From: Justin Bronder Date: Thu, 17 Jun 2010 03:24:50 +0000 (+0000) Subject: Removing outdated sci-biology/meme-3.5.x after checking with weaver. X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=7d58088610b87197fce560da9f6ada522d8bcb10;p=gentoo.git Removing outdated sci-biology/meme-3.5.x after checking with weaver. Package-Manager: portage-2.2_rc67/cvs/Linux x86_64 --- diff --git a/sci-biology/meme/ChangeLog b/sci-biology/meme/ChangeLog index 990b4987db5e..cdadd3af12e9 100644 --- a/sci-biology/meme/ChangeLog +++ b/sci-biology/meme/ChangeLog @@ -1,6 +1,10 @@ # 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jsbronder Exp $ + + 17 Jun 2010; Justin Bronder -meme-3.5.4-r1.ebuild, + -meme-3.5.7.ebuild: + Removing outdated meme-3.5.x *meme-4.4.0 (07 May 2010) diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest index 97891248c317..33107f1c42e0 100644 --- a/sci-biology/meme/Manifest +++ b/sci-biology/meme/Manifest @@ -1,15 +1,21 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + 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 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.14 (GNU/Linux) + +iEYEARECAAYFAkwZlYcACgkQ4MrvBE1wQ8lerACgq2eNF3b/FkeIiwGg9V/n+GQh +T9wAn15SPj3L+jnDqJfVBWK1iJaoyxxo +=DYxr +-----END PGP SIGNATURE----- diff --git a/sci-biology/meme/meme-3.5.4-r1.ebuild b/sci-biology/meme/meme-3.5.4-r1.ebuild deleted file mode 100644 index b80fd8f58831..000000000000 --- a/sci-biology/meme/meme-3.5.4-r1.ebuild +++ /dev/null @@ -1,90 +0,0 @@ -# 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." -} diff --git a/sci-biology/meme/meme-3.5.7.ebuild b/sci-biology/meme/meme-3.5.7.ebuild deleted file mode 100644 index 2361ebe9d539..000000000000 --- a/sci-biology/meme/meme-3.5.7.ebuild +++ /dev/null @@ -1,96 +0,0 @@ -# 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." -}