Tweaking ebuild, respect LDFLAGS #335629

Package-Manager: portage-2.2.0_alpha41/cvs/Linux x86_64

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() {