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* sci-biology/clustal-omega: Version bump, allow for compiling with GCC 6David Seifert2016-09-223-3/+36
| | | | | | Gentoo-bug: 594692 Package-Manager: portage-2.3.1
* sci-biology/tophat: Allow for compiling with GCC 6David Seifert2016-09-222-0/+15
| | | | | | Gentoo-bug: 594544 Package-Manager: portage-2.3.1
* sci-biology/iqpnni: fix cpp14 compilation; bug #594332Kacper Kołodziej2016-09-202-0/+54
| | | | | | Closes: https://github.com/gentoo/gentoo/pull/2365 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/prank: Remove old ebuildsDavid Seifert2016-09-204-89/+0
| | | | Package-Manager: portage-2.3.1
* sci-biology/prank: Allow for compiling with GCC 6David Seifert2016-09-202-3/+19
| | | | | | | Gentoo-bug: 594060 * EAPI=6 Package-Manager: portage-2.3.1
* sci-biology/abyss: pin boost subslot, noticed by SoapSergei Trofimovich2016-09-181-1/+1
| | | | Package-Manager: portage-2.3.0
* sci-biology/bowtie: Allow for compiling with GCC 6David Seifert2016-09-192-1/+31
| | | | | | Gentoo-bug: 593966 Package-Manager: portage-2.3.0
* sci-biology/abyss: bump up to 1.9.0, tweak for gcc-6, bug #594254Sergei Trofimovich2016-09-184-0/+106
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | On gcc-6 build failed as: ``` In file included from AssemblyAlgorithms.cpp:4:0: ../DataLayer/FastaReader.h: In member function ‘FastaReader::operator void*() const’: ../DataLayer/FastaReader.h:49:35: error: cannot convert ‘std::istream {aka std::basic_istream<char>}’ to ‘void*’ ... operator void*() const { return m_in; } ^~~~ ``` In the following source: ```c++ static bool existFile(const char* f) { ifstream file(f); return file; } ``` c++98 provides file->operator void*() c++11 provides file->explicit operator bool() Hence the failure on c++11. The change adds explicit casts around ifstream. Reported-by: Toralf Förster Bug: https://bugs.gentoo.org/594254 Package-Manager: portage-2.3.0
* sci-biology/lagan: Remove old ebuildsDavid Seifert2016-09-182-105/+0
| | | | Package-Manager: portage-2.3.0
* sci-biology/lagan: Allow for compiling with GCC 6David Seifert2016-09-183-0/+641
| | | | | | | | | Gentoo-bug: 594148 * EAPI=6 * Also fix QA violations due to implicit declarations and incorrectly formatted fprintf calls. Package-Manager: portage-2.3.0
* sci-biology/rebase: Version BumpJustin Lecher2016-09-102-0/+47
| | | | | Package-Manager: portage-2.3.0 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/mosaik: Version bump to 2.2.30David Seifert2016-09-045-0/+374
| | | | | | | | | | * EAPI=6 * Make build system verbose * Honour CPPFLAGS and LDFLAGS * Handle LFS properly * Fix -Werror=format-security errors Package-Manager: portage-2.3.0
* sci-biology/mafft: Version bump to 7.305David Seifert2016-09-042-0/+70
| | | | | | * EAPI=6 Package-Manager: portage-2.3.0
* sci-biology/yass: remove deprecated EAPI ebuildsDavid Seifert2016-09-042-58/+0
| | | | Package-Manager: portage-2.3.0
* sci-biology/yass: Port to EAPI=6David Seifert2016-09-041-0/+33
| | | | Package-Manager: portage-2.3.0
* sci-biology/biopython: Version bumpDavid Seifert2016-09-032-0/+57
| | | | Package-Manager: portage-2.3.0
* sci-biology/bwa: Version bump to 0.7.15David Seifert2016-09-033-7/+6
| | | | Package-Manager: portage-2.3.0
* sci-biology/tophat: Various QA fixes, handle python properlyDavid Seifert2016-09-031-4/+14
| | | | | | | | | | * Add subslot operator := for dev-libs/boost * DEPEND on virtual/pkgconfig * Add missing ${PYTHON_REQUIRED_USE} and ${PYTHON_DEPS} * Install python scripts and modules properly using 'python_doscript' and 'python_domodule' Package-Manager: portage-2.3.0
* sci-biology/allpathslg: Unconditionally require OpenMP supportDavid Seifert2016-08-131-10/+17
| | | | | | | | | Gentoo-bug: 591166 * The configure script of sci-biology/allpathslg allows for specifying --enable/--disable-openmp, without it actually being optional. Package-Manager: portage-2.3.0
* sci-biology/finchtv: Cleanup per bug #146900Pacho Ramos2016-08-061-4/+0
| | | | Package-Manager: portage-2.3.0
* sci-biology/fasta: Cleanup per bug #146900Pacho Ramos2016-08-061-4/+0
| | | | Package-Manager: portage-2.3.0
