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commit: efdfeb5e791069bf25575029a48cd572cb3bd792 |
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Author: Nicolas Bock <nicolasbock <AT> gmail <DOT> com> |
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AuthorDate: Sat Jan 25 22:37:07 2014 +0000 |
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Commit: Nicolas Bock <nicolasbock <AT> gmail <DOT> com> |
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CommitDate: Sat Jan 25 22:37:07 2014 +0000 |
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URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=efdfeb5e |
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Merge branch 'master' of github.com:gentoo-science/sci |
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CONTRIBUTING.md | 7 + |
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app-admin/eselect/ChangeLog | 11 +- |
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...elect-1.3.8-r100.ebuild => eselect-9999.ebuild} | 26 +- |
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dev-cpp/eigen/ChangeLog | 8 +- |
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dev-cpp/eigen/Manifest | 1 + |
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.../{eigen-9999.ebuild => eigen-3.2.0-r1.ebuild} | 11 +- |
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dev-cpp/eigen/metadata.xml | 14 +- |
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dev-lang/julia/julia-9999.ebuild | 18 +- |
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dev-lang/vtune/ChangeLog | 2 +- |
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dev-libs/asmjit/ChangeLog | 2 +- |
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dev-perl/Bio-BigFile/ChangeLog | 2 +- |
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dev-python/opal-client/ChangeLog | 2 +- |
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dev-python/pythonocc/ChangeLog | 8 +- |
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eclass/alternatives-2.eclass | 147 ++++-- |
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licenses/HSL | 222 --------- |
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media-gfx/librecad/ChangeLog | 3 + |
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media-gfx/librecad/Manifest | 1 + |
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profiles/package.mask | 1 + |
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profiles/package.use.mask | 9 +- |
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sci-biology/YASRA/ChangeLog | 2 +- |
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sci-biology/clover/ChangeLog | 2 +- |
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sci-biology/cutadapt/ChangeLog | 2 +- |
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sci-biology/fastx_toolkit/ChangeLog | 11 +- |
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sci-biology/fastx_toolkit/Manifest | 2 +- |
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...0.0.13.2.ebuild => fastx_toolkit-0.0.14.ebuild} | 7 +- |
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sci-biology/lastz/ChangeLog | 4 +- |
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sci-biology/mrfast/ChangeLog | 2 +- |
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sci-biology/mrsfast/ChangeLog | 2 +- |
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.../files/ncbi-tools++-12.0.0-as-needed.patch | 555 +++++++++++---------- |
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.../files/ncbi-tools++-12.0.0-conf-opts.patch | 183 +------ |
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.../ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 14 +- |
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sci-biology/sequin/ChangeLog | 2 +- |
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sci-biology/tablet-bin/ChangeLog | 13 +- |
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sci-biology/tablet-bin/Manifest | 2 +- |
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...3.05.17.ebuild => tablet-bin-1.13.12.17.ebuild} | 5 +- |
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sci-chemistry/avogadro2/ChangeLog | 13 + |
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sci-chemistry/avogadro2/Manifest | 1 + |
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sci-chemistry/avogadro2/avogadro2-0.7.2.ebuild | 48 ++ |
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sci-chemistry/{coot => avogadro2}/metadata.xml | 4 +- |
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sci-chemistry/chimera-bin/ChangeLog | 9 +- |
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sci-chemistry/chimera-bin/Manifest | 2 + |
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...era-bin-1.8.ebuild => chimera-bin-1.8.1.ebuild} | 2 +- |
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sci-chemistry/drawxtl/ChangeLog | 2 +- |
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sci-chemistry/mddnmr/ChangeLog | 2 +- |
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sci-chemistry/modeller/ChangeLog | 2 +- |
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sci-chemistry/nmrpipe/ChangeLog | 10 +- |
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sci-chemistry/pesto/ChangeLog | 12 + |
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sci-chemistry/{burrow-owl => pesto}/metadata.xml | 0 |
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sci-chemistry/pesto/pesto-9999.ebuild | 38 ++ |
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sci-chemistry/phenix-bin/ChangeLog | 2 +- |
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sci-chemistry/polygon/ChangeLog | 2 +- |
