gentoo resync : 25.11.2020

6 files changed, 0 insertions, 198 deletions

diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest
deleted file mode 100644
index 0de0a4ebedfe..000000000000
--- a/sci-biology/vienna-rna/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-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-2.1.8-bindir.patch 367 BLAKE2B 9bf3df6c604d5ac0661188d4f662ee12387f8bb30c2e3ecbd4a7bfd0a73ff5419f7a10b2fe70efd53e4b634bfdd3c1039ec000b26e7f5edbbcc4242a4edf5914 SHA512 aee16e7ff546aff38dd4a29d43502f4eb50778e6377a7d57f6a010dacc6a5f02162418fde27df03d1ba27f02361835d63dcefd866b8ac22f17a926c28fa4e9bf
-DIST ViennaRNA-2.1.8.tar.gz 5464683 BLAKE2B ed2086461b37c90de11638852680507c823495abacec1e797c589c22d07dc48b4833d8d6916e5c95083bb9b970c659bbfb14ca45e155486333a915593c4caf01 SHA512 84f9db1247ff7a77aa6550b6285d9bed31fa6ce179aab26eef798c65a07f5cbd89f944630dfa5d29a43401b12a439324b57ee69047a3985e3a4f1e88dffca60e
-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-impl-decl.patch b/sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch
deleted file mode 100644
index de457f318e8e..000000000000
--- 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 ee4aef5c3308..000000000000
--- 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 e54dff95b485..000000000000
--- 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 bbc3d41fb4a6..000000000000
--- 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>sci-biology@gentoo.org</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 7664f6d3dc6e..000000000000
--- 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
-}