Fixes for buffer overflow, #358195, USE=examples added

(Portage version: 2.2.0_alpha26/cvs/Linux x86_64)

3 files changed, 31 insertions, 13 deletions

diff --git a/sci-biology/recon/ChangeLog b/sci-biology/recon/ChangeLog
index 9eadd5462034..618f3a099331 100644
--- a/sci-biology/recon/ChangeLog
+++ b/sci-biology/recon/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/recon
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/recon/ChangeLog,v 1.1 2011/02/03 01:58:47 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/recon/ChangeLog,v 1.2 2011/03/10 11:12:46 jlec Exp $
+
+*recon-1.06-r1 (10 Mar 2011)
+
+  10 Mar 2011; Justin Lecher <jlec@gentoo.org>
+  +files/1.06-buffer-overflow.patch, -recon-1.06.ebuild, +recon-1.06-r1.ebuild:
+  Fixes for buffer overflow, #358195, USE=examples added
 
 *recon-1.06 (03 Feb 2011)
 
diff --git a/sci-biology/recon/files/1.06-buffer-overflow.patch b/sci-biology/recon/files/1.06-buffer-overflow.patch
new file mode 100644
index 000000000000..29d220c7310d
--- /dev/null
+++ b/sci-biology/recon/files/1.06-buffer-overflow.patch
@@ -0,0 +1,13 @@
+diff --git a/src/eledef.c b/src/eledef.c
+index 964890b..a001ec4 100644
+--- a/src/eledef.c
++++ b/src/eledef.c
+@@ -385,7 +385,7 @@ void ele_def(int method, FILE *frags, float cutoff, EPROT_t **all_epp, int *ecp,
+ 
+ void img_charge(IPROT_t **shadow, int ct, FILE *input) {
+   int i=0, pos=0;
+-  char line[100];
++  char line[256];
+   int scan_flag;
+   MSP_t msp;
+ 
diff --git a/sci-biology/recon/recon-1.06.ebuild b/sci-biology/recon/recon-1.06-r1.ebuild
index 2592816d1191..ce588df29cf4 100644
--- a/sci-biology/recon/recon-1.06.ebuild
+++ b/sci-biology/recon/recon-1.06-r1.ebuild
@@ -1,37 +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/recon/recon-1.06.ebuild,v 1.1 2011/02/03 01:58:47 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/recon/recon-1.06-r1.ebuild,v 1.1 2011/03/10 11:12:46 jlec Exp $
 
-EAPI="3"
+EAPI="4"
+
+inherit eutils
 
 DESCRIPTION="Automated de novo identification of repeat families from genomic sequences"
-HOMEPAGE="http://selab.janelia.org/recon.html
-	http://www.repeatmasker.org/RepeatModeler.html"
+HOMEPAGE="http://selab.janelia.org/recon.html http://www.repeatmasker.org/RepeatModeler.html"
 SRC_URI="http://www.repeatmasker.org/RECON${PV}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
-IUSE=""
+IUSE="examples"
 KEYWORDS="~amd64 ~x86"
 
-DEPEND=""
-RDEPEND="${DEPEND}"
-
 S="${WORKDIR}/RECON${PV}"
 
 src_prepare() {
+	epatch "${FILESDIR}"/${PV}-buffer-overflow.patch
 	sed -i 's|$path = "";|$path = "/usr/libexec/'${PN}'";|' scripts/recon.pl || die
 }
 
 src_compile() {
-	emake -C src || die
+	emake -C src
 }
 
 src_install() {
-	dobin scripts/* || die
+	dobin scripts/*
 	exeinto /usr/libexec/${PN}
-	doexe src/{edgeredef,eledef,eleredef,famdef,imagespread} || die
+	doexe src/{edgeredef,eledef,eleredef,famdef,imagespread}
 	dodoc 00README
 	insinto /usr/share/${PN}
-	doins -r Demos
+	use examples && doins -r Demos
 }