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| author |   David Seifert <soap@gentoo.org> | 2016-09-25 11:24:17 +0200 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2016-09-25 11:39:01 +0200 |
| commit | bdf7251db30941f3912dd646d37fb125fbabf018 (patch) | |
| tree | b3e9888c3084c07f8dae49138903d10a53f4f546 /sci-biology/vcftools/files | |
| parent | app-arch/snappy: x86 stable wrt bug #595026 (diff) | |
| download | gentoo-bdf7251db30941f3912dd646d37fb125fbabf018.tar.gz gentoo-bdf7251db30941f3912dd646d37fb125fbabf018.tar.bz2 gentoo-bdf7251db30941f3912dd646d37fb125fbabf018.zip | |
sci-biology/vcftools: Version bump to 0.1.14
Gentoo-bug: 594924
* EAPI=6
* Properly RDEPEND on dev-lang/perl
Package-Manager: portage-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/2407
Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology/vcftools/files')
| -rw-r--r-- | sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch | 50 |
1 files changed, 50 insertions, 0 deletions
diff --git a/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch b/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch new file mode 100644 index 000000000000..126a709385db --- /dev/null +++ b/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch @@ -0,0 +1,50 @@ +* Add prefix in Makefiles, not the configure script +* Use AC_SEARCH_LIBS instead of AC_CHECK_LIB, + as it is more flexible and helps us with LAPACK +* Use correct ZLIB_CFLAGS instead of non-existent ZLIB_CPPFLAGS + +--- a/configure.ac ++++ b/configure.ac +@@ -34,7 +34,7 @@ + [--with-pmdir=DIR], + [install Perl modules in DIR]), + [PMDIR=${withval}], +- [PMDIR='${prefix}'/"$pmdir_relative_path"]) ++ [PMDIR="$pmdir_relative_path"]) + + AC_SUBST([PMDIR]) + +@@ -73,9 +73,9 @@ + [pca=${enableval}], + [pca=no]) + +-if test "x${pca}" = "xyes" ; then +- AC_CHECK_LIB(lapack, dgeev_) +-fi ++AS_IF([test "x${pca}" = "xyes"],[ ++ AC_SEARCH_LIBS([dgeev_], [lapack]) ++]) + + # Generate output. + AC_CONFIG_FILES([Makefile +--- a/src/cpp/Makefile.am ++++ b/src/cpp/Makefile.am +@@ -1,6 +1,6 @@ + bin_PROGRAMS = vcftools + +-vcftools_CPPFLAGS = $(ZLIB_CPPFLAGS) ++vcftools_CPPFLAGS = $(ZLIB_CFLAGS) + vcftools_LDADD = $(ZLIB_LIBS) + + vcftools_SOURCES = \ +--- a/src/perl/Makefile.am ++++ b/src/perl/Makefile.am +@@ -24,7 +24,7 @@ + vcf-tstv \ + vcf-validator + +-pmdir = $(PMDIR) ++pmdir = $(exec_prefix)/$(PMDIR) + + dist_pm_DATA = \ + FaSlice.pm \ |