Git-Url: http://git.frugalware.org/gitweb/gitweb.cgi?p=frugalware-current.git;a=commitdiff;h=0ad130d260280c00d90cd5b451870dd2c869d8a9
commit 0ad130d260280c00d90cd5b451870dd2c869d8a9 Author: James Buren <[email protected]> Date: Sun Sep 28 04:10:41 2014 -0500 abyss-1.3.7-3-x86_64 * attempt to fix build time error on i686 * drop unused patch diff --git a/source/devel-extra/abyss/FrugalBuild b/source/devel-extra/abyss/FrugalBuild index 826440f..aefad3d 100644 --- a/source/devel-extra/abyss/FrugalBuild +++ b/source/devel-extra/abyss/FrugalBuild @@ -3,7 +3,7 @@ pkgname=abyss pkgver=1.3.7 -pkgrel=2 +pkgrel=3 pkgdesc="A de novo, parallel, paired-end sequence assembler" url="http://www.bcgsc.ca/platform/bioinfo/software/abyss"; depends=('openmpi>=1.8' 'libboost>=1.50.0') @@ -11,8 +11,9 @@ makedepends=('boost>=1.50.0' 'google-sparsehash') groups=('devel-extra') archs=('i686' 'x86_64') up2date="Flasttar $url" -source=(http://bcgsc.ca/downloads/$pkgname/$pkgname-$pkgver.tar.gz) -sha1sums=('3d0831b1b7fd0601ded7c2d01938a24b3fc1931a') +source=(http://bcgsc.ca/downloads/$pkgname/$pkgname-$pkgver.tar.gz fixes.patch) +sha1sums=('3d0831b1b7fd0601ded7c2d01938a24b3fc1931a' \ + '2d34d8e1fdc57c9b3f2b494b55076d10d596dc1c') CXXFLAGS="-Wno-unused-local-typedefs" # optimization OK diff --git a/source/devel-extra/abyss/abyss-fixmate.patch b/source/devel-extra/abyss/abyss-fixmate.patch deleted file mode 100644 index f3afc66..0000000 --- a/source/devel-extra/abyss/abyss-fixmate.patch +++ /dev/null @@ -1,14 +0,0 @@ -diff -rpN abyss-1.3.3~/ParseAligns/abyss-fixmate.cc abyss-1.3.3/ParseAligns/abyss-fixmate.cc -*** abyss-1.3.3~/ParseAligns/abyss-fixmate.cc 2012-05-27 11:17:52.808962276 -0500 ---- abyss-1.3.3/ParseAligns/abyss-fixmate.cc 2012-05-27 11:18:11.698858619 -0500 -*************** -*** 15,20 **** ---- 15,22 ---- - #include <iterator> - #include <sstream> - #include <string> -+ #include <inttypes.h> -+ #include <unistd.h> - - using namespace std; - diff --git a/source/devel-extra/abyss/fixes.patch b/source/devel-extra/abyss/fixes.patch new file mode 100644 index 0000000..d0db410 --- /dev/null +++ b/source/devel-extra/abyss/fixes.patch @@ -0,0 +1,12 @@ +diff -ur a/connectpairs/connectpairs.cc b/connectpairs/connectpairs.cc +--- a/connectpairs/connectpairs.cc 2013-12-10 14:11:49.000000000 -0600 ++++ b/connectpairs/connectpairs.cc 2014-09-28 04:09:15.624831649 -0500 +@@ -85,7 +85,7 @@ + unsigned k; + + /** An estimate of the size of the genome. */ +- size_t genomeSize = 3000000000; ++ size_t genomeSize = 3000000000UL; + + /** Write the de Bruijn graph to this file. */ + static string graphPath; _______________________________________________ Frugalware-git mailing list [email protected] http://frugalware.org/mailman/listinfo/frugalware-git
