* [gentoo-commits] proj/sci:master commit in: sci-chemistry/vmd/
@ 2012-11-26 22:02 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2012-11-26 22:02 UTC (permalink / raw
To: gentoo-commits
commit: d875fdfad6c699a8d163ac702afb1bd07d2775e4
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 26 12:10:39 2012 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 26 14:41:09 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d875fdfa
Imported from tree
---
sci-chemistry/vmd/ChangeLog | 235 +++++++++++++++++++++++++++++++++
sci-chemistry/vmd/metadata.xml | 15 ++
sci-chemistry/vmd/vmd-1.9.1-r1.ebuild | 230 ++++++++++++++++++++++++++++++++
3 files changed, 480 insertions(+), 0 deletions(-)
diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
new file mode 100644
index 0000000..cfca6cc
--- /dev/null
+++ b/sci-chemistry/vmd/ChangeLog
@@ -0,0 +1,235 @@
+# ChangeLog for sci-chemistry/vmd
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.50 2012/11/14 15:18:58 jlec Exp $
+
+*vmd-1.9.1-r1 (14 Nov 2012)
+
+ 14 Nov 2012; Justin Lecher <jlec@gentoo.org> +vmd-1.9.1-r1.ebuild:
+ Fix detection of netcdf; #406737, thanks Reinis Danne preparing the patch;
+ Loosen dep for cuda support, #406083
+
+ 24 Sep 2012; Mike Frysinger <vapier@gentoo.org> vmd-1.9.1.ebuild:
+ QA_DT_HASH (old/deprecated) -> QA_FLAGS_IGNORED (new hotness).
+
+ 05 Sep 2012; Justin Lecher <jlec@gentoo.org> -vmd-1.8.7-r2.ebuild,
+ -vmd-1.9.ebuild, vmd-1.9.1.ebuild:
+ Bumped to EAPI=4; use domenu; drop old
+
+ 14 Feb 2012; Alexey Shvetsov <alexxy@gentoo.org> vmd-1.9.1.ebuild:
+ Fix plugin install
+
+*vmd-1.9.1 (14 Feb 2012)
+
+ 14 Feb 2012; Alexey Shvetsov <alexxy@gentoo.org> +vmd-1.9.1.ebuild:
+ Version bump =D
+
+ 10 Jan 2012; Justin Lecher <jlec@gentoo.org> vmd-1.9.ebuild:
+ Remove USE=static-libs because this breaks build, #365051
+
+ 10 Jan 2012; Justin Lecher <jlec@gentoo.org> vmd-1.9.ebuild, metadata.xml:
+ Enhance nofetch msg, fix compilation with USE=cuda and gcc != 4.4*, thanks
+ xarthisius for the help
+
+ 20 Jul 2011; Pacho Ramos <pacho@gentoo.org> metadata.xml:
+ Drop maintainer due retirement, bug #105599
+
+ 15 Jun 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild,
+ vmd-1.9.ebuild:
+ FILESDIR is gone, wverything is mirrored now.
+
+ 13 Jun 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild,
+ vmd-1.9.ebuild:
+ Mirrored files aren't fetchrestricted
+
+ 13 Jun 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild,
+ -files/vmd-1.8.7-gentoo.patch, -files/vmd-1.8.7-respect-flags.patch,
+ vmd-1.9.ebuild, -files/vmd-1.9-gentoo-base.patch,
+ -files/vmd-1.9-gentoo-plugins.patch, -files/vmd.desktop, -files/vmd.png:
+ No binaryfiles in VCS please, #370915
+
+ 27 Mar 2011; Justin Lecher <jlec@gentoo.org> vmd-1.9.ebuild:
+ Correct version of cuda dep, #360401
+
+*vmd-1.9 (22 Mar 2011)
+
+ 22 Mar 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild,
+ +vmd-1.9.ebuild, +files/vmd-1.9-gentoo-base.patch,
+ +files/vmd-1.9-gentoo-plugins.patch, metadata.xml:
+ Version Bump, #358981; Dropped ppc due to missing KEYWORDS in DEPs
+
+ 22 Mar 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild:
+ Restrict fltk version being able to return includedir
+
+ 20 Mar 2011; Justin Lecher <jlec@gentoo.org> -vmd-1.8.7-r1.ebuild,
+ vmd-1.8.7-r2.ebuild:
+ x11-libs/fltk SLOTMOVE 1.1 -> 1, corrected ebuild accordingly
+
+ 11 Dec 2010; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild:
+ QA on quoting
+
+ 30 Oct 2010; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild:
+ Corrected msms DEP to sci-chemistry/msms-bin
+
+ 21 Aug 2010; Alexey Shvetsov <alexxy@gentoo.org> vmd-1.8.7-r2.ebuild,
+ metadata.xml:
+ Add msms and povray to RDEPS as per bug #293504
+
+*vmd-1.8.7-r2 (27 Jul 2010)
+
+ 27 Jul 2010; Justin Lecher <jlec@gentoo.org>
+ -files/vmd-1.8.5-config-gentoo.patch,
+ -files/vmd-1.8.6-config-gentoo.patch,
+ -files/vmd-1.8.6-fix-crash-on-tcl8.5.patch,
+ -files/vmd-1.8.6-python-2.5.patch, -files/vmd-1.8.6-tcltk8.5.patch,
+ vmd-1.8.7-r1.ebuild, +vmd-1.8.7-r2.ebuild, -files/vmd-1.8.7-config.patch,
+ files/vmd-1.8.7-gentoo.patch, +files/vmd-1.8.7-respect-flags.patch,
+ -files/vmd-1.8.7-use-bash-startup.patch:
+ Make it really prefix ready, don't mix CFLAGS/CXXFLAGS,clean old patches
+
+ 24 Jul 2010; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r1.ebuild:
+ Added prefix changes, thanks rei4dan #327517; keyworded for ~-linux prefix
+
+ 28 May 2010; Justin Lecher <jlec@gentoo.org> -vmd-1.8.6.ebuild,
+ -vmd-1.8.6-r1.ebuild, -vmd-1.8.7.ebuild:
+ Removed all non PythonABI compatible ebuilds
+
+*vmd-1.8.7-r1 (18 May 2010)
+
+ 18 May 2010; Justin Lecher <jlec@gentoo.org> +vmd-1.8.7-r1.ebuild,
+ files/vmd-1.8.7-config.patch, +files/vmd-1.8.7-gentoo.patch:
+ Fix for new python ABIs, #316187; building netcdf plugin, #306893, thanks
+ Kamil Kisiel for the patch; LDFLAGS are respected now; EAPI=3 and basic
+ fixes for prefix, usability has to be tested
+
+ 23 Feb 2010; Alexey Shvetsov <alexxy@gentoo.org> vmd-1.8.6-r1.ebuild,
+ vmd-1.8.7.ebuild, metadata.xml:
+ add tachyon raytracer as rdep
+
+ 18 Sep 2009; Petteri Räty <betelgeuse@gentoo.org> vmd-1.8.7.ebuild:
+ Remove built_with_use and use proper DEPEND atoms that work properly for
+ both tk 8.4 and 8.5 users.
