Hi everybody,
i install pymol via svn ebuild (attached). It crashes with a segfault but only
if i am inside my home directory. If i am outside, everything works fine.
Any ideas what this could be related to?
OpenGL graphics engine:
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: GeForce 6600/PCI/SSE2
GL_VERSION: 2.1.0 NVIDIA 96.29
Adapting to GeForce hardware.
Detected 2 CPUs. Enabled multithreaded rendering.
/usr/bin/pymol: line 6: 12230 Segmentation fault python
${PYMOL_PATH}/__init__.py $*
pymol start script says...
mar...@osgiliath ~ $ cat /usr/bin/pymol
#!/bin/sh
PYMOL_PATH=/usr/lib/python2.4/site-packages/pymol
PYMOL_DATA="/usr/share/pymol/data"
PYMOL_SCRIPTS="/usr/share/pymol/scripts"
export PYMOL_PATH PYMOL_DATA PYMOL_SCRIPTS
python ${PYMOL_PATH}/__init__.py $*
... which looks good to me.
Cheers
Martin
# Copyright 1999-2006 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header:
/var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-0.99_rc6-r2.ebuild,v 1.3
2006/10/22 18:41:55 ribosome Exp $
inherit subversion distutils eutils multilib
MY_PV=${PV/_}
MY_S_P="${PN}-${MY_PV}"
MY_PV=${MY_PV/./_}
MY_P="${PN}-${MY_PV}"
DESCRIPTION="A Python-extensible molecular graphics system."
HOMEPAGE="http://pymol.sourceforge.net/";
#SRC_URI="mirror://sourceforge/pymol/${MY_P}-src.tgz"
ESVN_REPO_URI="https://svn.sourceforge.net/svnroot/pymol/trunk/pymol/";
#ESVN_PATCHES="vmdplugin-pymol-svn.diff"
LICENSE="PSF-2.2"
IUSE="vmdplugins"
SLOT="0"
KEYWORDS="~amd64 ~ppc ~x86"
DEPEND="dev-lang/python
dev-python/pmw
dev-python/numeric
dev-lang/tk
media-libs/libpng
sys-libs/zlib
vmdplugins? ( sci-chemistry/vmd)
media-libs/glut"
S="${WORKDIR}/pymol"
src_unpack() {
subversion_src_unpack
cd ${S}
# Turn off splash screen. Please do make a project contribution
# if you are able though.
[[ -n "$WANT_NOSPLASH" ]] && epatch ${FILESDIR}/nosplash-gentoo.patch
use vmdplugins && epatch "${FILESDIR}/vmdplugin-pymol-svn.diff"
# Respect CFLAGS
sed -i \
-e "s:\(ext_comp_args=\).*:\1[]:g" \
${S}/setup.py
}
src_install() {
python_version
distutils_src_install
cd ${S}
#The following three lines probably do not do their jobs and should be
#changed
PYTHONPATH="${D}/usr/$(get_libdir)/site-packages" ${python} setup2.py
# Make our own wrapper
cat >> ${T}/pymol << EOF
#!/bin/sh
PYMOL_PATH=/usr/lib/python${PYVER}/site-packages/pymol
PYMOL_DATA="/usr/share/pymol/data"
PYMOL_SCRIPTS="/usr/share/pymol/scripts"
export PYMOL_PATH PYMOL_DATA PYMOL_SCRIPTS
${python} \${PYMOL_PATH}/__init__.py \$*
EOF
exeinto /usr/bin
doexe ${T}/pymol
dodoc DEVELOPERS CHANGES
mv examples ${D}/usr/share/doc/${PF}/
dodir /usr/share/pymol
mv test ${D}/usr/share/pymol/
mv data ${D}/usr/share/pymol/
mv scripts ${D}/usr/share/pymol/
}
--- modules/pymol/invocation.py.orig 2003-06-11 13:40:13.000000000 -0400
+++ modules/pymol/invocation.py 2003-06-11 13:40:29.000000000 -0400
@@ -179,5 +179,3 @@
else:
options.deferred.append(a)
- if options.show_splash and not options.no_gui:
- options.deferred.insert(0,"_do__ cmd.splash(1)")
--- /tmp/setup.py 2006-10-30 20:32:59.000000000 +0100
+++ setup.py 2006-10-30 20:33:31.000000000 +0100
@@ -69,8 +69,8 @@
"/usr/include/freetype2",
# "/users/warren/ext/include",
# VMD plugin support
-# "contrib/uiuc/plugins/include",
-# "contrib/uiuc/plugins/molfile_plugin/src",
+ "contrib/uiuc/plugins/include",
+ "contrib/uiuc/plugins/molfile_plugin/src",
]
libs=["GL","GLU","glut","png","z","freetype"
]
@@ -85,7 +85,7 @@
# Numeric Python support
# ("_PYMOL_NUMPY",None),
# VMD plugin support
-# ("_PYMOL_VMD_PLUGINS",None),
+ ("_PYMOL_VMD_PLUGINS",None),
("_HAVE_LIBPNG",None)]
ext_comp_args=["-ffast-math","-funroll-loops","-O3"]
ext_link_args=[]
@@ -230,52 +230,52 @@
"layer5/main.c",
# uncomment below for VMD molfile plugin support
# (incomplete at present -- only TRJ, TRR, XTC, DCD so far...)
-# "contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c",
-# "contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c",
-# "contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/carplugin.c",
-# "contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/corplugin.c",
-# "contrib/uiuc/plugins/molfile_plugin/src/cpmdplugin.c",
-# "contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c",
-# "contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c",
-# "contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c",
-# "contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/dxplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c",
-# "contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/mapplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c",
-# "contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c",
-# "contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c",
-# "contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c",
-# "contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c",
-# "contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c",
-# "contrib/uiuc/plugins/molfile_plugin/src/situsplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c",
-# "contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp",
-# "contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/carplugin.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/corplugin.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/cpmdplugin.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/dxplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/mapplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/situsplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c",
+ "contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp",
+ "contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c",
],
include_dirs = inc_dirs,
