Version bump

Package-Manager: portage-2.2.0_alpha74/cvs/Linux x86_64

10 files changed, 104 insertions, 164 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
+}
diff --git a/sci-biology/primer3/ChangeLog b/sci-biology/primer3/ChangeLog
index 5b9a2dab0ce0..13868f38f3a1 100644
--- a/sci-biology/primer3/ChangeLog
+++ b/sci-biology/primer3/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/primer3
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/ChangeLog,v 1.29 2011/12/03 10:58:16 hwoarang Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/ChangeLog,v 1.30 2012/02/28 05:41:15 weaver Exp $
+
+*primer3-2.3.0 (28 Feb 2012)
+
+  28 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> -primer3-1.1.4.ebuild,
+  +primer3-2.3.0.ebuild:
+  Version bump, remove old
 
   03 Dec 2011; Markos Chandras <hwoarang@gentoo.org> primer3-2.2.3.ebuild:
   convert test statement to if;fi block because || die does not work on a
diff --git a/sci-biology/primer3/Manifest b/sci-biology/primer3/Manifest
index 1656e56bdce0..de7a3d441473 100644
--- a/sci-biology/primer3/Manifest
+++ b/sci-biology/primer3/Manifest
@@ -1,28 +1,19 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
+Hash: SHA1
 
 AUX primer3-1.1.4-ldflags.patch 882 RMD160 c67d4e03fc68155d2a74276bbc7e409bc8e8096b SHA1 5346c976c80b6a474e352f3a27c6153648d58a2b SHA256 10ef0f1491df83c60f5919fcc461a0864e12a0303d8242f4e3ea1c2f8963c436
 DIST primer3-1.1.4.tar.gz 974628 RMD160 87535d123d4c00b64eb763e4e567c5c83fde6b54 SHA1 fcabf7d8aa31c5568bd130b318c3ead4a1b9aa3a SHA256 1cb045791afd3c4033956a65687ca0c1b1a6607ac84705bf4ed7d7151691980b
 DIST primer3-2.2.3.tar.gz 2284282 RMD160 040b41649f5bfc17214502b2ba5e98d1a5afd73f SHA1 20c6a00455b86a5712c1e297930f2624fca45881 SHA256 2e68d638119bfcac12571da351cf261e28a3dd4b32c89074ce17065931a98774
+DIST primer3-2.3.0.tar.gz 2596929 RMD160 4e27aeca7ffd78287e143088d2dffd99a6617d13 SHA1 22d4283e1fcc17c660c78e8b407d5051a414dbc2 SHA256 6b6721f8ae3b45dc8ac81d6a230012f79d56f840274e88dc5001ec718625e834
 EBUILD primer3-1.1.4-r2.ebuild 966 RMD160 36ddb7a39f54ee2650bcb2300ee7d14f594f7ae0 SHA1 2fe782c9bac2232e286439728ac1d55bffdf0c97 SHA256 fb2ea764406931476ae46e9878aa3591b8a23f972be52b57a76ae4fa2085347a
-EBUILD primer3-1.1.4.ebuild 777 RMD160 a7f7d260c80b4899568b11ec28a0431b215db2d1 SHA1 45485dafce00b8500267350041bc66c7c480b4e2 SHA256 cab7435d84362f2dd3b56d85db348662baa22e8ec5757acdffe45ecb08be7a74
 EBUILD primer3-2.2.3.ebuild 1335 RMD160 36c9a36ab5fa0fa3408432b9da7083abe437c794 SHA1 75015b4058a8b8c2268ca81a7365b0a5c6b699a4 SHA256 ed8de7c2dc7e7250de0e73f8af2298e6d8b385155c6a3605f1a539c20ec7dedd
-MISC ChangeLog 4599 RMD160 a42386e4bf7e25f160f482f4496b5292bd06ef3f SHA1 4172180b47c686765e1c38a851f2c8ed609cdc14 SHA256 6c8bf0edafc1833089f97b23defedb3c7e4f8730331f5ad7e4bf9e6654575279
+EBUILD primer3-2.3.0.ebuild 1335 RMD160 6d6b974fef83c515f9ece16def75a018f86cf8ad SHA1 7e066e63cbda084338458d7e5b5f45240053f33c SHA256 d45c932b849eb8cb45a886b0812bfdf8c621019522e5c52cc4b2626495ea03b4
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 MISC metadata.xml 624 RMD160 b9c9f7ed6eb37504dbe39d7fd2c12ea7c0e2b557 SHA1 ecbd008512496eeefae63e1d36bdbe66e71e63fc SHA256 f612edc94f6538c9acf99caadc2a7d6e33cac6f933db9deafae777c7a45505bb
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diff --git a/sci-biology/primer3/primer3-1.1.4.ebuild b/sci-biology/primer3/primer3-1.1.4.ebuild
deleted file mode 100644
index 441d554cd21a..000000000000
--- a/sci-biology/primer3/primer3-1.1.4.ebuild
+++ /dev/null
@@ -1,32 +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/primer3/primer3-1.1.4.ebuild,v 1.3 2011/11/23 08:10:50 jlec Exp $
-
-DESCRIPTION="Primer Design for PCR reactions"
-HOMEPAGE="http://primer3.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="whitehead"
-IUSE=""
-KEYWORDS="amd64 ~ppc ~ppc64 ~sparc x86"
-
-DEPEND="dev-lang/perl"
-RDEPEND=""
-
-S="${WORKDIR}/src"
-
-src_compile() {
-	emake -e || die
-}
-
-src_test () {
-	make primer_test || die
-}
-
-src_install () {
-	dobin long_seq_tm_test ntdpal oligotm primer3_core || die \
-			"Could not install program."
-	dodoc ../{how-to-cite.txt,README.txt,example} || die \
-			"Could not install documentation."
-}
diff --git a/sci-biology/primer3/primer3-2.3.0.ebuild b/sci-biology/primer3/primer3-2.3.0.ebuild
new file mode 100644
index 000000000000..eb61728f235a
--- /dev/null
+++ b/sci-biology/primer3/primer3-2.3.0.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/primer3-2.3.0.ebuild,v 1.1 2012/02/28 05:41:15 weaver Exp $
+
+EAPI="3"
+
+inherit toolchain-funcs
+
+DESCRIPTION="Primer Design for PCR reactions"
+HOMEPAGE="http://primer3.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-2"
+IUSE=""
+KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="dev-lang/perl"
+RDEPEND=""
+
+src_prepare() {
+	if [[ ${CHOST} == *-darwin* ]]; then
+		sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die
+	fi
+	perl -i -ne 's/\$\(CPP\)/'$(tc-getCXX)'/; print unless /^(CC|CPP|CFLAGS|LDFLAGS)\s*=/' src/Makefile || die
+	sed \
+		-e '/oligotm/s:-o $@:$(LDFLAGS) -o $@:g' \
+		-e '/long_seq_tm_test/s:-o $@:$(LDFLAGS) -o $@:g' \
+		-e 's:CFLAGS:CXXFLAGS:g' \
+		-i src/Makefile || die
+}
+
+src_compile() {
+	emake -C src || die
+}
+
+src_test () {
+	emake -C test || die
+}
+
+src_install () {
+	dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core} || die \
+		"Could not install program."
+	dodoc src/release_notes.txt example primer3_manual.htm || die \
+		"Could not install documentation."
+	insinto /opt/primer3_config
+	doins -r src/primer3_config/* primer3*settings.txt || die
+}