Version Bump

(Portage version: 2.2.0_alpha28/cvs/Linux x86_64)

4 files changed, 100 insertions, 16 deletions

diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog
index 03349a499abf..cc3ae6c7df59 100644
--- a/sci-biology/vienna-rna/ChangeLog
+++ b/sci-biology/vienna-rna/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/vienna-rna
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.34 2010/10/15 07:15:15 xarthisius Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.35 2011/03/20 12:15:50 jlec Exp $
+
+*vienna-rna-1.8.5 (20 Mar 2011)
+
+  20 Mar 2011; Justin Lecher <jlec@gentoo.org> vienna-rna-1.8.4-r1.ebuild,
+  vienna-rna-1.8.4-r2.ebuild, +vienna-rna-1.8.5.ebuild:
+  Version Bump
 
 *vienna-rna-1.8.4-r2 (15 Oct 2010)
 
diff --git a/sci-biology/vienna-rna/vienna-rna-1.8.4-r1.ebuild b/sci-biology/vienna-rna/vienna-rna-1.8.4-r1.ebuild
index 85685972ae08..03f87f752f23 100644
--- a/sci-biology/vienna-rna/vienna-rna-1.8.4-r1.ebuild
+++ b/sci-biology/vienna-rna/vienna-rna-1.8.4-r1.ebuild
@@ -1,21 +1,22 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.4-r1.ebuild,v 1.3 2010/07/15 09:11:27 fauli Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.4-r1.ebuild,v 1.4 2011/03/20 12:15:50 jlec Exp $
 
 EAPI="2"
 
 inherit toolchain-funcs multilib autotools perl-module
 
-DESCRIPTION="The Vienna RNA Package - RNA secondary structure prediction and comparison"
-LICENSE="vienna-rna"
-HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA"
+DESCRIPTION="RNA secondary structure prediction and comparison"
+HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"
 SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-${PV}.tar.gz"
 
+LICENSE="vienna-rna"
 SLOT="0"
 IUSE=""
 KEYWORDS="amd64 ~ppc x86"
 
-DEPEND="dev-lang/perl
+DEPEND="
+	dev-lang/perl
 	media-libs/gd"
 RDEPEND="${DEPEND}"
 
@@ -40,7 +41,7 @@ src_prepare() {
 }
 
 src_configure() {
-	econf --with-cluster || die "Configuration failed."
+	econf --with-cluster
 	sed -e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \
 		-e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \
 		-i RNAforester/g2-0.70/Makefile \
diff --git a/sci-biology/vienna-rna/vienna-rna-1.8.4-r2.ebuild b/sci-biology/vienna-rna/vienna-rna-1.8.4-r2.ebuild
index 0fffa5e85e05..7821e390c2d6 100644
--- a/sci-biology/vienna-rna/vienna-rna-1.8.4-r2.ebuild
+++ b/sci-biology/vienna-rna/vienna-rna-1.8.4-r2.ebuild
@@ -1,21 +1,22 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.4-r2.ebuild,v 1.1 2010/10/15 07:15:15 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.4-r2.ebuild,v 1.2 2011/03/20 12:15:50 jlec Exp $
 
 EAPI="2"
 
 inherit toolchain-funcs multilib autotools perl-module
 
-DESCRIPTION="The Vienna RNA Package - RNA secondary structure prediction and comparison"
-LICENSE="vienna-rna"
-HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA"
+DESCRIPTION="RNA secondary structure prediction and comparison"
+HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"
 SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-${PV}.tar.gz"
 
+LICENSE="vienna-rna"
 SLOT="0"
 IUSE=""
 KEYWORDS="~amd64 ~ppc ~x86"
 
-DEPEND="dev-lang/perl
+DEPEND="
+	dev-lang/perl
 	media-libs/gd"
 RDEPEND="${DEPEND}"
 
@@ -38,7 +39,7 @@ src_prepare() {
 	sed -i '1 i #include <cstdio>' RNAforester/src/rnafuncs.cpp || die
 
 	eautoreconf
-	(cd RNAforester; eautoreconf)
+	cd RNAforester && eautoreconf
 }
 
 src_configure() {
diff --git a/sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild b/sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild
new file mode 100644
index 000000000000..c31ba770d710
--- /dev/null
+++ b/sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild,v 1.1 2011/03/20 12:15:50 jlec Exp $
+
+EAPI="2"
+
+inherit toolchain-funcs multilib autotools perl-module
+
+DESCRIPTION="RNA secondary structure prediction and comparison"
+HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"
+SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-${PV}.tar.gz"
+
+LICENSE="vienna-rna"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~ppc ~x86"
+
+DEPEND="
+	dev-lang/perl
+	media-libs/gd"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/ViennaRNA-${PV}"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.6.5-c-fixes.patch
+	"${FILESDIR}"/${PN}-1.7.2-LDFLAGS.patch
+	"${FILESDIR}"/${PN}-1.8.3-gcc4.3.patch
+	"${FILESDIR}"/${PN}-1.8.3-disable-gd.patch
+	"${FILESDIR}"/${PN}-1.8.4-jobserver-fix.patch
+	"${FILESDIR}"/${PN}-1.8.4-bindir.patch
+	"${FILESDIR}"/${PN}-1.8.4-overflows.patch
+	"${FILESDIR}"/${PN}-1.8.4-implicits.patch
+)
+
+src_prepare() {
+	base_src_prepare
+	sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
+
+	eautoreconf
+	cd RNAforester && eautoreconf
+}
+
+src_configure() {
+	econf --with-cluster
+	sed -e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \
+		-e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \
+		-i RNAforester/g2-0.70/Makefile \
+			|| die "Failed patching RNAForester build system."
+	sed -e "s:CC=cc:CC=$(tc-getCC):" -e "s:CFLAGS=:CFLAGS=${CFLAGS}:" \
+		-i Readseq/Makefile || die "Failed patching readseq Makefile."
+}
+
+src_compile() {
+	emake clean || die
+	emake || die
+	emake -C Readseq || die "Failed to compile readseq."
+	# TODO: Add (optional?) support for the NCBI toolkit.
+}
+
+src_test() {
+	cd "${S}"/Perl && emake check || die "Perl tests failed"
+	cd "${S}"/Readseq && emake test || die "Readseq tests failed"
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die
+	dodoc AUTHORS ChangeLog NEWS README THANKS || die
+	newbin Readseq/readseq readseq-vienna || die
+	dodoc Readseq/Readseq.help || die
+	newdoc Readseq/Readme README.readseq || die
+	newdoc Readseq/Formats Formats.readseq || die
+
+	# remove perlocal.pod to avoid file collisions (see #240358)
+	fixlocalpod || die "Failed to remove perlocal.pod"
+}