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* sci-libs/dealii: bump patch level to 9.1.1Matthias Maier2019-08-012-2/+2
| | | | | Package-Manager: Portage-2.3.69, Repoman-2.3.16 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-libs/openblas: merge into ::gentoo and remove from overlay.Benda Xu2019-07-2511-1179/+0
| | | | | | | | | | | | | Closes: https://github.com/gentoo/sci/issues/917 Closes: https://github.com/gentoo/sci/issues/888 Closes: https://github.com/gentoo/sci/issues/859 Closes: https://github.com/gentoo/sci/issues/704 Closes: https://github.com/gentoo/sci/issues/686 Closes: https://github.com/gentoo/sci/issues/631 Closes: https://github.com/gentoo/sci/issues/628 Closes: https://github.com/gentoo/sci/issues/20 Signed-off-by: Benda Xu <heroxbd@gentoo.org>
* sci-biology/BRAKER: version bumpMartin Mokrejs2019-07-182-9/+8
| | | | | | | New HOMEPAGE, SRC_URI, layout of .tar.gz tarball Package-Manager: Portage-2.3.69, Repoman-2.3.16 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/jellyfish: version bumpMartin Mokrejs2019-07-182-2/+2
| | | | | Package-Manager: Portage-2.3.69, Repoman-2.3.16 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* dev-perl/Bio-EnsEMBL: update ensembl-api.tar.gz digestMartin Mokrejs2019-07-181-1/+1
| | | | | | | | | | !!! Fetched file: ensembl-api.tar.gz VERIFY FAILED! !!! Reason: Filesize does not match recorded size !!! Got: 65241091 !!! Expected: 59450373 Package-Manager: Portage-2.3.69, Repoman-2.3.16 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/portrait: Rewrite sed hackery (aka DOS2Unix)Martin Mokrejs2019-07-161-2/+2
| | | | | | | | Thanks to @mgorny for the hint. Reported-by: <mgorny@gentoo.org> Closes: https://bugs.gentoo.org/689816 Package-Manager: Portage-2.3.69, Repoman-2.3.16 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* dev-python/pyfftw: Remove from overlay, available as pyFFTW in treeMarius Brehler2019-07-135-129/+0
| | | | | | | Closes: https://github.com/gentoo/sci/pull/919 Signed-off-by: Marius Brehler <marius.brehler+gentoo@googlemail.com> Signed-off-by: Benda Xu <heroxbd@gentoo.org>
* sci-mathematics/petsc: switch back to EAPI 6 for the time beingMatthias Maier2019-07-121-1/+1
| | | | | Package-Manager: Portage-2.3.68, Repoman-2.3.16 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-mathematics/petsc: version bump to 3.11.3Matthias Maier2019-07-122-0/+192
| | | | | Package-Manager: Portage-2.3.68, Repoman-2.3.16 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-mathematics/slepc: drop oldMatthias Maier2019-07-124-225/+0
| | | | | Package-Manager: Portage-2.3.68, Repoman-2.3.16 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-mathematics/petsc: drop oldMatthias Maier2019-07-124-420/+0
| | | | | Package-Manager: Portage-2.3.68, Repoman-2.3.16 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-mathematics/petsc: also apply patches to 3.10.4 and 3.11.1Matthias Maier2019-07-122-18/+10
| | | | | Package-Manager: Portage-2.3.68, Repoman-2.3.16 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-mathematics/petsc: fix blas configuration errorBernd Waibel2019-07-121-9/+5
| | | | | | | | | | | | | | | * add blas to call to pkg-config for blas/lapack * make EAPI 7 compatible, remove versionator.eclass * change --with-cmake= variable to avoid warning Thanks to @ycoudier for hint on pkg-config Suggested-by: @ycoudier Closes: https://bugs.gentoo.org/669040 Closes: https://github.com/gentoo/sci/issues/892 Package-Manager: Portage-2.3.51, Repoman-2.3.12 Signed-off-by: Bernd Waibel <waebbl@gmail.com> Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* dev-python/ipykernel: drop from the overlay.Benda Xu2019-07-092-48/+0
| | | | The ebuilds are maintained in ::gentoo instead.
* Drop the extraneous license fileMartin Mokrejs2019-07-071-26/+0
| | | | It is just an ordinary 3-clause BSD license.
