Fix compile issue on x86, bug 279711

Package-Manager: portage-2.2_rc30/cvs/Linux x86_64
RepoMan-Options: --force

4 files changed, 46 insertions, 4 deletions

diff --git a/sci-biology/allpaths/ChangeLog b/sci-biology/allpaths/ChangeLog
index 470981c22678..56d1cae87f32 100644
--- a/sci-biology/allpaths/ChangeLog
+++ b/sci-biology/allpaths/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/allpaths
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/ChangeLog,v 1.2 2009/07/08 03:50:03 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/ChangeLog,v 1.3 2009/08/20 16:56:10 weaver Exp $
+
+  20 Aug 2009; Andrey Kislyuk <weaver@gentoo.org>
+  +files/allpaths-2.0-gcc-x86-no-autocast.patch, allpaths-2.0.ebuild:
+  Fix compile issue on x86, bug 279711
 
   07 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> allpaths-2.0.ebuild:
   Typo and collision fixes
diff --git a/sci-biology/allpaths/Manifest b/sci-biology/allpaths/Manifest
index 4c1e41e79758..1c2c3bdc07ae 100644
--- a/sci-biology/allpaths/Manifest
+++ b/sci-biology/allpaths/Manifest
@@ -1,5 +1,6 @@
+AUX allpaths-2.0-gcc-x86-no-autocast.patch 1481 RMD160 06ce2c1fe608621527e3af1b0e01e5efa8b8329a SHA1 565c480b4d48400b42af72c61919b2b52fd7c829 SHA256 933377d2066d6dd3c8015ad005a12fd60cb1b8e90e7a966d9ff52b8fa30c2338
 DIST allpaths-2.0.manual.docx 287123 RMD160 41a3792e2bc135462c22ee15c992a606b928145a SHA1 307bb76b8acedff289511d10a3e8a3b65278a4a4 SHA256 f89d15f31d511d6bad587562fa2539c1d5a37a097e4c3f33bb5a00d47fba7e69
 DIST allpaths-2.0.tar.gz 11211652 RMD160 cedffb29289c9229615c2ab72dca149722c4236a SHA1 a9cf07b59838aae714645f90cbf6f1407da69330 SHA256 16dce075e7b4ebd8924a79c765a7a7b87c01a68502e256ec200680ba42d95f02
-EBUILD allpaths-2.0.ebuild 1094 RMD160 fc02476303a5d831970297a16168c7bcdae210c2 SHA1 8a6ac609f89285244e9bb8b35a7fe06db9ee1c83 SHA256 96b6c4f15d20df1e9ae650c0d0e7389ed0b046ac2b4217c13e82026eaac9b267
-MISC ChangeLog 467 RMD160 cea1d6f7dfb4d8cc6933af8176ebdb97198b14ba SHA1 7389f01bd79b757e38b02d9cc14513cbf165a370 SHA256 ab26d30fe52c678c3e77e7282cbc84f9cecc8514addeefec9c19b99a1761ae8a
+EBUILD allpaths-2.0.ebuild 1185 RMD160 0f28968cc8dc9b8ce2ed06a9140ac3957c53ffce SHA1 ba46de00f351c4073f003ae100b7833f92051a17 SHA256 a814c18f62614f4ed0302ad197e3002151cb53e049762ed7c47868ceb271b3fb
+MISC ChangeLog 627 RMD160 008cb95a8a2a4ac42e5e44b1028f0329c5a15412 SHA1 2cc8d00613f95e1a2d8069f892d3dbeb5e78f4e4 SHA256 054b7a6637583c6a44385e2a9e438b1c31a8780a9d87285f24702543609b7c48
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/allpaths/allpaths-2.0.ebuild b/sci-biology/allpaths/allpaths-2.0.ebuild
index 3d8192db7c3f..5814ee571f3a 100644
--- a/sci-biology/allpaths/allpaths-2.0.ebuild
+++ b/sci-biology/allpaths/allpaths-2.0.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/allpaths/allpaths-2.0.ebuild,v 1.2 2009/07/08 03:50:03 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/allpaths-2.0.ebuild,v 1.3 2009/08/20 16:56:10 weaver Exp $
 
 EAPI="2"
 
+inherit base
+
 DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
 HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
 SRC_URI="ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-2-0/allpaths-2.0.tar.gz
@@ -18,9 +20,14 @@ KEYWORDS="~amd64 ~x86"
 DEPEND=">=sys-devel/gcc-4.3.2"
 RDEPEND=""
 
+PATCHES=(
+	"${FILESDIR}"/${P}-gcc-x86-no-autocast.patch
+)
+
 S="${WORKDIR}"
 
 src_prepare() {
+	base_src_prepare
 	rm -rf libxerces* xerces_include || die
 }
 
diff --git a/sci-biology/allpaths/files/allpaths-2.0-gcc-x86-no-autocast.patch b/sci-biology/allpaths/files/allpaths-2.0-gcc-x86-no-autocast.patch
new file mode 100644
index 000000000000..d4fe428efa26
--- /dev/null
+++ b/sci-biology/allpaths/files/allpaths-2.0-gcc-x86-no-autocast.patch
@@ -0,0 +1,30 @@
+diff -durr work.orig/SortKmersImpl.h work/SortKmersImpl.h
+--- work.orig/SortKmersImpl.h	2009-08-20 11:25:39.336695499 +0000
++++ work/SortKmersImpl.h	2009-08-20 11:25:51.431932630 +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);
+       }