commit: 2fd2b0673fc4a3a7c35c9cd18f45216fb1c488c4 Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> AuthorDate: Sun Jan 16 17:33:16 2022 +0000 Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> CommitDate: Sun Jan 16 17:33:16 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2fd2b067
sci-biology/gibbs: treeclean Bug: https://bugs.gentoo.org/829216 Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org> profiles/package.mask | 1 - sci-biology/gibbs/Manifest | 1 - sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch | 11 ----- sci-biology/gibbs/gibbs-3.1.ebuild | 47 ---------------------- sci-biology/gibbs/metadata.xml | 13 ------ 5 files changed, 73 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 5d104049d771..e64d3a456170 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -306,7 +306,6 @@ dev-go/blackfriday # Outdated, we are the only one who still have a package for them. # Removal in 30 days. # Bug #829216 sys-cluster/mpe2 -sci-biology/gibbs # Georgy Yakovlev <[email protected]> (2021-12-14) # AT&T decided to roll back community changes in March 2020 diff --git a/sci-biology/gibbs/Manifest b/sci-biology/gibbs/Manifest deleted file mode 100644 index 24b52453c962..000000000000 --- a/sci-biology/gibbs/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST gibbs-3.1.tar.gz 563300 BLAKE2B 74b97407ccdac49d19dd2fa5fe3a5384b52a3ae871f197c1212e818fb7ce2307f2d04a91cf8a1d14c82d57b6f7266bbae849091bec9e580b8d473b595a836212 SHA512 b1ffc0d0c7debaced3c3d850eb7d2c42e13358d1e7c6ff5e6be0273446edc50bd655c52c5ae904a9054d47d7a48abd54a7684534ba7681375b657ad77fb8cb52 diff --git a/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch b/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch deleted file mode 100644 index 6eaad637cfc8..000000000000 --- a/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/configure.in -+++ b/configure.in -@@ -51,7 +51,7 @@ - fi - ]) - --CFLAGS="$OPTFLAGS $MPIFLAGS -Wall -Werror $MACFLAG" -+CFLAGS="$CFLAGS $OPTFLAGS $MPIFLAGS -Wall $MACFLAG" - - AC_PROG_CC([$COMP_LIST]) - diff --git a/sci-biology/gibbs/gibbs-3.1.ebuild b/sci-biology/gibbs/gibbs-3.1.ebuild deleted file mode 100644 index a06d0880ee4d..000000000000 --- a/sci-biology/gibbs/gibbs-3.1.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit autotools - -DESCRIPTION="Identify motifs, conserved regions, in DNA or protein sequences" -HOMEPAGE="http://bayesweb.wadsworth.org/gibbs/gibbs.html"; -SRC_URI="mirror://gentoo/gibbs-${PV}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="mpi" - -DEPEND=" - mpi? ( - virtual/mpi - sys-cluster/mpe2 - )" -RDEPEND="${DEPEND}" - -PATCHES=( "${FILESDIR}"/${PN}-3.1-fix-CFLAGS.patch ) - -src_prepare() { - default - mv configure.{in,ac} || die - eautoreconf -} - -src_configure() { - use mpi && export CC=mpicc - econf $(use_enable mpi) -} - -src_install() { - default - - exeinto /usr/$(get_libdir)/${PN} - doexe *.pl -} - -pkg_postinst() { - einfo "Supplementary Perl scripts for Gibbs have been installed into ${EROOT}/usr/$(get_libdir)/${PN}." - einfo "These scripts require installation of sci-biology/bioperl." -} diff --git a/sci-biology/gibbs/metadata.xml b/sci-biology/gibbs/metadata.xml deleted file mode 100644 index a0cd7b42b3ab..000000000000 --- a/sci-biology/gibbs/metadata.xml +++ /dev/null @@ -1,13 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> - The Gibbs motif sampler stochastically examines candidate alignments - in an effort to find the best alignment as measured by the maximum - a posteriori (MAP) log-likelihood ratio. - </longdescription> -</pkgmetadata>
