From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 2E255138CA3 for ; Fri, 6 Mar 2015 10:07:20 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id B4C68E08F3; Fri, 6 Mar 2015 10:07:18 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 3BCC1E08F3 for ; Fri, 6 Mar 2015 10:07:18 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id C7846340693 for ; Fri, 6 Mar 2015 10:07:16 +0000 (UTC) Received: by oystercatcher.gentoo.org (Postfix, from userid 2264) id C31EF13281; Fri, 6 Mar 2015 10:07:11 +0000 (UTC) From: "Justin Lecher (jlec)" To: gentoo-commits@lists.gentoo.org Reply-To: gentoo-dev@lists.gentoo.org, jlec@gentoo.org Subject: [gentoo-commits] gentoo-x86 commit in sci-chemistry/vmd: metadata.xml vmd-1.9.2.ebuild ChangeLog vmd-1.9.1.ebuild vmd-1.9.1-r2.ebuild X-VCS-Repository: gentoo-x86 X-VCS-Files: metadata.xml vmd-1.9.2.ebuild ChangeLog vmd-1.9.1.ebuild vmd-1.9.1-r2.ebuild X-VCS-Directories: sci-chemistry/vmd X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit Message-Id: <20150306100711.C31EF13281@oystercatcher.gentoo.org> Date: Fri, 6 Mar 2015 10:07:11 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: d1bddf8c-0b9a-400e-aedd-5884edaa9c6b X-Archives-Hash: 32bdd7116e1440de8ca184db2b253c60 jlec 15/03/06 10:07:11 Modified: metadata.xml ChangeLog Added: vmd-1.9.2.ebuild Removed: vmd-1.9.1.ebuild vmd-1.9.1-r2.ebuild Log: Version BUmp; install optional plugins, #517886 (Portage version: 2.2.18/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!) Revision Changes Path 1.9 sci-chemistry/vmd/metadata.xml file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/vmd/metadata.xml?rev=1.9&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/vmd/metadata.xml?rev=1.9&content-type=text/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/vmd/metadata.xml?r1=1.8&r2=1.9 Index: metadata.xml =================================================================== RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/metadata.xml,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- metadata.xml 11 Jan 2013 09:29:35 -0000 1.8 +++ metadata.xml 6 Mar 2015 10:07:11 -0000 1.9 @@ -7,9 +7,10 @@ sci-chemistry + Use nvidia cuda toolkit for speeding up computations + Add support for TNG file format Add support for MSMS SAS calcualtion tool Add support for povray raytracer for HQ images Add support for tachyon raytracer for HQ images - Use nvidia cuda toolkit for speeding up computations 1.61 sci-chemistry/vmd/ChangeLog file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/vmd/ChangeLog?rev=1.61&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/vmd/ChangeLog?rev=1.61&content-type=text/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/vmd/ChangeLog?r1=1.60&r2=1.61 Index: ChangeLog =================================================================== RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v retrieving revision 1.60 retrieving revision 1.61 diff -u -r1.60 -r1.61 --- ChangeLog 10 Feb 2015 02:23:22 -0000 1.60 +++ ChangeLog 6 Mar 2015 10:07:11 -0000 1.61 @@ -1,6 +1,13 @@ # ChangeLog for sci-chemistry/vmd # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.60 2015/02/10 02:23:22 patrick Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.61 2015/03/06 10:07:11 jlec Exp $ + +*vmd-1.9.2 (06 Mar 2015) + + 06 Mar 2015; Justin Lecher + +files/vmd-1.9.2-format-security.patch, +vmd-1.9.2.ebuild, + -vmd-1.9.1-r2.ebuild, -vmd-1.9.1.ebuild, metadata.xml: + Version BUmp; install optional plugins, #517886 10 Feb 2015; Patrick Lauer -vmd-1.9.1-r1.ebuild: Remove version with unsatisfiable dependencies 1.1 sci-chemistry/vmd/vmd-1.9.2.ebuild file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/vmd/vmd-1.9.2.ebuild?rev=1.1&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/vmd/vmd-1.9.2.ebuild?rev=1.1&content-type=text/plain Index: vmd-1.9.2.ebuild =================================================================== # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.9.2.ebuild,v 1.1 2015/03/06 10:07:11 jlec Exp $ EAPI=5 PYTHON_COMPAT=( python2_7 ) inherit cuda eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs DESCRIPTION="Visual Molecular Dynamics" HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" SRC_URI=" http://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz ${P}.src.tar.gz" SLOT="0" LICENSE="vmd" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="cuda gromacs msms povray sqlite tachyon xinerama" RESTRICT="fetch" # currently, tk-8.5* with USE=truetype breaks some # tk apps such as Sequence Viewer or Timeline. CDEPEND=" || ( =dev-lang/tk-8.5*:0=[-truetype] >=dev-lang/tk-8.6.1 ) dev-lang/perl dev-libs/expat dev-python/numpy[${PYTHON_USEDEP}] sci-libs/netcdf virtual/opengl >=x11-libs/fltk-1.1.10-r2:1 