sci-biology/meme: Drop old; add examples handling

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

5 files changed, 14 insertions, 139 deletions

diff --git a/sci-biology/meme/ChangeLog b/sci-biology/meme/ChangeLog
index 1c602f60a71d..6315c0b51bd0 100644
--- a/sci-biology/meme/ChangeLog
+++ b/sci-biology/meme/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/meme
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.18 2012/08/26 16:03:01 jlec Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.19 2013/01/30 16:13:04 jlec Exp $
+
+  30 Jan 2013; Justin Lecher <jlec@gentoo.org> -meme-4.3.0-r1.ebuild,
+  -meme-4.4.0.ebuild, meme-4.8.1.ebuild, metadata.xml:
+  Drop old; add examples handling
 
 *meme-4.8.1 (26 Aug 2012)
 
diff --git a/sci-biology/meme/meme-4.3.0-r1.ebuild b/sci-biology/meme/meme-4.3.0-r1.ebuild
deleted file mode 100644
index 3d9b92351b1b..000000000000
--- a/sci-biology/meme/meme-4.3.0-r1.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# 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-4.3.0-r1.ebuild,v 1.2 2011/03/02 17:41:09 jlec Exp $
-
-EAPI="3"
-
-inherit autotools eutils
-
-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 ~amd64-linux ~x86-linux ~x86-macos"
-
-IUSE="mpi"
-
-DEPEND="
-	dev-libs/libxml2:2
-	dev-libs/libxslt
-	app-shells/tcsh
-	mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${PN}_${PV}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-4.0.0-Makefile.am.patch
-	eautoreconf
-}
-
-src_configure() {
-	MY_PREFIX="${EROOT}opt/meme"
-	USE_DISABLE_MPI=""; if ! use mpi; then USE_DISABLE_MPI="--enable-serial"; fi
-	econf --prefix=$MY_PREFIX --sysconfdir=${MY_PREFIX}/etc \
-		--with-logs="${EROOT}var/log/meme" \
-		$USE_DISABLE_MPI
-	# $(use_enable openmp)
-}
-
-#pkg_setup() {
-	# generate meme group to restrict logging to /var/log/meme
-#	enewgroup meme
-#}
-
-src_install() {
-	emake install DESTDIR="${D}" || die "Failed to install program files."
-	echo "PATH=${EPREFIX}/opt/${PN}/bin" > 99${PN}
-	doenvd 99${PN} || die
-	# 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.'
-#}
-
-src_test() {
-	# bug #297070
-	emake -j1 test || die "Regression tests failed."
-}
diff --git a/sci-biology/meme/meme-4.4.0.ebuild b/sci-biology/meme/meme-4.4.0.ebuild
deleted file mode 100644
index a3d0a3dc5d70..000000000000
--- a/sci-biology/meme/meme-4.4.0.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# 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-4.4.0.ebuild,v 1.2 2011/03/02 17:41:09 jlec Exp $
-
-EAPI="2"
-
-inherit autotools eutils
-
-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="mpi"
-
-DEPEND="
-	dev-libs/libxml2:2
-	dev-libs/libxslt
-	app-shells/tcsh
-	mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${PN}_${PV}"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PN}-4.0.0-Makefile.am.patch
-	eautoreconf
-}
-
-src_configure() {
-	MY_PREFIX="${ROOT}opt/meme"
-	USE_DISABLE_MPI=""; if ! use mpi; then USE_DISABLE_MPI="--enable-serial"; fi
-	econf --prefix=$MY_PREFIX --sysconfdir=${MY_PREFIX}/etc \
-		--with-logs="${ROOT}var/log/meme" \
-		$USE_DISABLE_MPI
-	# $(use_enable openmp)
-}
-
-#pkg_setup() {
-	# generate meme group to restrict logging to /var/log/meme
-#	enewgroup meme
-#}
-
-src_install() {
-	emake install DESTDIR="${D}" || die "Failed to install program files."
-	echo "PATH=/opt/${PN}/bin" > 99${PN}
-	doenvd 99${PN} || die
-	# 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.'
-#}
-
-src_test() {
-	# bug #297070
-	emake -j1 test || die "Regression tests failed."
-}
diff --git a/sci-biology/meme/meme-4.8.1.ebuild b/sci-biology/meme/meme-4.8.1.ebuild
index b143eeba05b8..4840fbc453bd 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 1.1 2012/08/26 16:03:01 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-4.8.1.ebuild,v 1.2 2013/01/30 16:13:04 jlec Exp $
 
 EAPI=4
 
@@ -15,7 +15,7 @@ SRC_URI="http://meme.nbcr.net/downloads/${PN}_${PV}.tar.gz"
 LICENSE="meme"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="debug mpi"
+IUSE="debug examples mpi"
 
 DEPEND="
 	dev-libs/libxml2:2
@@ -34,6 +34,7 @@ S="${WORKDIR}/${PN}_${PV}"
 #}
 
 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' \
diff --git a/sci-biology/meme/metadata.xml b/sci-biology/meme/metadata.xml
index 3302123e5718..fc7c76942a10 100644
--- a/sci-biology/meme/metadata.xml
+++ b/sci-biology/meme/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<herd>sci-biology</herd>
+  <maintainer>
+    <email>weaver@gentoo.org</email>
+    <name>Andrey Kislyuk</name>
+  </maintainer>
+  <herd>sci-biology</herd>
 </pkgmetadata>