sci-biology/meme: Drop old, fixes bug 297070 & bug 454662

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

4 files changed, 19 insertions, 72 deletions

diff --git a/sci-biology/meme/ChangeLog b/sci-biology/meme/ChangeLog
index 8fccd11c1e69..f29dcfe25542 100644
--- a/sci-biology/meme/ChangeLog
+++ b/sci-biology/meme/ChangeLog
@@ -1,6 +1,10 @@
 # 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 1.21 2013/01/30 22:44:02 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.22 2013/01/31 07:17:25 jlec Exp $
+
+  31 Jan 2013; Justin Lecher <jlec@gentoo.org> -meme-4.3.0.ebuild,
+  meme-4.8.1.ebuild:
+  Drop old, fixes bug 297070 & bug 454662
 
   30 Jan 2013; Agostino Sarubbo <ago@gentoo.org> meme-4.8.1.ebuild:
   Stable for x86, wrt bug #454698
diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest
index fcaa5521c613..bc2f0c204f62 100644
--- a/sci-biology/meme/Manifest
+++ b/sci-biology/meme/Manifest
@@ -1,11 +1,19 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA256
+
 AUX meme-3.5.4-Makefile.am.patch 377 SHA256 ef3f0d8ccca728325d9f9b4f485e8cd4db2ced50fc975f8b66f3b76fcf17b5e8 SHA512 87d4e552c51b45409093eeb7821dfa571b6d44dfdae4a899600da8c48bfe4806d5018d83a433cc88443d05ac6a5b4b7aa7f9abf9a027f5ce8ee7b8da7e4d7b12 WHIRLPOOL 16cc954f231868cd39be3dad5ec944a3e15c8946022a37e1a32c527237f045de70bc85e986a5a7ecadc2107992dd60859caa7f75b501eb256ebe208db89c38db
 AUX meme-3.5.4-patch1.patch 7443 SHA256 306cee9c3c831494cf264ded84d248e5773c9a56d259a02e8da9c6dc31457f04 SHA512 d0a1e362f664b90929316ed021d465c4bcb6d4ac52269858931bcb734ddc29fd2730d1e1e87f22d6ad173e1f719c741717be391835e677f78fa9d6a9a8110fff WHIRLPOOL 711311aa78c533aae6e9be47baf93c3b6ffb6b0e0c01064f160af8d8211efbc78314ff9375ed45c9c72ed998d3aa67b882b538c5c819323d447df6c28e5a1f07
 AUX meme-3.5.4-patch2.patch 2074 SHA256 bf74f09bcd6c247f464f15b17e3a0e8f95149fdc5b92d8f17d06ede430d2d7be SHA512 befadf63ce6181907d4a479e1508cb9f2b7d126b22644025d2715ec18cc5ff61b93ee9f7b3ebdeda2c8dca18691ca71b7842018e8f53603d10c0f9787ea5c0a1 WHIRLPOOL e8cdd07c74b20aa6f4ac252daca7a046ac192460eacc3d32a2653a88a2fa8eb021049d3a52c3aaf2918d1637f05c7d395c506cccfd754380b53bc7c1ca54feed
 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_4.3.0.tar.gz 4658395 SHA256 6a6a04f168f8ac6dbba022461701e0327bc8ececcb375b2dd387a084cd8ba17b
 DIST meme_4.8.1.tar.gz 8703632 SHA256 c3ad3ca26bc2a7130c5eceb64e1745275c317a5469e98fc8759a9e56babccb8c SHA512 31833169ffa9bd82387d1872be40b0fc4312f4a05bb7abb84daf372244ce3f2a68c89c96722c0453f7bcd9eb4fc84fd3d66e1278af55d556715b94b0df5f87ba WHIRLPOOL 4b5e8968e6964479081d1fe036ff3aa7a50dc56bafc0031890d2e47dbdc8e0273e62ffe01800d8908b2fa9824a4766254bb0fd94003d9ca14784073d5357793e
-EBUILD meme-4.3.0.ebuild 1583 SHA256 19ba4e94fef091a02108fe8928c292bdabf15a0d53f3915d997f15fb96bb8f46 SHA512 e4fcf052db62fd55e152fa816b227791951a2b7f68243878bb0696cc17ab6f183ef7253e56a45233862981802e4af688bd76922ca67746cfee0248ad6b7b7c1b WHIRLPOOL 71a5e33d6c5e5f868f7f527a0d9a62002d0c8e32dbac528a8c8b7fcf031bc0034272f19bc3028c91af980e01cc03427cb0c356b92108cd6b9aae48bb1c470ae1
-EBUILD meme-4.8.1.ebuild 1836 SHA256 52cc53a44b9508ee90d9f7ef57f6cc3f21eefea34e89e29056e5b6a00fbc580f SHA512 d546f9962ff277f56df6ef12a972e1a9a6b3baa9ccdff74a511d5b4f5b8504e0b8012ef596abea4baa987dbd7a908f08ecf16f6a6dc83f5c51da63f7d6158834 WHIRLPOOL 593d28ea44d04e8a3d52913bd8857c24da04ba8c0445770a418aaba861cf7d0e8c136b35dde2543d9697c0b2450ba7de3b43956a1b47c22e15c6efbcd2f91440
-MISC ChangeLog 3221 SHA256 a6bb3bb1c5d76ab70e248feac4f9b481558939e795ddb67a2e60635d2e3831a1 SHA512 d299b575700e6cfe5532dd9e44dee418444172f0c5638661fe724693a04e601b2819c3ccc83be2c836a2472a09879908a0f7df4c84366102571f50e1ddfedbf9 WHIRLPOOL 1e198f546f0611aa39a58487bf415276d7eee907ef614a1f2d8d060c6e8624d88c4f66c59dcecdc9301270d2998a8e162f98796a470b17c6fb5481504be6bf8d
+EBUILD meme-4.8.1.ebuild 1836 SHA256 bd19fb007d2e249b9eda3e7f5c01673d6fc2156ab5fd673a27b13e86f3c80b0b SHA512 9caf15d833490f89ed24fc80f6d2842ae012e4931ac42af7e6fc5fe2e40cedc98dfbb3c74529387456310fab8dc87ad3a87595b98edd4c2200242e5bec37a849 WHIRLPOOL f60b54d8733dc439018f978e7c0dfc096014cddca406cc6a79d2c8cdbb376f1f40b2ba031bd9da33cff02cb7304e203c9ad962bf94d429788d0a7c1cc846084d
+MISC ChangeLog 3353 SHA256 7721aee9dc8aae3d269e0887c531bf60ad0cda405d98691354ba68d465abf348 SHA512 8c158046545040114df4255d84d4a68f14a6e54ec7387e560b245139de541026fa407ea819ddfcba29c75846ab9e39b1a58c92f9bbd44557fdd0198b1b8beecd WHIRLPOOL 949219e4cd4eeb313d5f6ef7b4d73274e487cf1029bda30b349a498bdc5292ba4acee0c3a85b37dcad0920ca8a023fc2fa378a843f484d062498b03da50ccb3b
 MISC metadata.xml 266 SHA256 98c7d1da8a728a1f1d796a79d51f25e4164e24048ec1aacbbf0ae2ffb171ff35 SHA512 879cdcca092d4c82b8c63672c91e08e7b01e81419d2c7c7b766de96ba2a32dd1e21c18968ed7172eec8604f52c92b19a31773f428bce9461d9b8190384680194 WHIRLPOOL 0f46288ab7090ad3da5b31816792427e4ad1a950e39a503bb406ebe8789cffedd9c85b46bfbf040fffb8aad443f512c28716a0a6436d0c06309155277060cdcd
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.19 (GNU/Linux)
+
+iEYEAREIAAYFAlEKGoYACgkQgAnW8HDreRb2jwCeJKkqEUlOjdGasifyPa9z0UoN
+DbEAn23Isa5CYNzCd5sRSo1Ocqp7QJas
+=a0pZ
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/meme/meme-4.3.0.ebuild b/sci-biology/meme/meme-4.3.0.ebuild
deleted file mode 100644
index a55f684e36bb..000000000000
--- a/sci-biology/meme/meme-4.3.0.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-4.3.0.ebuild,v 1.5 2011/03/02 17:41:08 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 3bdcbe271e4f..19d3d29e1424 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 1.4 2013/01/30 22:44:02 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-4.8.1.ebuild,v 1.5 2013/01/31 07:17:25 jlec Exp $
 
 EAPI=4
 
@@ -34,7 +34,7 @@ S="${WORKDIR}/${PN}_${PV}"
 #}
 
 src_prepare() {
-	use examples || sed -e '/SUBDIRS/s:examples::g' -i doc/Makefile.am 
+	use examples || sed -e '/SUBDIRS/s:examples::g' -i doc/Makefile.am
 	sed \
 		-e '/flags/s:-O3::g' \
 		-e '/opt/s:-O::g' \