mirror of
https://github.com/gentoo-mirror/gentoo.git
synced 2026-09-24 17:09:10 -07:00
sci-biology/vienna-rna: Remove last-rited pkg
Closes: https://bugs.gentoo.org/735438 Signed-off-by: Michał Górny <mgorny@gentoo.org>
This commit is contained in:
Michał Górny
@@ -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@gmail.com> (2020-09-01)
|
||||
# Mismatched version (bug #695022). Masked to force upgrade to 2.0.4_pre20200306162733.
|
||||
|
||||
@@ -1 +0,0 @@
|
||||
DIST ViennaRNA-2.1.8.tar.gz 5464683 BLAKE2B ed2086461b37c90de11638852680507c823495abacec1e797c589c22d07dc48b4833d8d6916e5c95083bb9b970c659bbfb14ca45e155486333a915593c4caf01 SHA512 84f9db1247ff7a77aa6550b6285d9bed31fa6ce179aab26eef798c65a07f5cbd89f944630dfa5d29a43401b12a439324b57ee69047a3985e3a4f1e88dffca60e
|
||||
@@ -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"
|
||||
|
||||
@@ -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)
|
||||
@@ -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
|
||||
@@ -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>
|
||||
@@ -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
|
||||
}
|
||||
Reference in New Issue
Block a user