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sci-chemistry/pymol/ChangeLog | 8 +- |
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sci-chemistry/pymol/Manifest | 2 +- |
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sci-chemistry/pymol/pymol-9999.ebuild | 13 +- |
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sci-chemistry/simpson/ChangeLog | 2 +- |
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sci-chemistry/specView/ChangeLog | 2 +- |
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sci-chemistry/unio/ChangeLog | 7 +- |
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sci-chemistry/unio/Manifest | 1 + |
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.../{unio-2.0.2-r1.ebuild => unio-2.0.3.ebuild} | 4 +- |
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sci-geosciences/pydap/ChangeLog | 2 +- |
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sci-geosciences/pydap_handlers_hdf5/ChangeLog | 2 +- |
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sci-geosciences/pydap_handlers_netcdf/ChangeLog | 2 +- |
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sci-geosciences/pydap_handlers_sql/ChangeLog | 2 +- |
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sci-geosciences/pydap_responses_kml/ChangeLog | 2 +- |
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sci-geosciences/pydap_responses_matlab/ChangeLog | 2 +- |
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sci-geosciences/pydap_responses_netcdf/ChangeLog | 2 +- |
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sci-geosciences/pydap_responses_wms/ChangeLog | 2 +- |
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sci-libs/avogadro-libs/ChangeLog | 18 - |
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sci-libs/avogadro-libs/Manifest | 1 - |
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sci-libs/avogadro-libs/avogadro-libs-0.6.0.ebuild | 46 -- |
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.../files/avogadro-libs-0.6.0-underlinking.patch | 14 - |
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sci-libs/avogadro-libs/metadata.xml | 14 - |
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sci-libs/cblas-reference/ChangeLog | 6 +- |
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.../cblas-reference-20110218.ebuild | 5 +- |
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sci-libs/chemkit/ChangeLog | 10 - |
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sci-libs/chemkit/Manifest | 1 - |
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sci-libs/chemkit/chemkit-0.1.ebuild | 55 -- |
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sci-libs/chemkit/metadata.xml | 11 - |
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sci-libs/coinhsl/ChangeLog | 18 - |
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sci-libs/coinhsl/Manifest | 2 - |
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sci-libs/coinhsl/coinhsl-2012.12.21.ebuild | 36 -- |
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sci-libs/coinhsl/coinhsl-2013.06.18.ebuild | 32 -- |
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sci-libs/coinhsl/metadata.xml | 12 - |
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sci-libs/coinor-alps/ChangeLog | 30 -- |
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sci-libs/coinor-alps/Manifest | 1 - |
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sci-libs/coinor-alps/coinor-alps-1.4.7.ebuild | 67 --- |
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sci-libs/coinor-alps/metadata.xml | 13 - |
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sci-libs/coinor-bcp/ChangeLog | 21 - |
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sci-libs/coinor-bcp/Manifest | 1 - |
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sci-libs/coinor-bcp/coinor-bcp-1.3.7.ebuild | 56 --- |
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sci-libs/coinor-bcp/metadata.xml | 13 - |
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sci-libs/coinor-bcps/ChangeLog | 21 - |
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sci-libs/coinor-bcps/Manifest | 1 - |
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sci-libs/coinor-bcps/coinor-bcps-0.93.8.ebuild | 67 --- |
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sci-libs/coinor-bcps/metadata.xml | 13 - |
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sci-libs/coinor-blis/ChangeLog | 30 -- |
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sci-libs/coinor-blis/Manifest | 1 - |
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sci-libs/coinor-blis/coinor-blis-0.93.8.ebuild | 65 --- |
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sci-libs/coinor-blis/metadata.xml | 12 - |
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sci-libs/coinor-bonmin/ChangeLog | 24 - |
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sci-libs/coinor-bonmin/Manifest | 1 - |
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sci-libs/coinor-bonmin/coinor-bonmin-1.7.3.ebuild | 72 --- |
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sci-libs/coinor-bonmin/metadata.xml | 13 - |
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sci-libs/coinor-buildtools/ChangeLog | 15 - |
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.../coinor-buildtools-0.7.9.ebuild | 38 -- |
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sci-libs/coinor-buildtools/metadata.xml | 9 - |
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sci-libs/coinor-cbc/ChangeLog | 39 -- |
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sci-libs/coinor-cbc/Manifest | 1 - |
