Add patch for bug 279087

Package-Manager: portage-2.2_rc30/cvs/Linux x86_64

4 files changed, 54 insertions, 4 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/Manifest b/sci-biology/vaal/Manifest
index 8c3a31bc3fcd..74d91403e41e 100644
--- a/sci-biology/vaal/Manifest
+++ b/sci-biology/vaal/Manifest
@@ -1,5 +1,6 @@
+AUX vaal-1.2-gcc-x86-no-autocast.patch 1877 RMD160 dbcac734c896600c89c7c2ab73abeb03374a0bad SHA1 607371fad2443a65151b15ad6f08d4462056415b SHA256 a365d038dffdf6ea1ece2a0e55426c436f457b3cb0e640345decb00f2849a285
 DIST VAAL.1.2.tgz 978333 RMD160 f81c1a33348e7c2ef2a6b07c1ceeeda564b9b521 SHA1 f51a4000149cbd9ae674ee0d7781c27aee6e31a9 SHA256 cfb9d73fd4ac5720f65b54e7f763e28a503d65c61269939d5f43dbf88dd17375
 DIST VAAL_manual.doc 48128 RMD160 08d809c847f1842483ed653df9bb6ed5ee1d10a8 SHA1 836f8be0f0200358131c23174eeca5d2d7454a68 SHA256 08b662105e8db41b33ea5d6626b58d5a5d793b1dd40fdc663a7068d9abacdc83
-EBUILD vaal-1.2.ebuild 949 RMD160 2a8b9da80cc55398859756ea1ba6add9980bacf4 SHA1 85a4a693ebd6e9b8645183a1e13346085b811553 SHA256 2c8afcf6a8061ac1aa348f09c16c887e742a8b5c082064f343ee1d816337c927
-MISC ChangeLog 352 RMD160 486e5124d5021deba42184e8e1ca552998c6e803 SHA1 715b17c19a7a44ffcd6460be699bec2b829abce8 SHA256 835fae330ddd3a35614278b9bc98ac9ce68661eb158e5f6266677bdf69e7ba7f
+EBUILD vaal-1.2.ebuild 1022 RMD160 f32412dc1334abd2a37ba5c6de7aa59fa814c42d SHA1 6758a31d9e919314d7a1cec542afb7d5c4191842 SHA256 a20d3ee056326efa0070f31f6a88c0dbc155125453cc3bdfb9652ae9277fbb47
+MISC ChangeLog 492 RMD160 317d41aefeda3e1380c0ce6f19180543e187c9f8 SHA1 aa743688886fe7aed48c4e6652aa525e9efa4800 SHA256 281fe5106905a6cb80af821cb1a459fd7eabbec6eb5de07ed64b7fe616a0da85
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
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() {