chemistry/cnsface/metadata.xml | 5 +- sci-chemistry/concoord/metadata.xml | 2 +- sci-chemistry/coot/metadata.xml | 3 - sci-chemistry/cs-rosetta/metadata.xml | 2 +- sci-chemistry/curvefit/metadata.xml | 2 +- sci-chemistry/direx/metadata.xml | 3 - sci-chemistry/dssp2pdb/metadata.xml | 3 - sci-chemistry/freeon/ChangeLog | 9 + ...ch => freeon-2012.05.03-no_internal_hdf5.patch} | 32 +- .../files/freeon-9999-no_internal_hdf5.patch | 25 ++ .../files/freeon-9999-no_internal_libs.patch | 47 --- sci-chemistry/freeon/freeon-2012.05.03.ebuild | 7 +- sci-chemistry/freeon/freeon-9999.ebuild | 7 +- sci-chemistry/hydronmr/metadata.xml | 2 +- sci-chemistry/jana2000/metadata.xml | 3 - sci-chemistry/jligand/metadata.xml | 5 +- sci-chemistry/ligplot+/metadata.xml | 2 +- sci-chemistry/mage/metadata.xml | 3 - sci-chemistry/mddnmr/metadata.xml | 5 +- sci-chemistry/mics/ChangeLog | 10 + sci-chemistry/mics/Manifest | 1 + .../{mgltools-autodocktools => mics}/metadata.xml | 0 sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild | 51 +++ sci-chemistry/modelfree/metadata.xml | 2 +- sci-chemistry/modeller/ChangeLog | 6 + ...odeller-9.12.ebuild => modeller-9.12-r1.ebuild} | 2 +- sci-chemistry/mtz2hkl/metadata.xml | 3 - sci-chemistry/mtz2sca/metadata.xml | 3 - sci-chemistry/nMOLDYN/ChangeLog | 12 + sci-chemistry/nMOLDYN/Manifest | 1 + sci-chemistry/{trajng => nMOLDYN}/metadata.xml | 0 sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild | 24 ++ sci-chemistry/phenix-bin/metadata.xml | 2 +- sci-chemistry/polygon/metadata.xml | 5 +- sci-chemistry/pymol-apbs-plugin/metadata.xml | 5 +- sci-chemistry/rosetta-tools/metadata.xml | 3 - sci-chemistry/rosetta/metadata.xml | 23 +- sci-chemistry/shiftx/ChangeLog | 7 + sci-chemistry/shiftx/files/1.1-Makefile.patch | 15 +- sci-chemistry/shiftx/files/1.1-bfr-overflow.patch | 16 + sci-chemistry/shiftx/metadata.xml | 3 - sci-chemistry/shiftx/shiftx-1.1.ebuild | 7 +- sci-chemistry/shiftx2/metadata.xml | 2 +- sci-chemistry/simpson/metadata.xml | 2 +- sci-chemistry/smmp/metadata.xml | 5 +- sci-chemistry/specView/metadata.xml | 2 +- sci-chemistry/ssp/metadata.xml | 2 +- sci-chemistry/talosn/ChangeLog | 16 + sci-chemistry/talosn/Manifest | 1 + .../metadata.xml | 0 .../talosn/talosn-4.01.2013.148.15.55-r2.ebuild | 68 ++++ sci-chemistry/ucsf-tools/metadata.xml | 2 +- sci-chemistry/unio/metadata.xml | 5 +- sci-libs/Cgraph/metadata.xml | 5 +- sci-libs/bigdft-abi/ChangeLog | 29 ++ sci-libs/bigdft-abi/Manifest | 1 + .../bigdft-abi-1.0.4.ebuild} | 78 +++-- .../files/bigdft-abi-1.0.4-tests.tar.bz2 | Bin 0 -> 402968 bytes sci-libs/bigdft/metadata.xml | 19 +- sci-libs/cnsface-scripts/metadata.xml | 3 - sci-libs/coinor-clp/ChangeLog | 6 + sci-libs/coinor-clp/Manifest | 2 +- ...