remove old (fixes bug #392121)

Package-Manager: portage-2.2.0_alpha90/cvs/Linux i686

4 files changed, 21 insertions, 263 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index c4295e44c6ed..c3b053776947 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 1.106 2012/03/08 23:04:42 ranger Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.107 2012/03/09 00:59:11 ottxor Exp $
+
+  09 Mar 2012; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.4-r1.ebuild,
+  metadata.xml:
+  remove old (fixes bug #392121)
 
   08 Mar 2012; Brent Baude <ranger@gentoo.org> gromacs-4.5.5-r1.ebuild:
   Marking gromacs-4.5.5-r1 ppc64 for bug 391147
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 9fe16e1ee16d..2d3fdc28c996 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,12 +1,24 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX gromacs-4.5.5-cmake-cpp-asm.patch 2051 RMD160 dbb99d916aa7826de84e4621e7e6728759f0484f SHA1 55c0bf200891045680e5aed897386b18f37c0283 SHA256 b83f9252187caa3647a44166004191454257d8d187f2a3fb883824814b5379d4
 AUX gromacs-4.5.5-enable-see.patch 1916 RMD160 7867c9a9ea0720f0c0bb7f52021e0c417464044d SHA1 05fd406d35001d196edee3628397ffe4b0b32e9c SHA256 bd4cbe8b46de33c0a62cd7234265b3e27c6363959f4b97aad447ef18c4e16bb3
 DIST 0001-Make-stack-non-executable-for-GAS-assembly.patch.gz 3569527 RMD160 862efb96bee960f4bab4ce726d2524529bddde81 SHA1 a1d01348b421a1209d25d558ba6e0d8762c595f0 SHA256 17a948d221b67faeaf635a0b5ee9564067bc261e9279294c0c7c58ae9580ae5f
 DIST 0002-Make-stack-non-executable-for-ATT-assembly.patch.gz 3868244 RMD160 1b98ad7a1216b78aaa04f6f83a04d8be94cf234c SHA1 bc2a2ab012e42189710d6a38798add01e7813003 SHA256 af12b3632aaf4e3d0c49ce99e0a4ed5de61c40d293bc592b70f89e08738f2581
 DIST gmxtest-4.0.4.tgz 14845017 RMD160 c7c583415438bdef4c9996da9064254e9460cf16 SHA1 998179aa2bfbc4f80514f10ed774762f85c854c3 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361
-DIST gromacs-4.5.4.tar.gz 10353984 RMD160 96065d1a173231f75869764a08eb4feccc1ec597 SHA1 c7b3fbd2f3ddf915bc082e7effe76a8276563726 SHA256 301cc3d790f5036e230e02b1fb03c9b92e0db13df7ac6dbffb2a2fb03d7a1d1c
 DIST gromacs-4.5.5.tar.gz 10398178 RMD160 a3d40c3ac6ec9ee3e4607bd35afca1dd4715154e SHA1 ce4b4f9a0453dd2ffea72f28ea0bc7bb7a72f479 SHA256 e0605e4810b0d552a8761fef5540c545beeaf85893f4a6e21df9905a33f871ba
 DIST gromacs-manual-4.5.4.pdf 2463242 RMD160 309a1d9bc5f4821076d53f668c36f1c6bfc1714f SHA1 58c0261308212af29fa0c4f4a6d1b81da6d84766 SHA256 dc14504a7072b61e7aa576c48f04df03356824f3a9d9e744dfaf51529ab46252
-EBUILD gromacs-4.5.4-r1.ebuild 8073 RMD160 5a049f3ffb92c5842b3e1babc47e172db7fcaf78 SHA1 93e0ba7ca84bf9ffd06aa726f77cec9b9a4ede21 SHA256 8b06b2a5361d7a3d858f286350c8c6fd1fb8130642ca1f9418096fe93a17790a
 EBUILD gromacs-4.5.5-r1.ebuild 7904 RMD160 3f4d05933ec6c81c11e8749c5faf4245bbb14c8e SHA1 5f07aa52110aec8eb4b57f98ab985e4ff64dd460 SHA256 b47d5ce9dabc3d6770b62ec4b2a9680b4e4edcfcfe6d9481ba2cdec019b19d35
-MISC ChangeLog 18038 RMD160 c4393aa3092f0af9398500cbe874648d5c64694f SHA1 93616bc78f0f5517b72a53143eb8adf57cd0c350 SHA256 7f710f4713651ab77b781a17ae0ec6b8caea74e2a69a84b81ec599a18e8cefa2
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diff --git a/sci-chemistry/gromacs/gromacs-4.5.4-r1.ebuild b/sci-chemistry/gromacs/gromacs-4.5.4-r1.ebuild
deleted file mode 100644
index d68fbf406be2..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.5.4-r1.ebuild
+++ /dev/null
@@ -1,257 +0,0 @@
-# Copyright 1999-2012 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-r1.ebuild,v 1.13 2012/02/06 03:43:24 ottxor Exp $
-
-EAPI="4"
-
-LIBTOOLIZE="true"
-TEST_PV="4.0.4"
-MANUAL_PV="4.5.4"
-
-inherit autotools-utils bash-completion-r1 flag-o-matic 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-${TEST_PV}.tgz )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 ppc64 x86 ~amd64-linux ~x86-linux"
-IUSE="X altivec blas dmalloc doc -double-precision +fftw fkernels +gsl lapack
-mpi +single-precision sse2 static-libs test +threads +xml zsh-completion"
-REQUIRED_USE="fkernels? ( !threads )"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	dmalloc? ( dev-libs/dmalloc )
