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authorDavid Seifert <soap@gentoo.org>2020-06-21 19:40:58 +0200
committerDavid Seifert <soap@gentoo.org>2020-06-21 19:40:58 +0200
commit7e76d06f66573c6e22aed5b8dc0e9e8015b19c39 (patch)
treee41d6b6c8bb8087287b7539c56c50f598d649ff1 /sci-biology
parentsci-biology/infernal: [QA] Pass AR to build system (diff)
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sci-biology/vienna-rna: Remove old
Package-Manager: Portage-2.3.101, Repoman-2.3.22 Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/vienna-rna/Manifest1
-rw-r--r--sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch10
-rw-r--r--sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py27
-rw-r--r--sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild111
4 files changed, 0 insertions, 149 deletions
diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest
index 0ec5d7aa848..8acf7884e03 100644
--- a/sci-biology/vienna-rna/Manifest
+++ b/sci-biology/vienna-rna/Manifest
@@ -1,2 +1 @@
-DIST ViennaRNA-2.1.1.tar.gz 5327215 BLAKE2B 1319a13daafc3798b792f43488590b4d1d290cbbf41ed6e401255c082eceb1212c312179ea31c3e574c852b453a1641198768bf565e72a920b433420d259c53f SHA512 b272afa1146543b290db605debab2badbdbf04fcdfd6130ed3b10604255476b3472b184e9af8a0bbeaa0def266f1a167c125d6cfd02aa3f7ae463697dc5226d5
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-bindir.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-bindir.patch
deleted file mode 100644
index 6d35ecea9b0..00000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-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 = $(prefix)/bin
- pkgbin_PROGRAMS = b2ct popt
-
- pscript = b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl
diff --git a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py
deleted file mode 100644
index 57f6b712ba3..00000000000
--- a/sci-biology/vienna-rna/files/vienna-rna-2.1.1-setup.py
+++ /dev/null
@@ -1,27 +0,0 @@
-from distutils.core import setup, Extension
-import os
-import sys
-
-old_filename = os.path.join("Perl", "RNA.py")
-new_filename = os.path.join("Perl", "__init__.py")
-if os.path.exists(old_filename):
- os.rename(old_filename, new_filename)
-
-extra_link_args = []
-
-extension = Extension("_RNA",
- ["Perl/RNA_wrap.c"],
- libraries=['RNA'],
- library_dirs=['lib'],
- extra_link_args=extra_link_args
- )
-
-setup(name="RNA",
- version="2.1.1",
- description="Vienna RNA",
- author="Ivo Hofacker, Institute for Theoretical Chemistry, University of Vienna",
- url="http://www.tbi.univie.ac.at/RNA/",
- package_dir = {'RNA':'Perl'},
- packages = ['RNA'],
- ext_modules=[extension],
- )
diff --git a/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild b/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild
deleted file mode 100644
index 8b760b5a84b..00000000000
--- a/sci-biology/vienna-rna/vienna-rna-2.1.1.ebuild
+++ /dev/null
@@ -1,111 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-DISTUTILS_OPTIONAL=true
-AUTOTOOLS_AUTORECONF=true
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-inherit autotools-utils distutils-r1 multilib perl-module toolchain-funcs
-
-DESCRIPTION="RNA secondary structure prediction and comparison"
-HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"
-SRC_URI="http://www.tbi.univie.ac.at/~ronny/RNA/ViennaRNA-${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
- "${FILESDIR}"/${P}-prll.patch
- "${FILESDIR}"/${P}-impl-decl.patch
-)
-
-src_prepare() {
- sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
- sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' Perl/Makefile.am || die
-
- autotools-utils_src_prepare
-
- if use python; then
- cp "${FILESDIR}"/${P}-setup.py "${S}"/setup.py || die
- 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:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \
- -e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \
- -i RNAforester/g2-0.70/Makefile || die
- sed \
- -e "s:CC=gcc:CC=$(tc-getCC):" \
- -e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" \
- -i Readseq/Makefile || die
- use python && distutils-r1_src_configure
-}
-
-src_compile() {
- autotools-utils_src_compile
- autotools-utils_src_compile -C Readseq build CC=$(tc-getCC)
-
- # TODO: Add (optional?) support for the NCBI toolkit.
- if use python; then
- pushd Perl > /dev/null
- mv RNA_wrap.c{,-perl} || die
- swig -python RNA.i || die
- popd > /dev/null
- distutils-r1_src_compile
- mv Perl/RNA_wrap.c{-perl,} || die
- fi
-}
-
-src_test() {
- autotools-utils_src_compile -C Perl 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"
- use python && distutils-r1_src_install
-}