sci-libs/libmems: Version bump, fix bug 529770 and QA issues.

Package-Manager: portage-2.2.26

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 (file)
index 0000000..0bd922c
--- /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 ){\r
+               m_seq = seq;\r
+       }\r
+-      MatchLeftEndComparator( MatchLeftEndComparator& msc ){\r
++      MatchLeftEndComparator( const MatchLeftEndComparator& msc ){\r
+               m_seq = msc.m_seq;\r
+       }\r
+       // TODO??  make this do a wraparound comparison if all is equal?\r
+--- libmems-1.6_p1/libMems/Aligner.h
++++ libmems-1.6_p1/libMems/Aligner.h
+@@ -49,7 +49,7 @@
+       LabeledMemComparator( uint seq ){\r
+               m_seq = seq;\r
+       }\r
+-      LabeledMemComparator( LabeledMemComparator& lmc ){\r
++      LabeledMemComparator( const LabeledMemComparator& lmc ){\r
+               m_seq = lmc.m_seq;\r
+       }\r
+       boolean operator()(const LabeledMem& a, const LabeledMem& b) const{\r

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 63e5f121675666a005a63a985e7d2a9e43f38314..04d5dd9c82ac647a87292cb3be3ac1a292870b79 100644 (file)
--- 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 (file)
index 0000000..2e094ab
--- /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
+}