sci-biology/meme: Rename all binaries to meme-*; should fix all collisions in future, #458208; drop old

Package-Manager: portage-2.2.0_alpha163/cvs/Linux x86_64
RepoMan-Options: --force
Manifest-Sign-Key: 0x70EB7916

4 files changed, 18 insertions, 92 deletions

diff --git a/sci-biology/meme/ChangeLog b/sci-biology/meme/ChangeLog
index eda8367c9c41..b1baa394b9f0 100644
--- a/sci-biology/meme/ChangeLog
+++ b/sci-biology/meme/ChangeLog
@@ -1,6 +1,13 @@
 # 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 1.23 2013/02/01 14:51:24 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.24 2013/03/01 12:43:54 jlec Exp $
+
+*meme-4.8.1-r2 (01 Mar 2013)
+
+  01 Mar 2013; Justin Lecher <jlec@gentoo.org> -meme-4.8.1.ebuild,
+  -meme-4.8.1-r1.ebuild, +meme-4.8.1-r2.ebuild:
+  Rename all binaries to meme-*; should fix all collisions in future, #458208;
+  drop old
 
 *meme-4.8.1-r1 (01 Feb 2013)
 
diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest
index 9c23faf6e9fe..7b78e3307573 100644
--- a/sci-biology/meme/Manifest
+++ b/sci-biology/meme/Manifest
@@ -7,14 +7,13 @@ 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-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
+EBUILD meme-4.8.1-r2.ebuild 1870 SHA256 56dfc0c7e424124ff7eb6515452550e2bd80b289703d4f9f009a93a5e6234500 SHA512 cc89014303f12aa8f00f5b0df7f1957770f6d935d0daca87b4820e38ef9537cde7dab9f88ff3d3f41dc0d008e4d0d401d06e4ee08d9e2f6020d1c19b573d5495 WHIRLPOOL ae8b8caebc124a2860496cfd067dcd46a7007e2a4c744143d3c27f275e688bc232ee334e2570cba388d1da32e80abc88e323f82dedcd226a6e6b1e861cb0fd5b
+MISC ChangeLog 3783 SHA256 b6f8539874a3be1e392575991d6cf0a2319fdaf956b87be80c7ca685c305e53b SHA512 703c9d101311609c3bca741449fd640b61f962a7a97b0f387f559086a7e6a8f979e93f563e038660452f264649aa7ed51565477ee8d72b3c1f129f97f403ccc1 WHIRLPOOL 685fecaaef7bd75fa4a97f116e88b26c094cd97e21b95e3ee440ecd260719d0a44d00b864ca644d5fa828d75b8ab39211b1ceda7d7fadf2571388be7cc2d7b01
 MISC metadata.xml 266 SHA256 98c7d1da8a728a1f1d796a79d51f25e4164e24048ec1aacbbf0ae2ffb171ff35 SHA512 879cdcca092d4c82b8c63672c91e08e7b01e81419d2c7c7b766de96ba2a32dd1e21c18968ed7172eec8604f52c92b19a31773f428bce9461d9b8190384680194 WHIRLPOOL 0f46288ab7090ad3da5b31816792427e4ad1a950e39a503bb406ebe8789cffedd9c85b46bfbf040fffb8aad443f512c28716a0a6436d0c06309155277060cdcd
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.19 (GNU/Linux)
 
-iEYEAREIAAYFAlEL1m0ACgkQgAnW8HDreRYM5wCeNWRn7/6/v/6vUR+4UJRuN5rD
-hdMAn3QRczfkOryWCpGJXISrXRoWJJZu
-=VKC1
+iEYEAREIAAYFAlEwoosACgkQgAnW8HDreRb1fgCgiKfZjyXGfxjRMGRuTngxwyGX
+3ecAoMSBbOispbkIY/41SMvpNZQvWxh8
+=4mYY
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/meme/meme-4.8.1-r1.ebuild b/sci-biology/meme/meme-4.8.1-r2.ebuild
index 50c2f7fe6aee..abc810087e9a 100644
--- a/sci-biology/meme/meme-4.8.1-r1.ebuild
+++ b/sci-biology/meme/meme-4.8.1-r2.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-r1.ebuild,v 1.1 2013/02/01 14:51:24 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-4.8.1-r2.ebuild,v 1.1 2013/03/01 12:43:54 jlec Exp $
 
 EAPI=4
 
@@ -63,10 +63,12 @@ src_test() {
 }
 
 src_install() {
+	local i
 	default
 
-	mv "${ED}"/usr/bin/{,meme-}tree || die
-	mv "${ED}"/usr/bin/{,meme-}readseq || die
+	for i in "${ED}"/usr/bin/*; do
+		"${ED}"/usr/bin/{,meme-}${i} || die
+	done
 
 	echo "PATH=/opt/${PN}/bin" > 99${PN}
 	doenvd 99${PN}
diff --git a/sci-biology/meme/meme-4.8.1.ebuild b/sci-biology/meme/meme-4.8.1.ebuild
deleted file mode 100644
index dc154dd57195..000000000000
--- a/sci-biology/meme/meme-4.8.1.ebuild
+++ /dev/null
@@ -1,82 +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-4.8.1.ebuild,v 1.6 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-text/tree
-	app-shells/tcsh
-	dev-libs/libxml2:2
-	dev-libs/libxslt
-	!sci-biology/readseq
-	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) \
-		$USE_DISABLE_MPI
-}
-
-src_test() {
-	# bug #297070
-	emake -j1 test
-}
-
-src_install() {
-	default
-
-	echo "PATH=/opt/${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.'
-#}