diff options
author | Justin Lecher <jlec@gentoo.org> | 2012-07-10 18:58:02 +0000 |
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committer | Justin Lecher <jlec@gentoo.org> | 2012-07-10 18:58:02 +0000 |
commit | eb0708ad5f173f3592123f699922ac15409cee5d (patch) | |
tree | dc508647893c00677d9b133d49c91b45165fc211 /sci-biology/vienna-rna | |
parent | Marking tree-1.6.0-r1 ppc64 for bug 424469 (diff) | |
download | gentoo-2-eb0708ad5f173f3592123f699922ac15409cee5d.tar.gz gentoo-2-eb0708ad5f173f3592123f699922ac15409cee5d.tar.bz2 gentoo-2-eb0708ad5f173f3592123f699922ac15409cee5d.zip |
sci-biology/vienna-rna: Cleaned old
(Portage version: 2.2.0_alpha116/cvs/Linux x86_64)
Diffstat (limited to 'sci-biology/vienna-rna')
-rw-r--r-- | sci-biology/vienna-rna/ChangeLog | 6 | ||||
-rw-r--r-- | sci-biology/vienna-rna/metadata.xml | 4 | ||||
-rw-r--r-- | sci-biology/vienna-rna/vienna-rna-1.8.4-r1.ebuild | 80 | ||||
-rw-r--r-- | sci-biology/vienna-rna/vienna-rna-1.8.4-r2.ebuild | 78 |
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" -} |