* sci-libs/iRODS: drop the extraneous license fileMartin Mokrejs2019-07-071-2/+2
| | | | | | | It is just am ordinary 3-clause BSD license. Package-Manager: Portage-2.3.67, Repoman-2.3.16 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/lemur-brain-atlas: new data packageHorea Christian2019-07-073-0/+44
| | | | | Package-Manager: Portage-2.3.68, Repoman-2.3.16 Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/drlfom_bidsdata: new data packageHorea Christian2019-07-074-0/+59
| | | | | Package-Manager: Portage-2.3.68, Repoman-2.3.16 Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/maker-3.01.02_beta: mpi_evaluator is already goneMartin Mokrejs2019-07-011-2/+0
| | | | | | | | | The mpi_evaluator is not anymore in the distribution tarball. When rm is called with no arguments it obviously breaks. Drop the commands altogether. Package-Manager: Portage-2.3.67, Repoman-2.3.16 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sys-cluster/openmpi: bump 3.1.4Justin Bronder2019-06-102-2/+2
| | | | | Signed-off-by: Justin Bronder <jsbronder@gentoo.org> Package-Manager: Portage-2.3.66, Repoman-2.3.11
* sys-cluster/openmpi: bump 3.0.4Justin Bronder2019-06-102-2/+2
| | | | | Signed-off-by: Justin Bronder <jsbronder@gentoo.org> Package-Manager: Portage-2.3.66, Repoman-2.3.11
* sys-cluster/openmpi: drop unused numa flagJustin Bronder2019-06-101-2/+2
| | | | | Signed-off-by: Justin Bronder <jsbronder@gentoo.org> Package-Manager: Portage-2.3.66, Repoman-2.3.11
* sci-biology/opfvta_bidsdata: new packageHorea Christian2019-06-033-0/+54
| | | | | Package-Manager: Portage-2.3.67, Repoman-2.3.13 Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/samri_bindata: version bumpHorea Christian2019-05-292-0/+25
| | | | | | | and metadata update Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-biology/samri_bidsdata: added mirrorHorea Christian2019-05-271-2/+5
| | | | | Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-libs/mkl: version bump to 19.0.4.243Matthias Maier2019-05-252-0/+106
| | | | | Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-libs/ipp: version bump to 19.0.4.243Matthias Maier2019-05-252-0/+43
| | | | | Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* dev-lang/vtune: version bump to 19.0.4.0.597835Matthias Maier2019-05-253-0/+50
| | | | | Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* dev-lang/ifc: version bump to 19.0.4.243Matthias Maier2019-05-252-0/+40
| | | | | Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* dev-lang/icc: version bump to 19.0.4.243Matthias Maier2019-05-252-0/+42
| | | | | Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* dev-libs/intel-common: version bump to 19.0.4.243Matthias Maier2019-05-252-0/+102
| | | | | Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-libs/dealii: version bump to 9.1.0Matthias Maier2019-05-222-0/+147
| | | | | Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* dev-libs/intel-common: version bump to 19.0.3.199Oleg Höfling2019-05-222-0/+102
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.11 Signed-off-by: Horea Christian <chr@chymera.eu>
* dev-libs/intel-common: EAPI bump in intel-sdp-r1 eclassOleg Höfling2019-05-227-16/+16
| | | | | | | | | * removed versionator inheritance and usages in intel-sdp-r1.eclass * using EAPI=7 in intel-sdp-r1.eclass and inheriting ebuilds * updated copyright to pass repoman checks Package-Manager: Portage-2.3.62, Repoman-2.3.11 Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-libs/gmsh: version bump to 4.3.0Matthias Maier2019-05-182-0/+94
| | | | | Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-libs/trilinos: fix install phaseMatthias Maier2019-05-151-1/+1
| | | | | Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-mathematics/slepc: version bump to 3.11.1Matthias Maier2019-05-132-0/+75
| | | | | Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-mathematics/petsc: version bump to 3.11.1Matthias Maier2019-05-132-0/+196
| | | | | Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-biology/irsabi_bidsdata: deprecated releaseHorea Christian2019-05-052-36/+0
| | | | | | | due to upstream bugs Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-biology/irsabi_bidsdata: version bump 1.2Horea Christian2019-05-052-0/+34
| | | | | Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-biology/irsabi_bidsdata: version bump 1.1Horea Christian2019-05-032-0/+36
| | | | | Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-libs/nipype: revision for testing importsHorea Christian2019-05-011-0/+8
| | | | | Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-biology/irsabi_bidsdata: alternative mirrorsHorea Christian2019-05-011-1/+4
| | | | | Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* sci-biology/vague-bin: drop DEPEND on velvetkMartin Mokrejs2019-04-301-3/+2
| | | | | | | It is gone from the tree. Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
* sci-biology/samri: updated testsHorea Christian2019-04-281-0/+2
| | | | | Package-Manager: Portage-2.3.65, Repoman-2.3.12 Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-libs/dealii: update live ebuildMatthias Maier2019-04-253-5/+8
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
* sci-biology/afni: dependency updateHorea Christian2019-04-253-2/+5
| | | | | Package-Manager: Portage-2.3.63, Repoman-2.3.12 Signed-off-by: Horea Christian <chr@chymera.eu>
* dev-cpp/castxml: version bump 0.2.0Horea Christian2019-04-202-0/+32
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Horea Christian <horea.christ@yandex.com>
* dev-python/traits: version bump to 5.1.0Horea Christian2019-04-162-0/+44
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Horea Christian <chr@chymera.eu>
* sci-physics/mc-tester: add missing SLOT (non-maintainer commit)Martin Mokrejs2019-04-131-2/+2
| | | | | Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>