Version bump, fixing bug 545304

(Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key 0B08240A96F66571)

3 files changed, 106 insertions, 2 deletions

diff --git a/sci-biology/vcftools/ChangeLog b/sci-biology/vcftools/ChangeLog
index db5bddfe35af..cfc9dd1b0653 100644
--- a/sci-biology/vcftools/ChangeLog
+++ b/sci-biology/vcftools/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/vcftools
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vcftools/ChangeLog,v 1.6 2013/03/12 12:13:12 jlec Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vcftools/ChangeLog,v 1.7 2015/04/03 15:31:25 dilfridge Exp $
+
+*vcftools-0.1.12b (03 Apr 2015)
+
+  03 Apr 2015; Andreas K. Huettel <dilfridge@gentoo.org>
+  +vcftools-0.1.12b.ebuild, +files/vcftools-0.1.12b-buildsystem.patch:
+  Version bump, fixing bug 545304
 
   12 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
diff --git a/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch b/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch
new file mode 100644
index 000000000000..85197664a0d1
--- /dev/null
+++ b/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch
@@ -0,0 +1,53 @@
+diff -ur vcftools_0.1.12b.orig/cpp/Makefile vcftools_0.1.12b/cpp/Makefile
+--- vcftools_0.1.12b.orig/cpp/Makefile	2014-08-01 21:11:22.000000000 +0200
++++ vcftools_0.1.12b/cpp/Makefile	2015-04-03 17:24:38.830781049 +0200
+@@ -3,8 +3,8 @@
+ # ($Revision: 1.1 $)
+ 
+ # Compiler
+-CC = gcc
+-CPP = g++
++CC ?= gcc
++CPP ?= g++
+ # Output executable
+ EXECUTABLE = vcftools
+ # Flag used to turn on compilation of PCA routines
+@@ -12,9 +12,9 @@
+ 	VCFTOOLS_PCA = 0
+ endif
+ # Compiler flags
+-CFLAGS = -O2 -m64
++CFLAGS ?= -O2 -m64
+ #CFLAGS = -Wall -O2 -pg -m64
+-CPPFLAGS = -O2 -D_FILE_OFFSET_BITS=64 
++CPPFLAGS ?= -O2 -D_FILE_OFFSET_BITS=64 
+ #CPPFLAGS = -O2 -Wall -pg -D_FILE_OFFSET_BITS=64
+ # Included libraries (zlib)
+ LIB = -lz 
+@@ -29,13 +29,13 @@
+ 	# Define flag for PCA routine compilation
+ 	CPPFLAGS += -DVCFTOOLS_PCA
+ 	# Add LAPACK library
+-	LIB += -llapack	
++	LIB += `$(PKG_CONFIG) --libs lapack`
+ 	# Add PCA source code
+ 	OBJS+= dgeev.o
+ endif
+ 
+ vcftools: $(OBJS)
+-	$(CPP) $(CPPFLAGS) $(OBJS) -o vcftools $(LIB)
++	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(OBJS) -o vcftools $(LIB)
+ ifdef BINDIR
+ 	cp $(CURDIR)/$@ $(BINDIR)/$@
+ endif
+@@ -47,8 +47,8 @@
+ -include $(OBJS:.o=.d)
+ 
+ %.o: %.cpp
+-	$(CPP) -c $(CPPFLAGS) $*.cpp -o $*.o
+-	$(CPP) -MM $(CPPFLAGS) $*.cpp > $*.d
++	$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) $*.cpp -o $*.o
++	$(CXX) -MM $(CXXFLAGS) $(CPPFLAGS)  $*.cpp > $*.d
+ 
+ # remove compilation products
+ clean:
diff --git a/sci-biology/vcftools/vcftools-0.1.12b.ebuild b/sci-biology/vcftools/vcftools-0.1.12b.ebuild
new file mode 100644
index 000000000000..63914158fe86
--- /dev/null
+++ b/sci-biology/vcftools/vcftools-0.1.12b.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vcftools/vcftools-0.1.12b.ebuild,v 1.1 2015/04/03 15:31:25 dilfridge Exp $
+
+EAPI=5
+
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
+
+MY_P="${PN}_${PV}"
+
+DESCRIPTION="Tools for working with VCF (Variant Call Format) files"
+HOMEPAGE="http://vcftools.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="lapack"
+
+RDEPEND="lapack? ( virtual/lapack )"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-buildsystem.patch
+	tc-export CXX PKG_CONFIG
+}
+
+src_compile() {
+	local myconf
+	use lapack && myconf="VCFTOOLS_PCA=1"
+	emake -C cpp ${myconf}
+}
+
+src_install(){
+	perl_set_version
+	dobin cpp/${PN}
+	insinto ${VENDOR_LIB}
+	doins perl/*.pm
+	dobin perl/{fill,vcf}-*
+	dodoc README.txt
+}