-clp-1.15.0.ebuild => coinor-clp-1.15.1.ebuild} | 4 +- .../files/coinor-clp-1.15.1-mpi-header.patch | 12 + sci-libs/driftwood/metadata.xml | 5 +- sci-libs/etsf_io/ChangeLog | 13 +- ..._io-1.0.3-r1.ebuild => etsf_io-1.0.3-r2.ebuild} | 6 +- sci-libs/etsf_io/metadata.xml | 5 +- sci-libs/fox/ChangeLog | 14 +- ...patch => 4.1.2-r2-install-customizations.patch} | 4 +- .../{fox-4.1.2-r1.ebuild => fox-4.1.2-r2.ebuild} | 10 +- sci-libs/fox/metadata.xml | 19 +- sci-libs/libxc/ChangeLog | 11 +- sci-libs/libxc/Manifest | 2 +- ...libxc-1.1.0-r1.ebuild => libxc-1.2.0-r1.ebuild} | 26 +- .../{libxc-1.2.0.ebuild => libxc-2.0.1.ebuild} | 27 +- sci-libs/libxc/libxc-9999.ebuild | 27 +- sci-libs/libxc/metadata.xml | 5 +- sci-libs/med/metadata.xml | 5 +- sci-libs/msms/metadata.xml | 5 +- sci-libs/mumps/ChangeLog | 5 +- sci-libs/mumps/mumps-4.10.0-r2.ebuild | 5 +- sci-libs/pagmo/metadata.xml | 13 +- sci-libs/starparse/metadata.xml | 5 +- sci-libs/trilinos/ChangeLog | 7 +- sci-libs/trilinos/metadata.xml | 16 + sci-libs/trilinos/trilinos-11.2.3.ebuild | 186 +++++++++++ sci-libs/wannier90/ChangeLog | 7 + sci-libs/wannier90/metadata.xml | 5 +- ...annier90-1.2.ebuild => wannier90-1.2-r1.ebuild} | 0 sci-mathematics/alt-ergo/metadata.xml | 23 +- sci-mathematics/apron/metadata.xml | 31 +- sci-mathematics/flocq/metadata.xml | 17 +- sci-mathematics/frama-c/metadata.xml | 28 +- sci-mathematics/gap-guava/metadata.xml | 5 +- sci-mathematics/gappa/metadata.xml | 22 +- sci-mathematics/gappalib-coq/metadata.xml | 15 +- sci-mathematics/giac/metadata.xml | 24 +- sci-mathematics/ltl2ba/metadata.xml | 3 - sci-mathematics/pff/metadata.xml | 17 +- sci-mathematics/why/metadata.xml | 32 +- sci-physics/LoopTools/metadata.xml | 2 +- sci-physics/abinit/ChangeLog | 16 + sci-physics/abinit/Manifest | 3 +- sci-physics/abinit/abinit-7.0.5.ebuild | 356 --------------------- .../{abinit-7.0.4.ebuild => abinit-7.2.2.ebuild} | 75 +++-- sci-physics/abinit/files/6.0.3-fftw.patch | 14 - .../abinit/files/6.12.1-libabinit_options.patch | 57 ---- sci-physics/atompaw/ChangeLog | 7 + ...aw-3.0.1.9.ebuild => atompaw-3.0.1.9-r1.ebuild} | 11 +- sci-physics/atompaw/metadata.xml | 11 +- sci-physics/atompaw2abinit/metadata.xml | 5 +- {sci-libs => sci-physics}/bigdft/ChangeLog | 23 +- sci-physics/bigdft/Manifest | 1 + .../bigdft/bigdft-1.7_pre24.ebuild | 37 +-- .../files/bigdft-1.7-dev.24-nolib_mods.patch | 14 +- sci-physics/elk/ChangeLog | 4 + sci-physics/elk/elk-1.4.22.ebuild | 2 +- sci-physics/herwig++/metadata.xml | 2 +- sci-physics/openmx/ChangeLog | 7 + sci-physics/openmx/Manifest | 2 + sci-physics/openmx/files/3.7-fortran_objects.patch | 15 + sci-physics/openmx/metadata.xml | 2 +- sci-physics/openmx/openmx-3.7.3.ebuild | 161 ++++++++++ sci-physics/thepeg/metadata.xml | 2 +- sci-visualization/gnuplot/ChangeLog | 3 + sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild | 2 +- sci-visualization/v_sim/metadata.xml | 3 - www-apps/py-swish-e/metadata.xml | 5 +- x11-libs/tr/metadata.xml | 3 - 163 files changed, 1278 insertions(+), 1264 deletions(-) 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 87D0B1381F3 for ; Mon, 8 Jul 2013 12:08:08 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 999E4E0A45; Mon, 8 Jul 2013 12:08:05 +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 0BB59E09FE for ; Mon, 8 Jul 2013 12:08:04 +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 6A22533E8B0 for ; Mon, 8 Jul 2013 12:08:03 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 09FA1E5458 for ; Mon, 8 Jul 2013 12:08:02 +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: <1371811471.e2667d72a9cda457057fc4531574c2634dc92387.