Fix for _FORTIFY_SOURCE indicates presence of overflow, #363537; Don't mix FLAGS

(Portage version: 2.2.0_alpha30/cvs/Linux x86_64)

4 files changed, 85 insertions, 2 deletions

diff --git a/sci-biology/maq/ChangeLog b/sci-biology/maq/ChangeLog
index a6642084f26b..0905d89bc073 100644
--- a/sci-biology/maq/ChangeLog
+++ b/sci-biology/maq/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/maq
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/maq/ChangeLog,v 1.4 2009/04/04 19:19:39 maekke Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/maq/ChangeLog,v 1.5 2011/04/14 07:46:27 jlec Exp $
+
+*maq-0.7.1-r1 (14 Apr 2011)
+
+  14 Apr 2011; Justin Lecher <jlec@gentoo.org> +maq-0.7.1-r1.ebuild,
+  +files/maq-0.7.1-bfr-overfl.patch, +files/maq-0.7.1-flags.patch:
+  Fix for _FORTIFY_SOURCE indicates presence of overflow, #363537; Don't mix
+  FLAGS
 
   04 Apr 2009; Markus Meier <maekke@gentoo.org> maq-0.7.1.ebuild:
   amd64/x86 stable, bug #263735
diff --git a/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch b/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch
new file mode 100644
index 000000000000..9f4247d441f5
--- /dev/null
+++ b/sci-biology/maq/files/maq-0.7.1-bfr-overfl.patch
@@ -0,0 +1,16 @@
+ simulate.c |    2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/simulate.c b/simulate.c
+index 788c440..67ba2ba 100644
+--- a/simulate.c
++++ b/simulate.c
+@@ -383,7 +383,7 @@ static void simustat_core(gzFile fp, int Q_thres)
+ 	memset(wc_single, 0, 40); memset(tot_single, 0, 40);
+ 	memset(wc_pair, 0, 40); memset(tot_pair, 0, 40);
+ 	memset(abpair, 0, 4 * 256 * 10);
+-	memset(tc[2], 0, 4 * sizeof(int));
++	memset(tc, 0, 4 * sizeof(int));
+ 	while (maqmap_read1(fp, m1)) {
+ 		int is_correct;
+ 		bit32_t p1, p2;
diff --git a/sci-biology/maq/files/maq-0.7.1-flags.patch b/sci-biology/maq/files/maq-0.7.1-flags.patch
new file mode 100644
index 000000000000..721e53248b7a
--- /dev/null
+++ b/sci-biology/maq/files/maq-0.7.1-flags.patch
@@ -0,0 +1,24 @@
+ configure.ac |    3 ++-
+ 1 files changed, 2 insertions(+), 1 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index ad2f1e6..4f9d7be 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -8,6 +8,7 @@ AC_PROG_CXX
+ 
+ # set CFLAGS and CXXFLAGS
+ user_CFLAGS=${CFLAGS}
++user_CXXFLAGS=${CXXFLAGS}
+ generic_CFLAGS="-Wall"
+ ext_CFLAGS=""
+ case "${host_cpu}-${host_os}" in
+@@ -37,7 +38,7 @@ AC_ARG_ENABLE(shortread,    [  --enable-shortreads     use shortread mode],
+ AC_ARG_ENABLE(intel64,      [  --enable-intel64        optimize for Intel64 CPU such as Xeon and Core2],
+ 			  [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], [])
+ CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS}"
+-CXXFLAGS=$CFLAGS
++CXXFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CXXFLAGS}"
+ 
+ AC_STDC_HEADERS
+ AC_CHECK_HEADER(zlib.h)
diff --git a/sci-biology/maq/maq-0.7.1-r1.ebuild b/sci-biology/maq/maq-0.7.1-r1.ebuild
new file mode 100644
index 000000000000..dfcdfff7be40
--- /dev/null
+++ b/sci-biology/maq/maq-0.7.1-r1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/maq/maq-0.7.1-r1.ebuild,v 1.1 2011/04/14 07:46:27 jlec Exp $
+
+EAPI="4"
+
+inherit autotools eutils
+
+DESCRIPTION="Mapping and Assembly with Qualities - mapping Solexa and SOLiD reads to reference sequences"
+HOMEPAGE="http://maq.sourceforge.net/"
+SRC_URI="
+	mirror://sourceforge/${PN}/${P}.tar.bz2
+	mirror://sourceforge/${PN}/calib-36.dat.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND=""
+
+src_prepare() {
+	epatch \
+	"${FILESDIR}"/${P}-flags.patch \
+	"${FILESDIR}"/${P}-bfr-overfl.patch
+	eautoreconf
+}
+
+src_install() {
+	default
+	insinto /usr/share/maq
+	doins "${WORKDIR}"/*.dat || die
+	doman maq.1
+	dodoc ${PN}.pdf
+}