From f5526e274107be8a7514fec9912d1fd5dcde8125 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Fri, 1 Mar 2013 12:43:54 +0000 Subject: sci-biology/meme: Rename all binaries to meme-*; should fix all collisions in future, #458208; drop old (Portage version: 2.2.0_alpha163/cvs/Linux x86_64, RepoMan options: --force, signed Manifest commit with key 70EB7916) --- sci-biology/meme/ChangeLog | 9 +++- sci-biology/meme/meme-4.8.1-r1.ebuild | 83 ---------------------------------- sci-biology/meme/meme-4.8.1-r2.ebuild | 85 +++++++++++++++++++++++++++++++++++ sci-biology/meme/meme-4.8.1.ebuild | 82 --------------------------------- 4 files changed, 93 insertions(+), 166 deletions(-) delete mode 100644 sci-biology/meme/meme-4.8.1-r1.ebuild create mode 100644 sci-biology/meme/meme-4.8.1-r2.ebuild delete mode 100644 sci-biology/meme/meme-4.8.1.ebuild (limited to 'sci-biology/meme') 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 -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/meme-4.8.1-r1.ebuild b/sci-biology/meme/meme-4.8.1-r1.ebuild deleted file mode 100644 index 50c2f7fe6aee..000000000000 --- a/sci-biology/meme/meme-4.8.1-r1.ebuild +++ /dev/null @@ -1,83 +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-r1.ebuild,v 1.1 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-shells/tcsh - dev-libs/libxml2:2 - dev-libs/libxslt - 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) \ - $USE_DISABLE_MPI -} - -src_test() { - # bug #297070 - emake -j1 test -} - -src_install() { - default - - mv "${ED}"/usr/bin/{,meme-}tree || die - mv "${ED}"/usr/bin/{,meme-}readseq || die - - echo "PATH=/opt/${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.' -#} diff --git a/sci-biology/meme/meme-4.8.1-r2.ebuild b/sci-biology/meme/meme-4.8.1-r2.ebuild new file mode 100644 index 000000000000..abc810087e9a --- /dev/null +++ b/sci-biology/meme/meme-4.8.1-r2.ebuild @@ -0,0 +1,85 @@ +## 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-r2.ebuild,v 1.1 2013/03/01 12:43:54 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-shells/tcsh + dev-libs/libxml2:2 + dev-libs/libxslt + 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) \ + $USE_DISABLE_MPI +} + +src_test() { + # bug #297070 + emake -j1 test +} + +src_install() { + local i + default + + for i in "${ED}"/usr/bin/*; do + "${ED}"/usr/bin/{,meme-}${i} || die + done + + 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.' +#} 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.' -#} -- cgit v1.2.3-65-gdbad