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* virtual/blas: eigen needs the fortran useflag to provide blas.François Bissey2017-07-073-3/+3
| | | | | Package-Manager: portage-2.3.6 Closes: https://github.com/gentoo/sci/pull/795
* sci-libs/libmaus: Bump to EAPI 6Justin Lecher2017-07-072-3/+3
| | | | | Package-Manager: Portage-2.3.6-prefix, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-visualization/mayavi: committed to gentoo main repo.Benda Xu2017-07-034-168/+0
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* sci-mathematics/slepc: fix SRC_URIMatthias Maier2017-06-301-1/+1
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2
* sci-libs/atlas: version bump to 3.11.39Gergely Nagy2017-06-273-0/+300
| | | | | | Patch from upstream is required to build the shared library: https://sourceforge.net/p/math-atlas/bugs/260/ Closes: https://github.com/gentoo/sci/pull/794
* sci-libs/atlas: Sanitize default USE combinationJustin Lecher2017-06-263-4/+4
| | | | | | | Helps sorting out #794 Package-Manager: Portage-2.3.6-prefix, Repoman-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-geosciences/pydap_handlers_sql: Drop pacage due to dropped depsJustin Lecher2017-06-233-63/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-geosciences/pydap_handlers_cdms: Drop package due to masked depsJustin Lecher2017-06-233-48/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Drop www-client/casperjs due to broken revdepsJustin Lecher2017-06-237-54/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Add missing license for gamessJustin Lecher2017-06-231-0/+42
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-libs/itk: bump to 4.12.0tharvik2017-06-232-0/+137
| | | | | Package-Manager: Portage-2.3.5, Repoman-2.3.1 Closes: https://github.com/gentoo/sci/pull/792
* sci-libs/dealii: ebuild maintenanceMatthias Maier2017-06-181-2/+1
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2
* sci-chemistry/acpype: Move from treeAlexey Shvetsov2017-06-163-0/+42
| | | | Package-Manager: Portage-2.3.6, Repoman-2.3.2
* sci-libs/acml: fix missed opencl depAndrew Savchenko2017-06-101-0/+98
| | | | | | | | | | | | 1) acml is linked with opencl support: libclFFT.so.2.3.1, libclBLAS.so.2.3.0, libacml_bridge.so.1.1.28: libOpenCL.so.1 => not found 2) update to EAPI 6. Package-Manager: Portage-2.3.6, Repoman-2.3.2 Signed-off-by: Andrew Savchenko <bircoph@gentoo.org>
* sci-libs/openblas: remove redundant libdir from Libs in .pcBenda Xu2017-06-061-1/+1
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* numeric.eclass: use var reference in Libs and Cflags.Benda Xu2017-06-061-2/+2
| | | | Closes: https://github.com/gentoo/sci/issues/709
* sci-libs/cblas-reference: configure BLAS_LIBRARIES implicitlyBenda Xu2017-06-052-2/+0
| | | | | | | | | sci-libs/lapack-reference: configure BLAS_LIBRARIES implicitly cmake option USE_OPTIMIZED_BLAS uses pkg-config to figure out BLAS_LIBRARIES in Gentoo FindBLAS cmake patch. Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-libs/cblas-reference: guide cmake to find eselected blasBenda Xu2017-06-051-1/+1
| | | | | | | | | | same rational as commit e6181c66eac for lapack-reference. alternative.eclass blas.pc gives -L"${libdir}" -lxxx. The bare quotes confuses cmake parser. Escaping the quotes is tedious, but solves the problem. Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-libs/lapack-reference: guide cmake to find eselected blasBenda Xu2017-06-051-1/+1
| | | | | | | | alternative.eclass blas.pc gives -L"${libdir}" -lxxx. The bare quotes confuses cmake parser. Escaping the quotes is tedious, but solves the problem. Package-Manager: Portage-2.3.3, Repoman-2.3.1
* Update local USE descriptionJustin Lecher2017-06-041-6/+6
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-libs/pagmo: bump to pagmo2 and EAPI 6.Benda Xu2017-06-042-18/+18
| | | | | | Update the use flags. Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-libs/openblas: fix '??die' typos.Benda Xu2017-06-031-4/+4
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sys-cluster/openmpi: bump 2.0.3Justin Bronder2017-06-012-1/+1
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sys-cluster/openmpi: bump 1.10.7Justin Bronder2017-06-012-1/+1
