Version bump. Fixes bug 335608. Thanks to Diego for report.

(Portage version: 2.2_rc72/cvs/Linux x86_64)

3 files changed, 19 insertions, 62 deletions

diff --git a/sci-biology/paml/ChangeLog b/sci-biology/paml/ChangeLog
index 96ab6e81ee32..22b05b2c7c9d 100644
--- a/sci-biology/paml/ChangeLog
+++ b/sci-biology/paml/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/paml
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/ChangeLog,v 1.11 2010/02/09 11:17:38 pacho Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/ChangeLog,v 1.12 2010/09/02 06:56:14 xarthisius Exp $
+
+*paml-4.4c (02 Sep 2010)
+
+  02 Sep 2010; Kacper Kowalik <xarthisius@gentoo.org> -paml-4.1.ebuild,
+  -paml-4.2b-r1.ebuild, +paml-4.4c.ebuild:
+  Version bump. Fixes bug 335608. Thanks to Diego for report.
 
   09 Feb 2010; Pacho Ramos <pacho@gentoo.org> paml-4.3a.ebuild:
   amd64 stable, bug 298772
diff --git a/sci-biology/paml/paml-4.1.ebuild b/sci-biology/paml/paml-4.1.ebuild
deleted file mode 100644
index f2ea1263ca95..000000000000
--- a/sci-biology/paml/paml-4.1.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/paml-4.1.ebuild,v 1.1 2008/09/07 12:02:02 markusle Exp $
-
-inherit toolchain-funcs
-
-MY_PV="${PV/./}"
-DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
-HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
-SRC_URI="http://abacus.gene.ucl.ac.uk/software/${PN}${PV}.tar.gz"
-LICENSE="free-noncomm"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-RDEPEND=""
-DEPEND="${RDEPEND}"
-S="${WORKDIR}/${PN}${MY_PV}"
-
-src_compile() {
-	cd src
-	emake \
-		-f Makefile.UNIX \
-		CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS}" \
-		|| die "make failed"
-}
-
-src_install() {
-	pushd "${S}"/src
-	dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2 \
-		|| die "Failed to install binaries"
-	popd
-
-	dodoc README.txt doc/* || die "Failed to install docs"
-
-	insinto /usr/share/${PN}/control
-	doins *.ctl || die "Failed to install control files"
-
-	insinto /usr/share/${PN}/dat
-	doins stewart* *.dat dat/* || die "Failed to install data files"
-
-	insinto /usr/share/${PN}
-	doins -r examples/ || die "Failed to install examples"
-}
diff --git a/sci-biology/paml/paml-4.2b-r1.ebuild b/sci-biology/paml/paml-4.4c.ebuild
index 5159fee6c399..c828da151cae 100644
--- a/sci-biology/paml/paml-4.2b-r1.ebuild
+++ b/sci-biology/paml/paml-4.4c.ebuild
@@ -1,44 +1,39 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/paml-4.2b-r1.ebuild,v 1.1 2009/07/21 08:44:44 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/paml/paml-4.4c.ebuild,v 1.1 2010/09/02 06:56:14 xarthisius Exp $
 
 EAPI="2"
 
-inherit toolchain-funcs
+inherit toolchain-funcs versionator
+
+MY_P=$(version_format_string '${PN}$1$2')
 
-MY_P="${PN}42"
 DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
 HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
 SRC_URI="http://abacus.gene.ucl.ac.uk/software/${PN}${PV}.tar.gz"
 
 LICENSE="free-noncomm"
 SLOT="0"
-KEYWORDS="~x86 ~amd64"
+KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
+S=${WORKDIR}/${MY_P}
 
 src_prepare() {
-	sed -i 's/-static//' "${S}/src/Makefile.UNIX" || die
+	# Notice send by mail to prof. Ziheng Yang
+	sed -i "s/\$(CC)/& \$(LDFLAGS)/" src/Makefile || die #335608
 }
 
 src_compile() {
-	cd src
-	emake \
-		-f Makefile.UNIX \
-		CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS}" \
-		|| die "make failed"
+	emake -C src CC="$(tc-getCC)" \
+		CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" || die
 }
 
 src_install() {
 	pushd "${S}"/src
 	dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2 || die
 	popd
-	dodoc README.txt doc/*
+	dodoc README.txt doc/* || die
 	insinto /usr/share/${PN}/control
 	doins *.ctl || die "Failed to install control files"
 	insinto /usr/share/${PN}/dat