[gentoo-commits] gentoo-x86 commit in sci-biology/meme: ChangeLog meme-4.8.1-r1.ebuild meme-4.8.1.ebuild

[Justin Lecher (jlec)]

jlec        13/02/01 14:51:24

  Modified:             ChangeLog meme-4.8.1.ebuild
  Added:                meme-4.8.1-r1.ebuild
  Log:
  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)

Revision  Changes    Path
1.23                 sci-biology/meme/ChangeLog

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/meme/ChangeLog?rev=1.23&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/meme/ChangeLog?rev=1.23&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/meme/ChangeLog?r1=1.22&r2=1.23

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- ChangeLog	31 Jan 2013 07:17:25 -0000	1.22
+++ ChangeLog	1 Feb 2013 14:51:24 -0000	1.23
@@ -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@g.o> 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@g.o> -meme-4.3.0.ebuild,
   meme-4.8.1.ebuild:



1.6                  sci-biology/meme/meme-4.8.1.ebuild

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/meme/meme-4.8.1.ebuild?rev=1.6&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/meme/meme-4.8.1.ebuild?rev=1.6&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/meme/meme-4.8.1.ebuild?r1=1.5&r2=1.6

Index: meme-4.8.1.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-4.8.1.ebuild,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- meme-4.8.1.ebuild	31 Jan 2013 07:17:25 -0000	1.5
+++ meme-4.8.1.ebuild	1 Feb 2013 14:51:24 -0000	1.6
@@ -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 @@
 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_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}



1.1                  sci-biology/meme/meme-4.8.1-r1.ebuild

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/meme/meme-4.8.1-r1.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/meme/meme-4.8.1-r1.ebuild?rev=1.1&content-type=text/plain

Index: meme-4.8.1-r1.ebuild
===================================================================
## 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.'
#}