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-libs/gmsh: Drop oldMarius Brehler2017-05-292-90/+0
| | | | | | Required petsc versions were removed from the overlay. Package-Manager: Portage-2.3.5, Repoman-2.3.1
* Update README.mdMarius Brehler2017-05-291-3/+3
| | | | | | s/gentoo-sci/gentoo/g Signed-off-by: Marius Brehler <marbre@linux.sungazer.de>
* dev-python/nvidia-ml-py: Remove from overlayMarius Brehler2017-05-295-76/+0
| | | | | | | A matching version of nvidia-cuda-gdk is required, which is no longer available via the overlay. Signed-off-by: Marius Brehler <marbre@linux.sungazer.de>
* sci-libs/libsc: Removed, moved to ::gentooMatthias Maier2017-05-265-254/+0
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* sci-libs/p4est: Remove, moved to ::gentooMatthias Maier2017-05-265-343/+0
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* dev-util/numdiff: Remove, moved to ::gentooMatthias Maier2017-05-264-101/+0
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* sci-physics/quinoa: fix depsChristoph Junghans2017-05-251-1/+1
| | | | | | Ref: quinoacomputing/quinoa#140 Package-Manager: Portage-2.3.5, Repoman-2.3.1
* sci-mathematics/slepc: ensure that environment is saneMatthias Maier2017-05-251-0/+7
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/libStatGen: version bump, use ${PV}Martin Mokrejš2017-05-253-1/+23
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/verifyBamID: another attempt at removing the -WerrorMartin Mokrejš2017-05-251-4/+3
| | | | | | | Somehow the sed calls do not work, disable -Werror append by defining the variable non-empty Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/verifyBamID: work around compile error with g++-7.1.0Martin Mokrejš2017-05-251-0/+3
| | | | | | https://github.com/statgen/verifyBamID/issues/7 Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/dealii: add support for slepcMatthias Maier2017-05-253-3/+10
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-mathematics/slepc: initial commitMatthias Maier2017-05-253-0/+83
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-mathematics/petsc: fix licenseMatthias Maier2017-05-254-55/+5
| | | | | | petsc 3.5 and newer is released under a two-clause BSD license Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/dealii: update metadataMatthias Maier2017-05-251-1/+1
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-mathematics/petsc: update metadataMatthias Maier2017-05-251-15/+19
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-mathematics/petsc: version bump to 3.6.5, major overhaulMatthias Maier2017-05-259-452/+53
| | | | | | | | | | | | | - bump to EAPI 6 - respect upstream decision to install in a monolithic way. Now, the full petsc distribution is installed into /usr/lib/petsc - add metis support Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/dealii: remove erroneous package versionMatthias Maier2017-05-253-5/+2
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/trilinos: fix installation pathsMatthias Maier2017-05-241-0/+5
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/ncbi-tools++: do not add $(PCRE_LIBS) unless necessary (from ↵Martin Mokrejš2017-05-238-198/+97
| | | | | | Aaron Ucko) Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/fast5: remove blank lineMartin Mokrejš2017-05-231-1/+0
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/fast5: removing KEYWORDs until src_install is fixedMartin Mokrejš2017-05-231-1/+18
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-libs/fast5: new packageMartin Mokrejš2017-05-234-0/+65
| | | | | | Will be needed for sci-biology/nanopolish (once ebuild arrives in sci tree). Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/cortex_var: fix compilation error on PREFIXed hostsMartin Mokrejš2017-05-221-1/+2
| | | | Package-Manager: Portage-2.3.5, Repoman-2.3.2
* sci-biology/SOAPdenovo2: add Debian manpageMartin Mokrejš2017-05-223-5/+25
| | | | | | https://manpages.debian.org/testing/soapdenovo2/soapdenovo2.1.en.html Package-Manager: Portage-2.3.5, Repoman-2.3.2
* Drop obsolete maskJustin Lecher2017-05-221-5/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>