From: Justin Lecher <jlec@gentoo.org>
Date: Thu, 24 Jun 2010 19:03:18 +0000 (+0000)
Subject: Version BUmp, blocking sci-libs/libmuscle, #308707
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=ab1f0696f07f4744066c5f81b4f7d9fe9c8c91c8;p=gentoo.git

Version BUmp, blocking sci-libs/libmuscle, #308707
Package-Manager: portage-2.2_rc67/cvs/Linux x86_64
---

diff --git a/sci-biology/muscle/ChangeLog b/sci-biology/muscle/ChangeLog
index 98d26dd5e515..ca47dac333cc 100644
--- a/sci-biology/muscle/ChangeLog
+++ b/sci-biology/muscle/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/muscle
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/ChangeLog,v 1.9 2008/03/21 21:23:44 dberkholz Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/ChangeLog,v 1.10 2010/06/24 19:03:18 jlec Exp $
+
+*muscle-3.8.31 (24 Jun 2010)
+
+  24 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/3.8.31-make.patch,
+  muscle-3.6.ebuild, muscle-3.7.ebuild, +muscle-3.8.31.ebuild:
+  Version BUmp, blocking sci-libs/libmuscle, #308707
 
 *muscle-3.7 (21 Mar 2008)
 
diff --git a/sci-biology/muscle/Manifest b/sci-biology/muscle/Manifest
index fe3b0e3519eb..07695bd5b46c 100644
--- a/sci-biology/muscle/Manifest
+++ b/sci-biology/muscle/Manifest
@@ -1,16 +1,19 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA1
 
+AUX 3.8.31-make.patch 989 RMD160 22e88148f5701f5d7d6910c5f1bbd86e26220127 SHA1 2f55918397322ffe83464b3da5e3e5d972a40f63 SHA256 f5352a5fc8a792d7af177d1e829a33e59bc39dedb81baf17c6424f8520ea6879
 DIST muscle3.6_src.tar.gz 185267 RMD160 4afda92b982ec2b05853a582479c61a7d8814f51 SHA1 e8a4998ee10a8f067fd1ba63966e32e69da62d36 SHA256 32b818a51f421e1d687f513dc31374a330470950151a5e7df961e64781699431
 DIST muscle3.7_src.tar.gz 189907 RMD160 6eb64afd2032914781f453b925589c35e432b96c SHA1 6a3cbef3a8a00cf230f17bf90592f7108607d103 SHA256 a028f545612f9d260e35909959e98ae7aec552b1eac8806c3ae59cf1b00f7235
-EBUILD muscle-3.6.ebuild 825 RMD160 5c2e68629d7197f7e32cc4508a4a463e908fde9d SHA1 2e5dfe63244ee714fdfbd927672fc8d7dafdae6b SHA256 d855755012cbf3ad81a67cc1583bf58e080b35c2f78f756b7cc5a4c2b41470bd
-EBUILD muscle-3.7.ebuild 825 RMD160 e6c35313339f5fc88335ca67fff7e4b611dd0f71 SHA1 4dacfcc7bc9cdb2112fac98d20c56f0e9cb71f14 SHA256 71e7761587be1614148abad00578fd4fb19c7b7572ed86b136a4c2f5eefd3dca
-MISC ChangeLog 1350 RMD160 76fe19bc658b890017bfe317e47da53d31d0f755 SHA1 a971d9387c43a8fd11904627684dea0a72884084 SHA256 3574e30a3e43264e4c9c33f9697c45672a41c020538af52c29ba81ef8ce9af63
+DIST muscle3.8.31_src.tar.gz 515267 RMD160 18c9cf465f330a77d6a06ff9323c311a6f6be662 SHA1 2fe55db73ff4e7ac6d4ca692f8f213d1c5071dac SHA256 43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad
+EBUILD muscle-3.6.ebuild 847 RMD160 8a29fc7b68c5fb0c3680c513ede51aeaeaad4b11 SHA1 c38e5eebcf8f35e430f85f958de35083295ae0f0 SHA256 f3c041cb767be4e858a5854a03ee51e8424cd4197a7c723c4b28a46705a80c67
+EBUILD muscle-3.7.ebuild 842 RMD160 b37b66244779fadc518b6642b01b3c1ceebb8c53 SHA1 d100710640430e4b06191fcb526dba46284afe0a SHA256 0a44a1eb9895a94cb46e4fa7335a577c680cb9ee68d87df014a31dd1967a674c
+EBUILD muscle-3.8.31.ebuild 733 RMD160 e4139817205be0c2e14060b03f9de2468675d050 SHA1 c0d18e04a0ff065fff8113fca508628d48346ecd SHA256 cca4af8de32649c613201dbdadb0e5090bcb72eaf5c27652866a50635c806c30
+MISC ChangeLog 1566 RMD160 ec0a0be2de83cbf4c28222251abdd915e16ff898 SHA1 c0114c4e18b15bdd220532dda9335d2b16b3a0ae SHA256 8969930069aa640d6b8fd2a2fa01c9393e16b70c6a7850230728ee9fca281b5e
 MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.7 (GNU/Linux)
+Version: GnuPG v2.0.15 (GNU/Linux)
 
-iD8DBQFH5CdoXVaO67S1rtsRAngoAJ9YI33JVcuwZrcP9Mn7PVisGcN0KQCghk2a
-/fj7R28H1dXBluTWpUcyeo0=
-=Zt0f
+iEYEARECAAYFAkwjq/0ACgkQgAnW8HDreRZNHQCgvai8tZOZ7vSKuFkU32Jk05L/
+l3MAmQF+6C3sFLOjOqImoMnn+4jCYWPT
+=x/lJ
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/muscle/files/3.8.31-make.patch b/sci-biology/muscle/files/3.8.31-make.patch
new file mode 100644
index 000000000000..7c0e7308df54
--- /dev/null
+++ b/sci-biology/muscle/files/3.8.31-make.patch
@@ -0,0 +1,26 @@
+diff --git a/src/mk b/src/mk
+index 475d25a..d4b7e83 100755
+--- a/src/mk
++++ b/src/mk
+@@ -5,17 +5,14 @@ ObjNames='aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln
+ rm -f *.o muscle.make.stdout.txt muscle.make.stderr.txt
+ for CPPName in $CPPNames
+ do
+-  echo $CPPName >> /dev/tty
+-  g++ $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o  >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
++  echo "${CXX} ${CXXFLAGS} -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o"
++  ${CXX} ${CXXFLAGS} -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o
+ done
+ 
+ LINK_OPTS=
+ if [ `uname -s` == Linux ] ; then
+     LINK_OPTS=-static
+ fi
+-g++ $LINK_OPTS $ENV_LINK_OPTS -g -o muscle $ObjNames  >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
+-tail muscle.make.stderr.txt
+ 
+-strip muscle
+-ls -lh muscle
+-sum muscle
++echo "${CXX} ${LDFLAGS} -o muscle $ObjNames"
++${CXX} ${LDFLAGS} -o muscle $ObjNames
diff --git a/sci-biology/muscle/muscle-3.6.ebuild b/sci-biology/muscle/muscle-3.6.ebuild
index e181a618246b..f4fedf84f566 100644
--- a/sci-biology/muscle/muscle-3.6.ebuild
+++ b/sci-biology/muscle/muscle-3.6.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2007 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/muscle-3.6.ebuild,v 1.5 2007/12/26 10:25:01 drac Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/muscle-3.6.ebuild,v 1.6 2010/06/24 19:03:18 jlec Exp $
 
 inherit toolchain-funcs
 
@@ -9,11 +9,14 @@ DESCRIPTION="Multiple sequence comparison by log-expectation"
 HOMEPAGE="http://www.drive5.com/muscle/"
 SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz"
 LICENSE="public-domain"
+
 SLOT="0"
 KEYWORDS="amd64 ppc x86"
 IUSE=""
-RDEPEND=""
+
+RDEPEND="!sci-libs/libmuscle"
 DEPEND="${RDEPEND}"
+
 S="${WORKDIR}/${MY_P}"
 
 src_unpack() {
diff --git a/sci-biology/muscle/muscle-3.7.ebuild b/sci-biology/muscle/muscle-3.7.ebuild
index 346ccedb1ae5..64ee5b1820a4 100644
--- a/sci-biology/muscle/muscle-3.7.ebuild
+++ b/sci-biology/muscle/muscle-3.7.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/muscle-3.7.ebuild,v 1.1 2008/03/21 21:23:44 dberkholz Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/muscle-3.7.ebuild,v 1.2 2010/06/24 19:03:18 jlec Exp $
 
 inherit toolchain-funcs
 
@@ -8,12 +8,15 @@ MY_P="${PN}${PV}_src"
 DESCRIPTION="Multiple sequence comparison by log-expectation"
 HOMEPAGE="http://www.drive5.com/muscle/"
 SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz"
+
 LICENSE="public-domain"
 SLOT="0"
 KEYWORDS="~amd64 ~ppc ~x86"
 IUSE=""
-RDEPEND=""
+
+RDEPEND="!sci-libs/libmuscle"
 DEPEND="${RDEPEND}"
+
 S="${WORKDIR}"
 
 src_unpack() {
diff --git a/sci-biology/muscle/muscle-3.8.31.ebuild b/sci-biology/muscle/muscle-3.8.31.ebuild
new file mode 100644
index 000000000000..cfd0d79ac4c2
--- /dev/null
+++ b/sci-biology/muscle/muscle-3.8.31.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/muscle/muscle-3.8.31.ebuild,v 1.1 2010/06/24 19:03:18 jlec Exp $
+
+EAPI="3"
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}${PV}_src"
+
+DESCRIPTION="Multiple sequence comparison by log-expectation"
+HOMEPAGE="http://www.drive5.com/muscle/"
+SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+
+RDEPEND="!sci-libs/libmuscle"
+DEPEND=""
+
+S="${WORKDIR}"/${PN}${PV}/src
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-make.patch
+	tc-export CXX
+}
+
+src_install() {
+	dobin "${PN}" || die
+	dodoc *.txt || die
+}