remove obsolete

(Portage version: 2.2.0_alpha84/cvs/Linux i686)

3 files changed, 5 insertions, 491 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 0a50f170f547..a0716e8c8d63 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.102 2012/01/06 02:16:45 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.103 2012/01/06 02:21:02 ottxor Exp $
+
+  06 Jan 2012; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.4-r2.ebuild,
+  -gromacs-4.5.5.ebuild:
+  remove obsolete
 
   06 Jan 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.5-r1.ebuild:
   keyword ~x86-macos
diff --git a/sci-chemistry/gromacs/gromacs-4.5.4-r2.ebuild b/sci-chemistry/gromacs/gromacs-4.5.4-r2.ebuild
deleted file mode 100644
index bbcf8ae6fd31..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.5.4-r2.ebuild
+++ /dev/null
@@ -1,245 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.4-r2.ebuild,v 1.8 2011/09/10 14:47:53 ottxor Exp $
-
-EAPI="4"
-
-TEST_PV="4.0.4"
-MANUAL_PV="4.5.4"
-
-#to find external blas/lapack
-CMAKE_MIN_VERSION="2.8.5-r2"
-
-inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
-
-if [ "${PV%9999}" != "${PV}" ]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
-	EGIT_BRANCH="release-4-5-patches"
-	inherit git-2
-else
-	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
-fi
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="${SRC_URI}
-		http://dev.gentoo.org/~alexxy/gromacs/0001-Make-stack-non-executable-for-GAS-assembly.patch.gz
-		http://dev.gentoo.org/~alexxy/gromacs/0002-Make-stack-non-executable-for-ATT-assembly.patch.gz
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )
-		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux"
-IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
-mpi +single-precision sse2 test +threads xml zsh-completion"
-REQUIRED_USE="fkernels? ( !threads )"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	fkernels? ( virtual/fortran )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2:2 )"
-DEPEND="${CDEPEND}
-	dev-util/pkgconfig"
-RDEPEND="${CDEPEND}
-	app-shells/tcsh"
-
-RESTRICT="test"
-
-pkg_setup() {
-	use fkernels && fortran-2_pkg_setup
-}
-
-src_prepare() {
-	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
-	epatch_user
-
-	if use mpi && use threads; then
-		elog "mdrun uses only threads OR mpi, and gromacs favours the"
-		elog "use of mpi over threads, so a mpi-version of mdrun will"
-		elog "be compiled. If you want to run mdrun on shared memory"
-		elog "machines only, you can safely disable mpi"
-	fi
-
-	# Add patches for non-exec stack
-	epatch "${WORKDIR}/0001-Make-stack-non-executable-for-GAS-assembly.patch"
-	epatch "${WORKDIR}/0002-Make-stack-non-executable-for-ATT-assembly.patch"
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-	#if neither single-precision nor double-precision is enabled
-	#build at least default (single)
-	[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
-
-	for x in ${GMX_DIRS}; do
-		mkdir -p "${WORKDIR}/${P}_${x}" || die
-		use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
-	done
-}
-
-src_configure() {
-	local mycmakeargs_pre=( )
-	#from gromacs configure
-	if use fftw; then
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
-	else
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
-	fi
-
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
-
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-	fi
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
-	#go from slowest to fasterest acceleration
-	local acce="none"
-	use fkernels && acce="fortran"
-	use altivec && acce="altivec"
-	use ia64 && acce="ia64"
-	use sse2 && acce="sse"
-
-	mycmakeargs_pre+=(
-		$(cmake-utils_use X GMX_X11)
-		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use gsl GMX_GSL)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use threads GMX_THREADS)
-		$(cmake-utils_use xml GMX_XML)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_ACCELERATION="$acce"
-		-DLIB="$(get_libdir)"
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[ "${x}" = "double" ] && suffix="_d"
-		local p
-		[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile mdrun
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		local oldpath="${PATH}"
-		export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
-		cd "${WORKDIR}/${P}_${x}"
-		emake -j1 tests || die "${x} Precision test failed"
-		export PATH="${oldpath}"
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		use mpi || continue
-		#cmake-utils_src_install does not support args
-		#using cmake-utils_src_compile instead
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_make install-mdrun DESTDIR="${D}"
-	done
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
-
-	doenvd "${T}/80gromacs"
-	rm -f "${ED}"/usr/bin/GMXRC*
-
-	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${ED}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -f "${ED}"/usr/bin/completion.*
-
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL* README*
-	if use doc; then
-		newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
-		dohtml -r "${ED}usr/share/gromacs/html/"
-	fi
-	rm -rf "${ED}usr/share/gromacs/html/"
-}
-
-pkg_postinst() {
-	env-update && source /etc/profile
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	einfo
-	einfo  $(g_luck)
-	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
-	einfo
-	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
