Version bump and removed old ebuilds (fixes bug #235943).

Package-Manager: portage-2.2_rc8/cvs/Linux 2.6.26-SENTINEL-2 i686

5 files changed, 100 insertions, 69 deletions

diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog
index 72816ef39a7c..7b5d6edd2c62 100644
--- a/sci-biology/vienna-rna/ChangeLog
+++ b/sci-biology/vienna-rna/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/vienna-rna
 # Copyright 2000-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.16 2008/08/06 15:06:58 ulm Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.17 2008/08/29 01:21:38 markusle Exp $
+
+*vienna-rna-1.7.2 (28 Aug 2008)
+
+  28 Aug 2008; Markus Dittrich <markusle@gentoo.org>
+  +files/vienna-rna-1.7.2-gcc4.3.patch, -vienna-rna-1.6.1.ebuild,
+  -vienna-rna-1.6.5.ebuild, +vienna-rna-1.7.2.ebuild:
+  Version bump and removed old ebuilds (fixes bug #235943). Thanks much to
+  Chad A. Simmons <chad.simmons@member.fsf.org> for his ebuild and patches.
 
   06 Aug 2008; Ulrich Mueller <ulm@gentoo.org> metadata.xml:
   Add USE flag description to metadata wrt GLEP 56.
diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest
index 0551aa362ab6..5a4ff0ca75e5 100644
--- a/sci-biology/vienna-rna/Manifest
+++ b/sci-biology/vienna-rna/Manifest
@@ -1,21 +1,10 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 AUX vienna-rna-1.6.5-c-fixes.patch 728 RMD160 5f427bb976200f58599b1878ca7273844b21aac0 SHA1 7089237c787d780d53b92c4c38ba73ec60b81218 SHA256 49955a6244eb3be73f8d2472f3a4f9b8d1f8f92ba11327961b901a2c1f1e24d8
+AUX vienna-rna-1.7.2-gcc4.3.patch 2738 RMD160 c559c768b8c4e9b92f9bdbd66f5e3ff12ba5e5df SHA1 d1c1f8b9fa8109ad58613db53c72d8ae921990ce SHA256 234374db06aacef6cf7856fcb61642c501d8b03cd5bd579c167e1455774f5610
 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
-DIST ViennaRNA-1.6.5.tar.gz 1214312 RMD160 671f9ebd26c1c11db4f19821daea89feac8f2df2 SHA1 12a46718c684bb4f888b41df52a3a8009715ff10 SHA256 70a7bef5d6e67d31ee88089603c18b95e3a544880cddc56e5a04da28cdaa84b9
+DIST ViennaRNA-1.7.2.tar.gz 1298982 RMD160 768f53ba9e0f784b066ae485451eb0abd6f6631c SHA1 36a4bfcf88599afc479be14bc324ef4ce9d629a3 SHA256 202887653033de9e50644acd5c3d8607f215d6c84eef9d68a936837edf71a00e
 DIST ViennaRNA-1.7.tar.gz 1249073 RMD160 7f07ae00f0efbd992f7d7dfdb3c215dde7835355 SHA1 3856b4d18e09bc640e7e0aa344346efbe31b2421 SHA256 b1df6ec6c68ecaf5256cb0a3fbb3cbee4dc84138254499f3c471ca5afbb82c58
 EBUILD vienna-rna-1.4.ebuild 2411 RMD160 df875d116e09cb23ae6fbda5d59bf12202584aa2 SHA1 7cbe01e26e40d1fb92d6bece04f1ceba543c42b8 SHA256 db9071a8513e921026a11fcb1a57751dfdece8448e42f07d4b702af1736bf7d6
-EBUILD vienna-rna-1.6.1.ebuild 1587 RMD160 563cb491bc5c71347eaacd0d093924fbba79afa6 SHA1 5d30247bf97f0cc2197993673dc1d813f27b37e1 SHA256 04308a39ccf800a738a899ff93b1592532dab2886405b90b99815c5e9155bead
-EBUILD vienna-rna-1.6.5.ebuild 1744 RMD160 1b8d7dc72c02d815a21fc1398865c1d936afaf05 SHA1 e05f78a86fd59fcb13c3e57fe462b93bc6c39b16 SHA256 6e5b9eff1e28e5a0ec47886d743abd1b79909cd2331f87daee75f66dddd9925e