+
+ 11 Aug 2009; Markus Dittrich <markusle@gentoo.org> vmd-1.8.7.ebuild,
+ +files/vmd.desktop, +files/vmd.png:
+ Added desktop entry and vmd icon (#262275).
+ Thanks much to Bjoern Olausson for creating them.
+
+ 07 Aug 2009; Markus Dittrich <markusle@gentoo.org> vmd-1.8.7.ebuild,
+ files/vmd-1.8.7-config.patch:
+ Remove the EAPI2 check for -truetype and add explicit error logic
+ so tk-8.4 users can emerge vmd as well. Also updated the config
+ patch to handle tk8.4 better.
+
+*vmd-1.8.7 (05 Aug 2009)
+
+ 05 Aug 2009; Markus Dittrich <markusle@gentoo.org> +vmd-1.8.7.ebuild,
+ +files/vmd-1.8.7-config.patch, +files/vmd-1.8.7-use-bash-startup.patch:
+ Version bump (fixes bug #262275).
+
+ 07 Jul 2009; Diego E. Pettenò <flameeyes@gentoo.org> vmd-1.8.6-r1.ebuild:
+ Use elog for fetch error.
+
+ 18 May 2009; Jeff Gardner <je_fro@gentoo.org>
+ +files/vmd-1.8.6-fix-crash-on-tcl8.5.patch:
+ adding alexxy's patch :)
+
+ 17 May 2009; Jeff Gardner <je_fro@gentoo.org> +vmd-1.8.6-r1.ebuild:
+ Fixed by alexxy to work with tcl8.5
+
+*vmd-1.8.6-r1 (17 May 2009)
+
+ 17 May 2009; Jeff Gardner <je_fro@gentoo.org> +vmd-1.8.6-r1.ebuild:
+ Fixed by alexxy to work with tcl5.8
+
+ 12 Nov 2008; Markus Dittrich <markusle@gentoo.org> -vmd-1.8.5.ebuild,
+ vmd-1.8.6.ebuild:
+ Restrict fltk to 1.1 slot since vmd is not fltk-2 ready
+ (see bug #246445). Removed old ebuild.
+
+ 13 Mar 2008; Markus Dittrich <markusle@gentoo.org>
+ +files/vmd-1.8.6-tcltk8.5.patch, vmd-1.8.6.ebuild:
+ Added tcltk-8.5 support (fixes bug #212936).
+
+ 20 Sep 2007; Markus Dittrich <markusle@gentoo.org>
+ +files/vmd-1.8.6-python-2.5.patch, vmd-1.8.6.ebuild:
+ Added patch to fix python-2.5 compile issues on amd64 (fixes bug
+ #192902). Thanks much to milan hodoscek <milan@cmm.ki.si> for his
+ patch.
+
+ 22 Jul 2007; Donnie Berkholz <dberkholz@gentoo.org>; vmd-1.8.5.ebuild,
+ vmd-1.8.6.ebuild:
+ Drop virtual/x11 references.
+
+*vmd-1.8.6 (15 Apr 2007)
+
+ 15 Apr 2007; Markus Dittrich <markusle@gentoo.org>
+ -files/vmd-1.8.4-config-gentoo.patch, -files/vmd-1.8.4-paratool.patch,
+ -files/vmd-1.8.4-plugin-autopsf.patch,
+ +files/vmd-1.8.6-config-gentoo.patch, +vmd-1.8.6.ebuild:
+ Version bump (fixes bug #174595). Thanks much to Jeffrey Gardner
+ <je_fro@gentoo.org> for his patch and ebuild.
+
+ 08 Jan 2007; Danny van Dyk <kugelfang@gentoo.org> -vmd-1.8.4.ebuild,
+ -vmd-1.8.4-r1.ebuild:
+ QA: Removed unused versions.
+
+ 07 Jan 2007; Markus Dittrich <markusle@gentoo.org> vmd-1.8.5.ebuild:
+ Replaced backslashes with colons in some sed statements
+ (see bug #145467).
