[gentoo-commits] repo/gentoo:master commit in: sci-biology/vcftools/, sci-biology/vcftools/files/

["David Seifert" <soap@gentoo.org>]

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
-}