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

[Jakov Smolić]

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 # Outdated, we are the only one who still have a package for them.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 <gyakovlev@g.o> (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>sci-biology@g.o</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>