sci-chemistry/gromacs-4.0.7-r1: InCvs

(Portage version: 2.1.7.16/git/Linux i686)
 (Signed Manifest commit)

4 files changed, 8 insertions, 286 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 3dfb69cc6..3ac34e8d0 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -3,6 +3,10 @@
 # $Header: $
 
   06 Feb 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  -gromacs-4.0.7-r1.ebuild, -files/gromacs-4.0.9999-docdir.patch:
+  InCvs
+
+  06 Feb 2010; Christoph Junghans <kleiner_otti@gmx.de>
   gromacs-4.0.9999.ebuild, gromacs-9999.ebuild:
   docdir patch went upstream
 
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 13551c401..dbb555f65 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -3,20 +3,17 @@ Hash: SHA1
 
 AUX gromacs-4.0.9999-ccache.patch 678 RMD160 043d0e207e04a275fe00a3bd2b28f8dc0dfd4b7f SHA1 08bc5ac8bc0b28f68e1ede994d49616dd920af5d SHA256 ca477d54351c418f1d39dda29373a1426c9403ec0d2f21c28fc7568227d47632
 AUX gromacs-4.0.9999-configure-gfortran.patch 760 RMD160 1700579b0c2dfb8cbb743d795aa9f0f9f467c06b SHA1 e6924d3598b20195fcb6809e64f333def5b0f919 SHA256 1a59dfde8a3db8db729bd19691a5945e02be2725fa66ec0b125ab3b931518761
-AUX gromacs-4.0.9999-docdir.patch 1352 RMD160 336ab23b4b65430caf3205650a8787e8e33d2137 SHA1 77e0cc966c4d755f603b2d0ab9a075c0ee6b7361 SHA256 8ead457b06f7f943455a95494be4648e539934699d29e955d2e05ac02f1ca4ef
 AUX gromacs-9999-install-mdrun.patch 1367 RMD160 3d8e15fbc2d5bc721b907d36584ce69ee452f185 SHA1 729f2f882115603c5300116015dc4594a868b547 SHA256 4335c6bf26be4a990aae30df6cfbcdca60bbef02388deab8f79d22e0e14a7258
 DIST gmxtest-4.0.4.tgz 14845017 RMD160 c7c583415438bdef4c9996da9064254e9460cf16 SHA1 998179aa2bfbc4f80514f10ed774762f85c854c3 SHA256 6a7f787f4bb7cbecb688115ff0854a5ffd2ef33487d7bce4b031e63848b6f361
-DIST gromacs-4.0.7.tar.gz 8404518 RMD160 4fa8e5c90f549ef627a98a907a166676692a4c4b SHA1 8519bef2fa989fb487d54612b0a2d0228f228b30 SHA256 048f8ece2829f01d99f7e04e1d6e8f88d3a32273192274f2e9fcf71f41f212c1
 DIST manual-4.0.pdf 2135100 RMD160 b963642f8e1433f11328c3d0c4b1645c9de506da SHA1 8ae951ee15b2a7dc626331fce36511bc8766144c SHA256 646f810477eee2d710de6019c52056550413d0ba77baf9680195c835ddafe80a
-EBUILD gromacs-4.0.7-r1.ebuild 6991 RMD160 cf1550034a70f7f24c72b84c0ef2a40eef161670 SHA1 61115908912949884fe2b4d9551f2fc07a4c56d8 SHA256 56a2cb9ca8f38d2230e9250f755739fb00521084b96e133205cc1375d09b75dc
 EBUILD gromacs-4.0.9999.ebuild 6857 RMD160 727af5d38f52f5db01f6185c7ca0a7c05191be21 SHA1 2d1988574567e9c19af1d5624e51055a6b39d199 SHA256 b2304948a62c4e42c048e7912b24354265901ce6d9e7ac260ee65fa5ed7f56f5
 EBUILD gromacs-9999.ebuild 6619 RMD160 1025fdb695c8df84162a4702183e612dd8d22503 SHA1 a057576d6cdfb281b60cee352354ad490a3fe2d4 SHA256 da08b5a57acd130ffb20b68cec595d715428b65906cc402957390c01cc338892
-MISC ChangeLog 3056 RMD160 e4d1ef62be7fc815842b876672ef5315c4a5e3cf SHA1 f446da07aa7c773c1e187f16cfa678ad62f3741b SHA256 b6fb2dbbb9a41906e5ba928dd2d5774051e4155e463cd85fedf7e38c4100a9a8
+MISC ChangeLog 3187 RMD160 bd26ab83cccd549bd454bc53476b6f85579ba80d SHA1 b0ab4b2ea07a1f80c8abe2f4fdddd29f55353be1 SHA256 e4ae8ba91d1ac71c5ce5fd7fa89d451dd41e18e1bcaf31864c8cf87ee700e16b
 MISC metadata.xml 580 RMD160 06a95696ec536dd91eab06946d8787546f1e0582 SHA1 b6c5f5e50b518efa3014b69f97307d62734a288d SHA256 e976e31a9e16e9eea09d5ec147ce91d16b4e463453e71ebfb8092485589a6b49
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diff --git a/sci-chemistry/gromacs/files/gromacs-4.0.9999-docdir.patch b/sci-chemistry/gromacs/files/gromacs-4.0.9999-docdir.patch
deleted file mode 100644
index e32ddec90..000000000