+
+ 03 Jan 2007; Jeff Gardner <je_fro@gentoo.org> vmd-1.8.5.ebuild:
+ added ~amd64
+
+ 27 Dec 2006; Markus Dittrich <markusle@gentoo.org> vmd-1.8.5.ebuild:
+ Remove netcdf use flag and enable netcdf support by default
+ since it is needed by the catdcd plugin. This fixes bug #159081.
+
+ 22 Dec 2006; Markus Dittrich <markusle@gentoo.org>
+ files/vmd-1.8.5-config-gentoo.patch, vmd-1.8.5.ebuild:
+ Added netcdf support. This fixes bug #158771.
+
+ 09 Nov 2006; Markus Dittrich <markusle@gentoo.org> vmd-1.8.5.ebuild:
+ Enabled IMD functionality. Thanks to Stephane Gagne
+ <sgagne@rsvs.ulaval.ca> for pointing this out (see bug #154429).
+
+ 20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
+ (#148281) Change herd to sci-chemistry from sci.
+
+*vmd-1.8.5 (26 Aug 2006)
+
+ 26 Aug 2006; Markus Dittrich <markusle@gentoo.org>
+ -files/vmd-1.8.3-config-gentoo.patch,
+ +files/vmd-1.8.5-config-gentoo.patch, -vmd-1.8.3.ebuild,
+ +vmd-1.8.5.ebuild:
+ Version bump. Also removed some of the old ebuilds.
+
+*vmd-1.8.4-r1 (13 Aug 2006)
+
+ 13 Aug 2006; Markus Dittrich <markusle@gentoo.org>
+ +files/vmd-1.8.4-paratool.patch, +vmd-1.8.4-r1.ebuild:
+ VMD now depends on stride in order to properly display secondary
+ structure information. Also patched a paratool plugin error under
+ tcl-8.4.13.
+
+ 29 Apr 2006; Marien Zwart <marienz@gentoo.org> Manifest:
+ Fix SHA256 digests.
+
+*vmd-1.8.4 (18 Apr 2006)
+
+ 18 Apr 2006; Markus Dittrich <markusle@gentoo.org>
+ +files/vmd-1.8.4-config-gentoo.patch,
+ +files/vmd-1.8.4-plugin-autopsf.patch, +vmd-1.8.4.ebuild:
+ Version bump.
+
+ 21 Mar 2006; Donnie Berkholz <spyderous@gentoo.org>; vmd-1.8.3.ebuild:
+ Keyword ~ppc, and make changes to the wrapper script that may also fix amd64
+ and alpha.
+
+ 14 Feb 2006; Markus Dittrich <markusle@gentoo.org> Manifest:
+ Fixed bogus .Chanlog.swp file entry in Manifest.
+
+*vmd-1.8.3 (10 Feb 2006)
+
+ 10 Feb 2006; Markus Dittrich <markusle@gentoo.org>
+ +files/vmd-1.8.3-config-gentoo.patch, +metadata.xml, +vmd-1.8.3.ebuild:
+ Initial import.
diff --git a/sci-chemistry/vmd/metadata.xml b/sci-chemistry/vmd/metadata.xml
new file mode 100644
index 0000000..be76141
--- /dev/null
+++ b/sci-chemistry/vmd/metadata.xml
@@ -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>
diff --git a/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild
new file mode 100644
index 0000000..dc38b98
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild
@@ -0,0 +1,230 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild,v 1.1 2012/11/14 15:18:58 jlec Exp $
+
+EAPI=5
+
+PYTHON_DEPEND="2"
+
+inherit eutils multilib prefix python toolchain-funcs
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+SRC_URI="
+ http://dev.gentoo.org/~jlec/distifles/${P}-gentoo-patches-2.tar.xz
+ ${P}.src.tar.gz"
+
+SLOT="0"
+LICENSE="vmd"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cuda msms povray tachyon xinerama"
+
+RESTRICT="fetch"
+
+# currently, tk-8.5* with USE=truetype breaks some
+# tk apps such as Sequence Viewer or Timeline.
