From: "Justin Lecher" <jlec@gentoo.org>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:jlec commit in: /
Date: Wed, 26 Jun 2013 07:09:53 +0000 (UTC) [thread overview]
Message-ID: <1371811471.e2667d72a9cda457057fc4531574c2634dc92387.jlec@gentoo> (raw)
Message-ID: <20130626070953.04HhQ6fEwDKPTzQdy3YLU6ZUjjkWLaeOaVbldBO-f9I@z> (raw)
commit: e2667d72a9cda457057fc4531574c2634dc92387
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 21 10:44:31 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> 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(-)
next reply other threads:[~2013-06-26 7:10 UTC|newest]
Thread overview: 27+ messages / expand[flat|nested] mbox.gz Atom feed top
2013-07-11 20:26 Justin Lecher [this message]
2013-06-26 7:09 ` [gentoo-commits] proj/sci:jlec commit in: / Justin Lecher
2013-07-08 12:08 ` [gentoo-commits] proj/sci:master " Justin Lecher
-- strict thread matches above, loose matches on Subject: below --
2013-07-11 20:27 [gentoo-commits] proj/sci:vtk " Justin Lecher
2013-07-11 20:27 Justin Lecher
2013-07-11 20:27 Justin Lecher
2013-07-11 20:27 Justin Lecher
2013-07-11 20:27 Justin Lecher
2013-07-11 20:27 Justin Lecher
2013-07-11 20:27 Justin Lecher
2013-07-11 20:27 Justin Lecher
2013-07-11 20:27 Justin Lecher
2013-07-11 20:27 Justin Lecher
2013-07-11 20:27 Justin Lecher
2013-07-11 20:27 Justin Lecher
2013-07-11 20:27 Justin Lecher
2013-07-11 20:26 Justin Lecher
2013-07-11 20:26 Justin Lecher
2013-07-11 20:26 Justin Lecher
2013-07-11 20:26 Justin Lecher
2013-07-11 20:26 Justin Lecher
2013-07-11 20:26 Justin Lecher
2013-07-08 12:08 [gentoo-commits] proj/sci:master " Justin Lecher
2013-07-11 20:26 ` [gentoo-commits] proj/sci:vtk " Justin Lecher
2013-07-08 11:54 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-07-11 20:26 ` [gentoo-commits] proj/sci:vtk " Justin Lecher
2013-07-08 11:54 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-07-11 20:26 ` [gentoo-commits] proj/sci:vtk " Justin Lecher
2013-07-08 11:54 [gentoo-commits] proj/sci:ccp4 " Justin Lecher
2013-07-11 20:26 ` [gentoo-commits] proj/sci:vtk " Justin Lecher
2013-06-26 7:09 [gentoo-commits] proj/sci:jlec " Justin Lecher
2013-07-11 20:26 ` [gentoo-commits] proj/sci:vtk " Justin Lecher
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=1371811471.e2667d72a9cda457057fc4531574c2634dc92387.jlec@gentoo \
--to=jlec@gentoo.org \
--cc=gentoo-commits@lists.gentoo.org \
--cc=gentoo-dev@lists.gentoo.org \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox