01/01: gnu: vsearch: Update to 2.4.0.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 206af46fe1cc0627e4846167aa5e7c095b21afe3
Author: Ben Woodcroft <address@hidden>
Date:   Thu Feb 9 21:13:39 2017 +1000

    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.
---
 gnu/packages/bioinformatics.scm                    | 29 ++-------
 .../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 d708995..a448b51 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 0000000..b1ecb1f
--- /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"
+