# ChangeLog for sci-biology/meme
# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.15 2010/05/07 19:40:14 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.16 2010/06/17 03:24:50 jsbronder Exp $
+
+ 17 Jun 2010; Justin Bronder <jsbronder@gentoo.org> -meme-3.5.4-r1.ebuild,
+ -meme-3.5.7.ebuild:
+ Removing outdated meme-3.5.x
*meme-4.4.0 (07 May 2010)
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
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AUX meme-3.5.4-Makefile.am.patch 377 RMD160 a8d4551bcb53b66044ded24421cd2a17bf93b3ad SHA1 96530d5a58b8c01c99ae2b5463b7448758d7fb3d SHA256 ef3f0d8ccca728325d9f9b4f485e8cd4db2ced50fc975f8b66f3b76fcf17b5e8
AUX meme-3.5.4-patch1.patch 7443 RMD160 6d72e74d6139d8c29bfcda9da750dc454f08ef0a SHA1 336c91ad5ecd44d49de0e940bb18315b62569a2b SHA256 306cee9c3c831494cf264ded84d248e5773c9a56d259a02e8da9c6dc31457f04
AUX meme-3.5.4-patch2.patch 2074 RMD160 56520122dd1d35afa444414ea57199924e8492b5 SHA1 29edf295100721006aea8b76ff4c5bdfb9312020 SHA256 bf74f09bcd6c247f464f15b17e3a0e8f95149fdc5b92d8f17d06ede430d2d7be
AUX meme-4.0.0-Makefile.am.patch 377 RMD160 a8d4551bcb53b66044ded24421cd2a17bf93b3ad SHA1 96530d5a58b8c01c99ae2b5463b7448758d7fb3d SHA256 ef3f0d8ccca728325d9f9b4f485e8cd4db2ced50fc975f8b66f3b76fcf17b5e8
-DIST meme_3.5.4.tar.gz 1045501 RMD160 063a804c18f07349e95f4aba2a3c97cb025ed2a8 SHA1 d780dba0b900f840a599cf69cfeba4eefd4856b4 SHA256 b753ee276bc5eafeab8ff310e6d938977da11f466d26cfd3ae9c0f0a7a91de86
-DIST meme_3.5.7.tar.gz 1101383 RMD160 ab2c38873d30490933151520b09bec0644d2c492 SHA1 f04f233be63a75a78ea878d025a0476099e496cd SHA256 b5d84d969f69dbe02f2636e2161c53212f7c9a5b141ae2ed759f99a322f221a9
DIST meme_4.3.0.tar.gz 4658395 RMD160 32ddc2da3a361d737e70180198f8846a89f3aed5 SHA1 3e9def53eef96426fb3561b9de1de7901ac34f49 SHA256 6a6a04f168f8ac6dbba022461701e0327bc8ececcb375b2dd387a084cd8ba17b
DIST meme_4.4.0.tar.gz 4673815 RMD160 37b01dfd350617c2a41821396d353c6e952fb5c0 SHA1 5865e5994d4e76e9d9fc3460fc3949a873d6920d SHA256 3b61e1f4513da4ff60fd0c516d4edcefeb9c9e07a3ab7fa42c059576d6a0f992
-EBUILD meme-3.5.4-r1.ebuild 2830 RMD160 7d22f826e65582135face95b90cafefbd1cd97d0 SHA1 100a2254ec137006e75c2758ee6ba2457ded0935 SHA256 9c1604a7d2067b6bcf14ddb81f78fa609c6055ca8e6399fa866e7fae6b670cfd
-EBUILD meme-3.5.7.ebuild 2974 RMD160 40c253d011156412ca97efb4976341f3de3b0f1c SHA1 58771e53750ab5faf6893be18f39619cb98af0c8 SHA256 52de8a4de5715400ad8b0afda374fe38b962e5f11cb43b376b7a36c7ed200793
EBUILD meme-4.3.0-r1.ebuild 1631 RMD160 731ff9ca70a491c8302f3f35bced41464d5d364b SHA1 e3088c237d41a94a96af09b699b7bfda57a46052 SHA256 106c08daf8c38fc32fa6ca713f1bf24998b4c3f69bf2c6cd367c983dc3c3a9a3
EBUILD meme-4.3.0.ebuild 1580 RMD160 77272f4187fd76e6108f13555de396e5804d0e4c SHA1 8ac19251be1661a0b93b0c67953e811093958f6c SHA256 b9efea3a598c009f1ae57f18f1bbb4a8a8f90bcdda83169740b4c8a92e1edc97
