M gnu/packages/bioinformatics.scm => gnu/packages/bioinformatics.scm +5 -24
@@ 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")
A gnu/packages/patches/vsearch-unbundle-cityhash.patch => gnu/packages/patches/vsearch-unbundle-cityhash.patch +73 -0
@@ 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"
+