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authorBen Woodcroft <donttrustben@gmail.com>2017-07-15 16:31:40 +1000
committerBen Woodcroft <donttrustben@gmail.com>2017-07-23 10:29:36 +1000
commitf3f68a442c1c40438078c24c0869e22c08f30c48 (patch)
treefac25a3ea7df9189e101e0589be3fda917bfec77 /gnu/packages/patches
parent897ab082b23109d7710ff11bb18360153295bed2 (diff)
gnu: metabat: Update to 2.11.1.
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1. [source]: Add patch to fix compilation. [arguments]: Adjust regular expressions modifying 'SConstruct'. * gnu/packages/patches/metabat-fix-compilation.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
Diffstat (limited to 'gnu/packages/patches')
-rw-r--r--gnu/packages/patches/metabat-fix-compilation.patch39
1 files changed, 39 insertions, 0 deletions
diff --git a/gnu/packages/patches/metabat-fix-compilation.patch b/gnu/packages/patches/metabat-fix-compilation.patch
new file mode 100644
index 0000000000..7086a96e86
--- /dev/null
+++ b/gnu/packages/patches/metabat-fix-compilation.patch
@@ -0,0 +1,39 @@
+This patch changes metabat so that (1) it is not build statically, (2) it uses
+shared libraries rather than static libraries where possible.
+
+diff --git a/SConstruct b/SConstruct
+index 69cdc0a..ac99bcb 100644
+--- a/SConstruct
++++ b/SConstruct
+@@ -26,8 +26,6 @@ debug = ARGUMENTS.get('DEBUG', None)
+ build_flags = ['-Wall', '-g', '-std=c++11', '-fopenmp']
+ link_flags = ['-lstdc++', '-lm', '-fopenmp']
+
+-if platform.platform(True, True).find('Darwin') == -1:
+- link_flags.extend(['-static', '-static-libgcc', '-static-libstdc++'])
+
+ if debug is None:
+ build_flags.extend(['-O3', '-DNDEBUG', '-Wno-unknown-pragmas', '-Wno-deprecated-declarations', '-Wno-overflow', '-Wno-unused-variable'])
+@@ -110,17 +108,17 @@ def findStaticOrShared( lib, testPaths, static_source_list, link_flag_list, stat
+ for path in testPaths:
+ if not os.path.isdir(path):
+ continue
++ for testfile in ('%s/lib%s.so' % (path, lib), '%s/lib%s.dylib' % (path, lib)):
++ if os.path.isfile(testfile):
++ print "Found shared library %s as %s" % (lib, testfile)
++ link_flag_list.extend( ["-L%s" % (path), "-l%s" % (lib) ] )
++ return
+ for suffix in staticSuffixes:
+ testfile = '%s/lib%s%s' % (path, lib, suffix)
+ if os.path.isfile(testfile):
+ static_source_list.append(testfile)
+ print "Found static library %s as %s" % (lib, testfile)
+ return
+- for testfile in ('%s/lib%s.so' % (path, lib), '%s/lib%s.dylib' % (path, lib)):
+- if os.path.isfile(testfile):
+- print "Found shared library %s as %s" % (lib, testfile)
+- link_flag_list.extend( ["-L%s" % (path), "-l%s" % (lib) ] )
+- return
+ print "Could not find library for %s!!! Looked in %s" % (lib, testPaths)
+ return
+