Version bump (fixes bug #191882).

Package-Manager: portage-2.1.3.19

6 files changed, 109 insertions, 13 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/Manifest b/sci-biology/vienna-rna/Manifest
index c9f7d6a4a047..fcbd35c4714d 100644
--- a/sci-biology/vienna-rna/Manifest
+++ b/sci-biology/vienna-rna/Manifest
@@ -1,17 +1,26 @@
+AUX vienna-rna-1.6.5-c-fixes.patch 728 RMD160 5f427bb976200f58599b1878ca7273844b21aac0 SHA1 7089237c787d780d53b92c4c38ba73ec60b81218 SHA256 49955a6244eb3be73f8d2472f3a4f9b8d1f8f92ba11327961b901a2c1f1e24d8
+MD5 12551ebd039dc595be6654d87375b22d files/vienna-rna-1.6.5-c-fixes.patch 728
+RMD160 5f427bb976200f58599b1878ca7273844b21aac0 files/vienna-rna-1.6.5-c-fixes.patch 728
+SHA256 49955a6244eb3be73f8d2472f3a4f9b8d1f8f92ba11327961b901a2c1f1e24d8 files/vienna-rna-1.6.5-c-fixes.patch 728
 DIST ViennaRNA-1.4.tar.gz 483047 RMD160 31ce5f6e3f1adbd0c8e4759c243764523828a258 SHA1 fde493bfeeb443cb427bbe58b0d4daa446771ccf SHA256 8021ebe40d4fdf609fc9ad9aa7525736f69146666b6222d78d1016c20707522f
 DIST ViennaRNA-1.6.1.tar.gz 1149127 RMD160 37e4719e7ca03ced354976fa83f38d5f96776531 SHA1 afb35731c39893b17a21653a96ba5b3e39340934 SHA256 8036b6a562ec898dab4144cb5f18b42ff7c4290875572d05e7059b1ca2d5ddfd
-EBUILD vienna-rna-1.4.ebuild 2407 RMD160 1697ad7c9ea368107c2958429cc53ab35250d41c SHA1 0fabbd6bb11b7d1a5751245ec99a6c319e5a40a2 SHA256 c56b188f15a432c0749e075dab9cdc0a4a0631628b3992027d4718ed3dacd0e6
-MD5 3bb50b8cfbc48270128a17049473d2d4 vienna-rna-1.4.ebuild 2407
-RMD160 1697ad7c9ea368107c2958429cc53ab35250d41c vienna-rna-1.4.ebuild 2407
-SHA256 c56b188f15a432c0749e075dab9cdc0a4a0631628b3992027d4718ed3dacd0e6 vienna-rna-1.4.ebuild 2407
+DIST ViennaRNA-1.6.5.tar.gz 1214312 RMD160 671f9ebd26c1c11db4f19821daea89feac8f2df2 SHA1 12a46718c684bb4f888b41df52a3a8009715ff10 SHA256 70a7bef5d6e67d31ee88089603c18b95e3a544880cddc56e5a04da28cdaa84b9
+EBUILD vienna-rna-1.4.ebuild 2411 RMD160 df875d116e09cb23ae6fbda5d59bf12202584aa2 SHA1 7cbe01e26e40d1fb92d6bece04f1ceba543c42b8 SHA256 db9071a8513e921026a11fcb1a57751dfdece8448e42f07d4b702af1736bf7d6
+MD5 c17be19b856ff5ab5b684528acc33d44 vienna-rna-1.4.ebuild 2411
+RMD160 df875d116e09cb23ae6fbda5d59bf12202584aa2 vienna-rna-1.4.ebuild 2411
+SHA256 db9071a8513e921026a11fcb1a57751dfdece8448e42f07d4b702af1736bf7d6 vienna-rna-1.4.ebuild 2411
 EBUILD vienna-rna-1.6.1.ebuild 1587 RMD160 563cb491bc5c71347eaacd0d093924fbba79afa6 SHA1 5d30247bf97f0cc2197993673dc1d813f27b37e1 SHA256 04308a39ccf800a738a899ff93b1592532dab2886405b90b99815c5e9155bead
