sci-biology/raxml: Drop old; stop building when non sse3 capable CPU is detected, #375061

Package-Manager: portage-2.2.0_alpha163/cvs/Linux x86_64
Manifest-Sign-Key: 0x70EB7916

7 files changed, 32 insertions, 155 deletions

diff --git a/sci-biology/raxml/ChangeLog b/sci-biology/raxml/ChangeLog
index 18a21292326a..034eb24478d0 100644
--- a/sci-biology/raxml/ChangeLog
+++ b/sci-biology/raxml/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/raxml
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/ChangeLog,v 1.7 2011/06/27 05:59:01 jlec Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/ChangeLog,v 1.8 2013/02/18 12:20:50 jlec Exp $
+
+  18 Feb 2013; Justin Lecher <jlec@gentoo.org> -raxml-7.2.2.ebuild,
+  -raxml-7.2.5.ebuild, -raxml-7.2.5-r1.ebuild, raxml-7.2.6.ebuild,
+  metadata.xml:
+  Drop old; stop building when non sse3 capable CPU is detected, #375061
 
 *raxml-7.2.6 (27 Jun 2011)
 
diff --git a/sci-biology/raxml/Manifest b/sci-biology/raxml/Manifest
index cfd9bb706bc6..cfc069eb868e 100644
--- a/sci-biology/raxml/Manifest
+++ b/sci-biology/raxml/Manifest
@@ -1,21 +1,16 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA256
 
