Version bump and cleanup

(Portage version: 2.2_rc30/cvs/Linux x86_64)

6 files changed, 133 insertions, 99 deletions

diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog
index a84f1757b684..bd51332fff71 100644
--- a/sci-biology/vienna-rna/ChangeLog
+++ b/sci-biology/vienna-rna/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/vienna-rna
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.20 2009/07/30 08:31:01 ssuominen Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.21 2009/09/10 18:43:01 weaver Exp $
+
+*vienna-rna-1.8.3 (10 Sep 2009)
+
+  10 Sep 2009; Andrey Kislyuk <weaver@gentoo.org>
+  +files/vienna-rna-1.8.3-gcc4.3.patch, +vienna-rna-1.8.3.ebuild:
+  Version bump and cleanup
 
   30 Jul 2009; Samuli Suominen <ssuominen@gentoo.org>
   vienna-rna-1.7.2.ebuild, +files/vienna-rna-1.7.2-gcc4.4.patch:
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch
new file mode 100644
index 000000000000..2c5ac3041297
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch
@@ -0,0 +1,16 @@
+# unfortunately, vienna-rna's build system is a little broken and sometimes detects
+# gd in RNAforested but then realizes in g2 that it can't actually build it 
+# resulting in unresolved symbols.
+
+diff -durr ViennaRNA-1.8.3.orig/RNAforester/configure.in ViennaRNA-1.8.3/RNAforester/configure.in
+--- ViennaRNA-1.8.3.orig/RNAforester/configure.in	2009-09-10 13:05:40.507932827 +0000
++++ ViennaRNA-1.8.3/RNAforester/configure.in	2009-09-10 13:06:15.171952984 +0000
+@@ -47,7 +47,7 @@
+ save_CPPFLAGS=$CPPFLAGS	
+ CPPFLAGS=["-Ig2-0.70/src/ ${CPPFLAGS}"]
+ 
+-AC_CHECK_LIB(gd,main,,)
++dnl AC_CHECK_LIB(gd,main,,)
+ 		  
+ dnl Checks for header files.
+ AC_HEADER_STDC
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch
new file mode 100644
index 000000000000..025822f45c91
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch
@@ -0,0 +1,76 @@
+diff -durr ViennaRNA-1.8.3.orig/Cluster/AS_main.c ViennaRNA-1.8.3/Cluster/AS_main.c
+--- ViennaRNA-1.8.3.orig/Cluster/AS_main.c	2009-09-10 11:56:01.636674988 +0000
++++ ViennaRNA-1.8.3/Cluster/AS_main.c	2009-09-10 11:58:32.915952366 +0000
+@@ -1,5 +1,6 @@
+ #include <stdio.h>
+ #include <string.h>
++#include <stdlib.h>
+ #include "distance_matrix.h"
+ #include "statgeom.h"
+ #include "split.h"
+diff -durr ViennaRNA-1.8.3.orig/Cluster/statgeom.c ViennaRNA-1.8.3/Cluster/statgeom.c
+--- ViennaRNA-1.8.3.orig/Cluster/statgeom.c	2009-09-10 11:56:01.636674988 +0000
++++ ViennaRNA-1.8.3/Cluster/statgeom.c	2009-09-10 11:58:53.192452141 +0000
+@@ -7,6 +7,7 @@
+ #include <stdio.h>
+ #include <string.h>
+ #include <strings.h>
++#include <stdlib.h>
+ #include <ctype.h>
+ #include "utils.h"
+ #include "PS3D.h"
+diff -durr ViennaRNA-1.8.3.orig/Cluster/treeplot.c ViennaRNA-1.8.3/Cluster/treeplot.c
+--- ViennaRNA-1.8.3.orig/Cluster/treeplot.c	2009-09-10 11:56:01.636674988 +0000
++++ ViennaRNA-1.8.3/Cluster/treeplot.c	2009-09-10 11:59:22.457509165 +0000
+@@ -1,5 +1,6 @@
+ #include <stdio.h>
+ #include <string.h>
++#include <stdlib.h>
+ #include <math.h>
+ #include "distance_matrix.h"
+ #include "utils.h"
+diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/main.cpp ViennaRNA-1.8.3/RNAforester/src/main.cpp
+--- ViennaRNA-1.8.3.orig/RNAforester/src/main.cpp	2009-09-10 11:56:01.624743558 +0000
++++ ViennaRNA-1.8.3/RNAforester/src/main.cpp	2009-09-10 12:00:37.693252890 +0000
+@@ -19,6 +19,8 @@
+ #include <list>
+ #include <sstream>
+ #include <string>
++#include <cstring>
++#include <climits>
+ #include <map>
+ 
+ //#include <sys/timeb.h>
+diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/ppforestbase.h ViennaRNA-1.8.3/RNAforester/src/ppforestbase.h
+--- ViennaRNA-1.8.3.orig/RNAforester/src/ppforestbase.h	2009-09-10 11:56:01.624743558 +0000
++++ ViennaRNA-1.8.3/RNAforester/src/ppforestbase.h	2009-09-10 12:01:41.631932654 +0000
+@@ -16,6 +16,7 @@
+ 
+ #include <algorithm>
+ #include <cassert>
++#include <cstring>
+ 
+ #include "misc.h"
+ #include "types.h"
+diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/rna_algebra.h ViennaRNA-1.8.3/RNAforester/src/rna_algebra.h
+--- ViennaRNA-1.8.3.orig/RNAforester/src/rna_algebra.h	2009-09-10 11:56:01.620703294 +0000
