[gentoo-commits] repo/gentoo:master commit in: sci-biology/mrbayes/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/mrbayes/

[David Seifert]

commit:     c55800cb358f245934db72bc33a50b276d345621
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Tue Dec 10 23:48:22 2019 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Tue Dec 10 23:48:22 2019 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c55800cb

sci-biology/mrbayes: Remove old

Package-Manager: Portage-2.3.81, Repoman-2.3.20
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild | 51 -----------------------------
 1 file changed, 51 deletions(-)

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 b67b4b228f9..00000000000
--- a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-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
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/mrbayes/

[Andrew Ammerlaan]

commit:     e95dd20d9eaea3e8fa32f9337c8b3beb7ba5eddb
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 27 16:33:02 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Jan 27 16:37:38 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e95dd20d

sci-biology/mrbayes: add version 3.2.7

Closes: https://bugs.gentoo.org/521510
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/mrbayes/Manifest             |  1 +
 sci-biology/mrbayes/metadata.xml         | 19 +++++++-------
 sci-biology/mrbayes/mrbayes-3.2.7.ebuild | 45 ++++++++++++++++++++++++++++++++
 3 files changed, 56 insertions(+), 9 deletions(-)

diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest
index 799aafc484a4..3d68a52ee87a 100644
--- a/sci-biology/mrbayes/Manifest
+++ b/sci-biology/mrbayes/Manifest
@@ -1 +1,2 @@
 DIST mrbayes-3.1.2.tar.gz 545968 BLAKE2B f4c5bbdde765fb9e596c17d5fd890b168c22cefb0d24b67c1c68623e1dcfa4df716a896fe120f7a1cac4234125b6ed524973506e47492ba3ec26e389783d618a SHA512 2fb0ee7224cbb69c1acf2ffb0c6c8974f63002cda4f39a626eadf80fad9cfc23861f8c03f5545970f3a81e02093d62b6a0549ab7d7f7080557e91e21b2c3ee14
+DIST mrbayes-3.2.7.tar.gz 9787214 BLAKE2B 2d0ebbc376712e15fc1ed146053d977ad1af96f44c31b8fd0fdbd47ef9bafc41cbb8904db94bc8d30c753c0267a1dcce0d08c73d8b35c20e0f15206bc8fef6ff SHA512 4dc869cd07cf384b3a3945ac8d91a7cc2982e8c5cd8d1f097b46a479a071cb71e71c60e152aa4fc01b0bb296295c5fa9f5a48aa8e913b920c33e30cbb3a6ed37

diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml
index 348542381e73..2fbcd4fa4f98 100644
--- a/sci-biology/mrbayes/metadata.xml
+++ b/sci-biology/mrbayes/metadata.xml
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <longdescription>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<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
@@ -14,8 +14,9 @@ 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>
+	</longdescription>
+	<upstream>
+		<remote-id type="sourceforge">mrbayes</remote-id>
+		<remote-id type="github">NBISweden/MrBayes</remote-id>
+	</upstream>
 </pkgmetadata>

diff --git a/sci-biology/mrbayes/mrbayes-3.2.7.ebuild b/sci-biology/mrbayes/mrbayes-3.2.7.ebuild
new file mode 100644
index 000000000000..ad87554eb31e
--- /dev/null
+++ b/sci-biology/mrbayes/mrbayes-3.2.7.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Bayesian Inference of Phylogeny"
+HOMEPAGE="https://nbisweden.github.io/MrBayes/"
+SRC_URI="https://github.com/NBISweden/MrBayes/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+IUSE="debug mpi readline"
+# --with-readline was given, but MPI support requires readline to be disabled.
+REQUIRED_USE="mpi? ( !readline )"
+
+DEPEND="
+	sys-libs/ncurses:=
+	mpi? ( virtual/mpi )
+	readline? ( sys-libs/readline:= )
+"
+RDEPEND="${DEPEND}"
+
+src_configure() {
+	econf \
+		"$(use_with mpi)" \
+		"$(use_with readline)" \
+		"$(use_enable debug )" \
+		# configure checks cpuid and enables fma{3,4}, sse{1..4} if detected.
+		# Configure options only allow disabling the auto-detection, but do not
+		# actually allow toggling the individual cpu instruction sets. The only
+		# way to guarantee that cross-compiling and binpkgs will work on machines
+		# other than the host is to unconditionally disable sse/fma/avx.
+		#"$(use_enable cpu_flags_x86_sse sse )" \
+		#"$(use_enable cpu_flags_x86_avx avx )" \
+		#"$(use_enable cpu_flags_x86_fma3 fma )" \
+		# Has optional support for sci-biology/beagle::science
+		# "$(use_with beagle)"
+}
+
+src_compile() {
+	# The --disable options for the cpu instruction sets don't actually work so
+	# we override it here and also set the user specified CFLAGS.
+	emake SIMD_FLAGS= CPUEXT_FLAGS= CFLAGS="${CFLAGS}"
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/mrbayes/

[Sam James]

commit:     7761f837e81d76fa9d1637c4d6808e1a88f45f82
Author:     Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 20 18:49:38 2022 +0000
Commit:     Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Sun Mar 20 18:50:57 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7761f837

sci-biology/mrbayes: [QA] fix tc-get* quoting

This can cause build problems for e.g. 32-bit (gcc -m32 ...)

Signed-off-by: Sam James <sam <AT> gentoo.org>

 sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
index cee9e0f2d286..57c39ea21a94 100644
--- a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
+++ b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -44,7 +44,7 @@ src_compile() {
 	if use mpi; then
 		mycc=mpicc
 	else
-		mycc=$(tc-getCC)
+		mycc="$(tc-getCC)"
 	fi
 
 	use mpi && myconf="MPI=yes"