-AUX raxml-7.2.5-makefile.patch 1420 RMD160 55bfdf943c50d133986bd2f8a9da059b9cbf1f00 SHA1 666faa75663e6c520412f4ed3bf65fe9bde187a7 SHA256 f3c9d9eaacf7a7e0d1594e3d689f938ff82c2dbdb4c4c4f2ed81a861ebd7adb5
-AUX raxml-7.2.6-makefile.patch 777 RMD160 c561a8e5117295fdf094b165795098e1ac626569 SHA1 be59886d3ef00737507863d087a537266e40aa48 SHA256 0e87b5cd6375669e660ef6e3c37e51e751ea8846de6c52060f484380c28610d5
-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
-DIST RAxML-7.2.6.tar.bz2 202803 RMD160 8d31ca70e653917b198a482a2ed2e5acd9072486 SHA1 0e33022682ebabd353c38a1c766b68da266395df SHA256 d45bcbe45e3ed5f8d6ba3c99b9da9b202c72a9fb196a9d32d2961ee4cb791868
-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
-EBUILD raxml-7.2.6.ebuild 1022 RMD160 0bf1dcc2151a5a792c81c7434ddcacb90ef4691c SHA1 23bd6ead37ef405537df567690fed61cebfe8644 SHA256 19d92360d3e0042bed4f659caad3de986b750d290112d3d21e805a7b633562cc
-MISC ChangeLog 1245 RMD160 f4735fe883d52a1a56634b4329591ad985a20ecc SHA1 151fea6f58333e6b0e814c645cfe255acab10d7b SHA256 9c0aa287c55c3ee6f272926b6cf1481aadbe646c7a5820f4afca7b262a02734e
-MISC metadata.xml 344 RMD160 8ea584bc5a4b2cbefc385d178dc68d52ffb578e7 SHA1 7abc92a015607b3570d2aa8234345aec1b7396b8 SHA256 ed3d77b6cdfecc5005ad4e3eaefbb831660e05a85908f3e23f29f3cd2051ec16
+AUX raxml-7.2.5-makefile.patch 1420 SHA256 f3c9d9eaacf7a7e0d1594e3d689f938ff82c2dbdb4c4c4f2ed81a861ebd7adb5 SHA512 f905bfb638396c81ccd5f66deaf39c574bb9d97a94ff78b786214390f2ac715b7d4e251ba5d13701805f3928f450b6affefce565e7c30544d32e33ed6e5f20ca WHIRLPOOL d26222d935a8462cf10b6244ed043f1437038039c24486993c022332a7148bdd759704a9698242a1bbd60053afde0061edc31684c022085eb0e041e38818c42f
+AUX raxml-7.2.6-makefile.patch 777 SHA256 0e87b5cd6375669e660ef6e3c37e51e751ea8846de6c52060f484380c28610d5 SHA512 0cc326e8fed0882c56193fef9d1c98577f2252acc4dc25e650e0806d89ded0e2911e6967272a6d101cf830cfe63a190a8f5220fd7573864f5fa60106069ad74f WHIRLPOOL 896bb8f27d458e1d555ffb462abf89f55c487e595a604b3446c579a2e95719cfdfb1911873ca2570a73c3299ef49f0c489ee0c127fcb6e1acdcf907c748459b0
+DIST RAxML-7.2.6.tar.bz2 202803 SHA256 d45bcbe45e3ed5f8d6ba3c99b9da9b202c72a9fb196a9d32d2961ee4cb791868
+EBUILD raxml-7.2.6.ebuild 1104 SHA256 6c141557e09ffaac2d2d46f20b485b2ecce7ff12e319f6a47ea40289cf278e1b SHA512 4e7698a094f2b38b24ea81f4ccabbdcf63dd5e252dca889bb4fe50ffd9cd2123ad2565e265cd4663472e2a285f1682c6fac55603ef4e52a2dcda8a3f57e65c0a WHIRLPOOL 0ec5e308140d97f52c350e6c9c7ea727452b6f02139f97bc06d4415aac6d0c2a6a2132d3181b6c7996e5b2620fa3de33825bb216de5fd97e334fde3ab7071943
+MISC ChangeLog 1470 SHA256 16579f2db18dd46efa23763a62f4a4c20617ff03c36cc205e3752f8701999e09 SHA512 b76880a9d45056f509cb6eba07342b36e0ffaed9ee167829dbf2e8f71476bb5bcdbebc56a2e8a69602409cc16f16f72aa9a3312845291437f1d027897f843c3f WHIRLPOOL 444420b930db4bc2aa2b9452e1e93f48f478374c59b7aed7eaccb33a3cbf6a2e70d66513f7d10d1f8fb2539e7035fcc5f5f078a7c0c1af684c0a04e05f634691
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-=mK2y
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diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml
index 9fbd5c20ef5f..9d616102c9e4 100644
--- a/sci-biology/raxml/metadata.xml
+++ b/sci-biology/raxml/metadata.xml
@@ -1,12 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<herd>sci-biology</herd>
-	<use>
-		<flag name="sse3">Enable optimization for SSE3 capable chips</flag>
-	</use>
+  <maintainer>
+    <email>weaver@gentoo.org</email>
+    <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
deleted file mode 100644
index 27a52f2f18d2..000000000000
--- a/sci-biology/raxml/raxml-7.2.2.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# 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 1.4 2011/06/21 06:38:10 jlec Exp $
-
-EAPI=2
-
-inherit 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-${PV}.tar.bz2"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-IUSE="+threads"
-
-# mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS
-DEPEND="" # mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/RAxML-${PV}"
-
-src_prepare() {
-	sed \
-		-e 's/CFLAGS =/CFLAGS := ${CFLAGS}/' \
-		-e 's/CC = gcc/CC = '$(tc-getCC)'/' \
-		-i Makefile.* || die
-}
-
-src_compile() {
-	emake -f Makefile.gcc || die
-	emake -f Makefile.SSE3.gcc clean && emake -f Makefile.SSE3.gcc || die
-	if use threads; then
-		emake -f Makefile.PTHREADS.gcc clean && emake -f Makefile.PTHREADS.gcc || die
-		emake -f Makefile.SSE3.PTHREADS.gcc clean && emake -f Makefile.SSE3.PTHREADS.gcc || die
-	fi
-}
-
-src_install() {
-	dobin raxmlHPC raxmlHPC-SSE3 || die
-	if use threads; then dobin raxmlHPC-PTHREADS raxmlHPC-PTHREADS-SSE3 || die; fi
-}
diff --git a/sci-biology/raxml/raxml-7.2.5-r1.ebuild b/sci-biology/raxml/raxml-7.2.5-r1.ebuild
deleted file mode 100644
index 5ec6822f113d..000000000000
--- a/sci-biology/raxml/raxml-7.2.5-r1.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# 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
deleted file mode 100644
index b33622313705..000000000000
--- a/sci-biology/raxml/raxml-7.2.5.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# 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 1.2 2011/06/21 06:38:10 jlec Exp $
-
-EAPI=2
-
-inherit 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-${PV}.tar.bz2"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-IUSE="+threads"
-
-# mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS
-DEPEND="" # mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/RAxML-${PV}"
-
-src_prepare() {
-	sed \
-		-e 's/CFLAGS =/CFLAGS := ${CFLAGS}/' \
-		-e 's/CC = gcc/CC = '$(tc-getCC)'/' \
-		-i Makefile.* || die
-}
-
-src_compile() {
-	emake -f Makefile.gcc || die
-	emake -f Makefile.SSE3.gcc clean && emake -f Makefile.SSE3.gcc || die
-	if use threads; then
-		emake -f Makefile.PTHREADS.gcc clean && emake -f Makefile.PTHREADS.gcc || die
-		emake -f Makefile.SSE3.PTHREADS.gcc clean && emake -f Makefile.SSE3.PTHREADS.gcc || die
-	fi
-}
-
-src_install() {
-	dobin raxmlHPC raxmlHPC-SSE3 || die
-	if use threads; then dobin raxmlHPC-PTHREADS raxmlHPC-PTHREADS-SSE3 || die; fi
-}
diff --git a/sci-biology/raxml/raxml-7.2.6.ebuild b/sci-biology/raxml/raxml-7.2.6.ebuild
index 5d573e87651d..6339dd23bc1c 100644
--- a/sci-biology/raxml/raxml-7.2.6.ebuild
+++ b/sci-biology/raxml/raxml-7.2.6.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/raxml-7.2.6.ebuild,v 1.1 2011/06/27 05:59:01 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/raxml/raxml-7.2.6.ebuild,v 1.2 2013/02/18 12:20:50 jlec Exp $
 
 EAPI=4
 
@@ -21,6 +21,10 @@ RDEPEND="${DEPEND}"
 
 S="${WORKDIR}/RAxML-${PV}"
 
+pkg_pretend() {
+	use sse3 || die "This package needs sse3 support in your CPU"
+}
+
 src_prepare() {
 	epatch "${FILESDIR}"/${P}-makefile.patch