Version bump

(Portage version: 2.2.0_alpha74/cvs/Linux x86_64)

6 files changed, 40 insertions, 113 deletions

diff --git a/sci-biology/prank/ChangeLog b/sci-biology/prank/ChangeLog
index 1236f6930b9e..fcbbc89f24ab 100644
--- a/sci-biology/prank/ChangeLog
+++ b/sci-biology/prank/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/prank
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/prank/ChangeLog,v 1.7 2010/08/09 17:26:54 xarthisius Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/prank/ChangeLog,v 1.8 2012/02/28 05:37:06 weaver Exp $
+
+*prank-111130 (28 Feb 2012)
+
+  28 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> -prank-081202.ebuild,
+  -files/prank-081202-gcc44.patch, -prank-091016.ebuild,
+  -prank-100311.ebuild, +prank-111130.ebuild:
+  Version bump, remove old
 
   09 Aug 2010; Kacper Kowalik <xarthisius@gentoo.org> prank-100701.ebuild:
   Respect user FLAGS wrt bug 331799. Thanks to Diego for report. Drop perl
diff --git a/sci-biology/prank/files/prank-081202-gcc44.patch b/sci-biology/prank/files/prank-081202-gcc44.patch
deleted file mode 100644
index d3e25444bbaa..000000000000
--- a/sci-biology/prank/files/prank-081202-gcc44.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-diff -ur prank.orig/src/guidetree.cpp prank/src/guidetree.cpp
---- prank.orig/src/guidetree.cpp	2008-11-28 17:06:39.000000000 +0200
-+++ prank/src/guidetree.cpp	2009-08-10 10:58:57.000000000 +0300
-@@ -18,6 +18,8 @@
-  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
-  ***************************************************************************/
- 
-+#include <stdio.h>
-+
- #include "guidetree.h"
- #include "pwhirschberg.h"
- #include "pwsite.h"
-diff -ur prank.orig/src/node.cpp prank/src/node.cpp
---- prank.orig/src/node.cpp	2008-12-02 15:24:08.000000000 +0200
-+++ prank/src/node.cpp	2009-08-10 11:00:53.000000000 +0300
-@@ -18,6 +18,7 @@
-  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
-  ***************************************************************************/
- 
-+#include <cstdio>
- #include <cstdlib>
- #include <cmath>
- #include <iostream>
-diff -ur prank.orig/src/terminalnode.cpp prank/src/terminalnode.cpp
---- prank.orig/src/terminalnode.cpp	2008-09-04 16:13:51.000000000 +0300
-+++ prank/src/terminalnode.cpp	2009-08-10 11:01:41.000000000 +0300
-@@ -17,6 +17,8 @@
-  *   Free Software Foundation, Inc.,                                       *
-  *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
-  ***************************************************************************/
-+
-+#include <cstdio>
- #include <cstdlib>
- #include "terminalnode.h"
- #include "config.h"
diff --git a/sci-biology/prank/prank-081202.ebuild b/sci-biology/prank/prank-081202.ebuild
deleted file mode 100644
index 39a871fb684c..000000000000
--- a/sci-biology/prank/prank-081202.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/prank/prank-081202.ebuild,v 1.3 2009/08/10 08:00:34 ssuominen Exp $
-
-EAPI=2
-inherit eutils
-
-DESCRIPTION="Probabilistic Alignment Kit"
-HOMEPAGE="http://www.ebi.ac.uk/goldman-srv/prank/prank/"
-SRC_URI="http://www.ebi.ac.uk/goldman-srv/prank/src/prank.src.${PV}.tgz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-S=${WORKDIR}/src
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-gcc44.patch
-	perl -i -pe 's/(CC|CXX|CFLAGS|CXXFLAGS)\s*=/#/' "${S}/Makefile" || die
-}
-
-src_install() {
-	dobin prank || die "dobin failed"
-}
diff --git a/sci-biology/prank/prank-091016.ebuild b/sci-biology/prank/prank-091016.ebuild
deleted file mode 100644
index 7f4ada0f0c32..000000000000
--- a/sci-biology/prank/prank-091016.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/prank/prank-091016.ebuild,v 1.2 2009/10/29 02:04:18 weaver Exp $
-
-EAPI=2
-inherit eutils
-
-DESCRIPTION="Probabilistic Alignment Kit"
-HOMEPAGE="http://www.ebi.ac.uk/goldman-srv/prank/prank/"
-SRC_URI="http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.${PV}.tgz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-S=${WORKDIR}/src
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-081202-gcc44.patch
-	perl -i -pe 's/(CC|CXX|CFLAGS|CXXFLAGS)\s*=/#/' "${S}/Makefile" || die
-}
-
-src_install() {
-	dobin prank || die "dobin failed"
-}
diff --git a/sci-biology/prank/prank-100311.ebuild b/sci-biology/prank/prank-100311.ebuild
deleted file mode 100644
index b3985c573534..000000000000
--- a/sci-biology/prank/prank-100311.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/prank/prank-100311.ebuild,v 1.1 2010/03/23 07:41:51 weaver Exp $
-
-EAPI="2"
-
-DESCRIPTION="Probabilistic Alignment Kit"
-HOMEPAGE="http://www.ebi.ac.uk/goldman-srv/prank/prank/"
-SRC_URI="http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.${PV}.tgz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-S=${WORKDIR}/src
-
-src_prepare() {
-	perl -i -pe 's/(CC|CXX|CFLAGS|CXXFLAGS)\s*=/#/' "${S}/Makefile" || die
-}
-
-src_install() {
-	dobin prank || die "dobin failed"
-}
diff --git a/sci-biology/prank/prank-111130.ebuild b/sci-biology/prank/prank-111130.ebuild
new file mode 100644
index 000000000000..1f97dbf0ad4b
--- /dev/null
+++ b/sci-biology/prank/prank-111130.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/prank/prank-111130.ebuild,v 1.1 2012/02/28 05:37:06 weaver Exp $
+
+EAPI=4
+
+inherit toolchain-funcs
+
+DESCRIPTION="Probabilistic Alignment Kit"
+HOMEPAGE="http://code.google.com/p/prank-msa/ http://www.ebi.ac.uk/goldman-srv/prank/prank/"
+SRC_URI="http://prank-msa.googlecode.com/files/prank.src.${PV}.tgz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/prank-msa/src"
+
+src_prepare() {
+	sed -i -e "s/\$(LINK)/& \$(LDFLAGS)/" Makefile || die
+}
+
+src_compile() {
+	emake LINK="$(tc-getCXX)" CFLAGS="${CFLAGS}" \
+		CXX="$(tc-getCXX)" CXXFLAGS="${CXXFLAGS}" || die
+}
+
+src_install() {
+	dobin prank || die
+}