commit: 69b578f57aed0097521cb637b03a22139789cf84 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Jun 1 18:49:23 2014 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Jun 1 18:49:23 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=69b578f5
sci-biology/cd-hit-auxtools: new package, needs gcc<=4.6.4 or some CXXFLAG to loosen g++ strictness Package-Manager: portage-2.2.7 --- sci-biology/cd-hit-auxtools/ChangeLog | 10 +++++ .../cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild | 42 +++++++++++++++++++ sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch | 47 ++++++++++++++++++++++ sci-biology/cd-hit-auxtools/metadata.xml | 9 +++++ 4 files changed, 108 insertions(+) diff --git a/sci-biology/cd-hit-auxtools/ChangeLog b/sci-biology/cd-hit-auxtools/ChangeLog new file mode 100644 index 0000000..6bee545 --- /dev/null +++ b/sci-biology/cd-hit-auxtools/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/cd-hit-auxtools +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*cd-hit-auxtools-0.5 (01 Jun 2014) + + 01 Jun 2014; Martin Mokrejs <[email protected]> + +cd-hit-auxtools-0.5.ebuild, +files/0.5-gentoo.patch, +metadata.xml: + sci-biology/cd-hit-auxtools: new package, needs gcc<=4.6.4 or some CXXFLAG to + loosen g++ strictness diff --git a/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild b/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild new file mode 100644 index 0000000..c40e98b --- /dev/null +++ b/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/cd-hit-4.6.ebuild,v 1.1 2012/06/20 18:39:24 jlec Exp $ + +EAPI=4 + +inherit eutils flag-o-matic toolchain-funcs + +RELDATE="2012-03-07" +RELEASE="${PN}-v${PV}-${RELDATE}" + +DESCRIPTION="Additional cd-hit itools: read-linker, cd-hit-lap and cd-hit-dup" +HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"; +SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz"; + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="GPL-2" +IUSE="doc openmp" + +S="${WORKDIR}"/${RELEASE} + +pkg_setup() { + use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler" +} + +src_prepare() { + tc-export CXX + use openmp || append-flags -DNO_OPENMP + epatch "${FILESDIR}"/${PV}-gentoo.patch +} + +src_compile() { + local myconf= + use openmp && myconf="openmp=yes" + make ${myconf} || die "If compilation failed try gcc-4.6.4 or older, newer versions are too picky about quality of the source code" +} + +src_install() { + dodir /usr/bin + dobin read-linker cd-hit-lap cd-hit-dup +} diff --git a/sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch b/sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch new file mode 100644 index 0000000..3977cbe --- /dev/null +++ b/sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch @@ -0,0 +1,47 @@ +--- Makefile.ori 2014-06-01 20:25:53.000000000 +0200 ++++ Makefile 2014-06-01 20:27:15.000000000 +0200 +@@ -1,8 +1,8 @@ + +-CC = g++ ++CXX = g++ + +-CFLAGS = -Wall -Wno-unused -I. -Imintlib +-LFLAGS = -fPIC ++CXXFLAGS = -I. -Imintlib ++LDFLAGS = -fPIC + + + UNAME = $(shell uname) +@@ -16,9 +16,9 @@ + endif + + ifeq ($(debug),yes) +-CFLAGS += -ggdb ++CiXXFLAGS += + else +-CFLAGS += -O2 ++CXXFLAGS += + endif + + +@@ -32,16 +32,16 @@ + .SUFFIXES: .c .obj .cpp .cc .cxx .C + + .cxx.o: +- $(CC) -c $(CFLAGS) -o $@ $< ++ $(CXX) -c $(CXXFLAGS) -o $@ $< + + cd-hit-dup: $(OBJECTS) cdhit-dup.o +- $(CC) $(LFLAGS) $(OBJECTS) cdhit-dup.o -o cd-hit-dup ++ $(CXX) $(LDFLAGS) $(OBJECTS) cdhit-dup.o -o cd-hit-dup + + cd-hit-lap: $(OBJECTS) cdhit-lap.o +- $(CC) $(LFLAGS) $(OBJECTS) cdhit-lap.o -o cd-hit-lap ++ $(CXX) $(LDFLAGS) $(OBJECTS) cdhit-lap.o -o cd-hit-lap + + read-linker: $(OBJECTS) read-linker.o +- $(CC) $(LFLAGS) $(OBJECTS) read-linker.o -o read-linker ++ $(CXX) $(LDFLAGS) $(OBJECTS) read-linker.o -o read-linker + + clean: + rm $(OBJECTS) cdhit-dup.o cdhit-lap.o read-linker.o diff --git a/sci-biology/cd-hit-auxtools/metadata.xml b/sci-biology/cd-hit-auxtools/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/cd-hit-auxtools/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata>