++++ ViennaRNA-1.8.3/RNAforester/src/rna_algebra.h	2009-09-10 12:02:29.687952726 +0000
+@@ -4,6 +4,7 @@
+ #include <assert.h>
+ #include <algorithm>
+ #include <climits>
++#include <cstring>
+ 
+ #include "algebra.h"
+ #include "debug.h"
+diff -durr ViennaRNA-1.8.3.orig/Readseq/ureadseq.c ViennaRNA-1.8.3/Readseq/ureadseq.c
+--- ViennaRNA-1.8.3.orig/Readseq/ureadseq.c	2009-09-10 11:56:01.632743452 +0000
++++ ViennaRNA-1.8.3/Readseq/ureadseq.c	2009-09-10 12:03:15.343952776 +0000
+@@ -20,6 +20,7 @@
+ #include <stdio.h>
+ #include <ctype.h>
+ #include <string.h>
++#include <stdlib.h>
+ 
+ #define UREADSEQ_G
+ #include "ureadseq.h"
diff --git a/sci-biology/vienna-rna/metadata.xml b/sci-biology/vienna-rna/metadata.xml
index cec7b4a6ce48..925c942d9fed 100644
--- a/sci-biology/vienna-rna/metadata.xml
+++ b/sci-biology/vienna-rna/metadata.xml
@@ -19,10 +19,4 @@
 	(Shapiro and Zhang 1990). Finally, we provide an algorithm to design
 	sequences with a predefined structure (inverse folding).
 </longdescription>
-<use>
-  <flag name='no-readseq'>Do not include the modified version of Don Gilbert's
-    readseq program</flag>
-  <flag name='no-utils'>Do not include sequence format conversion and
-    representation utilities</flag>
-</use>
 </pkgmetadata>
diff --git a/sci-biology/vienna-rna/vienna-rna-1.4.ebuild b/sci-biology/vienna-rna/vienna-rna-1.4.ebuild
deleted file mode 100644
index 58ecaa73cb51..000000000000
--- a/sci-biology/vienna-rna/vienna-rna-1.4.ebuild
+++ /dev/null
@@ -1,76 +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-1.4.ebuild,v 1.4 2007/11/24 15:10:04 markusle Exp $
-
-inherit flag-o-matic
-
-DESCRIPTION="Vienna RNA Package - 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-${PV}.tar.gz"
-LICENSE="vienna-rna"
-
-SLOT=0
-KEYWORDS="x86 ~ppc"
-IUSE="no-utils no-readseq perl"
-
-DEPEND="perl? ( dev-lang/perl )
-	!no-utils? ( dev-lang/perl )"
-
-S="${WORKDIR}/ViennaRNA-${PV}"
-
-src_compile() {
-	sed -i -e 's:/usr/local/bin/perl:/usr/bin/perl:' Perl/RNAfold.pl || die
-	sed -i -e 's:/usr/local/bin/perl:/usr/bin/perl:' Utils/ct2b.pl || die
-	sed -i -e 's:/usr/local/bin/perl:/usr/bin/perl:' Utils/b2mt.pl || die
-	sed -i -e 's:/usr/local/bin/perl:/usr/bin/perl:' Utils/dpzoom.pl || die
-	sed -i -e 's:/usr/local/bin/perl:/usr/bin/perl:' Utils/mountain.pl || die
-	append-flags -I../H
-	make -e library programs gammel subopt || die
-	use perl && make -e perl || die
-	use no-utils || make -e util || die
-	use no-readseq || cd Readseq && make -e || die
-}
-
-src_install() {
-	insinto /usr/include/vienna-rna
-	doins H/*
-	dolib.a lib/libRNA.a
-	dobin Cluster/{AnalyseDists,AnalyseSeqs}
-	dobin Progs/RNA{distance,eval,fold,heat,inverse,pdist}
-	dobin Subopt/{RNAsubopt,popt}
-
-	dodoc CHANGES CREDITS README
-	doinfo man/RNAlib.info
-	newman man/AnalyseDists.man AnalyseDists.man.1
-	newman man/AnalyseSeqs.man AnalyseSeqs.man.1
-	newman man/RNAdistance.man RNAdistance.man.1
-	newman man/RNAeval.man RNAeval.man.1
-	newman man/RNAfold.man RNAfold.man.1
-	newman man/RNAheat.man RNAheat.man.1
-	newman man/RNAinverse.man RNAinverse.man.1
-	newman man/RNApdist.man RNApdist.man.1
-	newman Subopt/RNAsubopt.man RNAsubopt.man.1
-	dohtml man/RNAlib.html
-	insinto /usr/share/doc/${P}/pdf
-	doins man/RNAlib.pdf
-
-	if use perl; then
-		cd Perl
-		make install DESTDIR="${D}" || die
-		dodoc RNA_wrap.doc
-		cd "${S}"
-	fi
-
-	if ! use no-utils; then
-		dobin Utils/{b2ct,ct2b.pl,dpzoom.pl,mountain.pl,b2mt.pl,Fold,RNAplot}
-		newdoc Utils/README README.utils
-		newman Utils/RNAplot.man RNAplot.man.1
-	fi
-
-	if ! use no-readseq; then
-		newbin Readseq/readseq readseq-vienna
-		newdoc Readseq/Readme README.readseq
-		newdoc Readseq/Formats FORMATS.readseq
-		newdoc Readseq/README README.readseq-vienna
-	fi
-}
diff --git a/sci-biology/vienna-rna/vienna-rna-1.7.0.ebuild b/sci-biology/vienna-rna/vienna-rna-1.8.3.ebuild
index 98d5be613dc1..dd7cfd2583ad 100644
--- a/sci-biology/vienna-rna/vienna-rna-1.7.0.ebuild
+++ b/sci-biology/vienna-rna/vienna-rna-1.8.3.ebuild
@@ -1,15 +1,15 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.0.ebuild,v 1.1 2008/05/01 13:13:57 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.3.ebuild,v 1.1 2009/09/10 18:43:01 weaver Exp $
 
