jlec 15/02/28 10:51:24 Modified: samtools-1.2-buildsystem.patch Log: Fix depend rules in make which break due to unbundling of htslib, #541134; use LD_LIBRARY_PATH druing tests (Portage version: 2.2.17/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)
Revision Changes Path 1.2 sci-biology/samtools/files/samtools-1.2-buildsystem.patch file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/files/samtools-1.2-buildsystem.patch?rev=1.2&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/files/samtools-1.2-buildsystem.patch?rev=1.2&content-type=text/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/files/samtools-1.2-buildsystem.patch?r1=1.1&r2=1.2 Index: samtools-1.2-buildsystem.patch =================================================================== RCS file: /var/cvsroot/gentoo-x86/sci-biology/samtools/files/samtools-1.2-buildsystem.patch,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- samtools-1.2-buildsystem.patch 18 Feb 2015 10:21:10 -0000 1.1 +++ samtools-1.2-buildsystem.patch 28 Feb 2015 10:51:24 -0000 1.2 @@ -1,8 +1,8 @@ - Makefile | 76 ++++++++++++++++++++++++++++++++++++---------------------------- - 1 file changed, 43 insertions(+), 33 deletions(-) + Makefile | 94 +++++++++++++++++++++++++++++++++++----------------------------- + 1 file changed, 52 insertions(+), 42 deletions(-) diff --git a/Makefile b/Makefile -index e368cee..bebb7af 100644 +index e368cee..9054526 100644 --- a/Makefile +++ b/Makefile @@ -21,11 +21,12 @@ @@ -136,6 +136,47 @@ test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_pretty_header test/merge/test_rtrans_build +@@ -191,31 +201,31 @@ check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) + test/split/test_parse_args + + +-test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o $(HTSLIB) ++test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o + $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o $(HTSLIB) $(LDLIBS) -lz + +-test/merge/test_pretty_header: test/merge/test_pretty_header.o $(HTSLIB) ++test/merge/test_pretty_header: test/merge/test_pretty_header.o + $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_pretty_header.o $(HTSLIB) $(LDLIBS) -lz + +-test/merge/test_rtrans_build: test/merge/test_rtrans_build.o $(HTSLIB) ++test/merge/test_rtrans_build: test/merge/test_rtrans_build.o + $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o $(HTSLIB) $(LDLIBS) -lz + +-test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o $(HTSLIB) ++test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o + $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o $(HTSLIB) $(LDLIBS) -lz + +-test/split/test_count_rg: test/split/test_count_rg.o test/test.o $(HTSLIB) ++test/split/test_count_rg: test/split/test_count_rg.o test/test.o + $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz + +-test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o $(HTSLIB) ++test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o + $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o $(HTSLIB) $(LDLIBS) -lz + +-test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o $(HTSLIB) ++test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o + $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz + +-test/split/test_parse_args: test/split/test_parse_args.o test/test.o $(HTSLIB) ++test/split/test_parse_args: test/split/test_parse_args.o test/test.o + $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o $(HTSLIB) $(LDLIBS) -lz + +-test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) ++test/vcf-miniview: test/vcf-miniview.o + $(CC) -pthread $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB) $(LDLIBS) -lz + + test_test_h = test/test.h $(htslib_sam_h) @@ -252,10 +262,10 @@ misc/md5sum-lite: misc/md5sum-lite.o misc/wgsim: misc/wgsim.o $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz
