fix for bug 281734

5 files changed, 149 insertions, 0 deletions

diff --git a/sci-biology/clustalw/ChangeLog b/sci-biology/clustalw/ChangeLog
new file mode 100644
index 000000000..700b7cff1
--- /dev/null
+++ b/sci-biology/clustalw/ChangeLog
@@ -0,0 +1,100 @@
+# ChangeLog for sci-biology/clustalw
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/ChangeLog,v 1.16 2009/04/28 23:57:43 weaver Exp $
+
+  17 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/1.83-as-needed.patch, +clustalw-2.0.11.ebuild, +metadata.xml:
+  fixes for bug 281734
+
+*clustalw-2.0.11 (28 Apr 2009)
+
+  28 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> -clustalw-2.0.9.ebuild,
+  +clustalw-2.0.11.ebuild:
+  Version bump, remove old, assume maintainership
+
+  24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
+  Giving up maintainership of this package.
+
+  09 Sep 2008; Markus Dittrich <markusle@gentoo.org> clustalw-2.0.9.ebuild:
+  Keyworded amd64 since it works just fine.
+
+*clustalw-2.0.9 (28 Aug 2008)
+
+  28 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +clustalw-2.0.9.ebuild:
+  New upstream major version (complete rewrite, removing keywords). Slotted
+  to cohexist with version 1.x.
+
+*clustalw-1.83-r2 (27 Aug 2008)
+
+  27 Aug 2008; Olivier Fisette <ribosome@gentoo.org>
+  -clustalw-1.83-r1.ebuild, +clustalw-1.83-r2.ebuild:
+  Forcing bump to start using slots as ClustalW 2 should coexist with 1.83.
+
+  02 Nov 2006; Fabian Groffen <grobian@gentoo.org> clustalw-1.83-r1.ebuild:
+  Dropped ppc-macos, see you in prefix.
+
+  14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
+  Taking over maintainership.
+
+  04 Jan 2006; Olivier Fisette <ribosome@gentoo.org>
+  clustalw-1.83-r1.ebuild:
+  Do not depend on "virtual/libc" (package not in system target).
+
+  11 Oct 2005; Luis Medinas <metalgod@gentoo.org> clustalw-1.83-r1.ebuild:
+  Marked Stable on amd64.
+
+  19 Jun 2005; Markus Rothe <corsair@gentoo.org> clustalw-1.83-r1.ebuild:
+  Stable on ppc64
+
+  02 May 2005; Omkhar Arasaratnam <omkhar@gentoo.org>
+  clustalw-1.83-r1.ebuild:
+  Added ~ppc64
+
+  30 Jan 2005; Olivier Fisette <ribosome@gentoo.org>
+  clustalw-1.83-r1.ebuild:
+  Ebuild cleanup.
+
+  14 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> clustalw-1.83-r1.ebuild:
+  Stable ppc-macos.
+
+  02 Jan 2005; Olivier Fisette <ribosome@gentoo.org>
+  clustalw-1.83-r1.ebuild:
+  Use the toolchain-funcs rather than the gcc eclass.
+
+*clustalw-1.83-r1 (23 Dec 2004)
+
+  23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +clustalw-1.83-r1.ebuild:
+  Moved from app-sci/clustalw to sci-biology/clustalw.
+
+  21 Nov 2004; Karol Wojtaszek <sekretarz@gentoo.org>
+  clustalw-1.83-r1.ebuild:
+  Added to ~amd64, bug #71865
+
+  14 Oct 2004; Olivier Fisette <ribosome@gentoo.org> clustalw-1.83-r1.ebuild:
+  Fixed gcc with gcc.eclass. gongloo left some mistakes.
+
+  14 Oct 2004; Hasan Khalil <gongloo@gentoo.org> clustalw-1.83-r1.ebuild:
+  Fixed gcc with gcc.eclass. Keyworded ~ppc-macos.
+
+  05 Oct 2004; Olivier Fisette <ribosome@gentoo.org> clustalw-1.83-r1.ebuild:
+  Fixed overly verbose description.
+
+*clustalw-1.83-r1 (29 Sep 2004)
+
+  29 Sep 2004; Olivier Fisette <ribosome@gentoo.org> +clustalw-1.83-r1.ebuild,
+  -clustalw-1.83.ebuild:
+  Fixed bugs pertaining to "CFLAGS" and help files.
+
+  01 Jul 2004; Jeremy Huddleston <eradicator@gentoo.org> clustalw-1.83.ebuild:
+  virtual/glibc -> virtual/libc
+
+  19 Apr 2004; Patrick Kursawe <phosphan@gentoo.org> clustalw-1.83.ebuild:
+  Bumped to stable, using epatch now
+
+*clustalw-1.83 (04 Apr 2003)
+
+  04 Apr 2003; Michael Imhof <tantive@gentoo.org> :
+  Initial release.
+  This ebuild was submitted by Gontran Zepeda <gontran@gontran.net>.
+  Should close #18679.
diff --git a/sci-biology/clustalw/Manifest b/sci-biology/clustalw/Manifest
new file mode 100644
index 000000000..dd9d0b7df
--- /dev/null
+++ b/sci-biology/clustalw/Manifest
@@ -0,0 +1,5 @@
+AUX 1.83-as-needed.patch 460 RMD160 227750cedadad2ef790792d7e9dc2cf8b7978ca6 SHA1 8b1bc014f1906e65fbd21d22556296e632d6161b SHA256 82748081256727b2b75cf744828a4917434dcf9a662d02c87afd646a75ce80bc
+DIST clustalw-2.0.11.tar.gz 325936 RMD160 ea65bcda9ca1006ab498cd967ae82cc1409332af SHA1 c0491e7da01f5ceb3d651e51d1b38a0c12fd8f02 SHA256 3150344721b32fbec3eb0f8a54aa8a3d25fa674ecc0ab5a68ba3d5f1b07b4cb1
+EBUILD clustalw-2.0.11.ebuild 423 RMD160 542be0620b543fc50d21d1f78448feb53620440c SHA1 c60389bd51a3c6aacc86eac36330347dad899fba SHA256 282ead2091779e3674c29a90de2a6763f17c21d0f8554b2fd3aff301cb55f3ad
+MISC ChangeLog 3482 RMD160 afaa7915769e036233d7067269d61983c200a382 SHA1 33a0df288090d55c9396069288bee27a02ba8767 SHA256 766375918c56350017ef08235bdcd9170467b71078c19e7633c1d18d04f8cc43
+MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/clustalw/clustalw-2.0.11.ebuild b/sci-biology/clustalw/clustalw-2.0.11.ebuild
new file mode 100644
index 000000000..b010192ad
--- /dev/null
+++ b/sci-biology/clustalw/clustalw-2.0.11.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=2
+
+DESCRIPTION="General purpose multiple alignment program for DNA and proteins"
+HOMEPAGE="http://www.clustal.org/"
+SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz"
+
+LICENSE="clustalw"
+SLOT="2"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+src_install() {
+	einstall || die "Installation failed."
+}
diff --git a/sci-biology/clustalw/files/1.83-as-needed.patch b/sci-biology/clustalw/files/1.83-as-needed.patch
new file mode 100644
index 000000000..62b4654cd
--- /dev/null
+++ b/sci-biology/clustalw/files/1.83-as-needed.patch
@@ -0,0 +1,17 @@
+--- makefile	2003-01-29 09:53:45.000000000 +0100
++++ makefile.new	2009-08-17 08:33:16.000000000 +0200
+@@ -11,11 +11,11 @@
+ HEADERS = general.h clustalw.h
+ 
+ CC	= cc
+-CFLAGS  = -c -O
+-LFLAGS	= -O -lm 
++CFLAGS  += -c
++LIBS	= -lm 
+ 
+ clustalw : $(OBJECTS) amenu.o clustalw.o
+-	$(CC) -o $@ $(OBJECTS) amenu.o clustalw.o $(LFLAGS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJECTS) amenu.o clustalw.o $(LIBS)
+ 
+ interface.o : interface.c $(HEADERS) param.h
+ 	$(CC) $(CFLAGS) $*.c
diff --git a/sci-biology/clustalw/metadata.xml b/sci-biology/clustalw/metadata.xml
new file mode 100644
index 000000000..3302123e5
--- /dev/null
+++ b/sci-biology/clustalw/metadata.xml
@@ -0,0 +1,9 @@
+<?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>
+</pkgmetadata>