+CDEPEND="
+ || (
+ >=dev-lang/tk-8.5[-truetype]
+ =dev-lang/tk-8.4*
+ )
+ dev-lang/perl
+ dev-python/numpy
+ sci-libs/netcdf
+ virtual/opengl
+ >=x11-libs/fltk-1.1.10-r2:1
+ x11-libs/libXft
+ x11-libs/libXi
+ cuda? (
+ >=dev-util/nvidia-cuda-toolkit-3.1
+ || (
+ sys-devel/gcc:4.4
+ sys-devel/gcc:4.5 )
+ )
+ xinerama? ( x11-libs/libXinerama )"
+DEPEND="${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_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-2.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 = $(tc-getCXX) -shared:" \
+ -e "s:-ltcl8.5:-ltcl:" \
+ -i Make-arch || die "Failed to set up plugins Makefile"
+
+ sed \
+ -e '/^AR /s:=:?=:g' \
+ -e '/^RANLIB /s:=:?=:g' \
+ -i ../plugins/*/Makefile || die
+
+ tc-export AR RANLIB
+
+ sed \
+ -e "s:\$(CXXFLAGS)::g" \
+ -i hesstrans/Makefile || die
+
+ # prepare vmd itself
+ cd "${S}"
+
+ 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 gcc_bindir
+ if has_version sys-devel/gcc:4.5; then
+ gcc_bindir="$(ls -d ${EPREFIX}/usr/*pc-linux-gnu/gcc-bin/4.5*)"
+ elif has_version sys-devel/gcc:4.4; then
+ gcc_bindir="$(ls -d ${EPREFIX}/usr/*pc-linux-gnu/gcc-bin/4.4*)"
+ else
+ ewarn "Please install gcc with a version between 4.4* and 4.5*"
+ fi
+
+ sed \
+ -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
+ -e "/^\$arch_nvccflags/s:=:= \"--compiler-bindir=${gcc_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 "${WORKDIR}"/vmd.png
+ eprefixify "${WORKDIR}"/vmd.desktop
+ domenu "${WORKDIR}"/vmd.desktop
+}
^ permalink raw reply related [flat|nested] 7+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-chemistry/vmd/
@ 2013-01-14 7:11 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2013-01-14 7:11 UTC (permalink / raw
To: gentoo-commits
commit: df3026d93bc5980f71284d27b0290004625e8c26
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jan 11 13:48:56 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jan 11 13:48:56 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=df3026d9
moved to tree
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
---
sci-chemistry/vmd/ChangeLog | 244 ---------------------------------
sci-chemistry/vmd/metadata.xml | 15 --
sci-chemistry/vmd/vmd-1.9.1-r1.ebuild | 226 ------------------------------
3 files changed, 0 insertions(+), 485 deletions(-)
diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
deleted file mode 100644
index 296c399..0000000
--- a/sci-chemistry/vmd/ChangeLog
+++ /dev/null
@@ -1,244 +0,0 @@
-# ChangeLog for sci-chemistry/vmd
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.50 2012/11/14 15:18:58 jlec Exp $
-
- 23 Dec 2012; Christoph Junghans <ottxor@gentoo.org> vmd-1.9.1-r1.ebuild:
- fix build with !cuda and python=3 + qa
-
- 29 Nov 2012; Justin Lecher <jlec@gentoo.org> vmd-1.9.1-r1.ebuild:
- Drop dep on old tk
-
- 26 Nov 2012; Justin Lecher <jlec@gentoo.org> vmd-1.9.1-r1.ebuild:
- Using new cuda.eclass
-
-*vmd-1.9.1-r1 (14 Nov 2012)
-
- 14 Nov 2012; Justin Lecher <jlec@gentoo.org> +vmd-1.9.1-r1.ebuild:
- Fix detection of netcdf; #406737, thanks Reinis Danne preparing the patch;
- Loosen dep for cuda support, #406083
-
- 24 Sep 2012; Mike Frysinger <vapier@gentoo.org> vmd-1.9.1.ebuild:
- QA_DT_HASH (old/deprecated) -> QA_FLAGS_IGNORED (new hotness).
-
- 05 Sep 2012; Justin Lecher <jlec@gentoo.org> -vmd-1.8.7-r2.ebuild,
- -vmd-1.9.ebuild, vmd-1.9.1.ebuild:
- Bumped to EAPI=4; use domenu; drop old
-
- 14 Feb 2012; Alexey Shvetsov <alexxy@gentoo.org> vmd-1.9.1.ebuild:
- Fix plugin install
-
-*vmd-1.9.1 (14 Feb 2012)
-
- 14 Feb 2012; Alexey Shvetsov <alexxy@gentoo.org> +vmd-1.9.1.ebuild:
- Version bump =D
-
- 10 Jan 2012; Justin Lecher <jlec@gentoo.org> vmd-1.9.ebuild:
- Remove USE=static-libs because this breaks build, #365051
-
- 10 Jan 2012; Justin Lecher <jlec@gentoo.org> vmd-1.9.ebuild, metadata.xml:
- Enhance nofetch msg, fix compilation with USE=cuda and gcc != 4.4*, thanks
- xarthisius for the help
-
- 20 Jul 2011; Pacho Ramos <pacho@gentoo.org> metadata.xml:
- Drop maintainer due retirement, bug #105599
-
- 15 Jun 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild,
- vmd-1.9.ebuild:
- FILESDIR is gone, wverything is mirrored now.