EBUILD meme-4.4.0.ebuild 1583 RMD160 ded80f4d0a16cf7bf5d984def61e23e03831d332 SHA1 c6cf87d4b08334720460ecc9f0532b2fd3863188 SHA256 147fb3b14d9cec31d04bcc3b34af3459ddd6c6513950c1414faef069a4e3cb86
-MISC ChangeLog 2396 RMD160 e6b3d43e69fe6df5d1d789992e76ac96cc6b87bc SHA1 f638847674e9e32b0b8ec148b520bee24a8a238b SHA256 51a7778d92981307b9923916578778704e9cb6d8bc18870c997c96d1b57d756c
+MISC ChangeLog 2529 RMD160 3a4599b7d3aa602ca939cce2a7e2e4f45a9c57ae SHA1 ebd93d723dbd4d6836e0b3c0103230b7eeb85a9f SHA256 cc1fea18fed8da7968a2452f0cac8fcde7083c6f50f19ce15083c8833cf581bf
MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
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+++ /dev/null
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-3.5.4-r1.ebuild,v 1.4 2008/06/14 12:34:50 markusle Exp $
-
-inherit autotools eutils toolchain-funcs
-
-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="~x86 ~amd64"
-# Other possible USE flags include "debug", "client", "server", "web",
-# "queue". Other variables must be set at compile time, but only when
-# the Web server is built. Right now, Web server and client are disabled.
-IUSE="mpi"
-
-# Works only with LAM-MPI.
-DEPEND=">=dev-lang/perl-5.6.1
- mpi? ( sys-cluster/lam-mpi )"
-
-S="${WORKDIR}/${PN}_${PV}"
-
-src_unpack() {
- unpack ${A}
-
- cd "${S}"
- epatch "${FILESDIR}/${P}-Makefile.am.patch"
- epatch "${FILESDIR}/${P}-patch1.patch"
- epatch "${FILESDIR}/${P}-patch2.patch"
- einfo "Regenerating autotools files..."
- eautoreconf
-}
-
-src_compile() {
- local EXTRA_CONF
- # Build system is too bugy to make the programs use standard locations.
- # Put everything in "/opt" instead.
- EXTRA_CONF="${EXTRA_CONF} --prefix=/opt/${PN}"
- EXTRA_CONF="${EXTRA_CONF} --with-logs=/var/log/${PN}"
- # Connect hyperlinks to official Web site.
- EXTRA_CONF="${EXTRA_CONF} --with-url=http://meme.nbcr.net/meme"
- # Disable Web server, client and Web site.
- EXTRA_CONF="${EXTRA_CONF} --disable-server --disable-client --disable-web"
- # Parallel implementation
- if ! use mpi; then
- EXTRA_CONF="${EXTRA_CONF} --enable-serial"
- fi
-
- ./configure ${EXTRA_CONF} || die "Configure failed."
- CC="$(tc-getCC)" ac_cc_opt="${CFLAGS}" make -e || die "Make failed."
-
-# Install parallel files only on x86, otherwise the install fails with the error:
-# i386 architecture of input file `mp.o' is incompatible with i386:x86-64 output
- if [[ "${ARCH}" == "x86" ]] ; then
- if use mpi; then
- cd src/parallel
- make || die "Parallel make failed."
- fi
- fi
-}
-
-src_install() {
- make install DESTDIR="${D}" || die "Failed to install program files."
- exeinto "/opt/${PN}/bin"
- if [[ "${ARCH}" == "x86" ]] ; then
- if use mpi; then
- doexe "${S}/src/parallel/${PN}_p" || \
- die "Failed to install parallel MEME implementation."
