diff options
| author | Ben Woodcroft <donttrustben@gmail.com> | 2017-07-15 16:31:40 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2017-07-23 10:29:36 +1000 |
| commit | f3f68a442c1c40438078c24c0869e22c08f30c48 (patch) | |
| tree | fac25a3ea7df9189e101e0589be3fda917bfec77 /gnu/packages/patches | |
| parent | 897ab082b23109d7710ff11bb18360153295bed2 (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.patch | 39 |
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 + |