commit: bdf7251db30941f3912dd646d37fb125fbabf018 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Sep 25 09:24:17 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Sep 25 09:39:01 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bdf7251d
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 <AT> gentoo.org> sci-biology/vcftools/Manifest | 1 + .../files/vcftools-0.1.14-buildsystem.patch | 50 ++++++++++++++++++++++ sci-biology/vcftools/vcftools-0.1.14.ebuild | 39 +++++++++++++++++ 3 files changed, 90 insertions(+) diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest index acbb214..9a014b1 100644 --- a/sci-biology/vcftools/Manifest +++ b/sci-biology/vcftools/Manifest @@ -1 +1,2 @@ +DIST vcftools-0.1.14.tar.gz 342369 SHA256 76d799dd9afcb12f1ed42a07bc2886cd1a989858a4d047f24d91dcf40f608582 SHA512 863a16b3b20d392deba7f04310af95f1ab21be537273692aa104e22d737af2eb1bc54a768af954f06188e0500e4f7a032d1189886eb3a439b108cb8189b14eb7 WHIRLPOOL 6de2e33a9882cb5567e2e22605a14851a7b1b458ec4152c87986ef8f49882e9af17e860f24ff40201905ca7d4a54bcfd4f8e8178509aca0bf65172d1c385d2c8 DIST vcftools_0.1.12b.tar.gz 631374 SHA256 9d2324512e9f1237d5cece74ba63965eb43643e9eada8685afe8217760a20a91 SHA512 803790c8ddbfec1b006a5ce5c6d1c2e0f468978eb96d5ee61d38b863df5752f8b89e0c936803d690491e2d1a898d237ec8772c01b7e9d1a138c610f3a1decbfd WHIRLPOOL 3198f10cd97021f1878b4e2ab1cda3c0038061d301a99a36b1482c8d7bcc5e706f01d0bf3a46634d48dd2e741700032870da2a1dfe7a65022e318d4dde4c8863 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 00000000..126a709 --- /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 \ diff --git a/sci-biology/vcftools/vcftools-0.1.14.ebuild b/sci-biology/vcftools/vcftools-0.1.14.ebuild new file mode 100644 index 00000000..9281435 --- /dev/null +++ b/sci-biology/vcftools/vcftools-0.1.14.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit autotools flag-o-matic perl-functions toolchain-funcs + +DESCRIPTION="Tools for working with VCF (Variant Call Format) files" +HOMEPAGE="http://vcftools.sourceforge.net/"; +SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${P}.tar.gz"; + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="lapack" + +RDEPEND="dev-lang/perl:= + lapack? ( virtual/lapack )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( "${FILESDIR}/${PN}-0.1.14-buildsystem.patch" ) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + perl_set_version + + append-flags $($(tc-getPKG_CONFIG) --cflags lapack) + append-libs $($(tc-getPKG_CONFIG) --libs lapack) + + econf \ + $(use_enable lapack pca) \ + --with-pmdir="${VENDOR_LIB#${EPREFIX}/usr}" +}