diff --git a/sci-chemistry/gromacs/gromacs-4.5.5.ebuild b/sci-chemistry/gromacs/gromacs-4.5.5.ebuild
deleted file mode 100644
index 4a70357d3bb8..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.5.5.ebuild
+++ /dev/null
@@ -1,245 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.5.5.ebuild,v 1.4 2011/12/14 16:45:32 ago Exp $
-
-EAPI="4"
-
-TEST_PV="4.0.4"
-MANUAL_PV="4.5.4"
-
-#to find external blas/lapack
-CMAKE_MIN_VERSION="2.8.5-r2"
-
-inherit bash-completion-r1 cmake-utils eutils fortran-2 multilib toolchain-funcs
-
-if [ "${PV%9999}" != "${PV}" ]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs"
-	EGIT_BRANCH="release-4-5-patches"
-	inherit git-2
-else
-	SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz"
-fi
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="${SRC_URI}
-		http://dev.gentoo.org/~alexxy/gromacs/0001-Make-stack-non-executable-for-GAS-assembly.patch.gz
-		http://dev.gentoo.org/~alexxy/gromacs/0002-Make-stack-non-executable-for-ATT-assembly.patch.gz
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> gromacs-manual-${MANUAL_PV}.pdf )
-		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha amd64 ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux"
-IUSE="X altivec blas doc -double-precision +fftw fkernels gsl lapack
-mpi +single-precision sse2 test +threads xml zsh-completion"
-REQUIRED_USE="fkernels? ( !threads )"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	fkernels? ( virtual/fortran )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2:2 )"
-DEPEND="${CDEPEND}
-	dev-util/pkgconfig"
-RDEPEND="${CDEPEND}
-	app-shells/tcsh"
-
-RESTRICT="test"
-
-pkg_setup() {
-	use fkernels && fortran-2_pkg_setup
-}
-
-src_prepare() {
-	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
-	epatch_user
-
-	if use mpi && use threads; then
-		elog "mdrun uses only threads OR mpi, and gromacs favours the"
-		elog "use of mpi over threads, so a mpi-version of mdrun will"
-		elog "be compiled. If you want to run mdrun on shared memory"
-		elog "machines only, you can safely disable mpi"
-	fi
-
-	# Add patches for non-exec stack
-	epatch "${WORKDIR}/0001-Make-stack-non-executable-for-GAS-assembly.patch"
-	epatch "${WORKDIR}/0002-Make-stack-non-executable-for-ATT-assembly.patch"
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-	#if neither single-precision nor double-precision is enabled
-	#build at least default (single)
-	[ -z "$GMX_DIRS" ] && GMX_DIRS+=" float"
-
-	for x in ${GMX_DIRS}; do
-		mkdir -p "${WORKDIR}/${P}_${x}" || die
-		use test && cp -r "${WORKDIR}"/gmxtest "${WORKDIR}/${P}_${x}"
-	done
-}
-
-src_configure() {
-	local mycmakeargs_pre=( )
-	#from gromacs configure
-	if use fftw; then
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
-	else
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
-	fi
-
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
-
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-	fi
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
-	#go from slowest to fasterest acceleration
-	local acce="none"
-	use fkernels && acce="fortran"
-	use altivec && acce="altivec"
-	use ia64 && acce="ia64"
-	use sse2 && acce="sse"
-
-	mycmakeargs_pre+=(
-		$(cmake-utils_use X GMX_X11)
-		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use gsl GMX_GSL)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use threads GMX_THREADS)
-		$(cmake-utils_use xml GMX_XML)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_ACCELERATION="$acce"
-		-DGMXLIB="$(get_libdir)"
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[ "${x}" = "double" ] && suffix="_d"
-		local p
-		[ "${x}" = "double" ] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" cmake-utils_src_configure
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile mdrun
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		local oldpath="${PATH}"
-		export PATH="${WORKDIR}/${P}_${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
-		cd "${WORKDIR}/${P}_${x}"
-		emake -j1 tests || die "${x} Precision test failed"
-		export PATH="${oldpath}"
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		use mpi || continue
-		#cmake-utils_src_install does not support args
-		#using cmake-utils_src_compile instead
-		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_make install-mdrun DESTDIR="${D}"
-	done
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${ED}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	echo "VMD_PLUGIN_PATH=${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" >> "${T}/80gromacs"
-
-	doenvd "${T}/80gromacs"
-	rm -f "${ED}"/usr/bin/GMXRC*
-
-	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${ED}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -f "${ED}"/usr/bin/completion.*
-
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i "${ED}"usr/share/gromacs/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL* README*
-	if use doc; then
-		newdoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" "manual-${MANUAL_PV}.pdf"
-		dohtml -r "${ED}usr/share/gromacs/html/"
-	fi
-	rm -rf "${ED}usr/share/gromacs/html/"
-}
-
-pkg_postinst() {
-	env-update && source /etc/profile
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "http://dx.doi.org/10.1021/ct700301q"
-	einfo
-	einfo  $(g_luck)
-	einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
-	einfo
-	elog  "Gromacs can use sci-chemistry/vmd to read additional file formats"
-}