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 1C7911381F3 for ; Sat, 22 Jun 2013 10:49:27 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 9A0D2E0A52; Sat, 22 Jun 2013 10:49:26 +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 2743EE0A52 for ; Sat, 22 Jun 2013 10:49:26 +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 1288333E679 for ; Sat, 22 Jun 2013 10:49:25 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id A2AD5E545C for ; Sat, 22 Jun 2013 10:49:23 +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: <1371898140.cce50ebf51440b0d0b894465e42b13f88f4f0072.jlec@gentoo> Subject: [gentoo-commits] proj/sci:fixing commit in: / X-VCS-Repository: proj/sci X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: cce50ebf51440b0d0b894465e42b13f88f4f0072 X-VCS-Branch: fixing Date: Sat, 22 Jun 2013 10:49:23 +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: 7bf597eb-5948-403e-9319-25cd9c2fb198 X-Archives-Hash: d3872b504578c363911102d98e23bbd0 commit: cce50ebf51440b0d0b894465e42b13f88f4f0072 Author: Justin Lecher gentoo org> AuthorDate: Sat Jun 22 10:49:00 2013 +0000 Commit: Justin Lecher gentoo 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 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 +talosn-4.01.2013.148.15.55.ebuild, +metadata.xml: New package --