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vmd: Fix netcdf config, bug #406737

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1 parent 1b506b2 commit 260e6409c2209a794657ed50a21a68d9cb895602 @Reinis Reinis committed Oct 22, 2012
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  1. +10 −0 sci-chemistry/vmd/ChangeLog
  2. +2 −0 sci-chemistry/vmd/Manifest
  3. +15 −0 sci-chemistry/vmd/metadata.xml
  4. +215 −0 sci-chemistry/vmd/vmd-1.9.1.ebuild
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+# ChangeLog for sci-chemistry/vmd
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*vmd-1.9.1 (22 Oct 2012)
+
+ 22 Oct 2012; Reinis Danne <rei4dan@gmail.com> +vmd-1.9.1.ebuild,
+ +metadata.xml:
+ Fix netcdf config, bug #406737.
@jlec
jlec Oct 22, 2012 Gentoo Science Project member

Thanks for all the great help in fixing bugs. Could you please drop a message in the corresponding bugs, so that we can move your work to the tree?

+
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+DIST vmd-1.9.1-gentoo-patches.tar.xz 79240 SHA256 60fe1b017b1aed5cdd4a417d4a2dbd20f75eae24c83d1da68c504a31bfbdbcd8 SHA512 37856d5e00d3d4452324865190aef4ac05a7a49cbddffe83f568d3190b521f17e6e1e5323dee3127aadfb446ec0871bfd06dff47d640ed862547710ec4b0a421 WHIRLPOOL b3eebffe24a96ad1c7ce9ebc565e1b88d6f52894569a6d72c22e87fb3d6975d14779bd8c4305e3e9f2ecf9d981503b8bcea78a476a1a66eb37b78c759b3bdf60
+DIST vmd-1.9.1.src.tar.gz 30748110 SHA256 54aa88e03d86d763383e7b98592a152c9d68e78383e13af0dd2aca09b002491f SHA512 a54cb08e8a9ce801c2ca986f746bff0a041a25d5cffebc8d4af50813b6c05d04a3209a27830d580287230edaf3048a78923ae54bf367ab69c3d81388ab1787bd WHIRLPOOL 26d2a855c0768583cd45aed105fdd8f1ef59d59b8ce11c1903f5fc2008ea05989b8a32a0d817725e711613f8abfc22bb5301f20ea8d597efe9c7913790b25bb7
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer>
+ <email>alexxy@gentoo.org</email>
+ <name>Alexey Shvetsov</name>
+ </maintainer>
+ <herd>sci-chemistry</herd>
+ <use>
+ <flag name='msms'>Add support for MSMS SAS calcualtion tool</flag>
+ <flag name='povray'>Add support for povray raytracer for HQ images</flag>
+ <flag name='tachyon'>Add support for tachyon raytracer for HQ images</flag>
+ <flag name='cuda'>Use nvidia cuda toolkit for speeding up computations</flag>
+ </use>
+</pkgmetadata>
@@ -0,0 +1,215 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="5"
+
+PYTHON_DEPEND="2"
+
+inherit eutils multilib python toolchain-funcs
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+SRC_URI="
+ mirror://gentoo/${P}-gentoo-patches.tar.xz
+ ${P}.src.tar.gz"
+
+SLOT="0"
+LICENSE="vmd"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cuda msms povray tachyon xinerama"
+
+RESTRICT="fetch"
+
+# currently, tk-8.5* with USE=truetype breaks some
+# tk apps such as Sequence Viewer or Timeline.
+CDEPEND="
+ || (
+ >=dev-lang/tk-8.5[-truetype]
+ =dev-lang/tk-8.4*
+ )
+ dev-lang/perl
+ dev-python/numpy
+ sci-libs/netcdf
+ virtual/opengl
+ >=x11-libs/fltk-1.1.10-r2:1
+ x11-libs/libXft
+ x11-libs/libXi
+ cuda? ( >=dev-util/nvidia-cuda-toolkit-3.1 )
+ xinerama? ( x11-libs/libXinerama )"
+DEPEND="${CDEPEND}
+ dev-lang/swig"
+RDEPEND="${CDEPEND}
+ sci-biology/stride
+ sci-chemistry/surf
+ x11-terms/xterm
+ msms? ( sci-chemistry/msms-bin )
+ povray? ( media-gfx/povray )
+ tachyon? ( media-gfx/tachyon )"
+
+VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
+# Binary only plugin!!
