From fe8e9e48e1731b8ad61dbbb86c13d0a714e896cf Mon Sep 17 00:00:00 2001 From: Andrey Kislyuk Date: Thu, 10 Sep 2009 18:43:01 +0000 Subject: Version bump and cleanup (Portage version: 2.2_rc30/cvs/Linux x86_64) --- sci-biology/vienna-rna/ChangeLog | 8 ++- .../files/vienna-rna-1.8.3-disable-gd.patch | 16 +++++ .../vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch | 76 ++++++++++++++++++++++ sci-biology/vienna-rna/metadata.xml | 6 -- sci-biology/vienna-rna/vienna-rna-1.4.ebuild | 76 ---------------------- sci-biology/vienna-rna/vienna-rna-1.7.0.ebuild | 55 ---------------- sci-biology/vienna-rna/vienna-rna-1.8.3.ebuild | 73 +++++++++++++++++++++ 7 files changed, 172 insertions(+), 138 deletions(-) create mode 100644 sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch create mode 100644 sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch delete mode 100644 sci-biology/vienna-rna/vienna-rna-1.4.ebuild delete mode 100644 sci-biology/vienna-rna/vienna-rna-1.7.0.ebuild create mode 100644 sci-biology/vienna-rna/vienna-rna-1.8.3.ebuild (limited to 'sci-biology/vienna-rna') 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 + +files/vienna-rna-1.8.3-gcc4.3.patch, +vienna-rna-1.8.3.ebuild: + Version bump and cleanup 30 Jul 2009; Samuli Suominen 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 + #include ++#include + #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 + #include + #include ++#include + #include + #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 + #include ++#include + #include + #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 + #include + #include ++#include ++#include + #include + + //#include +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 + #include ++#include + + #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 + #include + #include ++#include + + #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 + #include + #include ++#include + + #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). - - Do not include the modified version of Don Gilbert's - readseq program - Do not include sequence format conversion and - representation utilities - 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-1.7.0.ebuild deleted file mode 100644 index 98d5be613dc1..000000000000 --- a/sci-biology/vienna-rna/vienna-rna-1.7.0.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# 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-1.7.0.ebuild,v 1.1 2008/05/01 13:13:57 markusle Exp $ - -inherit toolchain-funcs multilib eutils versionator - -MY_PV=$(get_version_component_range 1-2) - -DESCRIPTION="The Vienna RNA Package - RNA secondary structure prediction and comparison" -LICENSE="vienna-rna" -HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA" -SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-${MY_PV}.tar.gz" - -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86 ~ppc" - -DEPEND="dev-lang/perl - media-libs/gd" - -S="${WORKDIR}/ViennaRNA-${MY_PV}" - -src_unpack() { - unpack ${A} - cd "${S}" - epatch "${FILESDIR}"/${PN}-1.6.5-c-fixes.patch -} - -src_compile() { - 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." - # 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." -} diff --git a/sci-biology/vienna-rna/vienna-rna-1.8.3.ebuild b/sci-biology/vienna-rna/vienna-rna-1.8.3.ebuild new file mode 100644 index 000000000000..dd7cfd2583ad --- /dev/null +++ b/sci-biology/vienna-rna/vienna-rna-1.8.3.ebuild @@ -0,0 +1,73 @@ +# 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-1.8.3.ebuild,v 1.1 2009/09/10 18:43:01 weaver Exp $ + +EAPI="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-${PV}.tar.gz" + +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86 ~ppc" + +DEPEND="dev-lang/perl + media-libs/gd" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/ViennaRNA-${PV}" + +PATCHES=( + "${FILESDIR}"/${PN}-1.6.5-c-fixes.patch + "${FILESDIR}"/${PN}-1.7.2-LDFLAGS.patch + "${FILESDIR}"/${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_configure() { + econf --with-cluster || die "Configuration failed." + sed -e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \ + -e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \ + -i RNAforester/g2-0.70/Makefile \ + || die "Failed patching RNAForester build system." + sed -e "s:CC=cc:CC=$(tc-getCC):" -e "s:CFLAGS=:CFLAGS=${CFLAGS}:" \ + -i Readseq/Makefile || die "Failed patching readseq Makefile." +} + +src_compile() { + emake || die "Compilation failed." + emake -C Readseq || die "Failed to compile readseq." + # TODO: Add (optional?) support for the NCBI toolkit. +} + +src_test() { + cd "${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 \ + || 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" +} -- cgit v1.2.3-65-gdbad