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sci-libs/coinor-cbc/coinor-cbc-2.8.7.ebuild | 83 --- |
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sci-libs/coinor-cbc/metadata.xml | 11 - |
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sci-libs/coinor-cgl/ChangeLog | 36 -- |
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sci-libs/coinor-cgl/Manifest | 1 - |
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sci-libs/coinor-cgl/coinor-cgl-0.58.4.ebuild | 73 --- |
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sci-libs/coinor-cgl/metadata.xml | 12 - |
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sci-libs/coinor-clp/ChangeLog | 43 -- |
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sci-libs/coinor-clp/Manifest | 1 - |
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sci-libs/coinor-clp/coinor-clp-1.15.5.ebuild | 112 ----- |
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.../files/coinor-clp-1.15.1-mpi-header.patch | 12 - |
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sci-libs/coinor-clp/metadata.xml | 20 - |
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sci-libs/coinor-couenne/ChangeLog | 21 - |
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sci-libs/coinor-couenne/Manifest | 1 - |
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.../coinor-couenne/coinor-couenne-0.4.6.ebuild | 59 --- |
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sci-libs/coinor-couenne/metadata.xml | 12 - |
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sci-libs/coinor-cppad/ChangeLog | 37 -- |
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sci-libs/coinor-cppad/Manifest | 1 - |
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sci-libs/coinor-cppad/coinor-cppad-20131207.ebuild | 54 -- |
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sci-libs/coinor-cppad/metadata.xml | 14 - |
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sci-libs/coinor-csdp/ChangeLog | 12 - |
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sci-libs/coinor-csdp/Manifest | 1 - |
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sci-libs/coinor-csdp/coinor-csdp-6.1.1.ebuild | 100 ---- |
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sci-libs/coinor-csdp/metadata.xml | 16 - |
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sci-libs/coinor-dip/ChangeLog | 9 - |
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sci-libs/coinor-dip/Manifest | 1 - |
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sci-libs/coinor-dip/coinor-dip-0.83.2.ebuild | 62 --- |
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sci-libs/coinor-dip/metadata.xml | 14 - |
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sci-libs/coinor-dylp/ChangeLog | 21 - |
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sci-libs/coinor-dylp/Manifest | 1 - |
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sci-libs/coinor-dylp/coinor-dylp-1.9.3.ebuild | 66 --- |
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sci-libs/coinor-dylp/metadata.xml | 12 - |
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sci-libs/coinor-flopcpp/ChangeLog | 21 - |
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sci-libs/coinor-flopcpp/Manifest | 1 - |
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.../coinor-flopcpp/coinor-flopcpp-1.1.6.ebuild | 67 --- |
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sci-libs/coinor-flopcpp/metadata.xml | 14 - |
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sci-libs/coinor-mp/ChangeLog | 24 - |
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sci-libs/coinor-mp/Manifest | 1 - |
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sci-libs/coinor-mp/coinor-mp-1.7.5.ebuild | 56 --- |
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sci-libs/coinor-mp/metadata.xml | 11 - |
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sci-libs/coinor-netlib/ChangeLog | 25 - |
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sci-libs/coinor-netlib/Manifest | 1 - |
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sci-libs/coinor-netlib/coinor-netlib-1.2.6.ebuild | 23 - |
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sci-libs/coinor-netlib/metadata.xml | 9 - |
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sci-libs/coinor-os/ChangeLog | 15 - |
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sci-libs/coinor-os/Manifest | 1 - |
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sci-libs/coinor-os/coinor-os-2.8.2.ebuild | 67 --- |
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sci-libs/coinor-os/metadata.xml | 11 - |
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sci-libs/coinor-osi/ChangeLog | 33 -- |
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sci-libs/coinor-osi/Manifest | 1 - |
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sci-libs/coinor-osi/coinor-osi-0.106.4.ebuild | 76 --- |
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sci-libs/coinor-osi/metadata.xml | 15 - |
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sci-libs/coinor-sample/ChangeLog | 43 -- |
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sci-libs/coinor-sample/Manifest | 1 - |
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sci-libs/coinor-sample/coinor-sample-1.2.9.ebuild | 23 - |
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sci-libs/coinor-sample/metadata.xml | 9 - |
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sci-libs/coinor-smi/ChangeLog | 9 - |
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sci-libs/coinor-smi/Manifest | 1 - |
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sci-libs/coinor-smi/coinor-smi-0.93.3.ebuild | 69 --- |
