commit: 738b58d5c8eead005941421868ac2787b7ce570d Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Apr 28 20:11:15 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Apr 28 20:11:15 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=738b58d5
sci-biology/bedops: new package The patch does not expand properly CXXFLAGS for some reason. The package conatains bundled zlib. bzip2 and other 3rd-party stuff. It compile statically at least some binaries. Package-Manager: Portage-2.3.5, Repoman-2.3.2 sci-biology/bedops/bedops-2.4.26.ebuild | 25 ++++ .../files/bedops-2.4.26-respect-cxxflags.patch | 138 +++++++++++++++++++++ sci-biology/bedops/metadata.xml | 12 ++ 3 files changed, 175 insertions(+) diff --git a/sci-biology/bedops/bedops-2.4.26.ebuild b/sci-biology/bedops/bedops-2.4.26.ebuild new file mode 100644 index 000000000..d281fbede --- /dev/null +++ b/sci-biology/bedops/bedops-2.4.26.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2017 Gentoo Foundation +# 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 ${PATCHES[@]} +} diff --git a/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch new file mode 100644 index 000000000..16ac4e2b0 --- /dev/null +++ b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch @@ -0,0 +1,138 @@ +--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin.ori 2017-03-14 08:43:22.000000000 +0100 ++++ bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin 2017-04-28 21:53:55.811777276 +0200 +@@ -28,7 +28,7 @@ + LIBLOCATION = -L${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 diff --git a/sci-biology/bedops/metadata.xml b/sci-biology/bedops/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/bedops/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata>
