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* sci-biology/gmap: Clean metadata.xmlPacho Ramos2016-11-271-4/+0
| | | | Package-Manager: portage-2.3.2
* sci-biology/gmap: Drop old (#597984)Pacho Ramos2016-11-273-74/+0
| | | | Package-Manager: portage-2.3.2
* sci-biology/bedtools: This needs slot 0 of samtools (#597982)Pacho Ramos2016-11-271-1/+1
| | | | Package-Manager: portage-2.3.2
* sci-biology/treeviewx: Drop oldPacho Ramos2016-11-251-32/+0
| | | | Package-Manager: portage-2.3.2
* sci-biology/treeviewx: x86 stable, bug #584034Pacho Ramos2016-11-251-2/+2
| | | | Package-Manager: portage-2.3.2
* sci-biology/meme: Add $(DESTDIR) to install hooksDavid Seifert2016-11-201-1/+24
| | | | | | Gentoo-bug: 600316 Package-Manager: portage-2.3.2
* sci-biology/meme: Version bump to 4.11.2_p2David Seifert2016-11-195-0/+872
| | | | | | | | | | Gentoo-bug: 599860 * EAPI=6 * Install documentation and examples correctly * Install perl and python modules correctly * Add missing perl runtime dependencies Package-Manager: portage-2.3.2
* sci-biology/bioperl-run: Fix overlong DESCRIPTIONDavid Seifert2016-11-182-4/+4
| | | | Package-Manager: portage-2.3.2
* sci-biology/biogrep: Remove old ebuildsDavid Seifert2016-11-182-43/+0
| | | | Package-Manager: portage-2.3.2
* sci-biology/biogrep: Port to EAPI=6David Seifert2016-11-182-0/+37
| | | | | | | * Add USE="doc" and USE="examples" * Run 'eautoreconf' to modernize configure script Package-Manager: portage-2.3.2
* sci-biology/arb: Fix overlong DESCRIPTIONDavid Seifert2016-11-183-6/+6
| | | | Package-Manager: portage-2.3.2
* sci-biology/abyss: bump up to 2.0.2, bug #596018Sergei Trofimovich2016-11-063-1/+49
| | | | | | | | | Fixes gcc-6 and boost-1.62 build failures. Reported-by: Toralf Förster Bug: https://bugs.gentoo.org/596018 Package-Manager: portage-2.3.2
* global: Drop dead implementations from PYTHON_COMPATMichał Górny2016-11-014-4/+4
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* Revert "Temporarily remove Manifest files that were at risk of having broken ↵Michael Palimaka2016-10-311-0/+6
| | | | | | ChangeLog entries." This reverts commit 48b59c28052dbc9a1c410a8a5d93c1cc3c8c8d4b.
* Temporarily remove Manifest files that were at risk of having broken ↵Michael Palimaka2016-10-311-6/+0
| | | | | | | | | ChangeLog entries. This commit will be immediately reverted. The intention is to force the mtime to be bumped causing the updated Manifest to be propagated to mirrors. Gentoo-bug: 577722
* sci-biology/rebase: Bump to latest DBJustin Lecher2016-10-292-0/+47
| | | | | Package-Manager: portage-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/hmmer: Properly SLOT=2 hmmer-2.3.2David Seifert2016-10-093-0/+205
| | | | | | | | | Gentoo-bug: 328911, 586960 * EAPI=6 * Introduce SLOT=2 and rename binaries and static libraries Package-Manager: portage-2.3.1
* sci-biology/hmmer: Version bump to 3.1_beta2David Seifert2016-10-094-0/+470
| | | | | | | | * EAPI=6 * Make perl shebangs portable * Install headers into 'hmmer3' subdir Package-Manager: portage-2.3.1
* sci-biology/tophat: Do not wrap scriptsDavid Seifert2016-10-031-2/+2
| | | | Package-Manager: portage-2.3.1
* sci-biology/samtools: Use 'python-single-r1' instead of 'python-r1'David Seifert2016-10-031-17/+21
| | | | Package-Manager: portage-2.3.1
* sci-biology/consed: Remove old ebuildsDavid Seifert2016-10-033-165/+0
| | | | Package-Manager: portage-2.3.1
