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

Package-Manager: portage-2.2.0_alpha26/cvs/Linux x86_64

4 files changed, 44 insertions, 15 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/Manifest b/sci-biology/recon/Manifest
index c760ad24ecfe..6a3f92d2c7b0 100644
--- a/sci-biology/recon/Manifest
+++ b/sci-biology/recon/Manifest
@@ -1,4 +1,15 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 1.06-buffer-overflow.patch 361 RMD160 b53d960bd4b0f021727aecf53317ba136ac15a28 SHA1 d1b5855796904e4f5881532f53e6f382492f95a1 SHA256 e277cff1aa21475bc83f5d554092180ab2137aa9e2a0538bcfe5a54ecad21a1d
 DIST RECON1.06.tar.gz 109484 RMD160 c232cd052d360625d5d841ff29db75710988bf82 SHA1 a46d564a4a52fbd1b9a686897ffec97020334313 SHA256 6e106adb546952ecdfe7e9c1b56a4a80581383446c63abbe0c61c53af0e67461
-EBUILD recon-1.06.ebuild 917 RMD160 e4cb782a2ae4520eea61fdfcccf9ce54893ae609 SHA1 8e999cd0770ace94778ad5094df31a66091f8938 SHA256 280bf64fdad328bd5eb9eb671aae7adb63bb00c810b96ab2f700c470dd71bc7a
-MISC ChangeLog 399 RMD160 62763e81af6f3143d87c22d0c6778919b405d5c1 SHA1 deb29473f46763f6b5e765d877742fbf560d42cc SHA256 76b15b2e066060a28c6d6cd2f55d43818bed4068a22c4fdb8e6da14bf68a7b68
+EBUILD recon-1.06-r1.ebuild 955 RMD160 343e51a3e886cebfc8b34a2603d3f49da194f5fd SHA1 cdf2b11d88ac01cb6c015d1839931c663a5ec7fa SHA256 3c0d17a1f74da52b58592189eda9e0c9779d746175e473c03356ba0597d2a13d
+MISC ChangeLog 612 RMD160 8e61479a2c500fbc8c5a9f0f45ee5d0dc77507ad SHA1 921acd90cbfa30c9d04efbc976cea5b628d9665b SHA256 8649e6c6e5562c0a66347897ea2fa13d6a654192cf055b53262c3ad445943822
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.17 (GNU/Linux)
+
+iEYEARECAAYFAk14sjQACgkQgAnW8HDreRawZgCgqgt5LlAhCMamRL770EknhqbB
+DFYAn3HSYUoDYMPmOELrMb5PsMUszQAM
+=/aLn
+-----END PGP SIGNATURE-----
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
 }