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author | Justin Lecher <jlec@gentoo.org> | 2011-06-21 06:38:10 +0000 |
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committer | Justin Lecher <jlec@gentoo.org> | 2011-06-21 06:38:10 +0000 |
commit | 21a5b6b381a0495b1cb9684f538d7e9a6e4e0fcc (patch) | |
tree | acdbbc4aab841caaaac3136620db0902a44c1bb8 /sci-biology/raxml | |
parent | Maintainer changed to net-mail with dertobi123's permission (diff) | |
download | gentoo-2-21a5b6b381a0495b1cb9684f538d7e9a6e4e0fcc.tar.gz gentoo-2-21a5b6b381a0495b1cb9684f538d7e9a6e4e0fcc.tar.bz2 gentoo-2-21a5b6b381a0495b1cb9684f538d7e9a6e4e0fcc.zip |
Tweaking ebuild, respect LDFLAGS #335629
(Portage version: 2.2.0_alpha41/cvs/Linux x86_64)
Diffstat (limited to 'sci-biology/raxml')
-rw-r--r-- | sci-biology/raxml/ChangeLog | 11 | ||||
-rw-r--r-- | sci-biology/raxml/files/raxml-7.2.5-makefile.patch | 29 | ||||
-rw-r--r-- | sci-biology/raxml/metadata.xml | 1 | ||||
-rw-r--r-- | sci-biology/raxml/raxml-7.2.2.ebuild | 15 | ||||
-rw-r--r-- | sci-biology/raxml/raxml-7.2.5-r1.ebuild | 41 | ||||
-rw-r--r-- | sci-biology/raxml/raxml-7.2.5.ebuild | 15 |
6 files changed, 96 insertions, 16 deletions
diff --git a/sci-biology/raxml/ChangeLog b/sci-biology/raxml/ChangeLog index 3efdd7ff0089..12abc66afb9a 100644 --- a/sci-biology/raxml/ChangeLog +++ b/sci-biology/raxml/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-biology/raxml -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/ChangeLog,v 1.5 2010/01/27 15:58:33 weaver Exp $ +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/ChangeLog,v 1.6 2011/06/21 06:38:10 jlec Exp $ + +*raxml-7.2.5-r1 (21 Jun 2011) + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> raxml-7.2.2.ebuild, + raxml-7.2.5.ebuild, +raxml-7.2.5-r1.ebuild, + +files/raxml-7.2.5-makefile.patch, metadata.xml: + Tweaking ebuild, respect LDFLAGS #335629 *raxml-7.2.5 (27 Jan 2010) diff --git a/sci-biology/raxml/files/raxml-7.2.5-makefile.patch b/sci-biology/raxml/files/raxml-7.2.5-makefile.patch new file mode 100644 index 000000000000..8b381e50cb58 --- /dev/null +++ b/sci-biology/raxml/files/raxml-7.2.5-makefile.patch @@ -0,0 +1,29 @@ + Makefile.gcc | 6 +++--- + 1 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/Makefile.gcc b/Makefile.gcc +index 8d09549..59af556 100644 +--- a/Makefile.gcc ++++ b/Makefile.gcc +@@ -1,10 +1,10 @@ + # Makefile August 2006 by Alexandros Stamatakis + # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca> + +-CC = gcc ++CC ?= gcc + + +-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 ++CFLAGS += -D_GNU_SOURCE + #-Wall -std=c99 -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -pedantic-errors -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast + + +@@ -19,7 +19,7 @@ all : raxmlHPC + GLOBAL_DEPS = axml.h globalVariables.h + + raxmlHPC : $(objs) +- $(CC) -o raxmlHPC $(objs) $(LIBRARIES) ++ $(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) + + classify.o : classify.c $(GLOBAL_DEPS) + evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS) diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml index 3302123e5718..3f2ec4ab4025 100644 --- a/sci-biology/raxml/metadata.xml +++ b/sci-biology/raxml/metadata.xml @@ -6,4 +6,5 @@ <name>Andrey Kislyuk</name> </maintainer> <herd>sci-biology</herd> + <use><flag name='sse3'>Enable optimization for SSE3 capable chips</flag></use> </pkgmetadata> diff --git a/sci-biology/raxml/raxml-7.2.2.ebuild b/sci-biology/raxml/raxml-7.2.2.ebuild index 8c3610ac19e2..27a52f2f18d2 100644 --- a/sci-biology/raxml/raxml-7.2.2.ebuild +++ b/sci-biology/raxml/raxml-7.2.2.