-inherit toolchain-funcs multilib eutils versionator
+EAPI="2"
 
-MY_PV=$(get_version_component_range 1-2)
+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"
-SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-${MY_PV}.tar.gz"
+SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-${PV}.tar.gz"
 
 SLOT="0"
 IUSE=""
@@ -17,30 +17,45 @@ KEYWORDS="~amd64 ~x86 ~ppc"
 
 DEPEND="dev-lang/perl
 	media-libs/gd"
+RDEPEND="${DEPEND}"
 
-S="${WORKDIR}/ViennaRNA-${MY_PV}"
+S="${WORKDIR}/ViennaRNA-${PV}"
 
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}"/${PN}-1.6.5-c-fixes.patch
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.6.5-c-fixes.patch
+	"${FILESDIR}"/${PN}-1.7.2-LDFLAGS.patch
+	"${FILESDIR}"/${P}-gcc4.3.patch
+	"${FILESDIR}"/${P}-disable-gd.patch
+)
+
+src_prepare() {
+	base_src_prepare
+	sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
+	eautoreconf
+	(cd RNAforester; eautoreconf)
 }
 
-src_compile() {
+src_configure() {
 	econf --with-cluster || die "Configuration failed."
 	sed -e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \
 		-e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \
 		-i RNAforester/g2-0.70/Makefile \
 			|| die "Failed patching RNAForester build system."
-	emake || die "Compilation failed."
-
-	cd "${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."
+		-i Readseq/Makefile || die "Failed patching readseq Makefile."
+}
+
+src_compile() {
+	emake || die "Compilation failed."
+	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() {
 	make install DESTDIR="${D}" || die "Installation failed."
 	dodoc AUTHORS ChangeLog NEWS README THANKS \
@@ -52,4 +67,7 @@ src_install() {
 	newdoc Readseq/Readme README.readseq && \
 		newdoc Readseq/Formats Formats.readseq \
 		|| die "Installing readseq Readme failed."
+
+	# remove perlocal.pod to avoid file collisions (see #240358)
+	fixlocalpod || die "Failed to remove perlocal.pod"
 }