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commit: e81e21772377c90519cdd2e095b305e1039ecead |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sun Sep 25 09:26:02 2016 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sun Sep 25 09:39:05 2016 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e81e2177 |
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|
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sci-biology/vcftools: Remove old ebuild |
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|
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Package-Manager: portage-2.3.1 |
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Closes: https://github.com/gentoo/gentoo/pull/2407 |
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|
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Signed-off-by: David Seifert <soap <AT> gentoo.org> |
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|
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sci-biology/vcftools/Manifest | 1 - |
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.../files/vcftools-0.1.12b-buildsystem.patch | 53 ---------------------- |
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sci-biology/vcftools/vcftools-0.1.12b.ebuild | 45 ------------------ |
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3 files changed, 99 deletions(-) |
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|
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diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest |
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index 9a014b1..0e95b82 100644 |
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--- a/sci-biology/vcftools/Manifest |
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+++ b/sci-biology/vcftools/Manifest |
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@@ -1,2 +1 @@ |
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DIST vcftools-0.1.14.tar.gz 342369 SHA256 76d799dd9afcb12f1ed42a07bc2886cd1a989858a4d047f24d91dcf40f608582 SHA512 863a16b3b20d392deba7f04310af95f1ab21be537273692aa104e22d737af2eb1bc54a768af954f06188e0500e4f7a032d1189886eb3a439b108cb8189b14eb7 WHIRLPOOL 6de2e33a9882cb5567e2e22605a14851a7b1b458ec4152c87986ef8f49882e9af17e860f24ff40201905ca7d4a54bcfd4f8e8178509aca0bf65172d1c385d2c8 |
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-DIST vcftools_0.1.12b.tar.gz 631374 SHA256 9d2324512e9f1237d5cece74ba63965eb43643e9eada8685afe8217760a20a91 SHA512 803790c8ddbfec1b006a5ce5c6d1c2e0f468978eb96d5ee61d38b863df5752f8b89e0c936803d690491e2d1a898d237ec8772c01b7e9d1a138c610f3a1decbfd WHIRLPOOL 3198f10cd97021f1878b4e2ab1cda3c0038061d301a99a36b1482c8d7bcc5e706f01d0bf3a46634d48dd2e741700032870da2a1dfe7a65022e318d4dde4c8863 |
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|
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diff --git a/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch b/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch |
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deleted file mode 100644 |
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index 8519766..00000000 |
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--- a/sci-biology/vcftools/files/vcftools-0.1.12b-buildsystem.patch |
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+++ /dev/null |
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@@ -1,53 +0,0 @@ |
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-diff -ur vcftools_0.1.12b.orig/cpp/Makefile vcftools_0.1.12b/cpp/Makefile |
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---- vcftools_0.1.12b.orig/cpp/Makefile 2014-08-01 21:11:22.000000000 +0200 |
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-+++ vcftools_0.1.12b/cpp/Makefile 2015-04-03 17:24:38.830781049 +0200 |
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-@@ -3,8 +3,8 @@ |
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- # ($Revision: 1.1 $) |
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- |
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- # Compiler |
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--CC = gcc |
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--CPP = g++ |
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-+CC ?= gcc |
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-+CPP ?= g++ |
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- # Output executable |
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- EXECUTABLE = vcftools |
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- # Flag used to turn on compilation of PCA routines |
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-@@ -12,9 +12,9 @@ |
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- VCFTOOLS_PCA = 0 |
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- endif |
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- # Compiler flags |
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--CFLAGS = -O2 -m64 |
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-+CFLAGS ?= -O2 -m64 |
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- #CFLAGS = -Wall -O2 -pg -m64 |
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--CPPFLAGS = -O2 -D_FILE_OFFSET_BITS=64 |
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-+CPPFLAGS ?= -O2 -D_FILE_OFFSET_BITS=64 |
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- #CPPFLAGS = -O2 -Wall -pg -D_FILE_OFFSET_BITS=64 |
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- # Included libraries (zlib) |
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- LIB = -lz |
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-@@ -29,13 +29,13 @@ |
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- # Define flag for PCA routine compilation |
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- CPPFLAGS += -DVCFTOOLS_PCA |
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- # Add LAPACK library |
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-- LIB += -llapack |
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-+ LIB += `$(PKG_CONFIG) --libs lapack` |
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- # Add PCA source code |
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- OBJS+= dgeev.o |
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- endif |
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- |
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- vcftools: $(OBJS) |
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-- $(CPP) $(CPPFLAGS) $(OBJS) -o vcftools $(LIB) |
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-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(OBJS) -o vcftools $(LIB) |
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- ifdef BINDIR |
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- cp $(CURDIR)/$@ $(BINDIR)/$@ |
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- endif |
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-@@ -47,8 +47,8 @@ |
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- -include $(OBJS:.o=.d) |
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- |
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- %.o: %.cpp |
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-- $(CPP) -c $(CPPFLAGS) $*.cpp -o $*.o |
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-- $(CPP) -MM $(CPPFLAGS) $*.cpp > $*.d |
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-+ $(CXX) -c $(CXXFLAGS) $(CPPFLAGS) $*.cpp -o $*.o |
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-+ $(CXX) -MM $(CXXFLAGS) $(CPPFLAGS) $*.cpp > $*.d |
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- |
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- # remove compilation products |
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- clean: |
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|
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diff --git a/sci-biology/vcftools/vcftools-0.1.12b.ebuild b/sci-biology/vcftools/vcftools-0.1.12b.ebuild |
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deleted file mode 100644 |
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index ddc214c..00000000 |
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--- a/sci-biology/vcftools/vcftools-0.1.12b.ebuild |
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+++ /dev/null |
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@@ -1,45 +0,0 @@ |
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-# Copyright 1999-2015 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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-# $Id$ |
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- |
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-EAPI=5 |
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- |
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-PERL_EXPORT_PHASE_FUNCTIONS=no |
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-inherit perl-module eutils toolchain-funcs |
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- |
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-MY_P="${PN}_${PV}" |
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- |
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-DESCRIPTION="Tools for working with VCF (Variant Call Format) files" |
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-HOMEPAGE="http://vcftools.sourceforge.net/" |
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-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz" |
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- |
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-LICENSE="LGPL-3" |
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-SLOT="0" |
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-KEYWORDS="~x86 ~amd64" |
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-IUSE="lapack" |
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- |
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-RDEPEND="lapack? ( virtual/lapack )" |
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-DEPEND="${RDEPEND} |
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- virtual/pkgconfig" |
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- |
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-S="${WORKDIR}/${MY_P}" |
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- |
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-src_prepare() { |
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- epatch "${FILESDIR}"/${P}-buildsystem.patch |
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- tc-export CXX PKG_CONFIG |
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-} |
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- |
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-src_compile() { |
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- local myconf |
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- use lapack && myconf="VCFTOOLS_PCA=1" |
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- emake -C cpp ${myconf} |
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-} |
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- |
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-src_install(){ |
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- perl_set_version |
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- dobin cpp/${PN} |
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- insinto ${VENDOR_LIB} |
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- doins perl/*.pm |
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- dobin perl/{fill,vcf}-* |
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- dodoc README.txt |
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-} |
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