* sci-biology/exonerate: Cleanup per bug #146900Pacho Ramos2016-08-061-4/+0
| | | | Package-Manager: portage-2.3.0
* sci-biology/ApE: Cleanup per bug #146900Pacho Ramos2016-08-061-4/+0
| | | | Package-Manager: portage-2.3.0
* sci-biology/rebase: Version BumpJustin Lecher2016-07-312-0/+47
| | | | | Package-Manager: portage-2.3.0 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/seaview: version bumpDavid Seifert2016-07-312-0/+79
| | | | | | * EAPI=6 Package-Manager: portage-2.3.0
* sci-biology/seqan: version bumpDavid Seifert2016-07-302-2/+4
| | | | Package-Manager: portage-2.3.0
* sci-biology/emboss: add a blocker for games-action/xbomber #589918Austin English2016-07-281-1/+2
| | | | | | Gentoo-Bug: https://bugs.gentoo.org/589918 Package-Manager: portage-2.3.0
* sourceforge: switch to https:// URIsMike Frysinger2016-07-275-6/+6
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* sci-biology/bioruby: add ruby21Hans de Graaff2016-07-222-2/+2
| | | | Package-Manager: portage-2.2.28
* sci-biology/clustal-omega: Unconditionally prune .la filesDavid Seifert2016-07-021-4/+2
| | | | Package-Manager: portage-2.3.0
* sci-biology/clustal-omega: Version BumpJustin Lecher2016-07-022-0/+35
| | | | | Package-Manager: portage-2.3.0 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/rebase: Bump to latest versionJustin Lecher2016-07-022-2/+2
| | | | | Package-Manager: portage-2.3.0 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/bowtie: version bumpDavid Seifert2016-06-042-1/+1
| | | | Package-Manager: portage-2.3.0_rc1
* sci-biology/foldingathome: use #!/sbin/openrc-run instead of #!/sbin/runscriptAustin English2016-05-181-1/+1
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* sci-biology/abyss: add missing dev-libs/boost dependencySergei Trofimovich2016-05-151-0/+1
| | | | Package-Manager: portage-2.2.28
* sci-biology/vienna-rna: Fix QA MissingSlotDepDavid Seifert2016-05-151-2/+2
| | | | Package-Manager: portage-2.2.28
* sci-biology/vienna-rna: Fix QA MissingSlotDepDavid Seifert2016-05-151-2/+2
| | | | Package-Manager: portage-2.2.28
* sci-biology/mrbayes: Fix QA MissingSlotDepDavid Seifert2016-05-151-2/+2
| | | | Package-Manager: portage-2.2.28
* sci-biology/bwa: Version bumpDavid Seifert2016-05-083-0/+66
| | | | Package-Manager: portage-2.2.28
* sci-biology/allpathslg: replace isnan macro with proper std::isnan functionDavid Seifert2016-05-051-1/+21
| | | | | | Gentoo-Bug: 580086 Package-Manager: portage-2.2.28
* sci-biology/bioperl: Fix dependency on dev-perl/YAMLKent Fredric2016-04-291-1/+1
| | | | | Package-Manager: portage-2.2.28 RepoMan-Options: --include-arches="alpha amd64 amd64-fbsd arm arm64 hppa ia64 m68k mips nios2 ppc ppc64 riscv s390 sh sparc sparc-fbsd x86 x86-fbsd"
* sci-biology/emboss: Clean up of files dirJustin Lecher2016-04-268-838/+7
| | | | | | | | | Move to readme.gentoo-r1.eclass Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=579728 Package-Manager: portage-2.2.28 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/hmmer: cheamup of 2.3.2 versionIan Stakenvicius2016-04-193-68/+15
| | | | | | | | | * Bumped EAPI * Merged KEYWORDS between 2.3.2-r1 and 2.3.2-r2 * dropped IUSE="pvm" as package was dropped 5 years ago * fixed metadata.xml to match Package-Manager: portage-2.2.26
* sci-biology/bioperl: Fix dependency on dev-perl/Set-ScalarKent Fredric2016-04-152-4/+4
| | | | | Package-Manager: portage-2.2.28 RepoMan-Options: --include-arches="amd64 amd64-fbsd arm arm64 mips nios2 ppc ppc64 riscv s390 sh sparc-fbsd"
* sci-biology/goby: Clean up old.Patrice Clement2016-04-152-114/+0
| | | | Package-Manager: portage-2.2.26
* sci-biology/goby: Bump fastutil dependency SLOT to 0.Patrice Clement2016-04-152-0/+114
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* sci-biology/bowtie: Version bump to 2.2.8David Seifert2016-04-102-0/+62
| | | | | | * EAPI=6 Package-Manager: portage-2.2.28
* sci-biology/samtools: Remove lua dep, fix perl shebangsDavid Seifert2016-04-101-3/+14
| | | | Package-Manager: portage-2.2.28
* sci-biology/pysam: Remove oldDavid Seifert2016-04-102-26/+0
| | | | Package-Manager: portage-2.2.28
* sci-biology/pysam: Version bump, add py3 supportDavid Seifert2016-04-103-0/+87
| | | | Package-Manager: portage-2.2.28