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

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

6 files changed, 20 insertions, 149 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/Manifest b/sci-biology/meme/Manifest
index bfb418723485..354f1497a42d 100644
--- a/sci-biology/meme/Manifest
+++ b/sci-biology/meme/Manifest
@@ -7,19 +7,15 @@ 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_4.3.0.tar.gz 4658395 SHA256 6a6a04f168f8ac6dbba022461701e0327bc8ececcb375b2dd387a084cd8ba17b
-DIST meme_4.4.0.tar.gz 4673815 SHA256 3b61e1f4513da4ff60fd0c516d4edcefeb9c9e07a3ab7fa42c059576d6a0f992 SHA512 997e3652408ca0b9dbc647ff576c44fcb7021319b3f3395288e2fa321d98b96eccb5dc31e51dc96ec65b9fd1a5ecf35b28edc5398d161a114dc5d36b7b1dde85 WHIRLPOOL 8e03298e61387347f99ddf56f8a33866e926ccf71f3676ca227e1d72d8808aeb0aedb13f5b6a5a7d7f10b7687c2ce3e18d76c299954050b83058e765c0897b7d
 DIST meme_4.8.1.tar.gz 8703632 SHA256 c3ad3ca26bc2a7130c5eceb64e1745275c317a5469e98fc8759a9e56babccb8c SHA512 31833169ffa9bd82387d1872be40b0fc4312f4a05bb7abb84daf372244ce3f2a68c89c96722c0453f7bcd9eb4fc84fd3d66e1278af55d556715b94b0df5f87ba WHIRLPOOL 4b5e8968e6964479081d1fe036ff3aa7a50dc56bafc0031890d2e47dbdc8e0273e62ffe01800d8908b2fa9824a4766254bb0fd94003d9ca14784073d5357793e
-EBUILD meme-4.3.0-r1.ebuild 1635 SHA256 a557cb73935ef13ca457c5768606745c7af948856dd01c4ca524cb687b199c11 SHA512 12f2876d1984cbfb9c7f180a416bdde49433e9486292a820e6c3c8c0e8ceaa999301ef232df6a7fb9322b118ada3de2c348bc55d630a74d4100518fdd7ec5c9e WHIRLPOOL ff1800b8db99abb1a00acda8285300658a4385b23aeb54860fbf158b3384418f2afcc0b2482074ee3a02d81bf857c6dab74855152db66d6048988b208b6e10f9
 EBUILD meme-4.3.0.ebuild 1583 SHA256 19ba4e94fef091a02108fe8928c292bdabf15a0d53f3915d997f15fb96bb8f46 SHA512 e4fcf052db62fd55e152fa816b227791951a2b7f68243878bb0696cc17ab6f183ef7253e56a45233862981802e4af688bd76922ca67746cfee0248ad6b7b7c1b WHIRLPOOL 71a5e33d6c5e5f868f7f527a0d9a62002d0c8e32dbac528a8c8b7fcf031bc0034272f19bc3028c91af980e01cc03427cb0c356b92108cd6b9aae48bb1c470ae1
-EBUILD meme-4.4.0.ebuild 1585 SHA256 dfadfe550912c5eb2c3f7f8f25c32b64a63a782c5ae1ef70424d8f573abe2347 SHA512 feacd9f7d5091fc0cef0a1ed3c7b21e8a01de45e71bb7a907624e54bbac311ebaa21074fd7191ba0b81017f8a1ec4255f4204964c4507b0bf1b9eab4b1d3d586 WHIRLPOOL c43bf62e13a982c21eb4f77981f57ea400cb6fb3b87ce9a07706eed5ca63e1804097022d2a11eb925f2fdaf552f2e285025cffd4c35965a629c929eece537005
-EBUILD meme-4.8.1.ebuild 1761 SHA256 092222c8c3257e31b5627160e06260cac3337fdb753d0388d07a8e0b11879203 SHA512 2756a82caa019aed9be77ce3752290670a9c55ee3086d5eceed162a0dd5b8d58388744867e0e6b0e9bec87d12c1b86ca24100632618dc8069fa1adf6f010cbcc WHIRLPOOL 68a6f6a845912ebbe2a0ab98a74b65e63b23d8ac51ca97ebd5731325146770c5d78ed7e61cad2ac0ff54efb670a51bf7ce6f01cfe1ca38653f915efba8668780
-MISC ChangeLog 2855 SHA256 9c04efd9ef1604d6bd87e382af5c985d4f5863b81b4152d9a2022d659db4ef64 SHA512 0f14e8db92404f9998b379c683e2cac799ae51e50b27d4dd15181b70de214b01d624b65ff12a1d0143075c9fed4792a100a76260763e846fa66fca91d2862d38 WHIRLPOOL eb1d24641a0ef780fbd2afea2cd3bfe5f64af020a1b1c6d9a4bd54a054b0854dc248b1bf5c12f29eb86f7dbefd4e1259ccb96b0f63467ef9c9eb31751dfe570e
-MISC metadata.xml 259 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 SHA512 c3aea4d69d75075af0108a03b7e109cfed6a1fe324f8ccbda3d4e5ca8a5070f1b24ddeb46b64787e10fd22252d867abcee1f31316d602f7e32fe3c990ae60d74 WHIRLPOOL e50da2f26fd4c908446d22da3edb595d60e61d72def374be46440358802a211fc34045b7ad970c4f94b57f7b17ff24cfe64dc94254fea20e047f1fbbbcae0c64
+EBUILD meme-4.8.1.ebuild 1839 SHA256 1ec3af045ac77b061050e947bf6bf0121609b944b063095872719148ddbbb34a SHA512 1b0601ca5ff461e69e48237cdf3fcd2028bcce8c4f1d35fa7e5e6eed96e736cd91e4644efd97b58512b6d776a009428bcf822d4bc9d8f946766df51fe217a462 WHIRLPOOL 4656afda0ae6dd9a8cf6f03c2f777db4532bc1009c6b246d694141a7ff905c345b25e87db9f289af9d1806683b9ad36acda0daf68b78fcda92f4ed9e58ae2091
+MISC ChangeLog 3015 SHA256 9fde6ea95e2631aeca8f1a84b3cf448bfa22e299d9da0e3b74e731751d206188 SHA512 c559fe4e5e46e80c912f25175e701e5be40fb177b59159b720f7dacde9c1a0941c1a2ea2b4e90d1856595476af9c7bfc7abf697e84a051366f60cd83d498c778 WHIRLPOOL 37786df7303c7756fb1edf6a08b1aca81e5693e8f41068ade1491a8bf61d949116940503b929b6857bfcb490d9eaba3b068a1fa8b8aac7435e6bef9569c54f26
+MISC metadata.xml 266 SHA256 98c7d1da8a728a1f1d796a79d51f25e4164e24048ec1aacbbf0ae2ffb171ff35 SHA512 879cdcca092d4c82b8c63672c91e08e7b01e81419d2c7c7b766de96ba2a32dd1e21c18968ed7172eec8604f52c92b19a31773f428bce9461d9b8190384680194 WHIRLPOOL 0f46288ab7090ad3da5b31816792427e4ad1a950e39a503bb406ebe8789cffedd9c85b46bfbf040fffb8aad443f512c28716a0a6436d0c06309155277060cdcd
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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>