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sci-libs/coinor-smi/metadata.xml | 18 - |
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sci-libs/coinor-symphony/ChangeLog | 33 -- |
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sci-libs/coinor-symphony/Manifest | 1 - |
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.../coinor-symphony/coinor-symphony-5.5.6.ebuild | 89 ---- |
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sci-libs/coinor-symphony/metadata.xml | 18 - |
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sci-libs/coinor-utils/ChangeLog | 39 -- |
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sci-libs/coinor-utils/Manifest | 1 - |
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sci-libs/coinor-utils/coinor-utils-2.9.10.ebuild | 85 ---- |
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sci-libs/coinor-utils/metadata.xml | 15 - |
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sci-libs/coinor-vol/ChangeLog | 24 - |
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sci-libs/coinor-vol/Manifest | 1 - |
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sci-libs/coinor-vol/coinor-vol-1.4.3.ebuild | 71 --- |
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sci-libs/coinor-vol/metadata.xml | 10 - |
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sci-libs/ipopt/ChangeLog | 40 -- |
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sci-libs/ipopt/Manifest | 1 - |
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sci-libs/ipopt/files/ipopt-3.11.2-mpi-header.patch | 14 - |
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sci-libs/ipopt/ipopt-3.11.6.ebuild | 100 ---- |
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sci-libs/ipopt/metadata.xml | 18 - |
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sci-libs/lemon/ChangeLog | 30 -- |
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sci-libs/lemon/Manifest | 1 - |
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sci-libs/lemon/lemon-1.3.ebuild | 75 --- |
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sci-libs/lemon/metadata.xml | 23 - |
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sci-libs/libgeodecomp/Manifest | 1 + |
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...comp-0.2.0.ebuild => libgeodecomp-0.3.1.ebuild} | 0 |
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sci-libs/libxc/ChangeLog | 2 +- |
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sci-libs/magma/ChangeLog | 52 -- |
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sci-libs/magma/Manifest | 1 - |
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.../magma/files/magma-1.2.1-no-cuda-driver.patch | 38 -- |
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sci-libs/magma/magma-1.4.0.ebuild | 126 ----- |
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sci-libs/magma/metadata.xml | 15 - |
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sci-libs/mkl/ChangeLog | 2 +- |
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sci-libs/msms/ChangeLog | 4 +- |
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sci-libs/openlibm/ChangeLog | 4 + |
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.../openlibm/files/openlibm-extras-soname.patch | 11 - |
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sci-libs/openlibm/files/openlibm-soname.patch | 11 - |
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sci-libs/openlibm/openlibm-9999.ebuild | 10 +- |
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sci-libs/scalapack/ChangeLog | 8 +- |
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...pack-2.0.2.ebuild => scalapack-2.0.2-r1.ebuild} | 4 +- |
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sci-libs/silo/Manifest | 1 + |
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sci-libs/silo/files/silo-4.9.1-qtlibs.patch | 66 +++ |
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sci-libs/silo/metadata.xml | 18 + |
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sci-libs/silo/silo-4.9.1.ebuild | 35 ++ |
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.../gappalib-coq/gappalib-coq-0.18.0.ebuild | 2 +- |
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sci-mathematics/mdp/ChangeLog | 2 +- |
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sci-misc/nltk/ChangeLog | 2 +- |
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skel.ChangeLog | 2 +- |
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skel.ebuild | 2 +- |
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skel.metadata.xml | 1 - |
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sys-cluster/openmpi/Manifest | 1 + |
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sys-cluster/openmpi/metadata.xml | 2 + |
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.../{openmpi-1.6.5.ebuild => openmpi-1.7.3.ebuild} | 27 +- |
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sys-cluster/pyslice/ChangeLog | 2 +- |
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virtual/blas/ChangeLog | 6 +- |
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.../blas/{blas-2.1.ebuild => blas-2.1-r1.ebuild} | 19 +- |
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virtual/lapack/ChangeLog | 6 +- |
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.../{lapack-3.4.ebuild => lapack-3.4-r1.ebuild} | 18 +- |
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virtual/lapack/metadata.xml | 4 +- |
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223 files changed, 916 insertions(+), 4253 deletions(-) |
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