Fix for bufferoverflow, #309341

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

4 files changed, 79 insertions, 6 deletions

diff --git a/sci-biology/muscle/ChangeLog b/sci-biology/muscle/ChangeLog
index 5d63f944b8b3..5afcd999262a 100644
--- a/sci-biology/muscle/ChangeLog
+++ b/sci-biology/muscle/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/muscle
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/ChangeLog,v 1.11 2010/06/24 20:47:35 angelos Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/ChangeLog,v 1.12 2010/06/28 20:30:00 jlec Exp $
+
+*muscle-3.7-r1 (28 Jun 2010)
+
+  28 Jun 2010; Justin Lecher <jlec@gentoo.org>
+  +files/3.7-bufferoverflow.patch, +muscle-3.7-r1.ebuild:
+  Fix for bufferoverflow, #309341
 
   24 Jun 2010; Christoph Mende <angelos@gentoo.org> muscle-3.7.ebuild:
   Stable on amd64 wrt bug #277980
diff --git a/sci-biology/muscle/Manifest b/sci-biology/muscle/Manifest
index 0c445d6553f2..6e4bf2b42614 100644
--- a/sci-biology/muscle/Manifest
+++ b/sci-biology/muscle/Manifest
@@ -1,19 +1,21 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA1
 
+AUX 3.7-bufferoverflow.patch 575 RMD160 1052b974dfa00bf7ce0ef98dd190e654e5221218 SHA1 649dfbbc4db3b8d83f8a488b04b217cf48d79465 SHA256 c55e807cc0c80d3374ea6261b568aad5b7c581fa3b23a6224974ce70af4a06dd
 AUX 3.8.31-make.patch 989 RMD160 22e88148f5701f5d7d6910c5f1bbd86e26220127 SHA1 2f55918397322ffe83464b3da5e3e5d972a40f63 SHA256 f5352a5fc8a792d7af177d1e829a33e59bc39dedb81baf17c6424f8520ea6879
 DIST muscle3.6_src.tar.gz 185267 RMD160 4afda92b982ec2b05853a582479c61a7d8814f51 SHA1 e8a4998ee10a8f067fd1ba63966e32e69da62d36 SHA256 32b818a51f421e1d687f513dc31374a330470950151a5e7df961e64781699431
 DIST muscle3.7_src.tar.gz 189907 RMD160 6eb64afd2032914781f453b925589c35e432b96c SHA1 6a3cbef3a8a00cf230f17bf90592f7108607d103 SHA256 a028f545612f9d260e35909959e98ae7aec552b1eac8806c3ae59cf1b00f7235
 DIST muscle3.8.31_src.tar.gz 515267 RMD160 18c9cf465f330a77d6a06ff9323c311a6f6be662 SHA1 2fe55db73ff4e7ac6d4ca692f8f213d1c5071dac SHA256 43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad
 EBUILD muscle-3.6.ebuild 847 RMD160 8a29fc7b68c5fb0c3680c513ede51aeaeaad4b11 SHA1 c38e5eebcf8f35e430f85f958de35083295ae0f0 SHA256 f3c041cb767be4e858a5854a03ee51e8424cd4197a7c723c4b28a46705a80c67
+EBUILD muscle-3.7-r1.ebuild 889 RMD160 50388fc702b5d9d3cecb527b0ae4175f8763400e SHA1 ac9ceff54bd84270180be2f7d4cafef5bcec0fa1 SHA256 f8b12e052d95621b9604ebcc677ac40f54d9fba3290e3d5e95a6528f2930f9cf
 EBUILD muscle-3.7.ebuild 844 RMD160 1335020b6dcd0b8107165ada30a4c2ce4790ed86 SHA1 36c7c37bed6ac9c26e2a74646a39131630084b92 SHA256 9c6826b8d266d05f79f61c6940b36dbc54adea197eaf19cfad605543f6517d2b
 EBUILD muscle-3.8.31.ebuild 733 RMD160 e4139817205be0c2e14060b03f9de2468675d050 SHA1 c0d18e04a0ff065fff8113fca508628d48346ecd SHA256 cca4af8de32649c613201dbdadb0e5090bcb72eaf5c27652866a50635c806c30
-MISC ChangeLog 1675 RMD160 f6393c8767d4b81f2bb27c3537cf30c58ea3dd07 SHA1 379b5dd0564ce3aec9645dc4681cd77618394d4a SHA256 3111d3de286998692dca57b39eb39f810d8ea56dc86a56eee2ee954cf8a4e0d3
+MISC ChangeLog 1842 RMD160 25862c30c6158545eed1ad7dbde8d10b71fecf04 SHA1 b9de92f72f17472b226487d83e31cd69d0484670 SHA256 159c335a44e98ced0bed3dfb3db8cb7274667dd95ffffc160d42f9706ae5f6f7
 MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
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 Version: GnuPG v2.0.15 (GNU/Linux)
 