--- a/sci-chemistry/gromacs/files/gromacs-4.0.9999-docdir.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-diff -Naur gromacs-4.0.5.orig/share/html/Makefile.am gromacs-4.0.5/share/html/Makefile.am
---- gromacs-4.0.5.orig/share/html/Makefile.am	2006-03-06 10:52:20.000000000 +0100
-+++ gromacs-4.0.5/share/html/Makefile.am	2009-11-29 22:27:24.000000000 +0100
-@@ -4,7 +4,7 @@
- #
- SUBDIRS = .  images  online
- 
--htmldir = ${pkgdatadir}/html
-+htmldir = @htmldir@/html
- 
- html_DATA = online.html gmxfaq.html
- 
-diff -Naur gromacs-4.0.5.orig/share/html/images/Makefile.am gromacs-4.0.5/share/html/images/Makefile.am
---- gromacs-4.0.5.orig/share/html/images/Makefile.am	2006-03-06 10:52:20.000000000 +0100
-+++ gromacs-4.0.5/share/html/images/Makefile.am	2009-11-29 23:00:57.000000000 +0100
-@@ -2,7 +2,7 @@
- #
- # Don't edit - this file is generated automatically from Makefile.am
- #
--imagedir = ${pkgdatadir}/html/images
-+imagedir = @htmldir@/html/images
- 
- image_DATA = \
- 	features.gif					\
-diff -Naur gromacs-4.0.5.orig/share/html/online/Makefile.am gromacs-4.0.5/share/html/online/Makefile.am
---- gromacs-4.0.5.orig/share/html/online/Makefile.am	2008-08-11 11:46:17.000000000 +0200
-+++ gromacs-4.0.5/share/html/online/Makefile.am	2009-11-29 23:01:47.000000000 +0100
-@@ -2,7 +2,7 @@
- #
- # Don't edit - this file is generated automatically from Makefile.am
- #
--onlinedir = ${pkgdatadir}/html/online
-+onlinedir = @htmldir@/html/online
- 
- online_DATA = \
-   cpt.html	\
diff --git a/sci-chemistry/gromacs/gromacs-4.0.7-r1.ebuild b/sci-chemistry/gromacs/gromacs-4.0.7-r1.ebuild
deleted file mode 100644
index 4d2cd2607..000000000
--- a/sci-chemistry/gromacs/gromacs-4.0.7-r1.ebuild
+++ /dev/null
@@ -1,243 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.0.7.ebuild,v 1.2 2009/12/08 15:08:23 alexxy Exp $
-
-EAPI="2"
-
-LIBTOOLIZE="true"
-TEST_PV="4.0.4"
-
-inherit autotools bash-completion eutils fortran multilib
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-		test? ( ftp://ftp.gromacs.org/pub/tests/gmxtest-${TEST_PV}.tgz )
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86"
-IUSE="X blas dmalloc doc -double-precision +fftw fkernels +gsl lapack mpi +single-precision static test +xml zsh-completion"
-
-DEPEND="app-shells/tcsh
-	X? ( x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE )
-	dmalloc? ( dev-libs/dmalloc )
-	blas? ( virtual/blas )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mpi? ( virtual/mpi )
-	xml? ( dev-libs/libxml2 )"
-
-RDEPEND="${DEPEND}"
-
-RESTRICT="test"
-
-src_prepare() {
-
-	epatch "${FILESDIR}/${PN}-4.0.9999-docdir.patch"
-	epatch "${FILESDIR}/${PN}-4.0.9999-ccache.patch"
-	# Fix typos in a couple of files.
-	sed -e "s:+0f:-f:" -i share/tutor/gmxdemo/demo \
-		|| die "Failed to fixup demo script."
-
-	# Fix a sandbox violation that occurs when re-emerging with mpi.
-	sed "/libdir=\"\$(libdir)\"/ a\	temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed -e "s:\$\$libdir:\$temp_libdir:" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed "/libdir=\"\$(libdir)\"/ a\ temp_libdir=\"${D}usr/$( get_libdir )\" ; \\\\" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	sed -e "s:\$\$libdir:\$\$temp_libdir:" \
-	-i src/tools/Makefile.am \
-	|| die "sed tools/Makefile.am failed"
-
-	use fkernels && epatch "${FILESDIR}/${PN}-4.0.9999-configure-gfortran.patch"
-
-	eautoreconf
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" single"
-	use double-precision && GMX_DIRS+=" double"
-	for x in ${GMX_DIRS}; do
-		mkdir "${S}-${x}" || die
-		use test && cp -r "${WORKDIR}"/gmxtest "${S}-${x}"
-		use mpi || continue
-		mkdir "${S}-${x}_mpi" || die
-	done
-}
-
-src_configure() {
-	local myconf
-	local myconfsingle
