[gentoo-commits] repo/gentoo:master commit in: sci-biology/vienna-rna/files/, profiles/, sci-biology/vienna-rna/

[Michał Górny]

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 <arfrever.fta@×××××.com> (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>sci-biology@g.o</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
-}