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