-
- 13 Jun 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild,
- vmd-1.9.ebuild:
- Mirrored files aren't fetchrestricted
-
- 13 Jun 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild,
- -files/vmd-1.8.7-gentoo.patch, -files/vmd-1.8.7-respect-flags.patch,
- vmd-1.9.ebuild, -files/vmd-1.9-gentoo-base.patch,
- -files/vmd-1.9-gentoo-plugins.patch, -files/vmd.desktop, -files/vmd.png:
- No binaryfiles in VCS please, #370915
-
- 27 Mar 2011; Justin Lecher <jlec@gentoo.org> vmd-1.9.ebuild:
- Correct version of cuda dep, #360401
-
-*vmd-1.9 (22 Mar 2011)
-
- 22 Mar 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild,
- +vmd-1.9.ebuild, +files/vmd-1.9-gentoo-base.patch,
- +files/vmd-1.9-gentoo-plugins.patch, metadata.xml:
- Version Bump, #358981; Dropped ppc due to missing KEYWORDS in DEPs
-
- 22 Mar 2011; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild:
- Restrict fltk version being able to return includedir
-
- 20 Mar 2011; Justin Lecher <jlec@gentoo.org> -vmd-1.8.7-r1.ebuild,
- vmd-1.8.7-r2.ebuild:
- x11-libs/fltk SLOTMOVE 1.1 -> 1, corrected ebuild accordingly
-
- 11 Dec 2010; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild:
- QA on quoting
-
- 30 Oct 2010; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r2.ebuild:
- Corrected msms DEP to sci-chemistry/msms-bin
-
- 21 Aug 2010; Alexey Shvetsov <alexxy@gentoo.org> vmd-1.8.7-r2.ebuild,
- metadata.xml:
- Add msms and povray to RDEPS as per bug #293504
-
-*vmd-1.8.7-r2 (27 Jul 2010)
-
- 27 Jul 2010; Justin Lecher <jlec@gentoo.org>
- -files/vmd-1.8.5-config-gentoo.patch,
- -files/vmd-1.8.6-config-gentoo.patch,
- -files/vmd-1.8.6-fix-crash-on-tcl8.5.patch,
- -files/vmd-1.8.6-python-2.5.patch, -files/vmd-1.8.6-tcltk8.5.patch,
- vmd-1.8.7-r1.ebuild, +vmd-1.8.7-r2.ebuild, -files/vmd-1.8.7-config.patch,
- files/vmd-1.8.7-gentoo.patch, +files/vmd-1.8.7-respect-flags.patch,
- -files/vmd-1.8.7-use-bash-startup.patch:
- Make it really prefix ready, don't mix CFLAGS/CXXFLAGS,clean old patches
-
- 24 Jul 2010; Justin Lecher <jlec@gentoo.org> vmd-1.8.7-r1.ebuild:
- Added prefix changes, thanks rei4dan #327517; keyworded for ~-linux prefix
-
- 28 May 2010; Justin Lecher <jlec@gentoo.org> -vmd-1.8.6.ebuild,
- -vmd-1.8.6-r1.ebuild, -vmd-1.8.7.ebuild:
- Removed all non PythonABI compatible ebuilds
-
-*vmd-1.8.7-r1 (18 May 2010)
-
- 18 May 2010; Justin Lecher <jlec@gentoo.org> +vmd-1.8.7-r1.ebuild,
- files/vmd-1.8.7-config.patch, +files/vmd-1.8.7-gentoo.patch:
- Fix for new python ABIs, #316187; building netcdf plugin, #306893, thanks
- Kamil Kisiel for the patch; LDFLAGS are respected now; EAPI=3 and basic
- fixes for prefix, usability has to be tested
-
- 23 Feb 2010; Alexey Shvetsov <alexxy@gentoo.org> vmd-1.8.6-r1.ebuild,
- vmd-1.8.7.ebuild, metadata.xml:
- add tachyon raytracer as rdep
-
- 18 Sep 2009; Petteri Räty <betelgeuse@gentoo.org> vmd-1.8.7.ebuild:
- Remove built_with_use and use proper DEPEND atoms that work properly for
- both tk 8.4 and 8.5 users.
-
- 11 Aug 2009; Markus Dittrich <markusle@gentoo.org> vmd-1.8.7.ebuild,
- +files/vmd.desktop, +files/vmd.png:
- Added desktop entry and vmd icon (#262275).
- Thanks much to Bjoern Olausson for creating them.
-
- 07 Aug 2009; Markus Dittrich <markusle@gentoo.org> vmd-1.8.7.ebuild,
- files/vmd-1.8.7-config.patch:
- Remove the EAPI2 check for -truetype and add explicit error logic
- so tk-8.4 users can emerge vmd as well. Also updated the config
- patch to handle tk8.4 better.
-
-*vmd-1.8.7 (05 Aug 2009)
-
- 05 Aug 2009; Markus Dittrich <markusle@gentoo.org> +vmd-1.8.7.ebuild,
- +files/vmd-1.8.7-config.patch, +files/vmd-1.8.7-use-bash-startup.patch:
- Version bump (fixes bug #262275).
-
- 07 Jul 2009; Diego E. Pettenò <flameeyes@gentoo.org> vmd-1.8.6-r1.ebuild:
- Use elog for fetch error.
-
- 18 May 2009; Jeff Gardner <je_fro@gentoo.org>
- +files/vmd-1.8.6-fix-crash-on-tcl8.5.patch:
- adding alexxy's patch :)
-
- 17 May 2009; Jeff Gardner <je_fro@gentoo.org> +vmd-1.8.6-r1.ebuild:
- Fixed by alexxy to work with tcl8.5
-
-*vmd-1.8.6-r1 (17 May 2009)
-
- 17 May 2009; Jeff Gardner <je_fro@gentoo.org> +vmd-1.8.6-r1.ebuild:
- Fixed by alexxy to work with tcl5.8
-
- 12 Nov 2008; Markus Dittrich <markusle@gentoo.org> -vmd-1.8.5.ebuild,
- vmd-1.8.6.ebuild:
- Restrict fltk to 1.1 slot since vmd is not fltk-2 ready
- (see bug #246445). Removed old ebuild.
-
- 13 Mar 2008; Markus Dittrich <markusle@gentoo.org>
- +files/vmd-1.8.6-tcltk8.5.patch, vmd-1.8.6.ebuild:
- Added tcltk-8.5 support (fixes bug #212936).
-
- 20 Sep 2007; Markus Dittrich <markusle@gentoo.org>
- +files/vmd-1.8.6-python-2.5.patch, vmd-1.8.6.ebuild:
- Added patch to fix python-2.5 compile issues on amd64 (fixes bug
- #192902). Thanks much to milan hodoscek <milan@cmm.ki.si> for his
- patch.
-
- 22 Jul 2007; Donnie Berkholz <dberkholz@gentoo.org>; vmd-1.8.5.ebuild,
- vmd-1.8.6.ebuild:
- Drop virtual/x11 references.
