Import changes from science overlay

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

5 files changed, 81 insertions, 23 deletions

diff --git a/sci-biology/mrbayes/ChangeLog b/sci-biology/mrbayes/ChangeLog
index 6e131881219e..38863e55c8f8 100644
--- a/sci-biology/mrbayes/ChangeLog
+++ b/sci-biology/mrbayes/ChangeLog
@@ -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 <jlec@gentoo.org> +mrbayes-3.1.2-r2.ebuild,
+  metadata.xml, mrbayes-3.1.2-r1.ebuild:
+  Import changes from science overlay
 
   21 Dec 2011; Justin Lecher <jlec@gentoo.org> -mrbayes-3.1.2.ebuild:
   Cleaned old
@@ -96,4 +102,3 @@
 
   19 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> :
   Initial commit
-
diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest
index d721e34a27bf..829111f58e58 100644
--- a/sci-biology/mrbayes/Manifest
+++ b/sci-biology/mrbayes/Manifest
@@ -1,15 +1,6 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
-
-AUX mb_readline_312.patch 1108 RMD160 5901513567ef2198b4c9c1baeb1ecc295af3eee8 SHA1 c5526cf58fe15cb22c401de19de7056a66c37414 SHA256 6d7566cbe59eee9881b41a21ea561fd610816df768bb8fda42ef4435c84f5f22
-DIST mrbayes-3.1.2.tar.gz 545968 RMD160 b90b9406f34806bcd18bc49dc998b7ed444e93c3 SHA1 db73f53361688e1451ec155ccbdd130c3f889817 SHA256 c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4
-EBUILD mrbayes-3.1.2-r1.ebuild 1128 RMD160 52fd63f989b4a0e657935576d0227e3a7b3ca312 SHA1 0b755293aa999656bb1fa9ce92ed3bde7d415253 SHA256 4f71908fae072bb4d0f859b8e952f446e1f96995ab14ff34e2d5db0c249ebbc4
-MISC ChangeLog 3474 RMD160 02a4a14bd4f3106775339123edd1d28653ebeb22 SHA1 e52aa65ec306327c516ce319ed29ec8bcc7a5859 SHA256 8709b8744bdeddc27eb45d849267111e602c7eee4cf7e8172bcaa5a74ca7b0c2
-MISC metadata.xml 730 RMD160 46eda6e69c53a0e301343cfc645c343c5aa9fdd6 SHA1 06e33f8fa877635c7e771e74e3edeb8cba146fb3 SHA256 fe9b9273c53a7c502d6688d63557fe603f63a47c8ff17355b9db7cdc0b78f446
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.18 (GNU/Linux)
-
-iEYEAREKAAYFAk7xoV4ACgkQgAnW8HDreRYrIQCgsp1o180H55yrAIcJ5eprnl9f
-/3gAn1VLPD5Sv1XNTnQhBClvgO5m/4Dn
-=KpOk
------END PGP SIGNATURE-----
+AUX mb_readline_312.patch 1108 SHA256 6d7566cbe59eee9881b41a21ea561fd610816df768bb8fda42ef4435c84f5f22 SHA512 0a169b8560853dbff87c983bf8220384dcf22f53106ce5711bf3b1fc76d8a9adbf1860618176dde65a8657abe3ad888521bf5485fc00d4014adf1acb7ba3f114 WHIRLPOOL 925581e97278d36cdbfa4c53ab47a331640cf0d57c912eee7567d28805875a15e677a283f7a941c851783057cd606165ebccd6360e4f705eae53b2bf8df0fa89
+DIST mrbayes-3.1.2.tar.gz 545968 SHA256 c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4 SHA512 2fb0ee7224cbb69c1acf2ffb0c6c8974f63002cda4f39a626eadf80fad9cfc23861f8c03f5545970f3a81e02093d62b6a0549ab7d7f7080557e91e21b2c3ee14 WHIRLPOOL 45c9750a1e3e3ac85a1085bcaf8fc5c108b730a3dfa2f9e8d81cea8720bd6f02815c3145c19ee6c369a43f4565c2b234ec81cd5721672abded17186264de2e3f
+EBUILD mrbayes-3.1.2-r1.ebuild 1124 SHA256 175d30c618d3611e1534c3ab9ea731c3ebb19642a02abbbd6370033603ffaa9d SHA512 33c671fb95795ffdf81e005ee760a7d13f14ae4206d5ff650f7f4351e917b8e548b15579d0cf7cb30a16998ce9e56c148ccc4e4c6de1447badcd72535fd2aa85 WHIRLPOOL 268df71d0ad1c55f1b54f6deb0d8c00f01f70450336788fd410aeadc579a410e753d8674c771d7c3b92d2fc556f4dcede7d5fb119b37107c6bea497e72f9220f
+EBUILD mrbayes-3.1.2-r2.ebuild 1460 SHA256 a3ef239dd96f7dad2c5982ee72f11fe18b22ff5234810e00c94e4490393cecb0 SHA512 8a63704b623ca7e7e31e0d65817be305ff5a28492cdc8e1bc061d7e49c00abc9ab6ef0f77ed52fbf4ef603532fb63a0ebb38d39e920c5fb919023abda1cb2b37 WHIRLPOOL 73a2a660314bfd5366a1dfaf4a19c1cca320550a036d7379c079277479c0f9fc94265c6298dd17732d4ea8e3748e38b6bf3d1defe17c77eb3a0083e3d561dc27
+MISC ChangeLog 3659 SHA256 624f09b69c5d303e7dbcceae7cf41a0a0961a8affdea23e3a70ee4e5c10142af SHA512 68cb1b6c4177abf3ed1dd339edbff99c87bb70e16d637588f9d76ef798ca501a148a0a6b751c3fcc5df9b1b28305379a3b4e157973e6bbbce7bb10eb5c9dbdf3 WHIRLPOOL bd446c6d7ee8dba16098c97f203a52450ef924862838ffad53b75db387a8547c258f43dc65a81fc576699d5c99239736f7837e46518c5c7e8a656119111fd1b4
+MISC metadata.xml 734 SHA256 37b58f5ff4f1b6082bfe8f58f6153aefd6af27147c35276fe366fca2b09418cc SHA512 588700dc2913045980003f911d69c6a9cd221872aae612f91c57770bf735f65a07550d9df10c444305a8d643d1d8c2c43f2bc9b1855f4a8ebfdcfa7ce3af33b5 WHIRLPOOL c178c044cd536641b4d519fcb69a61b258a460702fb11f8e80c48ebeb07203c1f55bf08b055c3a78a0f6becac891f1abb59bfbc1ac1c2bb4d081efaedc1c9412
diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml
index d33282dbbb50..9b0503f3a779 100644
--- a/sci-biology/mrbayes/metadata.xml
+++ b/sci-biology/mrbayes/metadata.xml
@@ -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
diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild
index 69b7d11509bf..1e74c5fb27f8 100644
--- a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild
+++ b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild
@@ -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 @@ KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
 DEPEND="
 	sys-libs/ncurses
 	mpi? ( virtual/mpi )
-	readline? ( sys-libs/readline )"
+	readline? ( sys-libs/readline:0 )"
 RDEPEND="${DEPEND}"
 
 src_prepare() {
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..c60f61a93433
--- /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
+# $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
+}