From 572fb74e26fba60b7bd4af3b408ce30f65302ac6 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Sun, 11 Aug 2013 14:55:23 +0000 Subject: sci-biology/abyss: Version BUmp, respect AR, #477580 (Portage version: 2.2.0_alpha196/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!) --- sci-biology/abyss/ChangeLog | 9 ++++- sci-biology/abyss/abyss-1.3.3.ebuild | 10 +++-- sci-biology/abyss/abyss-1.3.4.ebuild | 8 +++- sci-biology/abyss/abyss-1.3.6.ebuild | 46 ++++++++++++++++++++++ .../abyss/files/abyss-1.3.3-ac_prog_ar.patch | 18 +++++++++ .../abyss/files/abyss-1.3.6-ac_prog_ar.patch | 18 +++++++++ sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch | 15 +++++++ 7 files changed, 118 insertions(+), 6 deletions(-) create mode 100644 sci-biology/abyss/abyss-1.3.6.ebuild create mode 100644 sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch create mode 100644 sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch create mode 100644 sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch (limited to 'sci-biology/abyss') diff --git a/sci-biology/abyss/ChangeLog b/sci-biology/abyss/ChangeLog index 62ae090239c6..7a534728cf26 100644 --- a/sci-biology/abyss/ChangeLog +++ b/sci-biology/abyss/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-biology/abyss # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/ChangeLog,v 1.18 2013/08/11 13:29:32 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/ChangeLog,v 1.19 2013/08/11 14:55:22 jlec Exp $ + +*abyss-1.3.6 (11 Aug 2013) + + 11 Aug 2013; Justin Lecher abyss-1.3.3.ebuild, + abyss-1.3.4.ebuild, +abyss-1.3.6.ebuild, +files/abyss-1.3.3-ac_prog_ar.patch, + +files/abyss-1.3.6-ac_prog_ar.patch, +files/abyss-1.3.6-gcc-4.7.patch: + Version BUmp, respect AR, #477580 11 Aug 2013; Justin Lecher -abyss-1.2.3.ebuild, -abyss-1.2.7.ebuild, -abyss-1.3.0.ebuild: diff --git a/sci-biology/abyss/abyss-1.3.3.ebuild b/sci-biology/abyss/abyss-1.3.3.ebuild index 752a131af6ab..9806da0ba4bb 100644 --- a/sci-biology/abyss/abyss-1.3.3.ebuild +++ b/sci-biology/abyss/abyss-1.3.3.ebuild @@ -1,10 +1,10 @@ # Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.3.ebuild,v 1.4 2013/07/27 22:22:05 ago Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.3.ebuild,v 1.5 2013/08/11 14:55:22 jlec Exp $ EAPI="4" -inherit autotools eutils +inherit autotools eutils toolchain-funcs DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" @@ -24,7 +24,11 @@ RDEPEND="${DEPEND}" # todo: fix automagic mpi toggling src_prepare() { - epatch "${FILESDIR}"/${P}-gcc-4.7.patch + tc-export AR + epatch \ + "${FILESDIR}"/${P}-gcc-4.7.patch \ + "${FILESDIR}"/${P}-ac_prog_ar.patch + sed -i -e "s/-Werror//" configure.ac || die #365195 sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die eautoreconf diff --git a/sci-biology/abyss/abyss-1.3.4.ebuild b/sci-biology/abyss/abyss-1.3.4.ebuild index 3e8e7fa36f4e..a6d4ea462569 100644 --- a/sci-biology/abyss/abyss-1.3.4.ebuild +++ b/sci-biology/abyss/abyss-1.3.4.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.4.ebuild,v 1.2 2013/07/17 07:32:04 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.4.ebuild,v 1.3 2013/08/11 14:55:22 jlec Exp $ EAPI=5 @@ -25,9 +25,13 @@ RDEPEND="${DEPEND}" # todo: --enable-maxk=N configure option # todo: fix automagic mpi toggling -PATCHES=( "${FILESDIR}"/${P}-gcc-4.7.patch ) +PATCHES=( + "${FILESDIR}"/${P}-gcc-4.7.patch + "${FILESDIR}"/${PN}-1.3.3-ac_prog_ar.patch + ) src_prepare() { + tc-export AR sed -i -e "s/-Werror//" configure.ac || die #365195 sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die autotools-utils_src_prepare diff --git a/sci-biology/abyss/abyss-1.3.6.ebuild b/sci-biology/abyss/abyss-1.3.6.ebuild new file mode 100644 index 000000000000..fe0006ac4b5b --- /dev/null +++ b/sci-biology/abyss/abyss-1.3.6.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.6.ebuild,v 1.1 2013/08/11 14:55:22 jlec Exp $ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" +SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz" + +LICENSE="abyss" +SLOT="0" +IUSE="+mpi openmp" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + dev-cpp/sparsehash + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +# todo: --enable-maxk=N configure option +# todo: fix automagic mpi toggling + +PATCHES=( + "${FILESDIR}"/${P}-gcc-4.7.patch + "${FILESDIR}"/${P}-ac_prog_ar.patch + ) + +src_prepare() { + tc-export AR + sed -i -e "s/-Werror//" configure.ac || die #365195 + sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --docdir="${EPREFIX}/usr/share/doc/${PF}" + $(use_enable openmp) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch new file mode 100644 index 000000000000..300868f52b76 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch @@ -0,0 +1,18 @@ + configure.ac | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/configure.ac b/configure.ac +index 5c6cb92..b99bedd 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -12,6 +12,10 @@ AC_PROG_CPP + AC_PROG_CXX + AC_PROG_INSTALL + AC_PROG_RANLIB ++AN_MAKEVAR([AR], [AC_PROG_AR]) ++AN_PROGRAM([ar], [AC_PROG_AR]) ++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)]) ++AC_PROG_AR + + # Checks for header files. + AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \ diff --git a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch new file mode 100644 index 000000000000..158e9b1262e4 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch @@ -0,0 +1,18 @@ + configure.ac | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/configure.ac b/configure.ac +index 9d4bb66..aa94364 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -12,6 +12,10 @@ AC_PROG_CPP + AC_PROG_CXX + AC_PROG_INSTALL + AC_PROG_RANLIB ++AN_MAKEVAR([AR], [AC_PROG_AR]) ++AN_PROGRAM([ar], [AC_PROG_AR]) ++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)]) ++AC_PROG_AR + AC_CHECK_TOOL(GHC, ghc) + AM_CONDITIONAL([HAVE_GHC], [test "$GHC"]) + diff --git a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch new file mode 100644 index 000000000000..c2cc35c31d98 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch @@ -0,0 +1,15 @@ + ParseAligns/abyss-fixmate.cc | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc +index 1a169cf..36cc05b 100644 +--- a/ParseAligns/abyss-fixmate.cc ++++ b/ParseAligns/abyss-fixmate.cc +@@ -16,6 +16,7 @@ + #include + #include + #include ++#include + + using namespace std; + -- cgit v1.2.3-65-gdbad