Version bump (fixes bug #191882).

(Portage version: 2.1.3.19)

5 files changed, 89 insertions, 5 deletions

diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog
index 4076748f62a0..167fc9e2791d 100644
--- a/sci-biology/vienna-rna/ChangeLog
+++ b/sci-biology/vienna-rna/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/vienna-rna
 # Copyright 2000-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.13 2007/04/29 01:06:35 je_fro Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.14 2007/11/24 15:10:04 markusle Exp $
+
+*vienna-rna-1.6.5 (24 Nov 2007)
+
+  24 Nov 2007; Markus Dittrich <markusle@gentoo.org>
+  +files/vienna-rna-1.6.5-c-fixes.patch, +vienna-rna-1.6.5.ebuild:
+  Version bump (fixes bug #191882).
 
   29 Apr 2007; Jeff Gardner <je_fro@gentoo.org> vienna-rna-1.6.1.ebuild:
   Adding ~amd64.
diff --git a/sci-biology/vienna-rna/files/digest-vienna-rna-1.6.5 b/sci-biology/vienna-rna/files/digest-vienna-rna-1.6.5
new file mode 100644
index 000000000000..480a80483521
--- /dev/null
+++ b/sci-biology/vienna-rna/files/digest-vienna-rna-1.6.5
@@ -0,0 +1,3 @@
+MD5 e03a98e6184a4b17eb071f6f67d7d741 ViennaRNA-1.6.5.tar.gz 1214312
+RMD160 671f9ebd26c1c11db4f19821daea89feac8f2df2 ViennaRNA-1.6.5.tar.gz 1214312
+SHA256 70a7bef5d6e67d31ee88089603c18b95e3a544880cddc56e5a04da28cdaa84b9 ViennaRNA-1.6.5.tar.gz 1214312
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.6.5-c-fixes.patch b/sci-biology/vienna-rna/files/vienna-rna-1.6.5-c-fixes.patch
new file mode 100644
index 000000000000..0a781667c70b
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.6.5-c-fixes.patch
@@ -0,0 +1,22 @@
+diff -Naur ViennaRNA-1.6.5/Cluster/statgeom.c ViennaRNA-1.6.5.new/Cluster/statgeom.c
+--- ViennaRNA-1.6.5/Cluster/statgeom.c	2001-04-05 04:36:41.000000000 -0400
++++ ViennaRNA-1.6.5.new/Cluster/statgeom.c	2007-11-24 08:55:17.000000000 -0500
+@@ -5,6 +5,7 @@
+ */
+ 
+ #include <stdio.h>
++#include <string.h>
+ #include <strings.h>
+ #include <ctype.h>
+ #include "utils.h"
+diff -Naur ViennaRNA-1.6.5/Readseq/readseq.c ViennaRNA-1.6.5.new/Readseq/readseq.c
+--- ViennaRNA-1.6.5/Readseq/readseq.c	1995-07-12 13:05:58.000000000 -0400
++++ ViennaRNA-1.6.5.new/Readseq/readseq.c	2007-11-24 08:56:16.000000000 -0500
+@@ -173,6 +173,7 @@
+ #include <stdio.h>
+ #include <string.h>
+ #include <ctype.h>
++#include <stdlib.h>
+ 
+ #include "ureadseq.h"
+ 
diff --git a/sci-biology/vienna-rna/vienna-rna-1.4.ebuild b/sci-biology/vienna-rna/vienna-rna-1.4.ebuild
index fd15d62688d2..58ecaa73cb51 100644
--- a/sci-biology/vienna-rna/vienna-rna-1.4.ebuild
+++ b/sci-biology/vienna-rna/vienna-rna-1.4.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2005 Gentoo Foundation
+# Copyright 1999-2007 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.4.ebuild,v 1.3 2005/01/30 18:21:09 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.4.ebuild,v 1.4 2007/11/24 15:10:04 markusle Exp $
 
 inherit flag-o-matic
 
@@ -56,9 +56,9 @@ src_install() {
 
 	if use perl; then
 		cd Perl
-		make install DESTDIR=${D} || die
+		make install DESTDIR="${D}" || die
 		dodoc RNA_wrap.doc
-		cd ${S}
+		cd "${S}"
 	fi
 
 	if ! use no-utils; then
diff --git a/sci-biology/vienna-rna/vienna-rna-1.6.5.ebuild b/sci-biology/vienna-rna/vienna-rna-1.6.5.ebuild
new file mode 100644
index 000000000000..44c09db8b71d
--- /dev/null
+++ b/sci-biology/vienna-rna/vienna-rna-1.6.5.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.6.5.ebuild,v 1.1 2007/11/24 15:10:04 markusle Exp $
+
+inherit toolchain-funcs multilib eutils
+
+DESCRIPTION="The Vienna RNA Package - RNA secondary structure prediction and comparison"
+LICENSE="vienna-rna"
+HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA"
+SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-${PV}.tar.gz"
+
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86 ~ppc"
+
+DEPEND="dev-lang/perl
+	media-libs/gd"
+
+S="${WORKDIR}/ViennaRNA-${PV}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${P}-c-fixes.patch
+}
+
+src_compile() {
+	econf --with-cluster || die "Configuration failed."
+	cd "${S}"/RNAforester/g2-0.70
+	sed -e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \
+		-e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \
+		-i Makefile || die "Failed patching RNAForester build system."
+	cd "${S}"
+	emake || die "Compilation failed."
+	cd "${S}"/Readseq
+	sed -e "s:CC=cc:CC=$(tc-getCC):" -e "s:CFLAGS=:CFLAGS=${CFLAGS}:" \
+		-i Makefile || die "Failed patching readseq Makefile."
+	make || die "Failed to compile readseq."
+	# TODO: Add (optional?) support for the NCBI toolkit.
+}
+
+src_install() {
+	make install DESTDIR="${D}" || die "Installation failed."
+	dodoc AUTHORS ChangeLog NEWS README THANKS \
+		|| die "Failed to install documentation."
+	newbin Readseq/readseq readseq-vienna \
+		|| die "Installing readseq failed."
+	dodoc Readseq/Readseq.help || die \
+		"Readseq Documentation installation failed."
+	newdoc Readseq/Readme README.readseq && \
+		newdoc Readseq/Formats Formats.readseq \
+		|| die "Installing readseq Readme failed."
+}