-
-*vmd-1.8.6 (15 Apr 2007)
-
- 15 Apr 2007; Markus Dittrich <markusle@gentoo.org>
- -files/vmd-1.8.4-config-gentoo.patch, -files/vmd-1.8.4-paratool.patch,
- -files/vmd-1.8.4-plugin-autopsf.patch,
- +files/vmd-1.8.6-config-gentoo.patch, +vmd-1.8.6.ebuild:
- Version bump (fixes bug #174595). Thanks much to Jeffrey Gardner
- <je_fro@gentoo.org> for his patch and ebuild.
-
- 08 Jan 2007; Danny van Dyk <kugelfang@gentoo.org> -vmd-1.8.4.ebuild,
- -vmd-1.8.4-r1.ebuild:
- QA: Removed unused versions.
-
- 07 Jan 2007; Markus Dittrich <markusle@gentoo.org> vmd-1.8.5.ebuild:
- Replaced backslashes with colons in some sed statements
- (see bug #145467).
-
- 03 Jan 2007; Jeff Gardner <je_fro@gentoo.org> vmd-1.8.5.ebuild:
- added ~amd64
-
- 27 Dec 2006; Markus Dittrich <markusle@gentoo.org> vmd-1.8.5.ebuild:
- Remove netcdf use flag and enable netcdf support by default
- since it is needed by the catdcd plugin. This fixes bug #159081.
-
- 22 Dec 2006; Markus Dittrich <markusle@gentoo.org>
- files/vmd-1.8.5-config-gentoo.patch, vmd-1.8.5.ebuild:
- Added netcdf support. This fixes bug #158771.
-
- 09 Nov 2006; Markus Dittrich <markusle@gentoo.org> vmd-1.8.5.ebuild:
- Enabled IMD functionality. Thanks to Stephane Gagne
- <sgagne@rsvs.ulaval.ca> for pointing this out (see bug #154429).
-
- 20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
- (#148281) Change herd to sci-chemistry from sci.
-
-*vmd-1.8.5 (26 Aug 2006)
-
- 26 Aug 2006; Markus Dittrich <markusle@gentoo.org>
- -files/vmd-1.8.3-config-gentoo.patch,
- +files/vmd-1.8.5-config-gentoo.patch, -vmd-1.8.3.ebuild,
- +vmd-1.8.5.ebuild:
- Version bump. Also removed some of the old ebuilds.
-
-*vmd-1.8.4-r1 (13 Aug 2006)
-
- 13 Aug 2006; Markus Dittrich <markusle@gentoo.org>
- +files/vmd-1.8.4-paratool.patch, +vmd-1.8.4-r1.ebuild:
- VMD now depends on stride in order to properly display secondary
- structure information. Also patched a paratool plugin error under
- tcl-8.4.13.
-
- 29 Apr 2006; Marien Zwart <marienz@gentoo.org> Manifest:
- Fix SHA256 digests.
-
-*vmd-1.8.4 (18 Apr 2006)
-
- 18 Apr 2006; Markus Dittrich <markusle@gentoo.org>
- +files/vmd-1.8.4-config-gentoo.patch,
- +files/vmd-1.8.4-plugin-autopsf.patch, +vmd-1.8.4.ebuild:
- Version bump.
-
- 21 Mar 2006; Donnie Berkholz <spyderous@gentoo.org>; vmd-1.8.3.ebuild:
- Keyword ~ppc, and make changes to the wrapper script that may also fix amd64
- and alpha.
-
- 14 Feb 2006; Markus Dittrich <markusle@gentoo.org> Manifest:
- Fixed bogus .Chanlog.swp file entry in Manifest.
-
-*vmd-1.8.3 (10 Feb 2006)
-
- 10 Feb 2006; Markus Dittrich <markusle@gentoo.org>
- +files/vmd-1.8.3-config-gentoo.patch, +metadata.xml, +vmd-1.8.3.ebuild:
- Initial import.
diff --git a/sci-chemistry/vmd/metadata.xml b/sci-chemistry/vmd/metadata.xml
deleted file mode 100644
index be76141..0000000
--- a/sci-chemistry/vmd/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?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>
diff --git a/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild
deleted file mode 100644
index 259c60c..0000000
--- a/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild
+++ /dev/null
@@ -1,226 +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/vmd/vmd-1.9.1-r1.ebuild,v 1.1 2012/11/14 15:18:58 jlec Exp $
-
-EAPI=5
-
-PYTHON_DEPEND="2"
-
-inherit cuda eutils multilib prefix python toolchain-funcs
-
-DESCRIPTION="Visual Molecular Dynamics"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
-SRC_URI="
- http://dev.gentoo.org/~jlec/distifles/${P}-gentoo-patches-2.tar.xz
- ${P}.src.tar.gz"
-
-SLOT="0"
-LICENSE="vmd"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cuda msms povray tachyon xinerama"
-
-RESTRICT="fetch"
-
-# currently, tk-8.5* with USE=truetype breaks some
-# tk apps such as Sequence Viewer or Timeline.
