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

Package-Manager: portage-2.2.0_alpha161/cvs/Linux x86_64
RepoMan-Options: --force
Manifest-Sign-Key: 0x70EB7916

4 files changed, 102 insertions, 10 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/Manifest b/sci-biology/meme/Manifest
index bc2f0c204f62..9c23faf6e9fe 100644
--- a/sci-biology/meme/Manifest
+++ b/sci-biology/meme/Manifest
@@ -7,13 +7,14 @@ AUX meme-3.5.4-patch2.patch 2074 SHA256 bf74f09bcd6c247f464f15b17e3a0e8f95149fdc
 AUX meme-4.0.0-Makefile.am.patch 377 SHA256 ef3f0d8ccca728325d9f9b4f485e8cd4db2ced50fc975f8b66f3b76fcf17b5e8 SHA512 87d4e552c51b45409093eeb7821dfa571b6d44dfdae4a899600da8c48bfe4806d5018d83a433cc88443d05ac6a5b4b7aa7f9abf9a027f5ce8ee7b8da7e4d7b12 WHIRLPOOL 16cc954f231868cd39be3dad5ec944a3e15c8946022a37e1a32c527237f045de70bc85e986a5a7ecadc2107992dd60859caa7f75b501eb256ebe208db89c38db
 AUX meme-4.8.1-Makefile.am.patch 4907 SHA256 a08c25df2ec74469f4586f9c11927cf775646b1cb744e72879fc24a6586a0ff0 SHA512 50c43b6e6f35e8898c073b95b1600df2c3a57bb5b9ab531fb060d3fb869d26284a081327d6624b5147a0e1209a714173540cb725dc54979b14e598ba831fd410 WHIRLPOOL 4ff6286ca9f45533996ab0d5e5554f6c77e5761c0c226f8c25c56d51270350d823e91da96a546d451dc0fc4a8df793ff29b9006b917ced149f3af5313b635cc8
 DIST meme_4.8.1.tar.gz 8703632 SHA256 c3ad3ca26bc2a7130c5eceb64e1745275c317a5469e98fc8759a9e56babccb8c SHA512 31833169ffa9bd82387d1872be40b0fc4312f4a05bb7abb84daf372244ce3f2a68c89c96722c0453f7bcd9eb4fc84fd3d66e1278af55d556715b94b0df5f87ba WHIRLPOOL 4b5e8968e6964479081d1fe036ff3aa7a50dc56bafc0031890d2e47dbdc8e0273e62ffe01800d8908b2fa9824a4766254bb0fd94003d9ca14784073d5357793e
-EBUILD meme-4.8.1.ebuild 1836 SHA256 bd19fb007d2e249b9eda3e7f5c01673d6fc2156ab5fd673a27b13e86f3c80b0b SHA512 9caf15d833490f89ed24fc80f6d2842ae012e4931ac42af7e6fc5fe2e40cedc98dfbb3c74529387456310fab8dc87ad3a87595b98edd4c2200242e5bec37a849 WHIRLPOOL f60b54d8733dc439018f978e7c0dfc096014cddca406cc6a79d2c8cdbb376f1f40b2ba031bd9da33cff02cb7304e203c9ad962bf94d429788d0a7c1cc846084d
-MISC ChangeLog 3353 SHA256 7721aee9dc8aae3d269e0887c531bf60ad0cda405d98691354ba68d465abf348 SHA512 8c158046545040114df4255d84d4a68f14a6e54ec7387e560b245139de541026fa407ea819ddfcba29c75846ab9e39b1a58c92f9bbd44557fdd0198b1b8beecd WHIRLPOOL 949219e4cd4eeb313d5f6ef7b4d73274e487cf1029bda30b349a498bdc5292ba4acee0c3a85b37dcad0920ca8a023fc2fa378a843f484d062498b03da50ccb3b
+EBUILD meme-4.8.1-r1.ebuild 1868 SHA256 5477a29a09fbacb83757b2974c5d8751ead9172028d1229c9c8e2316954f2150 SHA512 3ee3966ac64325c7b268d274a9808f203515545d1af88eeb6621a08ab29df8f24067ea8bbd3cf27b7dc1619106f0e5139085ad143585634e21daaac2cba0fba9 WHIRLPOOL e264f7ac9d8d1ff5d219598e60a9a25a5c6dbf68695b9af9121586d3762724f0ec253ffcc671af429b0fb6094708a719ece93e2ae4942051fe4ac97b87cae1eb
+EBUILD meme-4.8.1.ebuild 1819 SHA256 950b3e4eabd32427d1fb0dcaa624b4df54693b701270e9695fb18c6b286ff4aa SHA512 0db749a8d15dd12aa82a44094f57e2dd3d808d36992cbf19fa8adf9dddbcc6476591955d7d0c6da389b2a8d26cc583d98c575ebff05036398c6238e4a03d8781 WHIRLPOOL 6148614c50b413785c301addd9abf25b62041daa6ef884d85b1c646dea3011785702acbf644275ef971f472f8c5de1a02dc189af920ca5dda4077748018f7427
+MISC ChangeLog 3547 SHA256 c81d0a6046d3d3a5ae6be65b174717ceb4f744c458d97258fc98217166610a83 SHA512 fbd367b1fa547b9160f0abb7665920f29d2663468c30f1a6c8b90feaf2b00b6deb5ed251bd37f072aece51c6db009a1072dc17759cd192ae0473d13a324cf921 WHIRLPOOL 4ba05281b1a50fd6cae9dd708db0f74146348ba59f7db6425f64d4d7f5cbb9b7c257c9b46c22c02655ee4ec533297604fdb4e849d173d85cdfe3ecaf89bd6b37
 MISC metadata.xml 266 SHA256 98c7d1da8a728a1f1d796a79d51f25e4164e24048ec1aacbbf0ae2ffb171ff35 SHA512 879cdcca092d4c82b8c63672c91e08e7b01e81419d2c7c7b766de96ba2a32dd1e21c18968ed7172eec8604f52c92b19a31773f428bce9461d9b8190384680194 WHIRLPOOL 0f46288ab7090ad3da5b31816792427e4ad1a950e39a503bb406ebe8789cffedd9c85b46bfbf040fffb8aad443f512c28716a0a6436d0c06309155277060cdcd
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.19 (GNU/Linux)
 
-iEYEAREIAAYFAlEKGoYACgkQgAnW8HDreRb2jwCeJKkqEUlOjdGasifyPa9z0UoN
-DbEAn23Isa5CYNzCd5sRSo1Ocqp7QJas
-=a0pZ
+iEYEAREIAAYFAlEL1m0ACgkQgAnW8HDreRYM5wCeNWRn7/6/v/6vUR+4UJRuN5rD
+hdMAn3QRczfkOryWCpGJXISrXRoWJJZu
+=VKC1
 -----END PGP SIGNATURE-----
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}