x11-libs/libXft x11-libs/libXi cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1[tng] ) sqlite? ( dev-db/sqlite:3= ) tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) xinerama? ( x11-libs/libXinerama )" DEPEND="${CDEPEND} virtual/pkgconfig dev-lang/swig" RDEPEND="${CDEPEND} sci-biology/stride sci-chemistry/surf x11-terms/xterm msms? ( sci-chemistry/msms-bin ) povray? ( media-gfx/povray ) " VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" # Binary only plugin!! QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" pkg_nofetch() { elog "Please download ${P}.src.tar.gz from" elog "${VMD_DOWNLOAD}" elog "after agreeing to the license and get" elog "http://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" elog "Place both in ${DISTDIR}" } src_prepare() { use cuda && cuda_sanitize epatch "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch cd "${WORKDIR}"/plugins || die epatch \ "${WORKDIR}"/${P}-gentoo-plugins.patch \ "${FILESDIR}"/${P}-format-security.patch [[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) sed \ -e "s:CC = gcc:CC = $(tc-getCC):" \ -e "s:CXX = g++:CXX = $(tc-getCXX):" \ -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ -e "s:-ltcl8.5:-ltcl:" \ -i Make-arch || die "Failed to set up plugins Makefile" sed \ -e '/^AR /s:=:?=:g' \ -e '/^RANLIB /s:=:?=:g' \ -i ../plugins/*/Makefile || die tc-export AR RANLIB sed \ -e "s:\$(CXXFLAGS)::g" \ -i hesstrans/Makefile || die # prepare vmd itself cd "${S}" || die epatch "${WORKDIR}"/${P}-gentoo-base.patch # PREFIX sed \ -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ -i configure || die sed \ -e "s:gentoo-bindir:${ED}/usr/bin:g" \ -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ -e "s:gentoo-gcc:$(tc-getCC):g" \ -e "s:gentoo-g++:$(tc-getCXX):g" \ -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ -e "s:gentoo-cflags:${CFLAGS}:g" \ -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ -e "s:gentoo-nvflags::g" \ -e "s:gentoo-ldflags:${LDFLAGS}:g" \ -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ -i configure || die if use cuda; then sed \ -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ -i configure src/Makefile || die sed \ -e '/compute_/d' \ -i configure || die sed \ -e 's:-gencode .*code=sm_..::' \ -i src/Makefile || die fi sed \ -e "s:LINUXPPC:LINUX:g" \ -e "s:LINUXALPHA:LINUX:g" \ -e "s:LINUXAMD64:LINUX:g" \ -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" EMAKEOPTS=( TCLINC="-I${EPREFIX}/usr/include" TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" TCLLDFLAGS="-shared" NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf) ${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf) ${EPREFIX}/usr/include" NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" NETCDFDYNAMIC=1 EXPATINC="-I${EPREFIX}/usr/include" EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" EXPATLDFLAGS="-shared" EXPATDYNAMIC=1 ) if use gromacs; then EMAKEOPTS+=( TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" TNGINC="-I${EPREFIX}/usr/include" TNGLDFLAGS="-shared" TNGDYNAMIC=1 ) fi if use sqlite; then EMAKEOPTS+=( SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" SQLITEINC="-I${EPREFIX}/usr/include" SQLITELDFLAGS="-shared" SQLITEDYNAMIC=1 ) fi } src_configure() { local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" rm -f configure.options && echo $myconf >> configure.options use cuda && myconf+=" CUDA" # use mpi && myconf+=" MPI" use tachyon && myconf+=" LIBTACHYON" && append-cflags -I"${EPREFIX}/usr/include/tachyon" use xinerama && myconf+=" XINERAMA" export \ PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ PYTHON_LIBRARY="$(python_get_LIBS)" \ NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" perl ./configure LINUX \ ${myconf} || die } src_compile() { # build plugins cd "${WORKDIR}"/plugins || die emake \ ${EMAKEOPTS[@]} \ LINUX # build vmd cd "${S}"/src || die emake } src_install() { # install plugins cd "${WORKDIR}"/plugins || die emake \ PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ distrib # install vmd cd "${S}"/src || die emake install # install docs cd "${S}" || die dodoc Announcement README doc/ig.pdf doc/ug.pdf # remove some of the things we don't want and need in # /usr/lib cd "${ED}"/usr/$(get_libdir)/vmd || die rm -fr doc README Announcement LICENSE || \ die "failed to clean up /usr/lib/vmd directory" # adjust path in vmd wrapper sed \ -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ || die "failed to set up vmd wrapper script" # install icon and generate desktop entry insinto /usr/share/pixmaps doins "${WORKDIR}"/vmd.png eprefixify "${WORKDIR}"/vmd.desktop sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die domenu "${WORKDIR}"/vmd.desktop }