 EBUILD vienna-rna-1.7.0.ebuild 1795 RMD160 35771c487766583375c59d513bd3bac59e2aaaa6 SHA1 01da384c1830df80f232c4e361b96a28b77acc81 SHA256 4a2044beeb9070f2c415c491b94eadb74972db2987806e524da1c7927686c499
-MISC ChangeLog 2529 RMD160 de660b8d594fdcf6ba18ef4d29ad36f33e136a01 SHA1 5efc3d71998792750a265a7bb93320d9003ebbd7 SHA256 8b19d61deaa5672d40767abb837231c4373e39335281a4b37873fe114dbf1fd7
+EBUILD vienna-rna-1.7.2.ebuild 1787 RMD160 937574695e34e7a5b2dcaab38d14fd5801b21221 SHA1 97227df81bdd9eeba6cf5ae3dce88732f6f084c3 SHA256 8b6bb15d35bf5158251524dcfd6a0dca6d5ce06c02b04d8fc5067ec14b2eab14
+MISC ChangeLog 2892 RMD160 d6e093f408bb070b73f78ede64ccb162070b72b1 SHA1 75730c01f9c00cb04111b67af53880dc23a7c617 SHA256 27830b5fe43e4e696249963efaa0e9893cf7c6d7a7ea49821409e8d485d8edf0
 MISC metadata.xml 1435 RMD160 539ba60c7a5ca6656e5716b61e2bbf44bb5b9c27 SHA1 77777cd6e84bb6e799e0bfb357580c6a3edfbb91 SHA256 93f911332c6232466324a14891ee9ede4fb23633b12b8ea42ed8cfa2c32b294b
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diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.3.patch b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.3.patch
new file mode 100644
index 000000000000..4f5bd37f3a77
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.3.patch
@@ -0,0 +1,79 @@
+diff -Naur ViennaRNA-1.7/Cluster/AS_main.c ViennaRNA-1.7.new/Cluster/AS_main.c
+--- ViennaRNA-1.7/Cluster/AS_main.c	2001-04-05 04:36:41.000000000 -0400
++++ ViennaRNA-1.7.new/Cluster/AS_main.c	2008-08-28 10:53:11.000000000 -0400
+@@ -1,5 +1,6 @@
+ #include <stdio.h>
+ #include <string.h>
++#include <stdlib.h>
+ #include "distance_matrix.h"
+ #include "statgeom.h"
+ #include "split.h"
+diff -Naur ViennaRNA-1.7/Cluster/statgeom.c ViennaRNA-1.7.new/Cluster/statgeom.c
+--- ViennaRNA-1.7/Cluster/statgeom.c	2001-04-05 04:36:41.000000000 -0400
++++ ViennaRNA-1.7.new/Cluster/statgeom.c	2008-08-28 10:53:11.000000000 -0400
+@@ -7,6 +7,7 @@
+ #include <stdio.h>
+ #include <strings.h>
+ #include <ctype.h>
++#include <stdlib.h>
+ #include "utils.h"
+ #include "PS3D.h"
+ #include "distance_matrix.h"
+diff -Naur ViennaRNA-1.7/Cluster/treeplot.c ViennaRNA-1.7.new/Cluster/treeplot.c
+--- ViennaRNA-1.7/Cluster/treeplot.c	2001-04-05 04:36:41.000000000 -0400
++++ ViennaRNA-1.7.new/Cluster/treeplot.c	2008-08-28 10:53:11.000000000 -0400
+@@ -1,6 +1,7 @@
+ #include <stdio.h>
+ #include <string.h>
+ #include <math.h>
++#include <stdlib.h>
+ #include "distance_matrix.h"
+ #include "utils.h"
+ 
+diff -Naur ViennaRNA-1.7/RNAforester/src/main.cpp ViennaRNA-1.7.new/RNAforester/src/main.cpp
+--- ViennaRNA-1.7/RNAforester/src/main.cpp	2005-08-05 10:14:10.000000000 -0400
++++ ViennaRNA-1.7.new/RNAforester/src/main.cpp	2008-08-28 10:53:11.000000000 -0400
+@@ -19,6 +19,8 @@
+ #include <list>
+ #include <sstream>
+ #include <string>
++#include <cstring>
++#include <climits>
+ #include <map>
+ 
+ //#include <sys/timeb.h>

