commit: 79d0df0bd01844a81e723571b5ea2f52ac32dafa Author: Michał Górny <mgorny <AT> gentoo <DOT> org> AuthorDate: Fri Oct 9 07:22:37 2020 +0000 Commit: Michał Górny <mgorny <AT> gentoo <DOT> org> CommitDate: Fri Oct 9 07:22:37 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=79d0df0b
sci-biology/vienna-rna: Remove last-rited pkg Closes: https://bugs.gentoo.org/735438 Signed-off-by: Michał Górny <mgorny <AT> gentoo.org> profiles/package.mask | 2 - sci-biology/vienna-rna/Manifest | 1 - .../files/vienna-rna-2.1.1-impl-decl.patch | 15 --- .../vienna-rna/files/vienna-rna-2.1.1-prll.patch | 30 ------ .../vienna-rna/files/vienna-rna-2.1.8-bindir.patch | 10 -- sci-biology/vienna-rna/metadata.xml | 25 ----- sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild | 112 --------------------- 7 files changed, 195 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index eed0607c6c6..e017a399cbf 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -529,9 +529,7 @@ x11-misc/dsx # to build anyway. # # net-analyzer/mk-livestatus: py3 bug #735394, build failure bug #705430 -# sci-biology/vienna-rna: py3 bug #735438, build failure bug #707158 net-analyzer/mk-livestatus -sci-biology/vienna-rna # Arfrever Frehtes Taifersar Arahesis <[email protected]> (2020-09-01) # Mismatched version (bug #695022). Masked to force upgrade to 2.0.4_pre20200306162733. diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest deleted file mode 100644 index 8acf7884e03..00000000000 --- a/sci-biology/vienna-rna/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST ViennaRNA-2.1.8.tar.gz 5464683 BLAKE2B ed2086461b37c90de11638852680507c823495abacec1e797c589c22d07dc48b4833d8d6916e5c95083bb9b970c659bbfb14ca45e155486333a915593c4caf01 SHA512 84f9db1247ff7a77aa6550b6285d9bed31fa6ce179aab26eef798c65a07f5cbd89f944630dfa5d29a43401b12a439324b57ee69047a3985e3a4f1e88dffca60e diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch deleted file mode 100644 index de457f318e8..00000000000 --- a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch +++ /dev/null @@ -1,15 +0,0 @@ - Readseq/readseq.c | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/Readseq/readseq.c b/Readseq/readseq.c -index 8af7b39..56a25ae 100644 ---- a/Readseq/readseq.c -+++ b/Readseq/readseq.c -@@ -171,6 +171,7 @@ link -w -o readseq -t MPST -c 'MPS ' - #include <stdio.h> - #include <string.h> - #include <ctype.h> -+#include <stdlib.h> - - #include "ureadseq.h" - diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch deleted file mode 100644 index ee4aef5c330..00000000000 --- a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch +++ /dev/null @@ -1,30 +0,0 @@ - Readseq/Makefile | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - -diff --git a/Readseq/Makefile b/Readseq/Makefile -index f073aaa..05f2edd 100644 ---- a/Readseq/Makefile -+++ b/Readseq/Makefile -@@ -6,11 +6,11 @@ - # - - # pick an ANSI C compiler (the default Sun CC is not ANSI) --CC=gcc # Gnu C Compiler -+CC?=gcc # Gnu C Compiler - #CC=cc # SGI Irix - #CC=vcc # some DEC Ultrix - --CFLAGS= -+CFLAGS?= - #CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum - # instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software - -@@ -40,7 +40,7 @@ all: build test - - build: $(SOURCES) - @echo "Compiling readseq..." -- $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c -+ $(CC) $(LDFLAGS) $(CFLAGS) -o readseq readseq.c ureadseq.c ureadasn.c - - # if using NCBI, uncomment these lines in place of build: above - #build: $(SOURCES) diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch deleted file mode 100644 index e54dff95b48..00000000000 --- a/sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch +++ /dev/null @@ -1,10 +0,0 @@ -diff --git a/Utils/Makefile.am b/Utils/Makefile.am -index f42ebf4..d84a0f1 100644 ---- a/Utils/Makefile.am -+++ b/Utils/Makefile.am -@@ -1,4 +1,4 @@ --pkgbindir = $(pkgdatadir)/bin -+pkgbindir = $(prefix)/bin - pkgbin_PROGRAMS = b2ct popt ct2db - - pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl diff --git a/sci-biology/vienna-rna/metadata.xml b/sci-biology/vienna-rna/metadata.xml deleted file mode 100644 index bbc3d41fb4a..00000000000 --- a/sci-biology/vienna-rna/metadata.xml +++ /dev/null @@ -1,25 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <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 - minimization is the most used function in the package. We provide three - kinds of dynamic programming algorithms for structure prediction: the - minimum free energy algorithm of (Zuker and Stiegler 1981) which yields a - single optimal structure, the partition function algorithm of - (McCaskill 1990) which calculates base pair probabilities in the - thermodynamic ensemble, and the suboptimal folding algorithm of - (Wuchty et.al 1999) which generates all suboptimal structures within a - given energy range of the optimal energy. For secondary structure - comparison, the package contains several measures of distance - (dissimilarities) using either string alignment or tree-editing - (Shapiro and Zhang 1990). Finally, we provide an algorithm to design - sequences with a predefined structure (inverse folding). - </longdescription> -</pkgmetadata> diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild deleted file mode 100644 index 7664f6d3dc6..00000000000 --- a/sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild +++ /dev/null @@ -1,112 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -DISTUTILS_OPTIONAL=true -AUTOTOOLS_AUTORECONF=true -AUTOTOOLS_IN_SOURCE_BUILD=1 - -inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs - -DESCRIPTION="RNA secondary structure prediction and comparison" -HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"; -SRC_URI="http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-${PV}.tar.gz"; - -SLOT="0" -LICENSE="vienna-rna" -KEYWORDS="~amd64 ~ppc ~x86" -IUSE="doc openmp python static-libs" - -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" - -RDEPEND=" - dev-lang/perl - media-libs/gd - doc? ( dev-texlive/texlive-latex ) - python? ( ${PYTHON_DEPS} )" -DEPEND="${RDEPEND} - python? ( dev-lang/swig:0 )" - -S="${WORKDIR}/ViennaRNA-${PV}" - -PATCHES=( - "${FILESDIR}"/${P}-bindir.patch - "${FILESDIR}"/${PN}-2.1.1-prll.patch - "${FILESDIR}"/${PN}-2.1.1-impl-decl.patch -) - -src_prepare() { - sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die - sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' interfaces/Perl/Makefile.am || die - - autotools-utils_src_prepare - - if use python; then - cd interfaces/Python || die - local PATCHES=() - distutils-r1_src_prepare - fi -} - -src_configure() { - local myeconfargs=( - --with-cluster - $(use_enable openmp) - ) - - use doc || \ - myeconfargs+=( - --without-doc-pdf - --without-doc-html - --without-doc - ) - autotools-utils_src_configure - sed \ - -e "s:CC=gcc:CC=$(tc-getCC):" \ - -e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \ - -i Readseq/Makefile || die - if use python; then - cd interfaces/Python || die - distutils-r1_src_configure - fi -} - -src_compile() { - autotools-utils_src_compile - autotools-utils_src_compile -C Readseq build CC=$(tc-getCC) - - # TODO: Add (optional?) support for the NCBI toolkit. - if use python; then - cd interfaces/Python || die - emake RNA_wrap.c - distutils-r1_src_compile - fi -} - -src_test() { - autotools-utils_src_compile -C interfaces/Perl check - use python && autotools-utils_src_compile -C interfaces/Python check - autotools-utils_src_compile -C Readseq test -} - -src_install() { - autotools-utils_src_install - - if ! use static-libs; then - rm -f "${ED}"/usr/$(get_libdir)/*.a || die - fi - - newbin Readseq/readseq readseq-vienna - dodoc Readseq/Readseq.help - newdoc Readseq/Readme README.readseq - newdoc Readseq/Formats Formats.readseq - - # remove perlocal.pod to avoid file collisions (see #240358) - perl_delete_localpod || die "Failed to remove perlocal.pod" - if use python; then - cd interfaces/Python || die - distutils-r1_src_install - fi -}