-CDEPEND="
- >=dev-lang/tk-8.5[-truetype]
- dev-lang/perl
- dev-python/numpy
- sci-libs/netcdf
- virtual/opengl
- >=x11-libs/fltk-1.1.10-r2:1
- x11-libs/libXft
- x11-libs/libXi
- cuda? (
- >=dev-util/nvidia-cuda-toolkit-3.1
- || (
- sys-devel/gcc:4.4
- sys-devel/gcc:4.5 )
- )
- xinerama? ( x11-libs/libXinerama )"
-DEPEND="${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_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-2.tar.xz"
- elog "Place both in ${DISTDIR}"
-}
-
-pkg_setup() {
- python_set_active_version 2
- python_pkg_setup
-}
-
-src_prepare() {
- use cuda && cuda_sanitize
-
- cd "${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 = $(tc-getCXX) -shared:" \
- -e "s:-ltcl8.5:-ltcl:" \
- -i Make-arch || die "Failed to set up plugins Makefile"
-
- sed \
- -e '/^AR /s:=:?=:g' \
- -e '/^RANLIB /s:=:?=:g' \
- -i ../plugins/*/Makefile || die
-
- tc-export AR RANLIB
-
- sed \
- -e "s:\$(CXXFLAGS)::g" \
- -i hesstrans/Makefile || die
-
- # prepare vmd itself
- cd "${S}"
-
- 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
-
-# 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
- sed \
- -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
- -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
- -i configure src/Makefile || die
- fi
-
- sed \
- -e "s:LINUXPPC:LINUX:g" \
- -e "s:LINUXALPHA:LINUX:g" \
- -e "s:LINUXAMD64:LINUX:g" \
- -e "s:gentoo-stride:${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"
-}
-
-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 "${WORKDIR}"/vmd.png
- eprefixify "${WORKDIR}"/vmd.desktop
- sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
- domenu "${WORKDIR}"/vmd.desktop
-}
^ permalink raw reply related [flat|nested] 7+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-chemistry/vmd/
@ 2012-12-23 3:35 Christoph Junghans
0 siblings, 0 replies; 7+ messages in thread
From: Christoph Junghans @ 2012-12-23 3:35 UTC (permalink / raw
To: gentoo-commits
commit: 985c06cbeaeba817c34489a9c5af56de0c02740e
Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 23 03:34:43 2012 +0000
Commit: Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sun Dec 23 03:34:43 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=985c06cb
fix build with !cuda and python=3 + qa
Package-Manager: portage-2.2.0_alpha149
---
sci-chemistry/vmd/ChangeLog | 3 +++
sci-chemistry/vmd/vmd-1.9.1-r1.ebuild | 8 +++++++-
2 files changed, 10 insertions(+), 1 deletions(-)
diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
index 32fdd60..296c399 100644
--- a/sci-chemistry/vmd/ChangeLog
+++ b/sci-chemistry/vmd/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.50 2012/11/14 15:18:58 jlec Exp $
+ 23 Dec 2012; Christoph Junghans <ottxor@gentoo.org> vmd-1.9.1-r1.ebuild:
+ fix build with !cuda and python=3 + qa
+
29 Nov 2012; Justin Lecher <jlec@gentoo.org> vmd-1.9.1-r1.ebuild:
Drop dep on old tk
diff --git a/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild
index b361abd..259c60c 100644
--- a/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild
@@ -63,8 +63,13 @@ pkg_nofetch() {
elog "Place both in ${DISTDIR}"
}
+pkg_setup() {
+ python_set_active_version 2
+ python_pkg_setup
+}
+
src_prepare() {
- cuda_sanitize
+ use cuda && cuda_sanitize
cd "${WORKDIR}"/plugins
@@ -216,5 +221,6 @@ src_install() {
insinto /usr/share/pixmaps
doins "${WORKDIR}"/vmd.png
eprefixify "${WORKDIR}"/vmd.desktop
+ sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
domenu "${WORKDIR}"/vmd.desktop
}
^ permalink raw reply related [flat|nested] 7+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-chemistry/vmd/
@ 2012-11-29 21:05 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2012-11-29 21:05 UTC (permalink / raw
To: gentoo-commits
commit: 52b34118d2a87d729ed2ca92af5259786ca81839
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 29 15:13:43 2012 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Nov 29 15:13:43 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=52b34118
sci-chemistry/vmd: Drop dep on old tk
Package-Manager: portage-2.2.0_alpha142
---
sci-chemistry/vmd/ChangeLog | 3 +++
sci-chemistry/vmd/vmd-1.9.1-r1.ebuild | 5 +----
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
index 8707dea..32fdd60 100644
--- a/sci-chemistry/vmd/ChangeLog
+++ b/sci-chemistry/vmd/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.50 2012/11/14 15:18:58 jlec Exp $
+ 29 Nov 2012; Justin Lecher <jlec@gentoo.org> vmd-1.9.1-r1.ebuild:
+ Drop dep on old tk
+
26 Nov 2012; Justin Lecher <jlec@gentoo.org> vmd-1.9.1-r1.ebuild:
Using new cuda.eclass
diff --git a/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild
index a116445..b361abd 100644
--- a/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild
@@ -24,10 +24,7 @@ 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/tk-8.5[-truetype]
dev-lang/perl
dev-python/numpy
sci-libs/netcdf
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/vmd/
@ 2012-11-26 22:02 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2012-11-26 22:02 UTC (permalink / raw
To: gentoo-commits
commit: 46384de37eb72c21e1b25350e8afa40e0b6736a3
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 26 12:15:46 2012 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 26 14:41:09 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=46384de3
sci-chemistry/vmd: Using new cuda.eclass
