diff options
| -rw-r--r-- | sci-biology/raxml/ChangeLog | 11 | ||||
| -rw-r--r-- | sci-biology/raxml/Manifest | 20 | ||||
| -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 |
7 files changed, 112 insertions, 20 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/Manifest b/sci-biology/raxml/Manifest index f19f2a019425..4b2f9db674d7 100644 --- a/sci-biology/raxml/Manifest +++ b/sci-biology/raxml/Manifest @@ -1,6 +1,18 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +AUX raxml-7.2.5-makefile.patch 1420 RMD160 55bfdf943c50d133986bd2f8a9da059b9cbf1f00 SHA1 666faa75663e6c520412f4ed3bf65fe9bde187a7 SHA256 f3c9d9eaacf7a7e0d1594e3d689f938ff82c2dbdb4c4c4f2ed81a861ebd7adb5 DIST RAxML-7.2.2.tar.bz2 184132 RMD160 b2bec2d590c0899e245989d2f6e0ffba506d66cc SHA1 5c5bb777f150d6b7ee5051b82f8b3f398efd4ccf SHA256 294816da5e7c3ca6b766f6e95aa5f032447e22460518b6916853eb80b3491ba9 DIST RAxML-7.2.5.tar.bz2 198933 RMD160 d87541fcc73b4b6f662b1752ae2a7ec5376a05ca SHA1 9d75e0d4b0a136a82731feda7af9e0e2238ede6b SHA256 35ec543ad0e7879c86f1671d5f352dfe529c6684c6ea9d7fcc600423e37c3156 -EBUILD raxml-7.2.2.ebuild 1302 RMD160 d9faf5d1467d92a4713c5fe65614684d1b110f0a SHA1 44ca81922015263df5860b2755ae204dbd8aa073 SHA256 5306afbdd44a3dfa1ac901eff54d82c3c975daddce7d35fec6e4905f416fff8a -EBUILD raxml-7.2.5.ebuild 1304 RMD160 daac22281ba7c7d4a83d3565e48da277c24704ec SHA1 7a1ae21922c60c267f7029dc6dbec5a51000fe0e SHA256 469b8e57a10bdd20c688448b04a35c445b9d464a0f642546c463c5c9c206b548 -MISC ChangeLog 837 RMD160 b052546f781e8ad73e52fa9f2e44e7453f339ae1 SHA1 96b98bc7f575f61cd019a4cc6b40f0c743eaf66a SHA256 9a2499b65c0e7cc4ccc372e2b265d14d7a4e6dd0cc687b9dd0c0969a0caad1db -MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 +EBUILD raxml-7.2.2.ebuild 1304 RMD160 1e059aa2ef7a3f7665575d674a2d90ee9c8f21fa SHA1 2af59b45059e78064a9abc281148524f778975e2 SHA256 f41d0caa2e83661627fc21c312cb728074c76c6e5bbdbab1e6c07ac05046e22d +EBUILD raxml-7.2.5-r1.ebuild 1025 RMD160 23271fbcccfb2dbbd4d728ebce3cc57aee139f1c SHA1 c721f72719eacd662b234c935363ef62627cbcda SHA256 31cd2cbd9ff528177b003fe0775bd0c9589fb6e96c641b372a5a095d103a2654 +EBUILD raxml-7.2.5.ebuild 1304 RMD160 dbcceec05e567fd3af969309de45d03c44d9f6fb SHA1 eb599184d32592ee745a6fc4523d6f790c434040 SHA256 24653c9c70408aacc2728e5237f8303dc2e20bbc13d076d7a61bde2bbfd3c6cc +MISC ChangeLog 1074 RMD160 8df1680810c63cf427e220c7a0cc994715caddf5 SHA1 3e7d8bc5c1f9973655cd0ab5c301db09fdbab640 SHA256 f6872eed4b92b727117d445b4c1ca11dd8c9172bed26ea653d46de4bc3e93604 +MISC metadata.xml 339 RMD160 e204f70642579ae8d095983675851b681330c31a SHA1 21bb6e7ec4b97b6cbff33f0d34faf73dd018b5d5 SHA256 aac1952d3b2936edae355e265b85bda835bc53e8782778c495e214a05e1fb0e5 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.17 (GNU/Linux) + +iEYEARECAAYFAk4APFcACgkQgAnW8HDreRZR5QCghDOF85lOX8gN1fpZAJPLuBeT +ozQAnAkHgNEgZsGWftWuBU1aFfVT4MBv +=EDL5 +-----END PGP SIGNATURE----- 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() { |