From d934827bf44b7cfcf6711964418148fa60877668 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Wed, 25 Nov 2020 22:39:15 +0000 Subject: gentoo resync : 25.11.2020 --- sci-biology/vienna-rna/Manifest | 6 -- .../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 --------------------- 6 files changed, 198 deletions(-) delete mode 100644 sci-biology/vienna-rna/Manifest delete mode 100644 sci-biology/vienna-rna/files/vienna-rna-2.1.1-impl-decl.patch delete mode 100644 sci-biology/vienna-rna/files/vienna-rna-2.1.1-prll.patch delete mode 100644 sci-biology/vienna-rna/files/vienna-rna-2.1.8-bindir.patch delete mode 100644 sci-biology/vienna-rna/metadata.xml delete mode 100644 sci-biology/vienna-rna/vienna-rna-2.1.8.ebuild (limited to 'sci-biology/vienna-rna') 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 - #include - #include -+#include - - #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 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - - 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). - - 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 -} -- cgit v1.2.3