sci-biology/meme: Resolve file collision with app-text and sci-biology/readseq, #455010

(Portage version: 2.2.0_alpha161/cvs/Linux x86_64, RepoMan options: --force, signed Manifest commit with key 70EB7916)

3 files changed, 96 insertions, 5 deletions

diff --git a/sci-biology/meme/ChangeLog b/sci-biology/meme/ChangeLog
index f29dcfe25542..eda8367c9c41 100644
--- a/sci-biology/meme/ChangeLog
+++ b/sci-biology/meme/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/meme
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.22 2013/01/31 07:17:25 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.23 2013/02/01 14:51:24 jlec Exp $
+
+*meme-4.8.1-r1 (01 Feb 2013)
+
+  01 Feb 2013; Justin Lecher <jlec@gentoo.org> meme-4.8.1.ebuild,
+  +meme-4.8.1-r1.ebuild:
+  Resolve file collision with app-text and sci-biology/readseq, #455010
 
   31 Jan 2013; Justin Lecher <jlec@gentoo.org> -meme-4.3.0.ebuild,
   meme-4.8.1.ebuild:
diff --git a/sci-biology/meme/meme-4.8.1-r1.ebuild b/sci-biology/meme/meme-4.8.1-r1.ebuild
new file mode 100644
index 000000000000..50c2f7fe6aee
--- /dev/null
+++ b/sci-biology/meme/meme-4.8.1-r1.ebuild
@@ -0,0 +1,83 @@
+## Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-4.8.1-r1.ebuild,v 1.1 2013/02/01 14:51:24 jlec Exp $
+
+EAPI=4
+
+PYTHON_DEPEND="2"
+
+inherit autotools eutils python
+
+DESCRIPTION="The MEME/MAST system - Motif discovery and search"
+HOMEPAGE="http://meme.sdsc.edu/meme"
+SRC_URI="http://meme.nbcr.net/downloads/${PN}_${PV}.tar.gz"
+
+LICENSE="meme"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="debug examples mpi"
+
+DEPEND="
+	app-shells/tcsh
+	dev-libs/libxml2:2
+	dev-libs/libxslt
+	mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${PN}_${PV}"
+
+#pkg_setup() {
+	# generate meme group to restrict logging to /var/log/meme
+#	enewgroup meme
+#	python_pkg_setup
+#	python_set_active_version 2
+#}
+
+src_prepare() {
+	use examples || sed -e '/SUBDIRS/s:examples::g' -i doc/Makefile.am
+	sed \
+		-e '/flags/s:-O3::g' \
+		-e '/opt/s:-O::g' \
+		-e '/debug/s:-ggdb::' \
+		-e '/debug/s:-g::' \
+		-e 's:CFLAGS=:CFLAGS+=:g' \
+		-i configure.ac || die
+	epatch \
+		"${FILESDIR}"/${P}-Makefile.am.patch
+	eautoreconf
+}
+
+src_configure() {
+	MY_PREFIX="${ROOT}opt/meme"
+	USE_DISABLE_MPI=""; if ! use mpi; then USE_DISABLE_MPI="--enable-serial"; fi
+	econf \
+		--sysconfdir="${EPREFIX}/etc/meme" \
+		--with-logs="${ROOT}var/log/meme" \
+		$(use_enable debug) \
+		$USE_DISABLE_MPI
+}
+
+src_test() {
+	# bug #297070
+	emake -j1 test
+}
+
+src_install() {
+	default
+
+	mv "${ED}"/usr/bin/{,meme-}tree || die
+	mv "${ED}"/usr/bin/{,meme-}readseq || die
+
+	echo "PATH=/opt/${PN}/bin" > 99${PN}
+	doenvd 99${PN}
+
+	# allow logging only for members of meme group
+	# diropts -m 0770 -g meme -o root
+	diropts -m ugo+rwxt -o root
+	keepdir /var/log/meme
+}
+
+#pkg_postinst() {
+#	einfo 'Log files are produced in the "/var/log/meme" directory. Users'
+#	einfo 'need to be part of the meme group to use this facility.'
+#}
diff --git a/sci-biology/meme/meme-4.8.1.ebuild b/sci-biology/meme/meme-4.8.1.ebuild
index 19d3d29e1424..dc154dd57195 100644
--- a/sci-biology/meme/meme-4.8.1.ebuild
+++ b/sci-biology/meme/meme-4.8.1.ebuild
@@ -1,6 +1,6 @@
 ## Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-4.8.1.ebuild,v 1.5 2013/01/31 07:17:25 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-4.8.1.ebuild,v 1.6 2013/02/01 14:51:24 jlec Exp $
 
 EAPI=4
 
@@ -18,9 +18,11 @@ KEYWORDS="amd64 x86"
 IUSE="debug examples mpi"
 
 DEPEND="
+	!app-text/tree
+	app-shells/tcsh
 	dev-libs/libxml2:2
 	dev-libs/libxslt
-	app-shells/tcsh
+	!sci-biology/readseq
 	mpi? ( virtual/mpi )"
 RDEPEND="${DEPEND}"
 
@@ -59,11 +61,11 @@ src_configure() {
 
 src_test() {
 	# bug #297070
-	emake -j1 test || die "Regression tests failed."
+	emake -j1 test
 }
 
 src_install() {
-	emake install DESTDIR="${D}"
+	default
 
 	echo "PATH=/opt/${PN}/bin" > 99${PN}
 	doenvd 99${PN}