* sci-biology/consed: Version bump to 29David Seifert2016-10-036-0/+1662
| | | | | | | | | | * EAPI=6 * Allow for compiling with GCC 6 * [QA] Respect all user variables (CC, CXX, ...) * [QA] Fix various C and C++ related warnings * Fix perl shebangs to be portable Package-Manager: portage-2.3.1
* sci-biology/phrap: Revbump to EAPI=6David Seifert2016-10-033-6/+112
| | | | Package-Manager: portage-2.3.1
* sci-biology/phred: Revbump to EAPI=6David Seifert2016-10-035-41/+170
| | | | Package-Manager: portage-2.3.1
* sci-biology/tophat: Remove old and ancient 1.0 ebuildsDavid Seifert2016-09-272-39/+0
| | | | Package-Manager: portage-2.3.1
* sci-biology/rebase: amd64 stable wrt bug #590146Agostino Sarubbo2016-09-261-1/+1
| | | | | | Package-Manager: portage-2.2.28 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/biopython: amd64 stable wrt bug #584210Agostino Sarubbo2016-09-261-1/+1
| | | | | | Package-Manager: portage-2.2.28 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/treeviewx: amd64 stable wrt bug #584034Agostino Sarubbo2016-09-261-1/+1
| | | | | | Package-Manager: portage-2.2.28 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/tophat: USE="threads" dep on dev-libs/boostDavid Seifert2016-09-252-8/+61
| | | | | | | | Gentoo-bug: 594810 * Remove autoconf macros from archive, depend on sys-devel/autoconf instead for the latest versions. Package-Manager: portage-2.3.1
* sci-biology/vcftools: Add missing RDEPEND on sys-libs/zlibDavid Seifert2016-09-251-1/+2
| | | | Package-Manager: portage-2.3.1
* sci-biology/vcftools: Remove old ebuildDavid Seifert2016-09-253-99/+0
| | | | | | | Package-Manager: portage-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/2407 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/vcftools: Version bump to 0.1.14David Seifert2016-09-253-0/+90
| | | | | | | | | | | Gentoo-bug: 594924 * EAPI=6 * Properly RDEPEND on dev-lang/perl Package-Manager: portage-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/2407 Signed-off-by: David Seifert <soap@gentoo.org>
* sci-biology/bedtools: Add missing RDEPEND on sys-libs/zlibDavid Seifert2016-09-251-0/+1
| | | | Package-Manager: portage-2.3.1
* sci-biology/bedtools: Remove old ebuildsDavid Seifert2016-09-253-68/+0
| | | | Package-Manager: portage-2.3.1
* sci-biology/bedtools: Version bump to 2.26.0David Seifert2016-09-253-0/+912
| | | | | | | | | | | Gentoo-bug: 594994 * EAPI=6 * Make buildsystem output verbose * Inherit 'python-any-r1', due to python script * Add dependencies for test suite * Properly set CXX and CXXFLAGS Package-Manager: portage-2.3.1
* sci-biology/amos: Allow for compiling with GCC 6David Seifert2016-09-244-37/+185
| | | | | | | | Gentoo-bug: 594928 * EAPI=6 * [QA] fix implicit declarations Package-Manager: portage-2.3.1
* sci-biology/eugene: Bump to 4.1d from science-overlayDavid Seifert2016-09-244-0/+144
| | | | | | | | Gentoo-bug: 594700 * EAPI=6 * Fix -Wformat warnings Package-Manager: portage-2.3.1
* sci-biology/iqpnni: Remove old ebuildsDavid Seifert2016-09-243-61/+0
| | | | Package-Manager: portage-2.3.1
* sci-biology/iqpnni: Port to EAPI=6David Seifert2016-09-241-0/+31
| | | | Package-Manager: portage-2.3.1
* sci-biology/iqpnni: Fix CRLF line endings in patchDavid Seifert2016-09-241-24/+24
| | | | | | Gentoo-bug: 594654 Package-Manager: portage-2.3.1
* 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