jlec 15/04/17 06:49:59 Modified: metadata.xml mrbayes-3.1.2-r1.ebuild ChangeLog Added: mrbayes-3.1.2-r2.ebuild Log: Import changes from science overlay (Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)
Revision Changes Path 1.6 sci-biology/mrbayes/metadata.xml file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mrbayes/metadata.xml?rev=1.6&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mrbayes/metadata.xml?rev=1.6&content-type=text/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mrbayes/metadata.xml?r1=1.5&r2=1.6 Index: metadata.xml =================================================================== RCS file: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/metadata.xml,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- metadata.xml 14 Sep 2006 02:16:11 -0000 1.5 +++ metadata.xml 17 Apr 2015 06:49:59 -0000 1.6 @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> <pkgmetadata> -<herd>sci-biology</herd> -<longdescription> + <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 1.6 sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild?rev=1.6&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild?rev=1.6&content-type=text/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild?r1=1.5&r2=1.6 Index: mrbayes-3.1.2-r1.ebuild =================================================================== RCS file: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- mrbayes-3.1.2-r1.ebuild 21 Dec 2011 08:59:32 -0000 1.5 +++ mrbayes-3.1.2-r1.ebuild 17 Apr 2015 06:49:59 -0000 1.6 @@ -1,6 +1,6 @@ -# Copyright 1999-2011 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild,v 1.5 2011/12/21 08:59:32 phajdan.jr Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild,v 1.6 2015/04/17 06:49:59 jlec Exp $ EAPI=4 @@ -18,7 +18,7 @@ DEPEND=" sys-libs/ncurses mpi? ( virtual/mpi ) - readline? ( sys-libs/readline )" + readline? ( sys-libs/readline:0 )" RDEPEND="${DEPEND}" src_prepare() { 1.27 sci-biology/mrbayes/ChangeLog file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mrbayes/ChangeLog?rev=1.27&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mrbayes/ChangeLog?rev=1.27&content-type=text/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mrbayes/ChangeLog?r1=1.26&r2=1.27 Index: ChangeLog =================================================================== RCS file: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/ChangeLog,v retrieving revision 1.26 retrieving revision 1.27 diff -u -r1.26 -r1.27 --- ChangeLog 21 Dec 2011 09:05:28 -0000 1.26 +++ ChangeLog 17 Apr 2015 06:49:59 -0000 1.27 @@ -1,6 +1,12 @@ # ChangeLog for sci-biology/mrbayes -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/ChangeLog,v 1.26 2011/12/21 09:05:28 jlec Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/ChangeLog,v 1.27 2015/04/17 06:49:59 jlec Exp $ + +*mrbayes-3.1.2-r2 (17 Apr 2015) + + 17 Apr 2015; Justin Lecher <[email protected]> +mrbayes-3.1.2-r2.ebuild, + metadata.xml, mrbayes-3.1.2-r1.ebuild: + Import changes from science overlay 21 Dec 2011; Justin Lecher <[email protected]> -mrbayes-3.1.2.ebuild: Cleaned old @@ -96,4 +102,3 @@ 19 Jan 2005; Lina Pezzella <[email protected]> : Initial commit - 1.1 sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild?rev=1.1&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild?rev=1.1&content-type=text/plain Index: mrbayes-3.1.2-r2.ebuild =================================================================== # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild,v 1.1 2015/04/17 06:49:59 jlec Exp $ EAPI=5 inherit eutils 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 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" IUSE="debug mpi readline" DEPEND=" sys-libs/ncurses mpi? ( virtual/mpi ) readline? ( sys-libs/readline:0= )" RDEPEND="${DEPEND}" src_prepare() { if use mpi; then sed -e "s:MPI ?= no:MPI=yes:" -i Makefile || die "Patching MPI support." fi if ! use readline; then sed -e "s:USEREADLINE ?= yes:USEREADLINE=no:" \ -i Makefile || die "Patching readline support." else # Only needed for OSX with an old (4.x) version of # libreadline, but it doesn't hurt for other distributions. epatch "${FILESDIR}"/mb_readline_312.patch fi sed -e 's:-ggdb::g' -i Makefile || die } src_compile() { local myconf mycc if use mpi; then mycc=mpicc else mycc=$(tc-getCC) fi use mpi && myconf="MPI=yes" use readline || myconf="${myconf} USEREADLINE=no" use debug && myconf="${myconf} DEBUG=yes" emake \ OPTFLAGS="${CFLAGS}" \ LDFLAGS="${LDFLAGS}" \ CC=${mycc} \ ${myconf} } src_install() { dobin mb insinto /usr/share/${PN} doins *.nex }
