diff options
author | V3n3RiX <venerix@redcorelinux.org> | 2020-09-30 17:27:54 +0100 |
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committer | V3n3RiX <venerix@redcorelinux.org> | 2020-09-30 17:27:54 +0100 |
commit | f70a1bfc721336d4fc7dfb711c2f518a6b18cf16 (patch) | |
tree | e907cb121b30e3c1df1710719c0ddf4029597a47 /sci-biology/bwa/files | |
parent | db063b515939ab15261136b24e4bc44386335c0c (diff) |
gentoo resync : 30.09.2020
Diffstat (limited to 'sci-biology/bwa/files')
-rw-r--r-- | sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 | ||||
-rw-r--r-- | sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch | 7 | ||||
-rw-r--r-- | sci-biology/bwa/files/bwa-0.7.17-Makefile.patch | 42 | ||||
-rw-r--r-- | sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch | 11 |
4 files changed, 53 insertions, 34 deletions
diff --git a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch deleted file mode 100644 index 39b437a02897..000000000000 --- a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch +++ /dev/null @@ -1,27 +0,0 @@ ---- bwa-0.7.13/Makefile -+++ bwa-0.7.13/Makefile -@@ -1,8 +1,8 @@ --CC= gcc -+CC?= gcc - #CC= clang --analyze --CFLAGS= -g -Wall -Wno-unused-function -O2 -+CFLAGS?= -g -Wall -Wno-unused-function -O2 - WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS --AR= ar -+AR?= ar - DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) - LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o - AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ -@@ -26,10 +26,10 @@ - all:$(PROG) - - bwa:libbwa.a $(AOBJS) main.o -- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) - - bwamem-lite:libbwa.a example.o -- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) - - libbwa.a:$(LOBJS) - $(AR) -csru $@ $(LOBJS) diff --git a/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch b/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch deleted file mode 100644 index 40056ffeaaa9..000000000000 --- a/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch +++ /dev/null @@ -1,7 +0,0 @@ ---- a/rle.h -+++ b/rle.h -@@ -32,3 +32,3 @@ extern "C" { - --const uint8_t rle_auxtab[8]; -+extern const uint8_t rle_auxtab[8]; - diff --git a/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch new file mode 100644 index 000000000000..944369cb75e2 --- /dev/null +++ b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch @@ -0,0 +1,42 @@ +--- a/Makefile ++++ b/Makefile +@@ -1,9 +1,7 @@ +-CC= gcc + #CC= clang --analyze +-CFLAGS= -g -Wall -Wno-unused-function -O2 ++CFLAGS+= -Wall -Wno-unused-function + WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS +-AR= ar +-DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) ++CPPFLAGS+= -DHAVE_PTHREAD $(WRAP_MALLOC) + LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o \ + QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o + AOBJS= bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ +@@ -21,16 +19,13 @@ + + .SUFFIXES:.c .o .cc + +-.c.o: +- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ +- + all:$(PROG) + + bwa:libbwa.a $(AOBJS) main.o +- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) + + bwamem-lite:libbwa.a example.o +- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) example.o -o $@ -L. -lbwa $(LIBS) + + libbwa.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) +@@ -39,7 +34,7 @@ + rm -f gmon.out *.o a.out $(PROG) *~ *.a + + depend: +- ( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c ) ++ ( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c ) + + # DO NOT DELETE THIS LINE -- make depend depends on it. + diff --git a/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch b/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch new file mode 100644 index 000000000000..1babb8356c4a --- /dev/null +++ b/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch @@ -0,0 +1,11 @@ +--- a/rle.h ++++ b/rle.h +@@ -30,7 +30,7 @@ + *** 43+3 codec *** + ******************/ + +-const uint8_t rle_auxtab[8]; ++extern const uint8_t rle_auxtab[8]; + + #define RLE_MIN_SPACE 18 + #define rle_nptr(block) ((uint16_t*)(block)) |