commit: 380628fd5d035979ed5d371f67c01f2308354fd8 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Thu Apr 16 06:27:26 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Thu Apr 16 06:27:26 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=380628fd
In CVS Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> sci-biology/mrbayes/ChangeLog | 94 ------------------------- sci-biology/mrbayes/files/mb_readline_312.patch | 37 ---------- sci-biology/mrbayes/metadata.xml | 15 ---- sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild | 50 ------------- 4 files changed, 196 deletions(-) diff --git a/sci-biology/mrbayes/ChangeLog b/sci-biology/mrbayes/ChangeLog deleted file mode 100644 index ca36e0f..0000000 --- a/sci-biology/mrbayes/ChangeLog +++ /dev/null @@ -1,94 +0,0 @@ -# ChangeLog for sci-biology/mrbayes -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/ChangeLog,v 1.19 2008/06/11 18:10:48 ken69267 Exp $ - - 18 Feb 2015; Justin Lecher <[email protected]> mrbayes-3.1.2-r1.ebuild: - sci-biology/mrbayes: fix SLOT operators - - 10 Nov 2014; Justin Lecher <[email protected]> mrbayes-3.1.2-r1.ebuild, - metadata.xml: - Bump EAPI - - 25 Jun 2011; Justin Lecher <[email protected]> mrbayes-3.1.2-r1.ebuild, - metadata.xml: - RDEPEND is not explicitly assigned -> fixed - - 27 Jun 2010; Andreas K. Huettel (dilfridge) <[email protected]> - mrbayes-3.1.2-r1.ebuild: - QA fixes - - 05 Jun 2009; Justin Bronder <[email protected]> mrbayes-3.1.2-r1.ebuild: - +sci-biology/mrbayes/files/mb_readline_312.patch, - +sci-biology/mrbayes/metadata.xml: - Add an mpi.eclass version of mrbayes. - - 11 Jun 2008; Kenneth Prugh <[email protected]> mrbayes-3.1.2.ebuild: - amd64 stable, bug #213362 - - 17 Mar 2008; Donnie Berkholz <[email protected]>; mrbayes-3.1.2.ebuild: - (#213362) Keyword ~amd64. - - 25 Mar 2007; Danny van Dyk <[email protected]> mrbayes-3.1.2.ebuild: - QA: Cleaned up whitespaces. Removed redundant src_compile(). - - 06 Jan 2007; Danny van Dyk <[email protected]> -mrbayes-3.1.1.ebuild: - QA: Removed unused versions. - - 03 Nov 2006; Fabian Groffen <[email protected]> mrbayes-3.1.1.ebuild, - mrbayes-3.1.2.ebuild: - Dropped ppc-macos, see you in prefix. - - 14 Sep 2006; Olivier Fisette <[email protected]> metadata.xml: - Stepping down from maintaining this package. - - 12 Sep 2006; Olivier Fisette <[email protected]> mrbayes-3.1.1.ebuild, - mrbayes-3.1.2.ebuild: - Removed amd64 keywords because of bad pointer arithmetics causing segfaults - in the sumt function on all 64 bit architectures (see bug #143094). - - 09 Jul 2006; Donnie Berkholz <[email protected]>; mrbayes-3.1.2.ebuild: - x86 stable. - -*mrbayes-3.1.2 (03 Feb 2006) - - 03 Feb 2006; Olivier Fisette <[email protected]> - +files/mb_readline_312.patch, +mrbayes-3.1.2.ebuild: - New version. Added readline support. Thanks to Paul van der Mark for his - work on this ebuild. - - 09 Jan 2006; Homer Parker <[email protected]> mrbayes-3.1.1.ebuild: - Marked ~amd64. - - 09 Oct 2005; Olivier Fisette <[email protected]> -mrbayes-3.0.ebuild: - Pruning old version. - - 08 Oct 2005; Lina Pezzella <[email protected]> mrbayes-3.1.1.ebuild: - Stable ppc-macos, Bug 108333 - - 08 Oct 2005; Paul Varner <[email protected]> mrbayes-3.1.1.ebuild: - Stable on x86. Bug# 108333 - -*mrbayes-3.1.1 (14 Aug 2005) - - 14 Aug 2005; Olivier Fisette <[email protected]> metadata.xml, - +mrbayes-3.1.1.ebuild: - New version. Added MPI support. - - 20 Feb 2005; Lina Pezzella <[email protected]> mrbayes-3.0.ebuild: - Stable x86 and ppc-macos - - 09 Feb 2005; Lina Pezzella <[email protected]> mrbayes-3.0.ebuild: - Restricted fetching because of the license. Verified with GNU lawyers - -*mrbayes-3.0 (02 Feb 