diff options
Diffstat (limited to 'sci-biology/muscle')
| -rw-r--r-- | sci-biology/muscle/ChangeLog | 8 | ||||
| -rw-r--r-- | sci-biology/muscle/files/3.7-bufferoverflow.patch | 22 | ||||
| -rw-r--r-- | sci-biology/muscle/muscle-3.7-r1.ebuild | 43 |
3 files changed, 72 insertions, 1 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/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 +} |