+diff -Naur ViennaRNA-1.7/RNAforester/src/ppforestbase.h ViennaRNA-1.7.new/RNAforester/src/ppforestbase.h
+--- ViennaRNA-1.7/RNAforester/src/ppforestbase.h	2006-05-08 07:49:33.000000000 -0400
++++ ViennaRNA-1.7.new/RNAforester/src/ppforestbase.h	2008-08-28 10:53:11.000000000 -0400
+@@ -16,6 +16,7 @@
+ 
+ #include <algorithm>
+ #include <cassert>
++#include <cstring>
+ 
+ #include "misc.h"
+ #include "types.h"
+diff -Naur ViennaRNA-1.7/RNAforester/src/rna_algebra.h ViennaRNA-1.7.new/RNAforester/src/rna_algebra.h
+--- ViennaRNA-1.7/RNAforester/src/rna_algebra.h	2004-09-01 17:55:22.000000000 -0400
++++ ViennaRNA-1.7.new/RNAforester/src/rna_algebra.h	2008-08-28 10:53:11.000000000 -0400
+@@ -3,6 +3,8 @@
+ 

+ #include <assert.h>
+ #include <algorithm>
++#include <cstring>
++#include <climits>
+ 
+ #include "algebra.h"
+ #include "debug.h"
+diff -Naur ViennaRNA-1.7/Readseq/ureadseq.c ViennaRNA-1.7.new/Readseq/ureadseq.c
+--- ViennaRNA-1.7/Readseq/ureadseq.c	2002-11-27 06:23:56.000000000 -0500
++++ ViennaRNA-1.7.new/Readseq/ureadseq.c	2008-08-28 10:53:11.000000000 -0400
+@@ -16,7 +16,7 @@
+  *
+  */
+ 
+-
++#include <stdlib.h>
+ #include <stdio.h>
+ #include <ctype.h>
+ #include <string.h>
diff --git a/sci-biology/vienna-rna/vienna-rna-1.6.1.ebuild b/sci-biology/vienna-rna/vienna-rna-1.6.1.ebuild
deleted file mode 100644
index a7514b28edbb..000000000000
--- a/sci-biology/vienna-rna/vienna-rna-1.6.1.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# 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-1.6.1.ebuild,v 1.2 2007/04/29 01:06:35 je_fro Exp $
-
-inherit toolchain-funcs
-
-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-${PV}"
-
-src_compile() {
-	econf --with-cluster || die "Configuration failed."
-	cd "${S}"/RNAforester/g2-0.70
-	sed -e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/lib:" \
-		-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 || die \
-		"Installing readseq Readme failed."
-}
diff --git a/sci-biology/vienna-rna/vienna-rna-1.6.5.ebuild b/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild
index 44c09db8b71d..6e40c88002a0 100644
--- a/sci-biology/vienna-rna/vienna-rna-1.6.5.ebuild
+++ b/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2007 Gentoo Foundation
+# Copyright 1999-2008 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 $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild,v 1.1 2008/08/29 01:21:38 markusle Exp $
 
-inherit toolchain-funcs multilib eutils
+inherit toolchain-funcs multilib eutils versionator
 
 DESCRIPTION="The Vienna RNA Package - RNA secondary structure prediction and comparison"
 LICENSE="vienna-rna"
@@ -21,17 +21,18 @@ S="${WORKDIR}/ViennaRNA-${PV}"
 src_unpack() {
 	unpack ${A}
 	cd "${S}"
-	epatch "${FILESDIR}"/${P}-c-fixes.patch
+	epatch "${FILESDIR}"/${PN}-1.6.5-c-fixes.patch
+	epatch "${FILESDIR}"/${P}-gcc4.3.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}"
+		-i RNAforester/g2-0.70/Makefile \
+			|| die "Failed patching RNAForester build system."
 	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."