Fix bug 281734, thanks to Justin Lecher (jlec)

Package-Manager: portage-2.2_rc30/cvs/Linux x86_64

4 files changed, 41 insertions, 16 deletions

diff --git a/sci-biology/clustalw/ChangeLog b/sci-biology/clustalw/ChangeLog
index c3a51c4b741c..59d7abecdb7e 100644
--- a/sci-biology/clustalw/ChangeLog
+++ b/sci-biology/clustalw/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/clustalw
 # Copyright 2000-2009 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 $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/ChangeLog,v 1.17 2009/08/18 15:41:51 weaver Exp $
+
+*clustalw-1.83-r3 (18 Aug 2009)
+
+  18 Aug 2009; Andrey Kislyuk <weaver@gentoo.org>
+  +files/1.83-as-needed.patch, -clustalw-1.83-r2.ebuild,
+  +clustalw-1.83-r3.ebuild:
+  Fix bug 281734, thanks to Justin Lecher (jlec)
 
 *clustalw-2.0.11 (28 Apr 2009)
 
diff --git a/sci-biology/clustalw/Manifest b/sci-biology/clustalw/Manifest
index 7f11e0235887..147acb8de3b7 100644
--- a/sci-biology/clustalw/Manifest
+++ b/sci-biology/clustalw/Manifest
@@ -1,6 +1,7 @@
+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
 DIST clustalw1.83.UNIX.tar.gz 166863 RMD160 20c0ec7739be6747ae08220e5abf2bae412f039e SHA1 801ce911749171471b7964a1cff93c53c876c282 SHA256 8b757e02ae95ac0a0dd37db640497aa90f7a13a11784ce2a17f41b64e3059c60
-EBUILD clustalw-1.83-r2.ebuild 1031 RMD160 10d0c6c5c5922f3bd2fdfb0ef1fa014404e0a699 SHA1 e7f646bff6f5f6035d8ccab627fb5a3dc994cc8c SHA256 12c6d651d88d0b6d33fff91e701c10ef79ff3c36504e0b67dbd1c748f6bec67e
+EBUILD clustalw-1.83-r3.ebuild 965 RMD160 77e30c7efa37f2e4fce05dd18939de8e9f3b8f98 SHA1 0d4d736660df3362259f1041bcf754d9e158eb06 SHA256 340538bf07b91bc115a05cd1196a3e873be72b703aef9a99ee29d28fd7c829b7
 EBUILD clustalw-2.0.11.ebuild 528 RMD160 2c2c6b6166ef72cb6b7f69454ed8e949d84255b8 SHA1 c5e223dc30a3cad0be35743a4f1094e4908c8a5b SHA256 a4f06cc608a8185e0e01a41535585e2086279f6eb8147a496da555b158c35192
-MISC ChangeLog 3330 RMD160 13a44b712064aaf578d94fa17e59eb766588ff8c SHA1 9681ad79b28d7567ee8ffe2a8be541e0bed66a63 SHA256 8b2727d5ca8b46db9f0111125f6d72642c73e01e906063300c33342bcecb8290
+MISC ChangeLog 3548 RMD160 4b305e6e8cdf83e9036e360d851d2fc4ba0fa497 SHA1 2153298a8fe2c7d699a977945d821833ec8733cb SHA256 0248410c36963fe15f7bc25b2f9ae80abc25accd6df8c0da196a6a31b1ff450f
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/clustalw/clustalw-1.83-r2.ebuild b/sci-biology/clustalw/clustalw-1.83-r3.ebuild
index 03de96f97d1e..1c24269955ce 100644
--- a/sci-biology/clustalw/clustalw-1.83-r2.ebuild
+++ b/sci-biology/clustalw/clustalw-1.83-r3.ebuild
@@ -1,8 +1,10 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/clustalw-1.83-r2.ebuild,v 1.1 2008/08/27 22:51:42 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/clustalw-1.83-r3.ebuild,v 1.1 2009/08/18 15:41:51 weaver Exp $
 
-inherit toolchain-funcs
+EAPI="2"
+
+inherit base toolchain-funcs
 
 DESCRIPTION="General purpose multiple alignment program for DNA and proteins"
 HOMEPAGE="http://www.embl-heidelberg.de/~seqanal/"
@@ -10,24 +12,22 @@ SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/${PN}${PV}.UNIX.tar.gz"
 
 LICENSE="clustalw"
 SLOT="1"
-KEYWORDS="alpha amd64 ppc ppc64 sparc x86"
+KEYWORDS="~alpha ~amd64 ~ppc ~ppc64 ~sparc ~x86"
 IUSE=""
 
 S="${WORKDIR}"/${PN}${PV}
 
-src_unpack(){
-	unpack ${A}
-	cd "${S}"
+PATCHES=(
+	"${FILESDIR}"/${PV}-as-needed.patch
+)
+
+src_prepare() {
+	base_src_prepare
 	sed -i -e "s/CC	= cc/CC	= $(tc-getCC)/" \
-		-e "s/CFLAGS  = -c -O/CFLAGS  = -c ${CFLAGS}/" \
-		-e "s/LFLAGS	= -O -lm/LFLAGS	= -lm ${CFLAGS}/" makefile || die
+		makefile || die
 	sed -i -e "s%clustalw_help%/usr/share/doc/${PF}/clustalw_help%" clustalw.c || die
 }
 
-src_compile() {
-	emake || die
-}
-
 src_install() {
 	dobin clustalw || die
 	dodoc README clustalv.doc clustalw.doc clustalw.ms
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 000000000000..62b4654cddea
--- /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