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	fkernels? ( virtual/fortran )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2:2 )"
-DEPEND="${CDEPEND}
-	dev-util/pkgconfig"
-RDEPEND="${CDEPEND}
-	app-shells/tcsh"
-
-RESTRICT="test"
-
-pkg_setup() {
-	use fkernels && fortran-2_pkg_setup
-}
-
-src_prepare() {
-	if use mpi && use threads; then
-		elog "mdrun uses only threads OR mpi, and gromacs favours the"
-		elog "use of mpi over threads, so a mpi-version of mdrun will"
-		elog "be compiled. If you want to run mdrun on shared memory"
-		elog "machines only, you can safely disable mpi"
-	fi
-
-	# Add patches for non-exec stack
-	epatch "${WORKDIR}/0001-Make-stack-non-executable-for-GAS-assembly.patch"
-	epatch "${WORKDIR}/0002-Make-stack-non-executable-for-ATT-assembly.patch"
-
-	autotools-utils_src_prepare || die
-
-	eautoreconf || die
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-	#if neither single-precision nor double-precision is enabled
-	#build at least default (single)
-	[ -z "$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() {
-	#from gromacs configure
-	if ! use fftw; then
-		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
-
-	#fortran will gone in gromacs 5.0 anyway
-	#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
-
-	# if we need external blas or lapack
-	use blas && append-libs $(pkg-config blas --libs)
-	use lapack && append-libs $(pkg-config lapack --libs)
-	local sseflag="x86-64-sse"
-	use x86 && sseflag="ia32-sse"
-
-	#missing flag in autotools (bug #339837)
-	use sse2 && append-flags -msse2
-
-	for x in ${GMX_DIRS}; do
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[ "${x}" = "double" ] && suffix="_d"
-		myeconfargs=(
-			--bindir="${EPREFIX}"/usr/bin
-			--docdir="${EPREFIX}"/usr/share/doc/"${PF}"
-			--enable-"${x}"
-			$(use_with dmalloc)
-			$(use_with fftw fft fftw3)
-			$(use_with gsl)
-			$(use_with X x)
-			$(use_with xml)
-			$(use_enable threads)
-			$(use_enable altivec ppc-altivec)
-			$(use_enable ia64 ia64-asm)
-			$(use_with lapack external-lapack)
-			$(use_with blas external-blas)
-			$(use_enable fkernels fortran)
-			--disable-bluegene
-			--disable-la-files
-			--disable-power6
-			--disable-ia32-sse
-			--disable-x86-64-sse
-			$(use_enable sse2 $sseflag)
-		)
-		#disable ia32-sse and x86-64-sse and enable what we really need in last line
-
-		einfo "Configuring for ${x} precision"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			autotools-utils_src_configure --disable-mpi	--program-suffix="${suffix}" \
-			CC="$(tc-getCC)" F77="$(tc-getFC)"
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			autotools-utils_src_configure --enable-mpi --program-suffix="_mpi${suffix}" \
-			CC="$(tc-getCC)" F77="$(tc-getFC)"
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			autotools-utils_src_compile
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			autotools-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 ${GMX_DIRS}; do
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			autotools-utils_src_install
-		use mpi || continue
-		#autotools-utils_src_install does not support args
-		#using autotools-utils_src_compile instead
-		AUTOTOOLS_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			autotools-utils_src_compile install-mdrun DESTDIR="${D}"
-
-		#stolen from autotools-utils_src_install see comment above
-		local args
-		has static-libs ${IUSE//+} && ! use	static-libs || args='none'
-		remove_libtool_files ${args}
-	done
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${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() {
-	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/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index ac6daa0746fa..44b30a77c485 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -3,7 +3,6 @@
 <pkgmetadata>
 	<herd>sci-chemistry</herd>
 	<use>
-		<flag name="dmalloc">Enable use of Debug Malloc</flag>
 		<flag name="double-precision">More precise calculations at the expense of speed</flag>
 		<flag name="fkernels">Enable building of Fortran Kernels for platforms
 	  that dont have assembly loops</flag>