commit: 96b52ed1a41aa7598caeb8fef408a50dfd57715b Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Sat Mar 6 09:36:21 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Sat Mar 6 09:36:21 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=96b52ed1
sci-biology/bedops: drop old Package-Manager: Portage-3.0.16, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> sci-biology/bedops/bedops-2.4.26.ebuild | 31 ----- .../files/bedops-2.4.26-respect-cxxflags.patch | 138 --------------------- 2 files changed, 169 deletions(-) diff --git a/sci-biology/bedops/bedops-2.4.26.ebuild b/sci-biology/bedops/bedops-2.4.26.ebuild deleted file mode 100644 index 4ae167a08..000000000 --- a/sci-biology/bedops/bedops-2.4.26.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs eutils - -DESCRIPTION="Manipulate BED file (alternative to bedtools)" -HOMEPAGE="http://bedops.readthedocs.io - https://github.com/bedops/bedops"; -SRC_URI="https://github.com/bedops/bedops/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" - -src_prepare(){ - default - local PATCHES=("${FILESDIR}"/${P}-respect-cxxflags.patch) - epatch ${PATCHES[@]} -} - -src_install(){ - emake install - dobin bin/* - dodoc README.md -} diff --git a/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch deleted file mode 100644 index 16ac4e2b0..000000000 --- a/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch +++ /dev/null @@ -1,138 +0,0 @@ ---- bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100 -+++ bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin 2017-04-28 21:53:55.811777276 +0200 -@@ -28,7 +28,7 @@ - LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR} - LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB} - STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++ --BLDFLAGS = -O3 ${STDFLAGS} -+BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS} - - - FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES} ---- bedops-2.4.26/applications/bed/bedextract/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100 -+++ bedops-2.4.26/applications/bed/bedextract/src/Makefile 2017-04-28 21:54:05.952048644 +0200 -@@ -24,7 +24,7 @@ - INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR} - LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR} - LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB} --BLDFLAGS = -Wall -pedantic -O3 -std=c++11 -+BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11 - SFLAGS = -static - - dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding -@@ -64,4 +64,4 @@ - rm -rf $(OBJDIR) - rm -f $(BINDIR)/$(PROG) - rm -f $(BINDIR)/*.$(PROG) -- rm -rf $(BINDIR) -\ No newline at end of file -+ rm -rf $(BINDIR) ---- bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100 -+++ bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin 2017-04-28 21:54:12.162214836 +0200 -@@ -28,7 +28,7 @@ - LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR} - LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB} - STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++ --BLDFLAGS = -O3 ${STDFLAGS} -+BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS} - - FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES} - ---- bedops-2.4.26/applications/bed/bedmap/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100 -+++ bedops-2.4.26/applications/bed/bedmap/src/Makefile 2017-04-28 21:54:19.472410465 +0200 -@@ -23,7 +23,7 @@ - INCLUDES = -iquote${HEAD} -I${PARTY3} -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR} - LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR} - LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB} --BLDFLAGS = -Wall -pedantic -O3 -std=c++11 -+BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11 - SFLAGS = -static - - dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding ---- bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100 -+++ bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin 2017-04-28 21:54:25.422569698 +0200 -@@ -1,7 +1,7 @@ - MIN_OSX_VERSION = 10.7 - BLDFLAGS = -Wall -Wextra -pedantic -std=c99 - COMMONFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 --CFLAGS = -O3 -+CFLAGS = ${CXXFLAGS:--O3} - CDFLAGS = -DDEBUG=1 -g -O0 -fno-inline - CPFLAGS = -pg - LIBS = -lpthread ---- bedops-2.4.26/applications/bed/conversion/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100 -+++ bedops-2.4.26/applications/bed/conversion/src/Makefile 2017-04-28 21:54:30.832714482 +0200 -@@ -1,6 +1,6 @@ - BLDFLAGS = -Wall -Wextra -pedantic -std=c99 - COMMONFLAGS = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 --CFLAGS = -O3 -+CFLAGS = ${CXXFLAGS:--O3} - CDFLAGS = -DDEBUG=1 -g -O0 -fno-inline - CPFLAGS = -pg - LIBS = -lpthread ---- bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100 -+++ bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin 2017-04-28 21:54:37.312887898 +0200 -@@ -27,7 +27,7 @@ - LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR} - LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB} - STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++ --BLDFLAGS = -O3 ${STDFLAGS} -+BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS} - - FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES} - ---- bedops-2.4.26/applications/bed/bedops/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100 -+++ bedops-2.4.26/applications/bed/bedops/src/Makefile 2017-04-28 21:54:43.513053823 +0200 -@@ -25,7 +25,7 @@ - INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR} - LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR} - LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB} --BLDFLAGS = -Wall -pedantic -O3 -std=c++11 -+BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11 - SFLAGS = -static - - dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding ---- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100 -+++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin 2017-04-28 21:54:49.093203153 +0200 -@@ -28,7 +28,7 @@ - LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR} - LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB} - STDFLAGS = -Wall -pedantic -std=c++11 -stdlib=libc++ --BLDFLAGS = -O3 ${STDFLAGS} -+BLDFLAGS = ${CXXFLAGS:--O3} ${STDFLAGS} - - FLAGS = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES} - ---- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100 -+++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile 2017-04-28 21:54:54.283342049 +0200 -@@ -23,7 +23,7 @@ - INCLUDES = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR} - LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR} - LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB} --BLDFLAGS = -Wall -pedantic -O3 -std=c++11 -+BLDFLAGS = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11 - SFLAGS = -static - - dependency_names = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding ---- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100 -+++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin 2017-04-28 21:55:00.023495662 +0200 -@@ -7,7 +7,7 @@ - PROG = sort-bed - DIST_DIR = ../bin - OBJ_DIR = objects_${ARCH} --OPTIMIZE = -O3 -std=c++11 -stdlib=libc++ -+OPTIMIZE = ${CXXFLAGS:--O3} -std=c++11 -stdlib=libc++ - WARNINGS = -Wall - MAIN = ../../../.. - HEAD = ${MAIN}/interfaces/general-headers ---- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.ori 2017-03-14 08:43:22.000000000 +0100 -+++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile 2017-04-28 21:55:05.663646597 +0200 -@@ -29,7 +29,7 @@ - BINDIR = ../bin - OBJDIR = objects - WARNINGS = -Wall -Wextra -pedantic --BLDFLAGS = ${WARNINGS} -O3 -std=c++11 -+BLDFLAGS = ${WARNINGS} ${CXXFLAGS:--O3} -std=c++11 - SFLAGS = -static - - dependency_names = starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding SortDetails Sort CheckSort