2005) - - 02 Feb 2005; Lina Pezzella <[email protected]> +metadata.xml, +mrbayes-3.0.ebuild: - Moved from sci-biology/MrBayes to sci-biology/mrbayes. - -*MrBayes-3.0 (30 Jan 2005) - - 30 Jan 2005; Olivier Fisette <[email protected]> MrBayes-3.0.ebuild: - Check for "sed" exit code. - - 19 Jan 2005; Lina Pezzella <[email protected]> : - Initial commit diff --git a/sci-biology/mrbayes/files/mb_readline_312.patch b/sci-biology/mrbayes/files/mb_readline_312.patch deleted file mode 100644 index 2f8bab1..0000000 --- a/sci-biology/mrbayes/files/mb_readline_312.patch +++ /dev/null @@ -1,37 +0,0 @@ -Index: Makefile -=================================================================== -RCS file: /cvsroot/mrbayes/mrbayes/Makefile,v -retrieving revision 3.23 -retrieving revision 3.24 -diff -U2 -r3.23 -r3.24 ---- Makefile 22 Dec 2005 16:13:06 -0000 3.23 -+++ Makefile 3 Jan 2006 16:43:13 -0000 3.24 -@@ -50,4 +50,5 @@ - ifeq ($(strip $(USEREADLINE)),yes) - CFLAGS += -DUSE_READLINE -+# CFLAGS += -DCOMPLETIONMATCHES - LIBS += -lncurses -lreadline - endif -Index: bayes.c -=================================================================== -RCS file: /cvsroot/mrbayes/mrbayes/bayes.c,v -retrieving revision 3.39 -retrieving revision 3.40 -diff -U2 -r3.39 -r3.40 ---- bayes.c 23 Dec 2005 16:26:28 -0000 3.39 -+++ bayes.c 3 Jan 2006 16:43:13 -0000 3.40 -@@ -382,9 +382,11 @@ - char **readline_completion(const char *text, int start, int stop) { - char **matches = (char **) NULL; -- -+ -+#ifdef COMPLETIONMATCHES - if(start == 0) -- matches = rl_completion_matches (text, command_generator); -+ matches = rl_completion_matches (text, command_generator); -+#endif - -- return (matches); -+ return (matches); - } - #endif diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml deleted file mode 100644 index 9b0503f..0000000 --- a/sci-biology/mrbayes/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <herd>sci-biology</herd> - <longdescription> -MrBayes is a program for the Bayesian estimation of phylogeny. -Bayesian inference of phylogeny is based upon a quantity called the -posterior probability distribution of trees, which is the probability of a -tree conditioned on the observations. The conditioning is accomplished using -Bayes's theorem. The posterior probability distribution of trees is -impossible to calculate analytically; instead, MrBayes uses a simulation -technique called Markov chain Monte Carlo (or MCMC) to approximate the -posterior probabilities of trees. -</longdescription> -</pkgmetadata> diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild deleted file mode 100644 index 9ead9a6..0000000 --- a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit eutils mpi toolchain-funcs - -DESCRIPTION="Bayesian Inference of Phylogeny" -HOMEPAGE="http://mrbayes.csit.fsu.edu/"; -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86" -IUSE="mpi readline" - -DEPEND=" - mpi? ( $(mpi_pkg_deplist) ) - readline? ( sys-libs/readline:0 )" -RDEPEND="${DEPEND}" - -src_prepare() { - sed \ - -e "s:OPTFLAGS ?= -O3:CFLAGS = ${CFLAGS}:" \ - -e "s:CC = gcc:CC = $(tc-getCC):" \ - -e "s:CC = mpicc:CC = $(mpi_pkg_cc):" \ - -e "s:LDFLAGS =:LDFLAGS ?=:" \ - -i Makefile || die "Patching CC/CFLAGS." - if use mpi; then - sed -e "s:MPI ?= no:MPI=yes:" -i Makefile || die "Patching MPI support." - fi - if ! use readline; then - sed -e "s:USEREADLINE ?= yes:USEREADLINE=no:" \ - -i Makefile || die "Patching readline support." - else - # Only needed for OSX with an old (4.x) version of - # libreadline, but it doesn't hurt for other distributions. - epatch "${FILESDIR}"/mb_readline_312.patch - fi -} - -src_compile() { - mpi_pkg_set_env - emake -} - -src_install() { - mpi_dobin mb -}
