From: "Justin Lecher (jlec)" <jlec@gentoo.org>
To: gentoo-commits@lists.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
Date: Fri, 6 Mar 2015 10:07:11 +0000 (UTC) [thread overview]
Message-ID: <20150306100711.C31EF13281@oystercatcher.gentoo.org> (raw)
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 @@
</maintainer>
<herd>sci-chemistry</herd>
<use>
+ <flag name="cuda">Use nvidia cuda toolkit for speeding up computations</flag>
+ <flag name="gromacs">Add support for TNG file format</flag>
<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>
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 <jlec@gentoo.org>
+ +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 <patrick@gentoo.org> -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
}
reply other threads:[~2015-03-06 10:07 UTC|newest]
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