commit: 1ee6452972e294f0825ef450ec0f53cda42cb65f Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Jan 10 00:20:33 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue Jan 10 00:20:33 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1ee64529
sci-biology/abyss: removing old, 2.0.2 in main repo already sci-biology/abyss/abyss-1.9.0.ebuild | 53 ---------------------- .../abyss/files/abyss-1.9.0-ac_prog_ar.patch | 18 -------- sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch | 34 -------------- sci-biology/abyss/metadata.xml | 15 ------ 4 files changed, 120 deletions(-) diff --git a/sci-biology/abyss/abyss-1.9.0.ebuild b/sci-biology/abyss/abyss-1.9.0.ebuild deleted file mode 100644 index c32b477..0000000 --- a/sci-biology/abyss/abyss-1.9.0.ebuild +++ /dev/null @@ -1,53 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=6 - -inherit autotools toolchain-funcs - -DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" -HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"; -SRC_URI="https://github.com/bcgsc/abyss/archive/1.9.0.tar.gz -> ${P}.tar.gz" - -LICENSE="abyss" -SLOT="0" -IUSE="+mpi openmp misc-haskell" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-cpp/sparsehash - dev-libs/boost - misc-haskell? ( dev-libs/gmp:0= - virtual/libffi:0= - ) - mpi? ( virtual/mpi ) -" -DEPEND="${RDEPEND} - misc-haskell? ( dev-lang/ghc - dev-haskell/mmap ) -" - -# todo: --enable-maxk=N configure option -# todo: fix automagic mpi toggling - -PATCHES=( - "${FILESDIR}"/${P}-ac_prog_ar.patch - "${FILESDIR}"/${P}-gcc-6.patch -) - -src_prepare() { - default - tc-export AR - sed -i -e "s/-Werror//" configure.ac || die #365195 - sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die - eautoreconf -} - -src_configure() { - # disable building haskell tool Misc/samtobreak - # unless request by user: bug #534412 - use misc-haskell || export ac_cv_prog_ac_ct_GHC= - - econf $(use_enable openmp) -} diff --git a/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch deleted file mode 100644 index 158e9b1..0000000 --- a/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch +++ /dev/null @@ -1,18 +0,0 @@ - configure.ac | 4 ++++ - 1 file changed, 4 insertions(+) - -diff --git a/configure.ac b/configure.ac -index 9d4bb66..aa94364 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -12,6 +12,10 @@ AC_PROG_CPP - AC_PROG_CXX - AC_PROG_INSTALL - AC_PROG_RANLIB -+AN_MAKEVAR([AR], [AC_PROG_AR]) -+AN_PROGRAM([ar], [AC_PROG_AR]) -+AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)]) -+AC_PROG_AR - AC_CHECK_TOOL(GHC, ghc) - AM_CONDITIONAL([HAVE_GHC], [test "$GHC"]) - diff --git a/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch b/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch deleted file mode 100644 index 49a30f9..0000000 --- a/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch +++ /dev/null @@ -1,34 +0,0 @@ -diff --git a/DataBase/db-csv.cc b/DataBase/db-csv.cc -index 05cac19..48e3b44 100644 ---- a/DataBase/db-csv.cc -+++ b/DataBase/db-csv.cc -@@ -18,11 +18,11 @@ static const char TABLE_LIST[] = - typedef vector<string> vs; - - static bool existFile(const char* f) - { - ifstream file(f); -- return file; -+ return bool(file); - } - - template <typename D> - static bool existTable( - D& db, const string& t) -diff --git a/SimpleGraph/SimpleGraph.cpp b/SimpleGraph/SimpleGraph.cpp -index 373ec70..0a9ebd3 100644 ---- a/SimpleGraph/SimpleGraph.cpp -+++ b/SimpleGraph/SimpleGraph.cpp -@@ -645,11 +645,11 @@ static void* worker(void* pArg) - for (;;) { - /** Lock the input stream. */ - static pthread_mutex_t inMutex = PTHREAD_MUTEX_INITIALIZER; - pthread_mutex_lock(&inMutex); - EstimateRecord er; -- bool good = (*arg.in) >> er; -+ bool good = bool((*arg.in) >> er); - pthread_mutex_unlock(&inMutex); - if (!good) - break; - - // Flip the anterior distance estimates. diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml deleted file mode 100644 index c0c84f0..0000000 --- a/sci-biology/abyss/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Haskell</name> - </maintainer> - <use> - <flag name='misc-haskell'>build abyss-samtobreak tool, pull in haskell toolchain</flag> - </use> -</pkgmetadata>
