sci-biology/vienna-rna: Cleaned old

(Portage version: 2.2.0_alpha116/cvs/Linux x86_64)

4 files changed, 7 insertions, 161 deletions

diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog
index 6280263d5a5f..70f828adeae7 100644
--- a/sci-biology/vienna-rna/ChangeLog
+++ b/sci-biology/vienna-rna/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/vienna-rna
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.44 2012/07/10 18:02:37 ranger Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.45 2012/07/10 18:58:02 jlec Exp $
+
+  10 Jul 2012; Justin Lecher <jlec@gentoo.org> -vienna-rna-1.8.4-r1.ebuild,
+  -vienna-rna-1.8.4-r2.ebuild, metadata.xml:
+  Cleaned old
 
   10 Jul 2012; Brent Baude <ranger@gentoo.org> vienna-rna-1.8.5.ebuild:
   Marking vienna-rna-1.8.5 ppc for bug 393867
diff --git a/sci-biology/vienna-rna/metadata.xml b/sci-biology/vienna-rna/metadata.xml
index 925c942d9fed..a7da09cf6677 100644
--- a/sci-biology/vienna-rna/metadata.xml
+++ b/sci-biology/vienna-rna/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-biology</herd>
-<longdescription>
+	<herd>sci-biology</herd>
+	<longdescription>
 	The Vienna RNA Package consists of a C code library and several
 	stand-alone programs for the prediction and comparison of RNA secondary
 	structures. RNA secondary structure prediction through energy
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
deleted file mode 100644
index de0595b9a5fd..000000000000
--- a/sci-biology/vienna-rna/vienna-rna-1.8.4-r1.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2012 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 1.7 2012/02/26 01:44:58 patrick 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
-	"${FILESDIR}"/${P}-jobserver-fix.patch
-	"${FILESDIR}"/${P}-bindir.patch
-)
-
-src_prepare() {
-	base_src_prepare
-	sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
-	sed -i '1 i #include <cstdio>' RNAforester/src/rnafuncs.cpp || die
-	sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' Perl/Makefile.am || 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=${CFLAGS}:" \
-		-i Readseq/Makefile || die "Failed patching readseq Makefile."
-}
-
-src_compile() {
-	emake clean || die
-	emake || die "Compilation failed."
-	emake -C Readseq || die "Failed to compile readseq."
-	# TODO: Add (optional?) support for the NCBI toolkit.
-}
-
-src_test() {
-	cd "${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 \
-		|| 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."
-
-	# remove perlocal.pod to avoid file collisions (see #240358)
-	fixlocalpod || die "Failed to remove perlocal.pod"
-}
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
deleted file mode 100644
index 84f8fb36ab68..000000000000
--- a/sci-biology/vienna-rna/vienna-rna-1.8.4-r2.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# 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 1.3 2011/03/20 20:32:09 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
-	"${FILESDIR}"/${P}-jobserver-fix.patch
-	"${FILESDIR}"/${P}-bindir.patch
-	"${FILESDIR}"/${P}-overflows.patch
-	"${FILESDIR}"/${P}-implicits.patch
-)
-
-src_prepare() {
-	base_src_prepare
-	sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
-	sed -i '1 i #include <cstdio>' RNAforester/src/rnafuncs.cpp || die
-	sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' Perl/Makefile.am || 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"
-}