Get Gentoo!
gentoo.org sites
gentoo.org Wiki Bugs Forums Packages
Planet Archives Sources
Infra Status
aboutsummaryrefslogtreecommitdiff
Commit message (Collapse)AuthorAgeFilesLines
...
* sci-biology/picard: version bump (not working yet)Martin Mokrejs2018-04-123-61/+63
| | | | | | Bug: https://github.com/broadinstitute/picard/issues/605 Bug: https://bugs.gentoo.org/653012 Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/genometools: be more explicit with lua versionMartin Mokrejs2018-04-121-1/+1
| | | | Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/genometools: add missing SLOT for luaMartin Mokrejs2018-04-121-1/+1
| | | | Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/genometools: disable building using bundled libsMartin Mokrejs2018-04-121-4/+22
| | | | | | | | | | | | The build packaging system is suboptimal. Hand-edit the Makefile to force use of shared libs from system-wide. This brings us to a non-functional package because two lua-based packages are not yet in the tree. https://github.com/genometools/genometools/issues/742 https://github.com/genometools/genometools/pull/748 Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/genometools: bump to 1.5.10Martin Mokrejs2018-04-122-1/+1
| | | | | | | | | | | | | | | | | | | | | | https://github.com/genometools/genometools/blob/master/CHANGELOG changes in version 1.5.10 (2017-08-04) - bugfixes and cleanups - add Readjoiner output in GFA format - improve building on GCC 7 - add arbitrary N values for `gt seqstat` - install gtdata into $PREFIX/share/genometools by default - improve robustness of test suite - add Travis tests for Mac OS X - `gt seed_extend` now speaks GFA2 - improvements to `gt seed_extend` w.r.t. runtime and output format - new implementation of functionality for computing E-values for local alignments according to the Karlin-Altschul statistics Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/genometools: bump 1.5.7 to 1.5.9Martin Mokrejs2018-04-122-4/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | https://github.com/genometools/genometools/blob/master/CHANGELOG changes in version 1.5.9 (2016-07-21) - bugfixes and cleanups - update MD5 module to upstream version 1.2 - set verbatim dates in documentation files - add support for GCC 6 - gtlua: complete GtRegionMapping bindings - extend wording options for speck matchers - add tabular output format for speck - make unit tests compatible with Python 2.6 - improvements on `gt seed_extend' - improve compatibility with Ruby <1.9.2 - several changes to build system (verbosity etc.) - allow to sort sequences by header (`gt seqorder') changes in version 1.5.8 (2016-01-06) - bugfixes and cleanups - change number of spaces in GFF3 header - improve documentation of 'gt gff3 -checkids' - change GenBank and EMBL parsers to name sequences after LOCUS/ID fields - add Python 3 support for Python bindings - make build reproducible - allow speck templates to be given as files - updated genetic code table to most recent NCBI revision Package-Manager: Portage-2.3.27, Repoman-2.3.9
* dev-python/absl-py: new package, needed by sci-libs/tensorflowMartin Mokrejs2018-04-123-0/+35
| | | | Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-libs/tensorflow: more tweaks to use bazel build systemMartin Mokrejs2018-04-091-2/+38
| | | | | | | | | | It does not build for me and later runs in sandbox violation error. Possibly the build system could respect USE=mkl too. The autogenerated? BUILD file speaks of static libs being output instead of shared libs. It also mentions how to call linker when linking 3rd-party apps against these libs. Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-libs/tensorflow: version bumpMartin Mokrejs2018-04-073-2/+61
| | | | | | | | The ebuild does not compile for me still, it needs more work. Credits: Rok Kralj Closes: https://github.com/gentoo/sci/issues/857 Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-chemistry/modeller: Version bumpAlexey Shvetsov2018-04-062-0/+146
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* eclass/intel-sdp: dropMatthias Maier2018-04-031-608/+0
|
* dev-libs/intel-common: drop oldMatthias Maier2018-04-033-151/+0
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* dev-libs/intel-common: ebuild maintenanceMatthias Maier2018-04-031-1/+1
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* dev-lang/vtune: drop oldMatthias Maier2018-04-032-50/+0
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* dev-lang/idb: removeMatthias Maier2018-04-034-64/+0
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* dev-lang/ifc: drop oldMatthias Maier2018-04-032-56/+0
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* dev-lang/ifc: ebuild maintenanceMatthias Maier2018-04-031-1/+1
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* dev-lang/icc: drop oldMatthias Maier2018-04-032-53/+0
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* dev-lang/icc: ebuild maintenanceMatthias Maier2018-04-031-1/+1
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-libs/mkl: drop oldMatthias Maier2018-04-033-198/+0
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-libs/ipp: drop oldMatthias Maier2018-04-032-29/+0
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* dev-lang/vtune: version bump to 18.0.2.0.551022Matthias Maier2018-04-032-0/+50
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-libs/ipp: version bump to 18.0.2.199Matthias Maier2018-04-032-0/+44
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-libs/mkl: version bump to 18.0.2.199Matthias Maier2018-04-032-0/+109
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* eclass/intel-sdp-r1: MaintenanceMatthias Maier2018-04-031-108/+25
| | | | | | | | | | * remove IUSE l10n_ja * remove obsolete information * remove rpm automagic expansion: Intel changes naming and versioning convention with every release. Let's just give up and specify the full rpm file name in the ebuilds.