Package-Manager: portage-2.2.0_alpha142
---
sci-chemistry/vmd/ChangeLog | 3 +++
sci-chemistry/vmd/vmd-1.9.1-r1.ebuild | 19 ++++++-------------
2 files changed, 9 insertions(+), 13 deletions(-)
diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
index cfca6cc..8707dea 100644
--- a/sci-chemistry/vmd/ChangeLog
+++ b/sci-chemistry/vmd/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/vmd/ChangeLog,v 1.50 2012/11/14 15:18:58 jlec Exp $
+ 26 Nov 2012; Justin Lecher <jlec@gentoo.org> vmd-1.9.1-r1.ebuild:
+ Using new cuda.eclass
+
*vmd-1.9.1-r1 (14 Nov 2012)
14 Nov 2012; Justin Lecher <jlec@gentoo.org> +vmd-1.9.1-r1.ebuild:
diff --git a/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild
index dc38b98..a116445 100644
--- a/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.1-r1.ebuild
@@ -6,7 +6,7 @@ EAPI=5
PYTHON_DEPEND="2"
-inherit eutils multilib prefix python toolchain-funcs
+inherit cuda eutils multilib prefix python toolchain-funcs
DESCRIPTION="Visual Molecular Dynamics"
HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
@@ -67,6 +67,8 @@ pkg_nofetch() {
}
src_prepare() {
+ cuda_sanitize
+
cd "${WORKDIR}"/plugins
epatch "${WORKDIR}"/${P}-gentoo-plugins.patch
@@ -116,7 +118,7 @@ src_prepare() {
-e "s:gentoo-nvcc:${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-nvflags::g" \
-e "s:gentoo-ldflags:${LDFLAGS}:g" \
-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
@@ -133,19 +135,10 @@ src_prepare() {
# -i configure || die "failed setting up python"
if use cuda; then
- local gcc_bindir
- if has_version sys-devel/gcc:4.5; then
- gcc_bindir="$(ls -d ${EPREFIX}/usr/*pc-linux-gnu/gcc-bin/4.5*)"
- elif has_version sys-devel/gcc:4.4; then
- gcc_bindir="$(ls -d ${EPREFIX}/usr/*pc-linux-gnu/gcc-bin/4.4*)"
- else
- ewarn "Please install gcc with a version between 4.4* and 4.5*"
- fi
-
sed \
-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
- -e "/^\$arch_nvccflags/s:=:= \"--compiler-bindir=${gcc_bindir} \" . \n:1" \
- -i configure || die
+ -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
+ -i configure src/Makefile || die
fi
sed \
^ permalink raw reply related [flat|nested] 7+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-chemistry/vmd/
@ 2012-11-14 15:20 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2012-11-14 15:20 UTC (permalink / raw
To: gentoo-commits
commit: 044e9667653686b8fc406fc9361f5936e5815206
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Nov 14 15:20:03 2012 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Nov 14 15:20:03 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=044e9667
Moved to Tree
---
sci-chemistry/vmd/ChangeLog | 10 --
sci-chemistry/vmd/metadata.xml | 15 ---
sci-chemistry/vmd/vmd-1.9.1.ebuild | 215 ------------------------------------
3 files changed, 0 insertions(+), 240 deletions(-)
diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
deleted file mode 100644
index 764678c..0000000
--- a/sci-chemistry/vmd/ChangeLog
+++ /dev/null
@@ -1,10 +0,0 @@
-# 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.
-
diff --git a/sci-chemistry/vmd/metadata.xml b/sci-chemistry/vmd/metadata.xml
deleted file mode 100644
index 103ce95..0000000
--- a/sci-chemistry/vmd/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?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>
diff --git a/sci-chemistry/vmd/vmd-1.9.1.ebuild b/sci-chemistry/vmd/vmd-1.9.1.ebuild
deleted file mode 100644
index d9d2977..0000000
--- a/sci-chemistry/vmd/vmd-1.9.1.ebuild
+++ /dev/null
@@ -1,215 +0,0 @@
-# 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
-}
^ permalink raw reply related [flat|nested] 7+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-chemistry/vmd/
@ 2012-10-22 9:11 Reinis Danne
0 siblings, 0 replies; 7+ messages in thread
From: Reinis Danne @ 2012-10-22 9:11 UTC (permalink / raw
To: gentoo-commits
commit: 260e6409c2209a794657ed50a21a68d9cb895602
Author: Reinis Danne <rei4dan <AT> gmail <DOT> com>
AuthorDate: Mon Oct 22 09:09:58 2012 +0000
Commit: Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Mon Oct 22 09:09:58 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=260e6409
vmd: Fix netcdf config, bug #406737
---
sci-chemistry/vmd/ChangeLog | 10 ++
sci-chemistry/vmd/metadata.xml | 15 +++
sci-chemistry/vmd/vmd-1.9.1.ebuild | 215 ++++++++++++++++++++++++++++++++++++
3 files changed, 240 insertions(+), 0 deletions(-)
diff --git a/sci-chemistry/vmd/ChangeLog b/sci-chemistry/vmd/ChangeLog
new file mode 100644
index 0000000..764678c
--- /dev/null
+++ b/sci-chemistry/vmd/ChangeLog
@@ -0,0 +1,10 @@
+# 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.
+
diff --git a/sci-chemistry/vmd/metadata.xml b/sci-chemistry/vmd/metadata.xml
new file mode 100644
index 0000000..103ce95
--- /dev/null
+++ b/sci-chemistry/vmd/metadata.xml
@@ -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>
diff --git a/sci-chemistry/vmd/vmd-1.9.1.ebuild b/sci-chemistry/vmd/vmd-1.9.1.ebuild
new file mode 100644
index 0000000..d9d2977
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.1.ebuild
@@ -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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2012-11-26 22:02 [gentoo-commits] proj/sci:master commit in: sci-chemistry/vmd/ Justin Lecher
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