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| author |   Andrey Kislyuk <weaver@gentoo.org> | 2009-11-12 18:45:24 +0000 |
|---|---|---|
| committer | Andrey Kislyuk <weaver@gentoo.org> | 2009-11-12 18:45:24 +0000 |
| commit | e4b3f0b0559fb90c7cb00faebaa607390b274ce7 (patch) | |
| tree | 0a56dd4ebaf89a41ad7da357b3dcfdf14f126779 /sci-biology | |
| parent | Dropped vulnerable version, thank Alex Legler for request. (diff) | |
| download | gentoo-2-e4b3f0b0559fb90c7cb00faebaa607390b274ce7.tar.gz gentoo-2-e4b3f0b0559fb90c7cb00faebaa607390b274ce7.tar.bz2 gentoo-2-e4b3f0b0559fb90c7cb00faebaa607390b274ce7.zip | |
Add patch for bug 279087
(Portage version: 2.2_rc30/cvs/Linux x86_64)
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/vaal/ChangeLog | 6 | ||||
| -rw-r--r-- | sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch | 39 | ||||
| -rw-r--r-- | sci-biology/vaal/vaal-1.2.ebuild | 8 |
3 files changed, 51 insertions, 2 deletions
diff --git a/sci-biology/vaal/ChangeLog b/sci-biology/vaal/ChangeLog index 26188892693a..349ee153ecc3 100644 --- a/sci-biology/vaal/ChangeLog +++ b/sci-biology/vaal/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/vaal # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/ChangeLog,v 1.1 2009/07/08 03:52:35 weaver Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/ChangeLog,v 1.2 2009/11/12 18:45:22 weaver Exp $ + + 12 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> + +files/vaal-1.2-gcc-x86-no-autocast.patch, vaal-1.2.ebuild: + Add patch for bug 279087 *vaal-1.2 (07 Jul 2009) diff --git a/sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch b/sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch new file mode 100644 index 000000000000..c021fadb44b1 --- /dev/null +++ b/sci-biology/vaal/files/vaal-1.2-gcc-x86-no-autocast.patch @@ -0,0 +1,39 @@ +diff -durr VAAL.orig/SortKmersImpl.h VAAL/SortKmersImpl.h +--- VAAL.orig/SortKmersImpl.h 2009-11-12 13:02:40.116993289 +0000 ++++ VAAL/SortKmersImpl.h 2009-11-12 13:04:59.416388534 +0000 +@@ -98,7 +98,7 @@ + { if ( reads[l].size( ) < KSPAN ) continue; + unsigned int N = reads[l].size( ) - KSPAN + 1; + if ( S + 2*N >= R.size( ) ) { +- unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) ); ++ unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) ); + if ( nn < R.size( ) ) FatalErr( "SortKmers<1>: Unsigned-int overflow (R=" << R.size( ) << ")" ); + R.resize(nn); + } +@@ -180,7 +180,7 @@ + } + if ( q == N ) break; + if ( S + 2*N >= R.size( ) ) { +- unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) ); ++ unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) ); + if ( nn < R.size( ) ) FatalErr( "SortKmers<10>: Unsigned-int overflow (R=" << R.size( ) << ")" ); + R.resize(nn); + } +@@ -207,7 +207,7 @@ + top += Min( N - top, (unsigned int) 10000 ); + + if ( S + 20000 >= R.size( ) || S + 2*N >= R.size( ) ) { +- unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) ); ++ unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) ); + if ( nn < R.size( ) ) FatalErr( "SortKmers<10>: Unsigned-int overflow (R=" << R.size( ) << ")" ); + R.resize(nn); + } +@@ -318,7 +318,7 @@ + + top += Min( N - top, 10000 ); + if ( S + 2*(top - q) >= R.size( ) ) { +- unsigned nn = Max( (unsigned) ( 1.2 * R.size( ) ), (S + 2*(top - q)) ); ++ unsigned nn = Max( (unsigned) ( 1.2 * R.size( ) ), (unsigned) (S + 2*(top - q)) ); + if ( nn < R.size( ) ) FatalErr( "SortKmers<100>: Unsigned-int overflow (R=" << R.size( ) << ")" ); + R.resize(nn); + } diff --git a/sci-biology/vaal/vaal-1.2.ebuild b/sci-biology/vaal/vaal-1.2.ebuild index 7dc50a0c6ba9..b1331c1f320e 100644 --- a/sci-biology/vaal/vaal-1.2.ebuild +++ b/sci-biology/vaal/vaal-1.2.ebuild @@ -1,9 +1,11 @@ # Copyright 1999-2009 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/vaal-1.2.ebuild,v 1.1 2009/07/08 03:52:35 weaver Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/vaal-1.2.ebuild,v 1.2 2009/11/12 18:45:22 weaver Exp $ EAPI="2" +inherit base + DESCRIPTION="A variant ascertainment algorithm that can be used to detect SNPs, indels, and other polymorphisms" HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd" SRC_URI="ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL.1.2.tgz @@ -17,6 +19,10 @@ KEYWORDS="~amd64 ~x86" DEPEND=">=dev-libs/boost-1.37.0" RDEPEND="${DEPEND}" +PATCHES=( + "${FILESDIR}"/${P}-gcc-x86-no-autocast.patch +) + S="${WORKDIR}/VAAL" src_install() { |