* [gentoo-commits] gentoo-x86 commit in sci-biology/abyss: abyss-1.3.4.ebuild abyss-1.3.0.ebuild abyss-1.3.3.ebuild ChangeLog
@ 2012-06-20 20:48 Justin Lecher (jlec)
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From: Justin Lecher (jlec) @ 2012-06-20 20:48 UTC (permalink / raw
To: gentoo-commits
jlec 12/06/20 20:48:56
Modified: abyss-1.3.0.ebuild abyss-1.3.3.ebuild ChangeLog
Added: abyss-1.3.4.ebuild
Log:
sci-biology/abyss: Fix compilation with gcc-4.7, #422599; install docs inside /usr/share/doc/, #297205
(Portage version: 2.2.0_alpha110/cvs/Linux x86_64)
Revision Changes Path
1.2 sci-biology/abyss/abyss-1.3.0.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/abyss/abyss-1.3.0.ebuild?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/abyss/abyss-1.3.0.ebuild?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/abyss/abyss-1.3.0.ebuild?r1=1.1&r2=1.2
Index: abyss-1.3.0.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.0.ebuild,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- abyss-1.3.0.ebuild 24 Sep 2011 21:48:12 -0000 1.1
+++ abyss-1.3.0.ebuild 20 Jun 2012 20:48:56 -0000 1.2
@@ -1,6 +1,6 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.0.ebuild,v 1.1 2011/09/24 21:48:12 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.0.ebuild,v 1.2 2012/06/20 20:48:56 jlec Exp $
EAPI="4"
@@ -31,5 +31,6 @@
src_configure() {
econf \
+ --docdir="${EPREFIX}/usr/share/doc/${PF}" \
$(use_enable openmp)
}
1.2 sci-biology/abyss/abyss-1.3.3.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/abyss/abyss-1.3.3.ebuild?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/abyss/abyss-1.3.3.ebuild?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/abyss/abyss-1.3.3.ebuild?r1=1.1&r2=1.2
Index: abyss-1.3.3.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.3.ebuild,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- abyss-1.3.3.ebuild 29 May 2012 02:44:21 -0000 1.1
+++ abyss-1.3.3.ebuild 20 Jun 2012 20:48:56 -0000 1.2
@@ -1,10 +1,10 @@
# Copyright 1999-2012 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 1.1 2012/05/29 02:44:21 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.3.ebuild,v 1.2 2012/06/20 20:48:56 jlec Exp $
EAPI="4"
-inherit autotools
+inherit autotools eutils
DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
@@ -24,6 +24,7 @@
# todo: fix automagic mpi toggling
src_prepare() {
+ epatch "${FILESDIR}"/${P}-gcc-4.7.patch
sed -i -e "s/-Werror//" configure.ac || die #365195
sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
eautoreconf
@@ -31,5 +32,6 @@
src_configure() {
econf \
+ --docdir="${EPREFIX}/usr/share/doc/${PF}" \
$(use_enable openmp)
}
1.13 sci-biology/abyss/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/abyss/ChangeLog?rev=1.13&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/abyss/ChangeLog?rev=1.13&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/abyss/ChangeLog?r1=1.12&r2=1.13
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/abyss/ChangeLog,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- ChangeLog 29 May 2012 02:44:21 -0000 1.12
+++ ChangeLog 20 Jun 2012 20:48:56 -0000 1.13
@@ -1,6 +1,14 @@
# ChangeLog for sci-biology/abyss
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/ChangeLog,v 1.12 2012/05/29 02:44:21 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/ChangeLog,v 1.13 2012/06/20 20:48:56 jlec Exp $
+
+*abyss-1.3.4 (20 Jun 2012)
+
+ 20 Jun 2012; Justin Lecher <jlec@gentoo.org> abyss-1.3.0.ebuild,
+ abyss-1.3.3.ebuild, +files/abyss-1.3.3-gcc-4.7.patch, +abyss-1.3.4.ebuild,
+ +files/abyss-1.3.4-gcc-4.7.patch:
+ Fix compilation with gcc-4.7, #422599; install docs inside /usr/share/doc/,
+ #297205
*abyss-1.3.3 (29 May 2012)
1.1 sci-biology/abyss/abyss-1.3.4.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/abyss/abyss-1.3.4.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/abyss/abyss-1.3.4.ebuild?rev=1.1&content-type=text/plain
Index: abyss-1.3.4.ebuild
===================================================================
# Copyright 1999-2012 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 1.1 2012/06/20 20:48:56 jlec Exp $
EAPI="4"
inherit autotools eutils
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
src_prepare() {
epatch "${FILESDIR}"/${P}-gcc-4.7.patch
sed -i -e "s/-Werror//" configure.ac || die #365195
sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
eautoreconf
}
src_configure() {
econf \
--docdir="${EPREFIX}/usr/share/doc/${PF}" \
$(use_enable openmp)
}
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2012-06-20 20:48 [gentoo-commits] gentoo-x86 commit in sci-biology/abyss: abyss-1.3.4.ebuild abyss-1.3.0.ebuild abyss-1.3.3.ebuild ChangeLog Justin Lecher (jlec)
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