+QA_TEXTRELS="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+QA_PRESTRIPPED="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+QA_FLAGS_IGNORED_amd64="
+ usr/lib64/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so
+ usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
+QA_FLAGS_IGNORED_x86="
+ usr/lib/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so
+ 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 ${DISTDIR}"
+}
+
+src_prepare() {
+ cd "${WORKDIR}"/plugins
+
+ epatch "${WORKDIR}"/${P}-gentoo-plugins.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 = $(tc-getCXX) -shared:" \
+ -e "s:-ltcl8.5:-ltcl:" \
+ -i Make-arch || die "Failed to set up plugins Makefile"
+
+ sed \
+ -e "s:\$(CXXFLAGS)::g" \
+ -i hesstrans/Makefile || die
+
+ # prepare vmd itself
+ cd "${S}"
+
+ 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: -O3 -v: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
+
+# local NUMPY_INCLUDE="numpy/core/include"
+# sed -e "s:gentoo-python-include:${EPREFIX}$(python_get_includedir):" \
+# -e "s:gentoo-python-lib:${EPREFIX}$(python_get_libdir):" \
+# -e "s:gentoo-python-link:$(PYTHON):" \
+# -e "s:gentoo-numpy-include:${EPREFIX}$(python_get_sitedir)/${NUMPY_INCLUDE}:" \
+# -i configure || die "failed setting up python"
+
+ if use cuda; then
+ local gcc44_bindir="$(ls -d ${EPREFIX}/usr/*pc-linux-gnu/gcc-bin/4.4*)"
+
+ sed \
+ -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
+ -e "/^\$arch_nvccflags/s:=:= \"--compiler-bindir=${gcc44_bindir} \" . \n:1" \
+ -i configure || 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"
+}
+
+src_configure() {
+ local myconf="OPENGL FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
+ rm -f configure.options && echo $myconf >> configure.options
+
+ use cuda && myconf+=" CUDA"
+# use mpi && myconf+=" MPI"
+# use tachion && myconf+=" LIBTACHYON"
+ use xinerama && myconf+=" XINERAMA"
+
+ export \
+ PYTHON_INCLUDE_DIR="${EPREFIX}$(python_get_includedir)" \
+ PYTHON_LIBRARY_DIR="${EPREFIX}$(python_get_libdir)" \
+ PYTHON_LIBRARY="$(python_get_library -l)" \
+ NUMPY_INCLUDE_DIR="${EPREFIX}$(python_get_sitedir)/numpy/core/include" \
+ NUMPY_LIBRARY_DIR="${EPREFIX}$(python_get_sitedir)/numpy/core/include"
+
+ ./configure LINUX \
+ ${myconf} || die
+}
+
+src_compile() {
+ # build plugins
+ cd "${WORKDIR}"/plugins
+
+ emake \
+ TCLINC="-I${EPREFIX}/usr/include" \
+ TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" \
+ NETCDFLIB="$(pkg-config --libs-only-L netcdf) ${EPREFIX}/usr/lib64/libnetcdf.so" \
+ NETCDFINC="$(pkg-config --cflags-only-I netcdf) ${EPREFIX}/usr/include" \
+ NETCDFLDFLAGS="$(pkg-config --libs netcdf)" \
+ LINUX
+
+ # build vmd
+ cd "${S}"/src
+ emake
+}
+
+src_install() {
+ # install plugins
+ cd "${WORKDIR}"/plugins
+ emake \
+ PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
+ distrib
+
+ # install vmd
+ cd "${S}"/src
+ emake install
+
+ # install docs
+ cd "${S}"
+ dodoc Announcement README doc/ig.pdf doc/ug.pdf
+
+ # remove some of the things we don't want and need in
+ # /usr/lib
+ cd "${ED}"/usr/$(get_libdir)/vmd
+ rm -fr doc README Announcement LICENSE || \
+ die "failed to clean up /usr/lib/vmd directory"
+
+ # adjust path in vmd wrapper
+ sed \
+ -e "s:${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 "${WORKDIR}"/vmd.png
+ domenu "${WORKDIR}"/vmd.desktop
+}

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