- fi
- fi
- keepdir "/var/log/${PN}"
- fperms 777 "/var/log/${PN}"
-}
-
-pkg_postinst() {
- echo
- einfo 'Prior to using MEME/MAST, you should source "/opt/meme/etc/meme.sh"'
- einfo '(or "/opt/meme/etc/meme.csh" if you use a csh-style shell). To do'
- einfo 'this automatically with bash, add the following statement to your'
- einfo '"~/.bashrc" file (without the quotes): "source /opt/meme/etc/meme.sh".'
- echo
- einfo 'Log files are produced in the "/var/log/meme" directory.'
- echo
-}
-
-src_test() {
- make test || die "Regression tests failed."
-}
+++ /dev/null
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-3.5.7.ebuild,v 1.2 2008/09/12 18:24:11 mr_bones_ Exp $
-
-inherit autotools eutils toolchain-funcs
-
-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="~x86 ~amd64"
-# Other possible USE flags include "debug", "client", "server", "web",
-# "queue". Other variables must be set at compile time, but only when
-# the Web server is built. Right now, Web server and client are disabled.
-IUSE="mpi"
-
-# Works only with LAM-MPI.
-DEPEND=">=dev-lang/perl-5.6.1
- mpi? ( sys-cluster/lam-mpi )"
-
-S="${WORKDIR}/${PN}_${PV}"
-
-pkg_setup() {
- # generate meme group to restrict logging to
- # /var/log/meme
- enewgroup meme
-}
-
-src_unpack() {
- unpack ${A}
- cd "${S}"
- epatch "${FILESDIR}/${PN}-3.5.4-Makefile.am.patch"
- einfo "Regenerating autotools files..."
- eautoreconf
-}
-
-src_compile() {
- local EXTRA_CONF
- # Build system is too bugy to make the programs use standard locations.
- # Put everything in "/opt" instead.
- EXTRA_CONF="${EXTRA_CONF} --prefix=/opt/${PN}"
- EXTRA_CONF="${EXTRA_CONF} --with-logs=/var/log/${PN}"
- # Connect hyperlinks to official Web site.
- EXTRA_CONF="${EXTRA_CONF} --with-url=http://meme.nbcr.net/meme"
- # Disable Web server, client and Web site.
- EXTRA_CONF="${EXTRA_CONF} --disable-server --disable-client --disable-web"
- # Parallel implementation
- if ! use mpi; then
- EXTRA_CONF="${EXTRA_CONF} --enable-serial"
- fi
-
- ./configure ${EXTRA_CONF} || die "Configure failed."
- CC="$(tc-getCC)" ac_cc_opt="${CFLAGS}" make -e || die "Make failed."
-
-# Install parallel files only on x86, otherwise the install fails with the error:
-# i386 architecture of input file `mp.o' is incompatible with i386:x86-64 output
- if [[ "${ARCH}" == "x86" ]] ; then
- if use mpi; then
- cd src/parallel
- make || die "Parallel make failed."
- fi
- fi
-}
-
-src_install() {
- make install DESTDIR="${D}" || die "Failed to install program files."
- exeinto "/opt/${PN}/bin"
- if [[ "${ARCH}" == "x86" ]] ; then
- if use mpi; then
- doexe "${S}/src/parallel/${PN}_p" || \
- die "Failed to install parallel MEME implementation."
- fi
- fi
-
- # allow logging only for members of meme group
- diropts -m 0770 -g meme -o root
- keepdir "/var/log/${PN}"
-}
-
-pkg_postinst() {
- echo
- einfo 'Prior to using MEME/MAST, you should source "/opt/meme/etc/meme.sh"'
- einfo '(or "/opt/meme/etc/meme.csh" if you use a csh-style shell). To do'
- einfo 'this automatically with bash, add the following statement to your'
- einfo '"~/.bashrc" file (without the quotes): "source /opt/meme/etc/meme.sh".'
- echo
- 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.'
- echo
-}
-
-src_test() {
- make test || die "Regression tests failed."
-}
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