diff options
| author | Ben Woodcroft <donttrustben@gmail.com> | 2017-02-09 21:13:39 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2017-02-09 21:21:29 +1000 |
| commit | 206af46fe1cc0627e4846167aa5e7c095b21afe3 (patch) | |
| tree | df744fa0a06d890d3c3baed843f9f765fdb705f6 /gnu/packages/patches/vsearch-unbundle-cityhash.patch | |
| parent | c8916c3336154f1933a59883d4e1da9f23249a09 (diff) | |
gnu: vsearch: Update to 2.4.0.
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.0.
[source]: Convert most operations in the snippet to patch form and adjust
for 2.4.0.
* gnu/packages/patches/vsearch-unbundle-cityhash.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
Diffstat (limited to 'gnu/packages/patches/vsearch-unbundle-cityhash.patch')
| -rw-r--r-- | gnu/packages/patches/vsearch-unbundle-cityhash.patch | 73 |
1 files changed, 73 insertions, 0 deletions
diff --git a/gnu/packages/patches/vsearch-unbundle-cityhash.patch b/gnu/packages/patches/vsearch-unbundle-cityhash.patch new file mode 100644 index 0000000000..b1ecb1f063 --- /dev/null +++ b/gnu/packages/patches/vsearch-unbundle-cityhash.patch @@ -0,0 +1,73 @@ +diff --git a/src/Makefile.am b/src/Makefile.am +index e56a8a2..4adcc48 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -3,7 +3,7 @@ bin_PROGRAMS = $(top_builddir)/bin/vsearch + if TARGET_PPC + AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8 + else +-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g ++AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -lcityhash + endif + + AM_CFLAGS=$(AM_CXXFLAGS) +@@ -18,8 +18,6 @@ allpairs.h \ + arch.h \ + bitmap.h \ + chimera.h \ +-city.h \ +-citycrc.h \ + cluster.h \ + cpu.h \ + db.h \ +@@ -59,31 +57,26 @@ xstring.h + + if TARGET_PPC + libcpu_a_SOURCES = cpu.cc $(VSEARCHHEADERS) +-noinst_LIBRARIES = libcpu.a libcityhash.a ++noinst_LIBRARIES = libcpu.a + else + libcpu_sse2_a_SOURCES = cpu.cc $(VSEARCHHEADERS) + libcpu_sse2_a_CXXFLAGS = $(AM_CXXFLAGS) -msse2 + libcpu_ssse3_a_SOURCES = cpu.cc $(VSEARCHHEADERS) + libcpu_ssse3_a_CXXFLAGS = $(AM_CXXFLAGS) -mssse3 -DSSSE3 +-noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a libcityhash.a ++noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a + endif + +-libcityhash_a_SOURCES = city.cc city.h +- + if TARGET_WIN + +-libcityhash_a_CXXFLAGS = -Wall -Wno-sign-compare -O3 -g -D_MSC_VER +-__top_builddir__bin_vsearch_LDFLAGS = -static +-__top_builddir__bin_vsearch_LDADD = libregex.a libcityhash.a libcpu_ssse3.a libcpu_sse2.a ++__top_builddir__bin_vsearch_LDFLAGS = -static -lcityhash ++__top_builddir__bin_vsearch_LDADD = libregex.a libcpu_ssse3.a libcpu_sse2.a + + else + +-libcityhash_a_CXXFLAGS = -Wall -Wno-sign-compare -O3 -g +- + if TARGET_PPC +-__top_builddir__bin_vsearch_LDADD = libcityhash.a libcpu.a ++__top_builddir__bin_vsearch_LDADD = libcpu.a + else +-__top_builddir__bin_vsearch_LDADD = libcityhash.a libcpu_ssse3.a libcpu_sse2.a ++__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a libcpu_sse2.a + endif + + endif +diff --git a/src/vsearch.h b/src/vsearch.h +index f2c244b..5f51bbe 100644 +--- a/src/vsearch.h ++++ b/src/vsearch.h +@@ -148,7 +148,7 @@ + #include <bzlib.h> + #endif + +-#include "city.h" ++#include <city.h> + #include "md5.h" + #include "sha1.h" + |