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| author |   Ted Tanberry <ted.tanberry@gmail.com> | 2015-12-25 00:32:17 +0100 |
|---|---|---|
| committer |   Justin Lecher <jlec@gentoo.org> | 2015-12-25 12:44:51 +0100 |
| commit | 319e280a8e026786b319d48de907e440049f490c (patch) | |
| tree | dc4bd9d17371d75576fed0a64daa76f6441305d1 | |
| parent | sci-biology/mcl: Version bump, fix bug 569040 and QA issues. (diff) | |
| download | gentoo-319e280a8e026786b319d48de907e440049f490c.tar.gz gentoo-319e280a8e026786b319d48de907e440049f490c.tar.bz2 gentoo-319e280a8e026786b319d48de907e440049f490c.zip | |
sci-libs/libmems: Version bump, fix bug 529770 and QA issues.
Package-Manager: portage-2.2.26
| -rw-r--r-- | sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch | 24 | ||||
| -rw-r--r-- | sci-libs/libmems/files/libmems-1.6_p1-build.patch | 10 | ||||
| -rw-r--r-- | sci-libs/libmems/libmems-1.6_p1-r1.ebuild | 36 |
3 files changed, 70 insertions, 0 deletions
diff --git a/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch b/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch new file mode 100644 index 000000000000..0bd922c9e111 --- /dev/null +++ b/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch @@ -0,0 +1,24 @@ +Fix bug 529770 caused by non-const copy constructor. + +--- libmems-1.6_p1/libMems/Aligner.cpp ++++ libmems-1.6_p1/libMems/Aligner.cpp +@@ -939,7 +939,7 @@ + MatchLeftEndComparator( unsigned seq = 0 ){
+ m_seq = seq;
+ }
+- MatchLeftEndComparator( MatchLeftEndComparator& msc ){
++ MatchLeftEndComparator( const MatchLeftEndComparator& msc ){
+ m_seq = msc.m_seq;
+ }
+ // TODO?? make this do a wraparound comparison if all is equal?
+--- libmems-1.6_p1/libMems/Aligner.h ++++ libmems-1.6_p1/libMems/Aligner.h +@@ -49,7 +49,7 @@ + LabeledMemComparator( uint seq ){
+ m_seq = seq;
+ }
+- LabeledMemComparator( LabeledMemComparator& lmc ){
++ LabeledMemComparator( const LabeledMemComparator& lmc ){
+ m_seq = lmc.m_seq;
+ }
+ boolean operator()(const LabeledMem& a, const LabeledMem& b) const{
diff --git a/sci-libs/libmems/files/libmems-1.6_p1-build.patch b/sci-libs/libmems/files/libmems-1.6_p1-build.patch index 63e5f1216756..04d5dd9c82ac 100644 --- a/sci-libs/libmems/files/libmems-1.6_p1-build.patch +++ b/sci-libs/libmems/files/libmems-1.6_p1-build.patch @@ -17,3 +17,13 @@ index 6101f71..d66053d 100644 LIBMEMS_H = \ RepeatHash.h MatchHashEntry.h \ +--- a/libMems/dmSML/util.c ++++ b/libMems/dmSML/util.c +@@ -2,6 +2,7 @@ + #include "config.h" + #endif + ++#include <stdlib.h> + #include <stdio.h> + #include "libMems/dmSML/util.h" + diff --git a/sci-libs/libmems/libmems-1.6_p1-r1.ebuild b/sci-libs/libmems/libmems-1.6_p1-r1.ebuild new file mode 100644 index 000000000000..2e094ab42ce2 --- /dev/null +++ b/sci-libs/libmems/libmems-1.6_p1-r1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit autotools + +DESCRIPTION="Library for sci-biology/mauve" +HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/" +SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="GPL-2" +IUSE="doc" +KEYWORDS="~amd64 ~x86" + +CDEPEND=" + dev-libs/boost + sci-libs/libgenome + sci-libs/libmuscle" +DEPEND="${CDEPEND} + doc? ( app-doc/doxygen )" +RDEPEND="${CDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-build.patch + "${FILESDIR}"/${P}-boost.patch + "${FILESDIR}"/${P}-gcc-4.7.patch + "${FILESDIR}"/${P}-broken-constness.patch + ) + +src_prepare() { + default + eautoreconf +} |