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/raxml-7.2.2.ebuild,v 1.3 2009/10/31 17:56:05 maekke Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/raxml-7.2.2.ebuild,v 1.4 2011/06/21 06:38:10 jlec Exp $ -EAPI="2" +EAPI=2 inherit toolchain-funcs @@ -10,10 +10,10 @@ DESCRIPTION="A Program for Sequential, Parallel & Distributed Inference of Large HOMEPAGE="http://wwwkramer.in.tum.de/exelixis/software.html" SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2" -LICENSE="GPL-2" SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86" IUSE="+threads" -KEYWORDS="amd64 x86" # mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS DEPEND="" # mpi? ( virtual/mpi )" @@ -22,9 +22,10 @@ RDEPEND="${DEPEND}" S="${WORKDIR}/RAxML-${PV}" src_prepare() { - sed -i -e 's/CFLAGS =/CFLAGS := ${CFLAGS}/' \ + sed \ + -e 's/CFLAGS =/CFLAGS := ${CFLAGS}/' \ -e 's/CC = gcc/CC = '$(tc-getCC)'/' \ - Makefile.* || die + -i Makefile.* || die } src_compile() { diff --git a/sci-biology/raxml/raxml-7.2.5-r1.ebuild b/sci-biology/raxml/raxml-7.2.5-r1.ebuild new file mode 100644 index 000000000000..5ec6822f113d --- /dev/null +++ b/sci-biology/raxml/raxml-7.2.5-r1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/raxml-7.2.5-r1.ebuild,v 1.1 2011/06/21 06:38:10 jlec Exp $ + +EAPI=4 + +inherit eutils flag-o-matic toolchain-funcs + +DESCRIPTION="A Program for Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees" +HOMEPAGE="http://wwwkramer.in.tum.de/exelixis/software.html" +SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86" +IUSE="sse3 +threads" + +# mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS +DEPEND="" # mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/RAxML-${PV}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-makefile.patch + + use sse3 && append-cflags -D__SIM_SSE3 + use threads && \ + append-cflags -D_USE_PTHREADS && \ + append-ldflags -pthread + + tc-export CC +} + +src_compile() { + emake -f Makefile.gcc +} + +src_install() { + dobin raxmlHPC +} diff --git a/sci-biology/raxml/raxml-7.2.5.ebuild b/sci-biology/raxml/raxml-7.2.5.ebuild index 6f3a6a52161b..b33622313705 100644 --- a/sci-biology/raxml/raxml-7.2.5.ebuild +++ b/sci-biology/raxml/raxml-7.2.5.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/raxml-7.2.5.ebuild,v 1.1 2010/01/27 15:58:33 weaver Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/raxml-7.2.5.ebuild,v 1.2 2011/06/21 06:38:10 jlec Exp $ -EAPI="2" +EAPI=2 inherit toolchain-funcs @@ -10,10 +10,10 @@ DESCRIPTION="A Program for Sequential, Parallel & Distributed Inference of Large HOMEPAGE="http://wwwkramer.in.tum.de/exelixis/software.html" SRC_URI="http://wwwkramer.in.tum.de/exelixis/software/RAxML-${PV}.tar.bz2" -LICENSE="GPL-2" SLOT="0" -IUSE="+threads" +LICENSE="GPL-2" KEYWORDS="~amd64 ~x86" +IUSE="+threads" # mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS DEPEND="" # mpi? ( virtual/mpi )" @@ -22,9 +22,10 @@ RDEPEND="${DEPEND}" S="${WORKDIR}/RAxML-${PV}" src_prepare() { - sed -i -e 's/CFLAGS =/CFLAGS := ${CFLAGS}/' \ + sed \ + -e 's/CFLAGS =/CFLAGS := ${CFLAGS}/' \ -e 's/CC = gcc/CC = '$(tc-getCC)'/' \ - Makefile.* || die + -i Makefile.* || die } src_compile() { |