proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

5 files changed, 170 insertions, 0 deletions

diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest
new file mode 100644
index 000000000000..d932da527753
--- /dev/null
+++ b/sci-biology/mrbayes/Manifest
@@ -0,0 +1 @@
+DIST mrbayes-3.1.2.tar.gz 545968 SHA256 c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4 SHA512 2fb0ee7224cbb69c1acf2ffb0c6c8974f63002cda4f39a626eadf80fad9cfc23861f8c03f5545970f3a81e02093d62b6a0549ab7d7f7080557e91e21b2c3ee14 WHIRLPOOL 45c9750a1e3e3ac85a1085bcaf8fc5c108b730a3dfa2f9e8d81cea8720bd6f02815c3145c19ee6c369a43f4565c2b234ec81cd5721672abded17186264de2e3f
diff --git a/sci-biology/mrbayes/files/mb_readline_312.patch b/sci-biology/mrbayes/files/mb_readline_312.patch
new file mode 100644
index 000000000000..2f8bab1e7665
--- /dev/null
+++ b/sci-biology/mrbayes/files/mb_readline_312.patch
@@ -0,0 +1,37 @@
+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
new file mode 100644
index 000000000000..8a6a5b986dc7
--- /dev/null
+++ b/sci-biology/mrbayes/metadata.xml
@@ -0,0 +1,18 @@
+<?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>
+  <upstream>
+    <remote-id type="sourceforge">mrbayes</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild
new file mode 100644
index 000000000000..b4303b8f90b3
--- /dev/null
+++ b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Bayesian Inference of Phylogeny"
+HOMEPAGE="http://mrbayes.csit.fsu.edu/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE="debug mpi readline"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="
+	sys-libs/ncurses
+	mpi? ( virtual/mpi )
+	readline? ( sys-libs/readline:0 )"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+	use readline && epatch "${FILESDIR}"/mb_readline_312.patch
+	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
+}
diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
new file mode 100644
index 000000000000..0c5a5015ecc7
--- /dev/null
+++ b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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
+}