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: e2667d72a9cda457057fc4531574c2634dc92387 X-VCS-Branch: master Date: Mon, 8 Jul 2013 12:08:02 +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: 18deda86-085c-4603-b60c-38109f538f0a X-Archives-Hash: 253a0d89fd6739b52ae2f1d4ea8da202 Message-ID: <20130708120802.A5eIXN4AM994D127lxNYQvdaliMX9KFROWEftx_ko2s@z> commit: e2667d72a9cda457057fc4531574c2634dc92387 Author: Justin Lecher gentoo org> AuthorDate: Fri Jun 21 10:44:31 2013 +0000 Commit: Justin Lecher gentoo org> CommitDate: Fri Jun 21 10:44:31 2013 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e2667d72 Merge branch 'master' into jlec * master: (29 commits) sci-chemistry/shiftx: Block shiftx2 at runtime sci-chemistry/shiftx: Fix patch and add patch for buffer overflow fix The announced, but forgotten, change in sci-libs/fox-4.1.2-r2 actually done. The announced, but forgotten, change in sci-libs/etsf_io-1.0.3-r2 actually done. sci-physics/abinit/files/6.12.3-gui-makefiles.tbz put back, its deletion was a mistake. sci-libs/trilinos: Version bump and rewrite sci-libs/coinor-clp: Version bump and patch for mpi For sci-libs/bigdft-abi and sci-physics/bigdft, filter LDFLAGS for cuda use not to break nvcc. To sci-libs/bigdft-abi and sci-physics/bigdft added dev-util/gdbus-codegen among dependencies. Spaces in the testing snippet of fortran code in sci-libs/bigdft-abi-1.0.4.ebuild protected from reformatting. fixed qt4 build fixing manifests big fixes of metadata and package sub-herd re-distribution sci-physics/openmx upgraded to 3.7.3 with some openMP and MPI C/F90 juggling, previous sci-physics/openmx-3.6 preserved for the time being. sci-chemistry/talosn: drop upstream path in favour of our sci-chemistry/modeller: Fix broken symlink, #473680 sci-chemistry/mics: New package sci-chemistry/talosn: New package Abinit & friends upgraded to sci-physics/abinit-7.2.2. BigDFT moved from sci-libs to sci-physics, sci-physics/abinit uses sci-libs/bigdft-abi instead. Usage of LIBDIR/finclude abandoned in favour of /usr/include, as mostly used upstream. Old files cleaned up. Version of bigdft bumped to 1.7_pre24, moved from sci-libs to sci-physics. No longer used as a library by sci-physics/abinit. Usage of LIBDIR/finclude abandoned in favour of /usr/include, as used upstream. ... app-text/dgs/metadata.xml | 3 - app-text/jabref/ChangeLog | 10 + ...jabref-2.10b.ebuild => jabref-2.10_beta.ebuild} | 8 +- app-vim/freefem++-syntax/metadata.xml | 7 +- app-vim/vim-gromacs/metadata.xml | 5 +- dev-db/cppdb/metadata.xml | 19 +- dev-libs/simclist/metadata.xml | 17 +- dev-ml/mlgmpidl/metadata.xml | 23 +- dev-ml/ocamlgraph/metadata.xml | 47 ++- dev-ml/zarith/metadata.xml | 20 +- dev-perl/opal-client/metadata.xml | 3 - dev-python/opal-client/metadata.xml | 5 +- dev-tcltk/img_rotate/metadata.xml | 5 +- dev-tcltk/togl/metadata.xml | 3 - media-gfx/librecad/ChangeLog | 6 + media-gfx/librecad/Manifest | 4 +- media-gfx/librecad/files/1.0.0_rc2-gcc4.6.patch | 38 --- .../files/librecad-1.0.0_rc2-version.patch | 11 - media-gfx/librecad/librecad-1.0.2.ebuild | 45 --- media-gfx/librecad/librecad-2.0.0_beta5.ebuild | 48 --- media-gfx/librecad/librecad-2.0.0_rc1.ebuild | 27 +- media-gfx/librecad/metadata.xml | 23 +- media-libs/OpenMOIV/metadata.xml | 3 - media-libs/libgfx/metadata.xml | 3 - profiles/package.mask | 6 + sci-biology/perlprimer/metadata.xml | 3 - sci-chemistry/GromacsWrapper/metadata.xml | 2 +- sci-chemistry/ball/metadata.xml | 2 +- sci-chemistry/burrow-owl/metadata.xml | 5 +- sci-chemistry/camshift/metadata.xml | 5 +- sci-chemistry/chemBuild/metadata.xml | 2 +- sci-chemistry/chimera-bin/metadata.xml | 2 +- sci-chemistry/chooch/metadata.xml | 5 +- sci-chemistry/cnsface/metadata.xml | 5 +- sci-chemistry/concoord/metadata.xml | 2 +- sci-chemistry/coot/metadata.xml | 3 - sci-chemistry/cs-rosetta/metadata.xml | 2 +- sci-chemistry/curvefit/metadata.xml | 2 +- sci-chemistry/direx/metadata.xml | 3 - sci-chemistry/dssp2pdb/metadata.xml | 3 - sci-chemistry/freeon/ChangeLog | 9 + ...ch => freeon-2012.05.03-no_internal_hdf5.patch} | 32 +- .../files/freeon-9999-no_internal_hdf5.patch | 25 ++ .../files/freeon-9999-no_internal_libs.patch | 47 --- sci-chemistry/freeon/freeon-2012.05.03.ebuild | 7 +- sci-chemistry/freeon/freeon-9999.ebuild | 7 +- sci-chemistry/hydronmr/metadata.xml | 2 +- sci-chemistry/jana2000/metadata.xml | 3 - sci-chemistry/jligand/metadata.xml | 5 +- sci-chemistry/ligplot+/metadata.xml | 2 +- sci-chemistry/mage/metadata.xml | 3 - sci-chemistry/mddnmr/metadata.xml | 5 +- sci-chemistry/mics/ChangeLog | 10 + sci-chemistry/mics/Manifest | 1 + .../{mgltools-autodocktools => mics}/metadata.xml | 0 sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild | 51 +++ sci-chemistry/modelfree/metadata.xml | 2 +- sci-chemistry/modeller/ChangeLog | 6 + ...odeller-9.12.ebuild => modeller-9.12-r1.ebuild} | 2 +- sci-chemistry/mtz2hkl/metadata.xml | 3 - sci-chemistry/mtz2sca/metadata.xml | 3 - sci-chemistry/nMOLDYN/ChangeLog | 12 + sci-chemistry/nMOLDYN/Manifest | 1 + sci-chemistry/{trajng => nMOLDYN}/metadata.xml | 0 sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild | 24 ++ sci-chemistry/phenix-bin/metadata.xml | 2 +- sci-chemistry/polygon/metadata.xml | 5 +- sci-chemistry/pymol-apbs-plugin/metadata.xml | 5 +- sci-chemistry/rosetta-tools/metadata.xml | 3 - sci-chemistry/rosetta/metadata.xml | 23 +- sci-chemistry/shiftx/ChangeLog | 7 + sci-chemistry/shiftx/files/1.1-Makefile.patch | 15 +- sci-chemistry/shiftx/files/1.1-bfr-overflow.patch | 16 + sci-chemistry/shiftx/metadata.xml | 3 - sci-chemistry/shiftx/shiftx-1.1.ebuild | 7 +- sci-chemistry/shiftx2/metadata.xml | 2 +- sci-chemistry/simpson/metadata.xml | 2 +- sci-chemistry/smmp/metadata.xml | 5 +- sci-chemistry/specView/metadata.xml | 2 +- sci-chemistry/ssp/metadata.xml | 2 +- sci-chemistry/talosn/ChangeLog | 16 + sci-chemistry/talosn/Manifest | 1 + .../metadata.xml | 0 .../talosn/talosn-4.01.2013.148.15.55-r2.ebuild | 68 ++++ sci-chemistry/ucsf-tools/metadata.xml | 2 +- sci-chemistry/unio/metadata.xml | 5 +- sci-libs/Cgraph/metadata.xml | 5 +- sci-libs/bigdft-abi/ChangeLog | 29 ++ sci-libs/bigdft-abi/Manifest | 1 + .../bigdft-abi-1.0.4.ebuild} | 78 +++-- .../files/bigdft-abi-1.0.4-tests.tar.bz2 | Bin 0 -> 402968 bytes sci-libs/bigdft/metadata.xml | 19 +- sci-libs/cnsface-scripts/metadata.xml | 3 - sci-libs/coinor-clp/ChangeLog | 6 + sci-libs/coinor-clp/Manifest | 2 +- ...