gentoo resync : 29.06.2020

4 files changed, 0 insertions, 152 deletions

diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest
index 93ed6d8adf22..0de0a4ebedfe 100644
--- a/sci-biology/vienna-rna/Manifest
+++ b/sci-biology/vienna-rna/Manifest
@@ -1,10 +1,6 @@
-AUX vienna-rna-2.1.1-bindir.patch 361 BLAKE2B c05d660b422519274f3c88c922d9eac79a8af055df17b78ecfd13561e76f02820d0bdc0462b66100858a8e6b1f3f8bba41cacbc142b9684e47aeb11295edef93 SHA512 f2e9da29f1ae3c1d3e7594367ef13ad0d44ebbcf1d9badf9d55c415e50b7e5af170dba7bcdad6438505786b941518f84ddb154cf1a6df60a229f3856cf333a94
 AUX vienna-rna-2.1.1-impl-decl.patch 354 BLAKE2B d9d7a4e749a2c8681dc619961291f5e082681f15729a72ee1423bc4af71e8f745a558506e7147846c84df8fb7e5d316d1bc253f8125487a4ea6aab3c05b19bd8 SHA512 7c288b4889f11b5cc4e6db5b5db6dfcd70843aa135181e8d819ae86c90faed4a43e08f99b47f418caa23643642e68bf5e153f4d279f7566433af1c9093ec6e8b
 AUX vienna-rna-2.1.1-prll.patch 885 BLAKE2B 168d4b1a4c5ff0eb92379fe5762e7f0d6b7676c774c659422923c894bfcdb9efbbe20979ed87129c688b6ced9ad19cc51716164a0056b19fbc80fc27bbd32d57 SHA512 1b80636b43e1ce9ca54431358b45f2503ef3f49b8cd049b5ef501058e1771bda3628c88e63cc1bea9a32aff5a004ccef663b47dae385a5df6071793f292dff94
-AUX vienna-rna-2.1.1-setup.py 810 BLAKE2B 7db99496739eaf21a8964d8a545204c05026ae6e5de1070d14e820e64760ffb2544a2a0247543415cc909d8938ac423be7d57dddd68103e3d9cc007ac7db7833 SHA512 57feac6d5701a25fcda01f93f506a422d4639595a7d0ef73575af88f283fabc3730a8ea3e116ccfd417b015611c813f08ff047c9e362eaa74d2ce275ae65f8b8
 AUX vienna-rna-2.1.8-bindir.patch 367 BLAKE2B 9bf3df6c604d5ac0661188d4f662ee12387f8bb30c2e3ecbd4a7bfd0a73ff5419f7a10b2fe70efd53e4b634bfdd3c1039ec000b26e7f5edbbcc4242a4edf5914 SHA512 aee16e7ff546aff38dd4a29d43502f4eb50778e6377a7d57f6a010dacc6a5f02162418fde27df03d1ba27f02361835d63dcefd866b8ac22f17a926c28fa4e9bf
-DIST ViennaRNA-2.1.1.tar.gz 5327215 BLAKE2B 1319a13daafc3798b792f43488590b4d1d290cbbf41ed6e401255c082eceb1212c312179ea31c3e574c852b453a1641198768bf565e72a920b433420d259c53f SHA512 b272afa1146543b290db605debab2badbdbf04fcdfd6130ed3b10604255476b3472b184e9af8a0bbeaa0def266f1a167c125d6cfd02aa3f7ae463697dc5226d5
 DIST ViennaRNA-2.1.8.tar.gz 5464683 BLAKE2B ed2086461b37c90de11638852680507c823495abacec1e797c589c22d07dc48b4833d8d6916e5c95083bb9b970c659bbfb14ca45e155486333a915593c4caf01 SHA512 84f9db1247ff7a77aa6550b6285d9bed31fa6ce179aab26eef798c65a07f5cbd89f944630dfa5d29a43401b12a439324b57ee69047a3985e3a4f1e88dffca60e
-EBUILD vienna-rna-2.1.1.ebuild 2667 BLAKE2B f81e3a8fd09cc846b570831ee21081e246163cfa36990a42c1e582b47adb8f59b137bd656277ed1b990a0fdddbfbc67e6c49d22a896c78842362bd1e16eaab0d SHA512 22b96fce6750fd8094e6943abd8085ec5e3035f66766f56a6a840f591faaebbffece2b0174e7db078d4e96bae30762bc6d15e21bc2e45a6e086115ddb2ca4bc1
 EBUILD vienna-rna-2.1.8.ebuild 2588 BLAKE2B 5a1692be0a587cc85dcf0a60c609ff0c4eade92e5da98ce05bf2d90a195e606d9ca9262774c2c6875b1d9d53451b5043d7c4ae8a3446d4ebf3607effe039cd92 SHA512 4474f2bf042a31e02fd7b9882f6b5ec17fef4ba9f23eab29a39e9c09ea29414e836c029e568a905a2c315370c763384f9d84547a56a8806216dc825d51c3d378
 MISC metadata.xml 1324 BLAKE2B ba9d5e1f5893344fd1899e3723e1b86bac75546cde97b311fe7ef9dc2068f1a063cd5a5d2ac65d1195f532441194e8943ad2ec44db9a5c614ed0c8d894a900bb SHA512 8198db695aea5244b62fab23fd0a53a0657f8d37cc741f60869a39374e97c725b564086d852e37216c584083168881eba246f59b840d6a41bfe9246d3bd88d4b
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 6d35ecea9b0f..000000000000
--- 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 57f6b712ba3d..000000000000
--- 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 8b760b5a84bf..000000000000
--- 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
-}