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

Package-Manager: portage-2.2.0_alpha30/cvs/Linux x86_64

5 files changed, 93 insertions, 7 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/Manifest b/sci-biology/maq/Manifest
index a734b37423eb..22e692399037 100644
--- a/sci-biology/maq/Manifest
+++ b/sci-biology/maq/Manifest
@@ -1,15 +1,18 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA1
 
+AUX maq-0.7.1-bfr-overfl.patch 527 RMD160 80f3917a4ead2f2b7c2e9907d7df2772e834e21e SHA1 42a3e32bc19827559344d343c4b15db047ed45c2 SHA256 ff7521f696d4deb311f3dec07997bd8cce068749369d6cd3d3e65fb6cce19e56
+AUX maq-0.7.1-flags.patch 799 RMD160 2053550e04b27b1e53d60f4ac098f90c41106faf SHA1 16dd6cf8e295db16046c147d440e22c4936f29bb SHA256 f1949b063ed015182e403668dc19466d079eacc6d351d11cc5d099d2aeeb18f9
 DIST calib-36.dat.gz 196371 RMD160 34d6845c41388009970f478af14382334118ca9c SHA1 3af6e7b07c26a8d79f595412aed64d191614e8f0 SHA256 d4480e04446eb273f1908add709dd5a24262c08a59a1647b9a2d053f4d30181b
 DIST maq-0.7.1.tar.bz2 368645 RMD160 98b514dba887c63b567e8c6a2ed09f02812d8fb1 SHA1 3a455817fc6e98c2d06533d630e22c47649afa97 SHA256 e1671e0408b0895f5ab943839ee8f28747cf5f55dc64032c7469b133202b6de2
+EBUILD maq-0.7.1-r1.ebuild 800 RMD160 3e0ecbc699214941f7e92194d00fe8c9015b6ef5 SHA1 0e5844a59b2f79782a6dd0ed3fa4cbf5a2ee93bd SHA256 7e17ef47042851a0ea11cc749f417fb846b7657fdd65e1234b76f1e8cd865840
 EBUILD maq-0.7.1.ebuild 695 RMD160 2ffecbd9508ed2420dc2d61adfcb6d12c7935123 SHA1 d97cd72cfd5b246b86d82092e2a3d45282da3e06 SHA256 4ecb74414902b3522e3076e3dee11618a255f42ca485e0d47fdaeb0705c9a5e2
-MISC ChangeLog 602 RMD160 376dfe13a2f5373ab564509176c53e9cd0b4a130 SHA1 ee881430ac79783808e0fc6b6576ce7090728ac9 SHA256 84a75212f478040dfcf2a2103a90f48e27ff7ed73592f4a5c6b4b430e89b0c2f
+MISC ChangeLog 851 RMD160 b22c51e07f07d05c881299ed4a6a65ab5fa1a707 SHA1 7ace2ad3ea19b6c4fa6b037b0debe585a5ee2a0e SHA256 030eaed537c295945db43d29633d41a6118578f90ed98a34ff821fc5e3a89bee
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.10 (GNU/Linux)
+Version: GnuPG v2.0.17 (GNU/Linux)
 
-iEYEARECAAYFAknXsuMACgkQkKaRLQcq0GKIUwCfUq5jVbhEiqpn9LZJe3yvLzyV
-pSQAnjZ7IFBXycPj48Or5Ny1FH/euVia
-=ei7e
+iEYEARECAAYFAk2mplkACgkQgAnW8HDreRZxaQCcCxfwki6ofE4/N2rNQamWVGd9
+JuIAn3z5aNCBOE7ZvbAiUjdTT72GNL0a
+=oRC9
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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
+}