diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 29 | ||||
| -rw-r--r-- | gnu/packages/patches/vsearch-unbundle-cityhash.patch | 73 |
2 files changed, 78 insertions, 24 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d7089959ea..a448b51c6c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5748,7 +5748,7 @@ track. The database is exposed as a @code{TxDb} object.") (define-public vsearch (package (name "vsearch") - (version "2.3.4") + (version "2.4.0") (source (origin (method url-fetch) @@ -5758,31 +5758,12 @@ track. The database is exposed as a @code{TxDb} object.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1xyraxmhyx62mxx8z7c8waygvcijwkh48ms1ar60w2cv2y2sn4al")) - (modules '((guix build utils))) + "007q9a50hdw4vs2iajabvbw7qccml4r8cbqzyi5ipkkf42jk3vnr")) + (patches (search-patches "vsearch-unbundle-cityhash.patch")) (snippet '(begin - ;; Remove bundled cityhash and '-mtune=native'. - (substitute* "src/Makefile.am" - (("^AM_CXXFLAGS=-I\\$\\{srcdir\\}/cityhash \ --O3 -mtune=native -Wall -Wsign-compare") - (string-append "AM_CXXFLAGS=-lcityhash" - " -O3 -Wall -Wsign-compare")) - (("^__top_builddir__bin_vsearch_SOURCES = city.h \\\\") - "__top_builddir__bin_vsearch_SOURCES = \\") - (("^city.h \\\\") "\\") - (("^citycrc.h \\\\") "\\") - (("^libcityhash_a.*") "") - (("noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a \ -libcityhash.a") - "noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a") - (("__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a \ -libcpu_sse2.a libcityhash.a") - "__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a \ -libcpu_sse2.a -lcityhash")) - (substitute* "src/vsearch.h" - (("^\\#include \"city.h\"") "#include <city.h>") - (("^\\#include \"citycrc.h\"") "#include <citycrc.h>")) + ;; Remove bundled cityhash sources. The vsearch source is adjusted + ;; for this in the patch. (delete-file "src/city.h") (delete-file "src/citycrc.h") (delete-file "src/city.cc") 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" + |