-	local myconfdouble
-	local suffixdouble
-
-	#leave all assembly options enabled mdrun is smart enough to deside itself
-	#there so no gentoo on bluegene!
-	myconf="${myconf} --disable-bluegene"
-
-	#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 [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
-
-	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
-
-	#fortran will gone in gromacs 4.1 anyway
-	#note for gentoo-PREFIX on aix, fortran (xlf) is still much faster
-	if use fkernels; then
-		ewarn "Fortran kernels are usually not faster than C kernels and assembly"
-		ewarn "I hope, you know what are you doing..."
-		FORTRAN="g77 gfortran ifc"
-		myconf="${myconf} --enable-fortran" && fortran_pkg_setup
-	else
-		myconf="${myconf} --disable-fortran"
-	fi
-
-	# if we need external blas
-	if use blas; then
-		export LIBS="${LIBS} -lblas"
-		myconf="${myconf} $(use_with blas external-blas)"
-	fi
-
-	# if we need external lapack
-	if use lapack; then
-		export LIBS="${LIBS} -llapack"
-		myconf="${myconf} $(use_with lapack external-lapack)"
-	fi
-
-	# by default its better to have dynamicaly linked binaries
-	if use static; then
-		myconf="${myconf} $(use_enable static all-static)"
-	else
-		myconf="${myconf} --enable-shared"
-	fi
-
-	myconf="--datadir=/usr/share \
-			--bindir=/usr/bin \
-			--libdir=/usr/$(get_libdir) \
-			--docdir=/usr/share/doc/"${PF}" \
-			$(use_with dmalloc) \
-			$(use_with fftw fft fftw3) \
-			$(use_with gsl) \
-			$(use_with X x) \
-			$(use_with xml) \
-			${myconf}"
-
-	#if we build single and double - double is suffixed
-	if ( use double-precision && use single-precision ); then
-		suffixdouble="_d"
-	else
-		suffixdouble=""
-	fi
-
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
-	myconfdouble="${myconf} --enable-double --program-suffix='${suffixdouble}'"
-	myconfsingle="${myconf} --enable-float --program-suffix=''"
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		cd "${S}-${x}"
-		local p=myconf${x}
-		ECONF_SOURCE="${S}" econf ${!p} --disable-mpi
-		use mpi || continue
-		cd "${S}-${x}_mpi"
-		ECONF_SOURCE="${S}" econf ${!p} --enable-mpi
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		cd "${S}-${x}"
-		einfo "Compiling for ${x} precision"
-		emake || die "emake for ${x} precision failed"
-		use mpi || continue
-		cd "${S}-${x}_mpi"
-		emake mdrun || die "emake mdrun for ${x} precision failed"
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		local oldpath="${PATH}"
-		export PATH="${S}-${x}/src/kernel:${S}-{x}/src/tools:${PATH}"
-		cd "${S}-${x}"
-		emake -j1 tests || die "${x} Precision test failed"
-		export PATH="${oldpath}"
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		cd "${S}-${x}"
-		emake DESTDIR="${D}" install || die "emake install for ${x} failed"
-		use mpi || continue
-		cd "${S}-${x}_mpi"
-		emake DESTDIR="${D}" install-mdrun || die "emake install-mdrun for ${x} failed"
-	done
-
-	sed -n -e '/^GMXBIN/,/^GMXDATA/p' "${D}"/usr/bin/GMXRC.bash > "${T}/80gromacs"
-	doenvd "${T}/80gromacs"
-	rm -f "${D}"/usr/bin/GMXRC*
-
-	dobashcompletion "${D}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${D}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -r "${D}"/usr/bin/completion.*
-
-	cd "${S}"
-	dodoc AUTHORS INSTALL README
-	use doc && dodoc "${DISTDIR}"/manual-4.0.pdf
-}
-
-pkg_postinst() {
-	env-update && source /etc/profile
-	elog
-	elog "Please read and cite:"
-	elog "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	elog "http://dx.doi.org/10.1021/ct700301q"
-	elog
-	bash-completion_pkg_postinst
-	elog
-	elog $(luck)
-	elog "For more Gromacs cool quotes (gcq) add luck to your .bashrc"
-	elog
-}