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-+PCMS8nQGxyhg3zKgtgA/1tzX5EYttfm4R3yx31dGB87i4zMUAPa+mMLruZOxm0H
-=CwSi
+iEYEARECAAYFAkwpBk0ACgkQgAnW8HDreRb05ACfbkAApihWWkoLVPr73deAmqa1
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+=tKEG
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diff --git a/sci-biology/muscle/files/3.7-bufferoverflow.patch b/sci-biology/muscle/files/3.7-bufferoverflow.patch
new file mode 100644
index 000000000000..62dab42e3cb5
--- /dev/null
+++ b/sci-biology/muscle/files/3.7-bufferoverflow.patch
@@ -0,0 +1,22 @@
+--- libMUSCLE/globalslinux.cpp.old	2010-03-14 19:03:14.000000000 +1300
++++ libMUSCLE/globalslinux.cpp	2010-03-14 19:11:09.000000000 +1300
+@@ -159,7 +159,7 @@
+ 			}
+ 		return DEFAULT_RAM;
+ 		}
+-	int Bytes = atoi(pMem+9)*1000;
++	long Bytes = atol(pMem+9)*1000;
+ 	return ((double) Bytes)/1e6;
+ 	}
+ 
+--- libMUSCLE/progress.cpp.old	2010-03-14 19:50:27.000000000 +1300
++++ libMUSCLE/progress.cpp	2010-03-14 19:51:07.000000000 +1300
+@@ -48,7 +48,7 @@
+ 	if (MB < 0)
+ 		return "";
+ 
+-	static char Str[9];
++	static char Str[16];
+ 	static double MaxMB = 0;
+ 	static double RAMMB = 0;
+ 
diff --git a/sci-biology/muscle/muscle-3.7-r1.ebuild b/sci-biology/muscle/muscle-3.7-r1.ebuild
new file mode 100644
index 000000000000..e2b1b7ca4b0c
--- /dev/null
+++ b/sci-biology/muscle/muscle-3.7-r1.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/muscle-3.7-r1.ebuild,v 1.1 2010/06/28 20:30:00 jlec Exp $
+
+EAPI="3"
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}${PV}_src"
+DESCRIPTION="Multiple sequence comparison by log-expectation"
+HOMEPAGE="http://www.drive5.com/muscle/"
+SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+
+RDEPEND="!sci-libs/libmuscle"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
+
+src_prepare() {
+	epatch"${FILESDIR}"/${PV}-bufferoverflow.patch
+	sed -i \
+		"s:-static::g" \
+		"${S}/Makefile"
+	sed -i \
+		"/strip/d" \
+		"${S}/Makefile"
+}
+
+src_compile() {
+	emake \
+		GPP="$(tc-getCXX)" \
+		CFLAGS="${CXXFLAGS}" \
+		|| die "make failed"
+}
+
+src_install() {
+	dobin muscle || die
+}