commit: e81e21772377c90519cdd2e095b305e1039ecead Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Sep 25 09:26:02 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Sep 25 09:39:05 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e81e2177
sci-biology/vcftools: Remove old ebuild 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-0.1.12b-buildsystem.patch | 53 ---------------------- sci-biology/vcftools/vcftools-0.1.12b.ebuild | 45 ------------------ 3 files changed, 99 deletions(-) diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest index 9a014b1..0e95b82 100644 --- a/sci-biology/vcftools/Manifest +++ b/sci-biology/vcftools/Manifest @@ -1,2 +1 @@ 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-0.1.12b-buildsystem.patch b/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch deleted file mode 100644 index 8519766..00000000 --- a/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch +++ /dev/null @@ -1,53 +0,0 @@ -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 deleted file mode 100644 index ddc214c..00000000 --- a/sci-biology/vcftools/vcftools-0.1.12b.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -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 -}