* dev-lang/ifc: version bump to 18.0.2.199Matthias Maier2018-04-022-0/+41
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* dev-lang/icc: version bump to 18.0.2.199Matthias Maier2018-04-022-0/+42
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* dev-libs/intel-common: version bump to 18.0.2.199Matthias Maier2018-04-022-0/+96
| | | | Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-libs/trilinos: remove qt4 use flagMatthias Maier2018-04-021-3/+1
| | | | | | | | I have no idea what graphical interface is constructed when qt support is enabled but it isn't essential for trilinos at all and Trilinos doesn't support Qt5... So let's just remove that. Package-Manager: Portage-2.3.28, Repoman-2.3.9
* sci-mathematics/open-axiom: Broken deps, drop keywordJustin Lecher2018-04-021-3/+3
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/proovread: Fix licenseJustin Lecher2018-04-021-1/+1
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-libs/trilinos: Drop oldJustin Lecher2018-04-027-1716/+0
| | | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.27, Repoman-2.3.9 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/tablet-bin: FIX specify an explicit slotJustin Lecher2018-04-021-5/+4
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/pilon-bin: FIX Stale CVS header on line: 3Justin Lecher2018-04-021-2/+2
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/atsas: Drop oldJustin Lecher2018-04-023-152/+0
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/atsas: FIX Stale CVS header on line: 3Justin Lecher2018-04-021-1/+0
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.27, Repoman-2.3.9
* net-misc/cernbox-client: Fix USE-depsJustin Lecher2018-04-023-110/+7
| | | | | | | Drop old Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-libs/trilinos: Change USE=qt to qt5Justin Lecher2018-04-021-3/+3
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-libs/tensorflow: Update metadata.xml for USE=cudaJustin Lecher2018-04-021-0/+3
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.27, Repoman-2.3.9
* Bump dep versionJustin Lecher2018-04-021-1/+1
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* Drop deprecated archesJustin Lecher2018-04-021-2/+0
| | | | Signed-off-by: Justin Lecher <jlec@gentoo.org>
* app-admin/eselect: Version BumpJustin Lecher2018-04-024-6/+6
| | | | | Signed-off-by: Justin Lecher <jlec@gentoo.org> Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/proovread: call perl_domodule to install *.pm filesMartin Mokrejs2018-04-021-0/+4
| | | | Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/proovread: new packageMartin Mokrejs2018-04-012-0/+62
| | | | | | Will need more work from upstream to make it into Gentoo. Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/diamond: new packageMartin Mokrejs2018-04-013-0/+40
| | | | | | | Do not know if the SSE instruction calls can be protected with CPU_FLAGS or similar. See page 2 in diamond_manual.pdf . Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/genepop: switch to httpsMartin Mokrejs2018-04-011-2/+2
| | | | Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/genepop: version bumpMartin Mokrejs2018-04-012-8/+8
| | | | | | | Upstream does not version the release tarballs, now 4.7 is being actually exposed on the website. Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/seq_crumbs: new packageMartin Mokrejs2018-04-013-0/+59
| | | | | | | The fix to setup.py to respect DESTDIR is probably not ideal. Needs a fix to avoid file collisions. Package-Manager: Portage-2.3.27, Repoman-2.3.9
* sci-biology/augustus: update file checksumMartin Mokrejs2018-03-311-1/+1
| | | | | | | | | | | | | | | | Seems upstream re-released the binary tarball with sources $ gzip -dc /usr/portage/distfiles/augustus-3.3.tar.gz | tar tvf - | grep 2018 drwxrwxr-x mario/mario 0 2018-01-26 14:09 augustus/auxprogs/homGeneMapping/src/ drwx------ mario/mario 0 2018-01-26 14:07 augustus/auxprogs/joingenes/ drwx------ mario/mario 0 2018-01-26 14:07 augustus/auxprogs/bam2hints/ drwx------ mario/mario 0 2018-01-26 14:09 augustus/auxprogs/filterBam/src/ drwxrwxr-x mario/mario 0 2018-01-26 14:09 augustus/auxprogs/filterBam/bin/ drwxrwxr-x mario/mario 0 2018-01-26 14:07 augustus/auxprogs/compileSpliceCands/ drwx------ mario/mario 0 2018-01-26 14:08 augustus/auxprogs/bam2wig/ drwx------ mario/mario 0 2018-01-26 14:08 augustus/bin/ Package-Manager: Portage-2.3.24, Repoman-2.3.6
* sci-biology/BRAKER: version bump, update LICENSEMartin Mokrejs2018-03-312-19/+13
| | | | Package-Manager: Portage-2.3.24, Repoman-2.3.6