-clp-1.15.0.ebuild => coinor-clp-1.15.1.ebuild} | 4 +- .../files/coinor-clp-1.15.1-mpi-header.patch | 12 + sci-libs/driftwood/metadata.xml | 5 +- sci-libs/etsf_io/ChangeLog | 13 +- ..._io-1.0.3-r1.ebuild => etsf_io-1.0.3-r2.ebuild} | 6 +- sci-libs/etsf_io/metadata.xml | 5 +- sci-libs/fox/ChangeLog | 14 +- ...patch => 4.1.2-r2-install-customizations.patch} | 4 +- .../{fox-4.1.2-r1.ebuild => fox-4.1.2-r2.ebuild} | 10 +- sci-libs/fox/metadata.xml | 19 +- sci-libs/libxc/ChangeLog | 11 +- sci-libs/libxc/Manifest | 2 +- ...libxc-1.1.0-r1.ebuild => libxc-1.2.0-r1.ebuild} | 26 +- .../{libxc-1.2.0.ebuild => libxc-2.0.1.ebuild} | 27 +- sci-libs/libxc/libxc-9999.ebuild | 27 +- sci-libs/libxc/metadata.xml | 5 +- sci-libs/med/metadata.xml | 5 +- sci-libs/msms/metadata.xml | 5 +- sci-libs/mumps/ChangeLog | 5 +- sci-libs/mumps/mumps-4.10.0-r2.ebuild | 5 +- sci-libs/pagmo/metadata.xml | 13 +- sci-libs/starparse/metadata.xml | 5 +- sci-libs/trilinos/ChangeLog | 7 +- sci-libs/trilinos/metadata.xml | 16 + sci-libs/trilinos/trilinos-11.2.3.ebuild | 186 +++++++++++ sci-libs/wannier90/ChangeLog | 7 + sci-libs/wannier90/metadata.xml | 5 +- ...annier90-1.2.ebuild => wannier90-1.2-r1.ebuild} | 0 sci-mathematics/alt-ergo/metadata.xml | 23 +- sci-mathematics/apron/metadata.xml | 31 +- sci-mathematics/flocq/metadata.xml | 17 +- sci-mathematics/frama-c/metadata.xml | 28 +- sci-mathematics/gap-guava/metadata.xml | 5 +- sci-mathematics/gappa/metadata.xml | 22 +- sci-mathematics/gappalib-coq/metadata.xml | 15 +- sci-mathematics/giac/metadata.xml | 24 +- sci-mathematics/ltl2ba/metadata.xml | 3 - sci-mathematics/pff/metadata.xml | 17 +- sci-mathematics/why/metadata.xml | 32 +- sci-physics/LoopTools/metadata.xml | 2 +- sci-physics/abinit/ChangeLog | 16 + sci-physics/abinit/Manifest | 3 +- sci-physics/abinit/abinit-7.0.5.ebuild | 356 --------------------- .../{abinit-7.0.4.ebuild => abinit-7.2.2.ebuild} | 75 +++-- sci-physics/abinit/files/6.0.3-fftw.patch | 14 - .../abinit/files/6.12.1-libabinit_options.patch | 57 ---- sci-physics/atompaw/ChangeLog | 7 + ...aw-3.0.1.9.ebuild => atompaw-3.0.1.9-r1.ebuild} | 11 +- sci-physics/atompaw/metadata.xml | 11 +- sci-physics/atompaw2abinit/metadata.xml | 5 +- {sci-libs => sci-physics}/bigdft/ChangeLog | 23 +- sci-physics/bigdft/Manifest | 1 + .../bigdft/bigdft-1.7_pre24.ebuild | 37 +-- .../files/bigdft-1.7-dev.24-nolib_mods.patch | 14 +- sci-physics/elk/ChangeLog | 4 + sci-physics/elk/elk-1.4.22.ebuild | 2 +- sci-physics/herwig++/metadata.xml | 2 +- sci-physics/openmx/ChangeLog | 7 + sci-physics/openmx/Manifest | 2 + sci-physics/openmx/files/3.7-fortran_objects.patch | 15 + sci-physics/openmx/metadata.xml | 2 +- sci-physics/openmx/openmx-3.7.3.ebuild | 161 ++++++++++ sci-physics/thepeg/metadata.xml | 2 +- sci-visualization/gnuplot/ChangeLog | 3 + sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild | 2 +- sci-visualization/v_sim/metadata.xml | 3 - www-apps/py-swish-e/metadata.xml | 5 +- x11-libs/tr/metadata.xml | 3 - 163 files changed, 1278 insertions(+), 1264 deletions(-)