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ESMTP id 2212C18730 for ; Sat, 18 Jan 2014 07:39:22 +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: <1389866729.37c147172bcabefca0bad3163e9e54919a781336.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: 37c147172bcabefca0bad3163e9e54919a781336 X-VCS-Branch: master Date: Sat, 18 Jan 2014 07:39:22 +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: 7490ddcd-668f-4b91-b2ca-046d0c3b8121 X-Archives-Hash: fef42d3c5dcb14ba6592178c8bcbd747 commit: 37c147172bcabefca0bad3163e9e54919a781336 Author: Andreas Schäfer gmx de> AuthorDate: Thu Jan 16 10:05:29 2014 +0000 Commit: Justin Lecher gentoo org> CommitDate: Thu Jan 16 10:05:29 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=37c14717 merge app-benchmarks/numbench/ChangeLog | 5 +- app-benchmarks/numbench/numbench-9999.ebuild | 4 +- app-portage/g-octave/ChangeLog | 5 +- app-portage/g-octave/g-octave-9999.ebuild | 5 +- app-text/jabref/ChangeLog | 51 ++- app-text/jabref/Manifest | 2 + app-text/jabref/jabref-2.10_beta-r1.ebuild | 65 +++ app-text/jabref/jabref-2.10_beta2-r1.ebuild | 69 +++ ...f-2.10_beta.ebuild => jabref-2.10_beta2.ebuild} | 12 +- ...ref-2.10_beta.ebuild => jabref-2.9.2-r1.ebuild} | 22 +- app-text/jabref/metadata.xml | 8 +- app-vim/vim-gromacs/ChangeLog | 6 +- app-vim/vim-gromacs/metadata.xml | 4 +- app-vim/vim-gromacs/vim-gromacs-9999.ebuild | 10 +- dev-java/gluegen/ChangeLog | 16 +- dev-java/gluegen/Manifest | 1 + .../gluegen/files/2.1.4_rc1-dont-copy-jars.patch | 17 + dev-java/gluegen/files/2.1.4_rc1-dont-strip.patch | 22 + .../files/2.1.4_rc1-dont-test-archive.patch | 16 + dev-java/gluegen/gluegen-2.1.4_rc1.ebuild | 74 +++ dev-java/jogl/ChangeLog | 12 +- dev-java/jogl/Manifest | 3 +- .../jogl/{jogl-1.1.1.ebuild => jogl-1.1.1a.ebuild} | 18 +- dev-java/jogl/jogl-2.1.4_rc1.ebuild | 74 +++ dev-lang/ispc/ChangeLog | 8 +- dev-lang/ispc/ispc-9999.ebuild | 16 +- dev-lang/julia/ChangeLog | 5 +- dev-lang/julia/julia-9999.ebuild | 9 +- dev-lang/julia/metadata.xml | 4 +- dev-lang/path64/ChangeLog | 5 +- dev-lang/path64/path64-9999.ebuild | 18 +- dev-libs/libcuda/ChangeLog | 8 +- dev-libs/libcuda/libcuda-9999.ebuild | 25 +- dev-libs/libcuda/metadata.xml | 8 +- dev-libs/libgdev/ChangeLog | 8 +- dev-libs/libgdev/libgdev-9999.ebuild | 28 +- dev-libs/libgdev/metadata.xml | 8 +- dev-python/RecSQL/ChangeLog | 5 +- dev-python/RecSQL/RecSQL-9999.ebuild | 4 +- dev-python/astropy/ChangeLog | 5 +- dev-python/astropy/astropy-9999.ebuild | 6 +- dev-python/astropysics/ChangeLog | 5 +- dev-python/astropysics/astropysics-9999.ebuild | 4 +- dev-python/dimensionful/ChangeLog | 5 +- dev-python/dimensionful/dimensionful-9999.ebuild | 4 +- dev-tex/pythontex/ChangeLog | 8 + .../pythontex}/metadata.xml | 2 +- dev-tex/pythontex/pythontex-0.12.ebuild | 24 +- dev-tex/pythontex/pythontex-9999.ebuild | 33 +- eclass/alternatives-2.eclass | 2 +- media-gfx/librecad/ChangeLog | 9 +- media-gfx/librecad/Manifest | 2 +- media-gfx/librecad/librecad-9999.ebuild | 4 +- media-gfx/librecad/metadata.xml | 20 +- profiles/package.use.mask | 7 + sci-biology/BG7/BG7-9999.ebuild | 22 +- sci-biology/BG7/ChangeLog | 5 +- .../omniorbpy => sci-biology/BG7}/metadata.xml | 0 sci-biology/artemis/ChangeLog | 6 +- sci-biology/artemis/artemis-9999.ebuild | 34 +- sci-biology/artemis/metadata.xml | 10 +- sci-biology/bamtools/ChangeLog | 6 +- sci-biology/bamtools/bamtools-9999.ebuild | 10 +- sci-biology/bamtools/metadata.xml | 12 +- sci-biology/blasr/ChangeLog | 5 +- sci-biology/blasr/blasr-9999.ebuild | 6 +- sci-biology/est2uni/ChangeLog | 6 +- sci-biology/est2uni/est2uni-9999.ebuild | 23 +- sci-biology/est2uni/metadata.xml | 10 +- sci-biology/fastx_toolkit/ChangeLog | 6 +- .../fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild | 9 +- .../fastx_toolkit}/metadata.xml | 0 sci-biology/genepop/ChangeLog | 6 +- sci-biology/genepop/Manifest | 2 +- ...{genepop-4.0.10.ebuild => genepop-4.2.1.ebuild} | 31 +- sci-biology/genepop/metadata.xml | 10 +- sci-biology/mira/ChangeLog | 7 +- sci-biology/mira/Manifest | 6 - sci-biology/mira/mira-3.4.0.1.ebuild | 62 --- sci-biology/mira/mira-3.4.1.1.ebuild | 61 --- sci-biology/mira/mira-3.9.15.ebuild | 64 --- sci-biology/mira/mira-3.9.9.ebuild | 61 --- sci-biology/mira/mira-4.0_rc2.ebuild | 80 ---- sci-biology/mira/mira-4.0_rc4.ebuild | 6 +- sci-biology/miranda/ChangeLog | 6 +- sci-biology/miranda/metadata.xml | 10 +- sci-biology/miranda/miranda-3.3a.ebuild | 4 +- sci-biology/mne-python/ChangeLog | 8 + .../mne-python}/metadata.xml | 0 sci-biology/mne-python/mne-python-0.7.ebuild | 56 +-- sci-biology/mne-python/mne-python-9999.ebuild | 56 +-- sci-biology/mosaik/ChangeLog | 6 +- sci-biology/mosaik/Manifest | 1 - sci-biology/mosaik/metadata.xml | 10 +- sci-biology/mosaik/mosaik-1.1.0021.ebuild | 40 -- sci-biology/mosaik/mosaik-2.1.33.ebuild | 38 +- sci-biology/mosaik/mosaik-9999.ebuild | 36 +- sci-biology/mrfast/ChangeLog | 9 + sci-biology/mrfast/Manifest | 2 +- .../mrfast-2.1.0.3-disc_buffer_overflow.patch | 52 --- sci-biology/mrfast/metadata.xml | 10 +- ...mrfast-2.1.0.3.ebuild => mrfast-2.6.0.1.ebuild} | 23 +- sci-biology/mrsfast/ChangeLog | 8 + sci-biology/mrsfast/Manifest | 2 +- sci-biology/mrsfast/metadata.xml | 10 +- sci-biology/mrsfast/mrsfast-2.3.0.2.ebuild | 30 -- .../mrsfast-2.6.0.4.ebuild} | 25 +- sci-biology/psychopy/ChangeLog | 5 +- sci-biology/psychopy/psychopy-9999.ebuild | 10 +- sci-biology/pybrain/ChangeLog | 5 +- sci-biology/pybrain/pybrain-9999.ebuild | 7 +- sci-biology/pysurfer/ChangeLog | 8 + .../pysurfer}/metadata.xml | 0 sci-biology/pysurfer/pysurfer-0.4.ebuild | 14 +- sci-biology/pysurfer/pysurfer-9999.ebuild | 16 +- sci-biology/staden/ChangeLog | 6 +- sci-biology/staden/metadata.xml | 10 +- sci-biology/staden/staden-2.0.0_beta9.ebuild | 4 +- sci-biology/staden/staden-9999.ebuild | 70 ++- sci-biology/symap/ChangeLog | 5 +- .../omniorbpy => sci-biology/symap}/metadata.xml | 0 sci-biology/symap/symap-4.0.ebuild | 19 +- sci-chemistry/GromacsWrapper/ChangeLog | 5 +- .../GromacsWrapper/GromacsWrapper-9999.ebuild | 10 +- sci-chemistry/ball/ChangeLog | 5 +- sci-chemistry/ball/ball-9999.ebuild | 4 +- sci-chemistry/bist/ChangeLog | 6 +- sci-chemistry/bist/bist-0.5.1-r1.ebuild | 6 +- sci-chemistry/bist/metadata.xml | 8 +- sci-chemistry/chemBuild/ChangeLog | 5 +- sci-chemistry/chemBuild/chemBuild-1.0.3.ebuild | 4 +- sci-chemistry/drawxtl/ChangeLog | 9 +- sci-chemistry/drawxtl/Manifest | 4 +- .../{drawxtl-44.ebuild => drawxtl-45.ebuild} | 40 +- .../{drawxtl-54.ebuild => drawxtl-55.ebuild} | 30 +- sci-chemistry/drawxtl/files/54-gcc44.patch | 11 - sci-chemistry/drawxtl/files/54-ldflags.patch | 11 - .../{44-gentoo.patch => drawxtl-45-gentoo.patch} | 40 +- .../{54-gentoo.patch => drawxtl-55-gentoo.patch} | 35 +- sci-chemistry/drawxtl/metadata.xml | 4 +- sci-chemistry/freeon/ChangeLog | 6 +- sci-chemistry/freeon/freeon-9999.ebuild | 13 +- sci-chemistry/freeon/metadata.xml | 2 +- sci-chemistry/gromacs/ChangeLog | 10 +- sci-chemistry/gromacs/gromacs-4.6.9999.ebuild | 10 +- sci-chemistry/gromacs/gromacs-5.0_beta1.ebuild | 8 +- sci-chemistry/gromacs/gromacs-9999.ebuild | 8 +- sci-chemistry/hydronmr/ChangeLog | 5 +- sci-chemistry/hydronmr/hydronmr-7c.ebuild | 4 +- sci-chemistry/mtz2hkl/ChangeLog | 6 +- sci-chemistry/mtz2hkl/metadata.xml | 2 +- sci-chemistry/mtz2hkl/mtz2hkl-0.3.ebuild | 17 +- sci-chemistry/mtz2sca/ChangeLog | 6 +- sci-chemistry/mtz2sca/metadata.xml | 2 +- sci-chemistry/mtz2sca/mtz2sca-0.3.ebuild | 17 +- sci-chemistry/openbabel-java/ChangeLog | 5 +- .../openbabel-java/openbabel-java-9999.ebuild | 15 +- sci-chemistry/openbabel-perl/ChangeLog | 5 +- .../openbabel-perl/openbabel-perl-9999.ebuild | 6 +- sci-chemistry/openbabel-python/ChangeLog | 5 +- .../openbabel-python/openbabel-python-9999.ebuild | 5 +- sci-chemistry/openbabel-ruby/ChangeLog | 5 +- .../openbabel-ruby/openbabel-ruby-9999.ebuild | 7 +- sci-chemistry/openbabel/ChangeLog | 6 +- sci-chemistry/openbabel/metadata.xml | 18 +- sci-chemistry/openbabel/openbabel-9999.ebuild | 9 +- sci-chemistry/pesto/ChangeLog | 9 + sci-chemistry/{burrow-owl => pesto}/metadata.xml | 0 sci-chemistry/pesto/pesto-9999.ebuild | 29 ++ sci-chemistry/shiftx/ChangeLog | 5 +- sci-chemistry/shiftx/shiftx-1.1.ebuild | 16 +- sci-chemistry/specView/ChangeLog | 5 +- sci-chemistry/specView/specView-1.0.3.ebuild | 4 +- sci-chemistry/wxmacmolplt/ChangeLog | 19 - sci-chemistry/wxmacmolplt/Manifest | 2 - .../wxmacmolplt/files/wxmacmolplt-7.4.3-glew.patch | 12 - sci-chemistry/wxmacmolplt/metadata.xml | 11 - sci-chemistry/wxmacmolplt/wxmacmolplt-7.4.3.ebuild | 44 -- sci-chemistry/wxmacmolplt/wxmacmolplt-7.5.ebuild | 44 -- sci-electronics/tnt/ChangeLog | 6 +- sci-electronics/tnt/Manifest | 2 +- .../tnt/files/tnt-1.2.2-autotools.patch | 277 ++++++++++++ sci-electronics/tnt/metadata.xml | 2 +- sci-electronics/tnt/tnt-1.2.2.ebuild | 40 +- sci-libs/dealii/ChangeLog | 9 + sci-libs/dealii/Manifest | 2 + .../{dealii-8.0.0.ebuild => dealii-8.1.0.ebuild} | 0 sci-libs/dealii/dealii-9999.ebuild | 46 +- sci-libs/dealii/metadata.xml | 42 +- sci-libs/fftw/ChangeLog | 5 +- sci-libs/fftw/fftw-9999.ebuild | 4 +- sci-libs/fgsl/ChangeLog | 6 +- sci-libs/fgsl/fgsl-0.9.3.ebuild | 30 +- sci-libs/fgsl/fgsl-0.9.4.ebuild | 29 +- sci-libs/fgsl/metadata.xml | 12 +- sci-libs/itk/ChangeLog | 5 +- sci-libs/itk/metadata.xml | 20 +- sci-libs/nibabel/ChangeLog | 8 + sci-libs/nibabel/metadata.xml | 18 +- sci-libs/nibabel/nibabel-1.3.0.ebuild | 4 +- sci-libs/nibabel/nibabel-9999.ebuild | 8 +- sci-libs/nipy/ChangeLog | 8 + sci-libs/nipy/metadata.xml | 12 +- sci-libs/nipy/nipy-0.3.0.ebuild | 10 +- sci-libs/nipy/nipy-9999.ebuild | 12 +- sci-libs/nipype/ChangeLog | 8 + sci-libs/nipype/metadata.xml | 12 +- sci-libs/nipype/nipype-9999.ebuild | 9 +- sci-libs/openblas/ChangeLog | 6 +- sci-libs/openblas/metadata.xml | 12 +- sci-libs/openblas/openblas-9999.ebuild | 19 +- sci-libs/openlibm/ChangeLog | 6 +- sci-libs/openlibm/metadata.xml | 4 +- sci-libs/openlibm/openlibm-9999.ebuild | 16 +- sci-libs/pagmo/ChangeLog | 8 +- sci-libs/pagmo/metadata.xml | 10 +- sci-libs/pagmo/pagmo-9999.ebuild | 20 +- sci-libs/pmx/ChangeLog | 10 + sci-libs/pmx/metadata.xml | 13 + sci-libs/pmx/pmx-9999.ebuild | 26 ++ sci-libs/pydicom/ChangeLog | 8 + .../omniorbpy => sci-libs/pydicom}/metadata.xml | 0 sci-libs/pydicom/pydicom-0.9.8.ebuild | 6 +- sci-libs/trilinos/ChangeLog | 9 +- sci-libs/trilinos/metadata.xml | 64 +-- sci-libs/trilinos/trilinos-11.0.3.ebuild | 11 +- sci-libs/trilinos/trilinos-11.4.2.ebuild | 4 +- sci-libs/vtk/ChangeLog | 495 +++++++++++++++++++++ sci-libs/vtk/Manifest | 2 + sci-libs/vtk/files/vtk-6.0.0-install.patch | 19 + sci-libs/vtk/files/vtk-6.0.0-netcdf.patch | 75 ++++ sci-libs/vtk/files/vtk-6.0.0-system.patch | 27 ++ sci-libs/vtk/files/vtk-6.0.0-vtkpython.patch | 12 + sci-libs/vtk/metadata.xml | 19 + sci-libs/vtk/vtk-6.0.0.ebuild | 321 +++++++++++++ sci-mathematics/cipi/ChangeLog | 5 +- sci-mathematics/cipi/Manifest | 1 + sci-mathematics/cipi/cipi-1.0.ebuild | 9 +- sci-mathematics/cipi/metadata.xml | 12 +- sci-mathematics/petsc/ChangeLog | 6 +- sci-mathematics/petsc/Manifest | 1 - sci-mathematics/petsc/metadata.xml | 2 + sci-mathematics/petsc/petsc-3.3_p5.ebuild | 223 ---------- sci-mathematics/petsc/petsc-3.4.2.ebuild | 22 +- .../scilab/files/scilab-5.5.0_beta1-nogui.patch | 13 + sci-mathematics/scilab/scilab-5.5.0_beta1.ebuild | 64 ++- sci-misc/elmer-meta/ChangeLog | 6 +- sci-misc/elmer-meta/elmer-meta-6.0_p4651.ebuild | 5 +- sci-misc/elmer-meta/elmer-meta-9999.ebuild | 5 +- sci-misc/simx/ChangeLog | 6 +- sci-misc/simx/metadata.xml | 2 +- sci-misc/simx/simx-0.1.ebuild | 16 +- sci-misc/simx/simx-9999.ebuild | 18 +- sci-physics/geant-vmc/ChangeLog | 13 +- sci-physics/geant-vmc/Manifest | 1 + sci-physics/geant-vmc/geant-vmc-4.2.14b.ebuild | 14 +- ...-vmc-4.2.14b.ebuild => geant-vmc-4.2.15.ebuild} | 13 +- sci-physics/geant-vmc/metadata.xml | 10 +- sci-physics/root/ChangeLog | 5 +- sci-physics/root/root-9999.ebuild | 4 +- sci-visualization/labplot/ChangeLog | 8 + sci-visualization/labplot/labplot-9999.ebuild | 5 +- sci-visualization/labplot/metadata.xml | 2 +- sys-cluster/charm/ChangeLog | 20 +- sys-cluster/charm/Manifest | 2 +- sys-cluster/charm/charm-6.5.1-r2.ebuild | 209 --------- ...m-6.5.1-r3.ebuild => charm-6.6.0_rc1-r1.ebuild} | 48 +- sys-cluster/lustre/ChangeLog | 5 +- sys-cluster/lustre/lustre-9999.ebuild | 6 +- sys-cluster/nullmpi/ChangeLog | 5 +- sys-cluster/nullmpi/nullmpi-9999.ebuild | 8 +- x11-misc/envytools/ChangeLog | 5 +- x11-misc/envytools/envytools-9999.ebuild | 4 +- 273 files changed, 3174 insertions(+), 2143 deletions(-) diff --cc profiles/package.use.mask index 9e3e91a,136fec3..f7f1044 --- a/profiles/package.use.mask +++ b/profiles/package.use.mask @@@ -16,10 -16,13 +16,17 @@@ ## =media-video/mplayer-0.90_pre5-r1 foo # + # Justin Lecher (06 Jan 2014) + # Missing dep dev-python/scikits-cuda + sci-biology/mne-python cuda + +# Andreas Schäfer (21 Nov 2013) +# cuda only works on x86 and amd64 +sys-cluster/openmpi -cuda + + # sci-libs/parmetis-4* is masked + sci-libs/dealii metis + # Christoph Junghans (05 Nov 2013) # gui sandbox error dev-lang/conceptual gui