 MD5 aef9c18a51a387759b34f06342bb5d9f vienna-rna-1.6.1.ebuild 1587
 RMD160 563cb491bc5c71347eaacd0d093924fbba79afa6 vienna-rna-1.6.1.ebuild 1587
 SHA256 04308a39ccf800a738a899ff93b1592532dab2886405b90b99815c5e9155bead vienna-rna-1.6.1.ebuild 1587
-MISC ChangeLog 2097 RMD160 d0c2669f15701a33d5def85e8d2c5de6fdabdd1a SHA1 ed5b17c4831cbe32bf058c86ad6ba0992a07e940 SHA256 801e24a9743d565e8b995ba5e33972c301b15beb99dff1ecf76685a6c9f6a0f9
-MD5 2ca4f68e2703e2e88c6311c46fa793cd ChangeLog 2097
-RMD160 d0c2669f15701a33d5def85e8d2c5de6fdabdd1a ChangeLog 2097
-SHA256 801e24a9743d565e8b995ba5e33972c301b15beb99dff1ecf76685a6c9f6a0f9 ChangeLog 2097
+EBUILD vienna-rna-1.6.5.ebuild 1744 RMD160 1b8d7dc72c02d815a21fc1398865c1d936afaf05 SHA1 e05f78a86fd59fcb13c3e57fe462b93bc6c39b16 SHA256 6e5b9eff1e28e5a0ec47886d743abd1b79909cd2331f87daee75f66dddd9925e
+MD5 3c703e0a65951975078c3d6abb0e3290 vienna-rna-1.6.5.ebuild 1744
+RMD160 1b8d7dc72c02d815a21fc1398865c1d936afaf05 vienna-rna-1.6.5.ebuild 1744
+SHA256 6e5b9eff1e28e5a0ec47886d743abd1b79909cd2331f87daee75f66dddd9925e vienna-rna-1.6.5.ebuild 1744
+MISC ChangeLog 2289 RMD160 352226578ec3e2d6fadaeefe426ebb613ecc8e9f SHA1 fa7a49ddd07a8e280b9eab911c608d31ec3bad96 SHA256 04e84f5d262fa2c1438f7199cb3c6c1c8737f9da9cf09c6f24ce698df5ced095
+MD5 88b1de721d6af322db6c223bbf406f71 ChangeLog 2289
+RMD160 352226578ec3e2d6fadaeefe426ebb613ecc8e9f ChangeLog 2289
+SHA256 04e84f5d262fa2c1438f7199cb3c6c1c8737f9da9cf09c6f24ce698df5ced095 ChangeLog 2289
 MISC metadata.xml 1228 RMD160 8db8df2ec48d6a7e8dd4c592f7f4a9c7f8810cf9 SHA1 e46645ad44f1236a471a0ba79e08e4f6fe752dcb SHA256 7c558ba2568a5ec64654465c4c45784a32c4dccd6adf33518cf1f3daca2acd16
 MD5 3f7b19f43a1d86838c7947446337f2a8 metadata.xml 1228
 RMD160 8db8df2ec48d6a7e8dd4c592f7f4a9c7f8810cf9 metadata.xml 1228
@@ -22,3 +31,6 @@ SHA256 459b7bbca590c52d3bb60e3279fd55d121a43fb4f655e6e62af475430a597295 files/di
 MD5 eb193013e189f83146d7327383271be0 files/digest-vienna-rna-1.6.1 250
 RMD160 caf402e2c2f9d9cbf9182f4c79195bef66f39f53 files/digest-vienna-rna-1.6.1 250
 SHA256 cfbe4a4bc1a18ddbd121ff08e6b67fcaf93a7ca8e28068f4f837a8b53fc3adf0 files/digest-vienna-rna-1.6.1 250
+MD5 f39324f28a684c8edd2c450292e15c1b files/digest-vienna-rna-1.6.5 250
+RMD160 51401de45b9ebc58ab3e1f53b5018d2b803d1b9e files/digest-vienna-rna-1.6.5 250
+SHA256 9c9b6c4cd300347d959b1d649ea6cb78cf38b622a418e78b48c1e61e5c8732c1 files/digest-vienna-rna-1.6.5 250
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."
+}