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| author |   Andrey Kislyuk <weaver@gentoo.org> | 2009-08-20 16:56:10 +0000 |
|---|---|---|
| committer | Andrey Kislyuk <weaver@gentoo.org> | 2009-08-20 16:56:10 +0000 |
| commit | 50fb05b65e184e9b3ead9fb1587587959b1cacc2 (patch) | |
| tree | 7064304505a28b01acc909b66b174ba149d45ad0 /sci-biology/allpaths | |
| parent | With thanks to Ondrej Filip, the build system can now handle parallel make. T... (diff) | |
| download | gentoo-2-50fb05b65e184e9b3ead9fb1587587959b1cacc2.tar.gz gentoo-2-50fb05b65e184e9b3ead9fb1587587959b1cacc2.tar.bz2 gentoo-2-50fb05b65e184e9b3ead9fb1587587959b1cacc2.zip | |
Fix compile issue on x86, bug 279711
(Portage version: 2.2_rc30/cvs/Linux x86_64, RepoMan options: --force)
Diffstat (limited to 'sci-biology/allpaths')
| -rw-r--r-- | sci-biology/allpaths/ChangeLog | 6 | ||||
| -rw-r--r-- | sci-biology/allpaths/allpaths-2.0.ebuild | 9 | ||||
| -rw-r--r-- | sci-biology/allpaths/files/allpaths-2.0-gcc-x86-no-autocast.patch | 30 |
3 files changed, 43 insertions, 2 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/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); + } |