Hi all, As suggested by Peter, I tried compiling PyMol from src (pymol-0_99rc6-src.tgz). Unfortunately it fell over :(
Attached is the output. The error occurs in layer0/Crystal.c. I've look at the file in vim and there does not seem to be anything untowards (weird characters etc...) in it. I tried to compile from pymol-0_99rc1-src.tgz and got the same error. Any pointers?? Many thanks Noel On Friday 25 August 2006 23:49, you wrote: > <snip> > > > Dose anyone have any idea's? This occurs when I single click left or > > right in > > the main display. > > If you're using the binary distribution, try using the source distribution > and see if the problem persists (if compilation fails, then the error > message might provide some information as to what's going on). You could > also try different graphics drivers (if possible). > > Failing that, it sounds like an issue w\ the mouse event listener in the > glut stuff. Unfortunately I don't know of an easy fix or work-around if > this is the case (hopefully Warren will chime in on this). > > Good luck, > > Pete -- PhD Student Department of Biochemistry and Molecular Biology Monash University Clayton, Victoria Australia Ph: +61 3 9905 1418 e-mail: noel.f...@med.monash.edu.au website: http://vbc.med.monash.edu.au/~fauxn
13:13:12-fa...@~/software/pymol-0.99rc6$ python setup.py install 1> pymol_setup.log 1>&2 running install running build running build_py creating build creating build/lib.linux-i686-2.4 creating build/lib.linux-i686-2.4/chempy copying modules/chempy/bond_amber.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/hetatm.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/lst.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/protein_amber99.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/dictdb.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/protein_mmff.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/arc.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/protein_amber.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/water_amber.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/solvate.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/protein.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/models.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/water_residues.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/mmd.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/cex.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/io.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/charge.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/sdf.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/map.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/bond_mmff.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/mass.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/xyz.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/place.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/mol.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/gms.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/pdb.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/cc1.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/cpv.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/mae.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/pkl.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/neighbor.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/gamess1.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/protein_residues.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/brick.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/__init__.py -> build/lib.linux-i686-2.4/chempy copying modules/chempy/bonds.py -> build/lib.linux-i686-2.4/chempy creating build/lib.linux-i686-2.4/chempy/bmin copying modules/chempy/bmin/commands.py -> build/lib.linux-i686-2.4/chempy/bmin copying modules/chempy/bmin/realtime.py -> build/lib.linux-i686-2.4/chempy/bmin copying modules/chempy/bmin/state.py -> build/lib.linux-i686-2.4/chempy/bmin copying modules/chempy/bmin/util.py -> build/lib.linux-i686-2.4/chempy/bmin copying modules/chempy/bmin/__init__.py -> build/lib.linux-i686-2.4/chempy/bmin creating build/lib.linux-i686-2.4/chempy/champ copying modules/chempy/champ/formal_charges.py -> build/lib.linux-i686-2.4/chempy/champ copying modules/chempy/champ/assign.py -> build/lib.linux-i686-2.4/chempy/champ copying modules/chempy/champ/amber99.py -> build/lib.linux-i686-2.4/chempy/champ copying modules/chempy/champ/__init__.py -> build/lib.linux-i686-2.4/chempy/champ creating build/lib.linux-i686-2.4/chempy/fast copying modules/chempy/fast/__init__.py -> build/lib.linux-i686-2.4/chempy/fast creating build/lib.linux-i686-2.4/chempy/fragments copying modules/chempy/fragments/__init__.py -> build/lib.linux-i686-2.4/chempy/fragments creating build/lib.linux-i686-2.4/chempy/tinker copying modules/chempy/tinker/realtime.py -> build/lib.linux-i686-2.4/chempy/tinker copying modules/chempy/tinker/state.py -> build/lib.linux-i686-2.4/chempy/tinker copying modules/chempy/tinker/amber.py -> build/lib.linux-i686-2.4/chempy/tinker copying modules/chempy/tinker/__init__.py -> build/lib.linux-i686-2.4/chempy/tinker copying modules/chempy/tinker/keyword.py -> build/lib.linux-i686-2.4/chempy/tinker creating build/lib.linux-i686-2.4/pmg_tk copying modules/pmg_tk/PMGApp.py -> build/lib.linux-i686-2.4/pmg_tk copying modules/pmg_tk/ColorEditor.py -> build/lib.linux-i686-2.4/pmg_tk copying modules/pmg_tk/Setting.py -> build/lib.linux-i686-2.4/pmg_tk copying modules/pmg_tk/__init__.py -> build/lib.linux-i686-2.4/pmg_tk copying modules/pmg_tk/Demo.py -> build/lib.linux-i686-2.4/pmg_tk copying modules/pmg_tk/SetEditor.py -> build/lib.linux-i686-2.4/pmg_tk creating build/lib.linux-i686-2.4/pmg_tk/startup copying modules/pmg_tk/startup/apbs_tools.py -> build/lib.linux-i686-2.4/pmg_tk/startup copying modules/pmg_tk/startup/remote_pdb_load.py -> build/lib.linux-i686-2.4/pmg_tk/startup copying modules/pmg_tk/startup/__init__.py -> build/lib.linux-i686-2.4/pmg_tk/startup creating build/lib.linux-i686-2.4/pmg_tk/skins copying modules/pmg_tk/skins/__init__.py -> build/lib.linux-i686-2.4/pmg_tk/skins creating build/lib.linux-i686-2.4/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/builder.py -> build/lib.linux-i686-2.4/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/__init__.py -> build/lib.linux-i686-2.4/pmg_tk/skins/normal creating build/lib.linux-i686-2.4/pmg_wx copying modules/pmg_wx/__init__.py -> build/lib.linux-i686-2.4/pmg_wx creating build/lib.linux-i686-2.4/pymol copying modules/pymol/movie.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/experimenting.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/moving.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/cmd.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/importing.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/commanding.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/callback.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/parser.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/creating.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/editing.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/parsing.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/editor.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/controlling.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/vfont.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/helping.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/setting.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/exporting.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/externing.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/wizarding.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/fitting.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/viewing.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/selector.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/xray.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/querying.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/contrib.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/preset.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/menu.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/util.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/xwin.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/povray.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/shortcut.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/__init__.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/selecting.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/m4x.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/cgo.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/invocation.py -> build/lib.linux-i686-2.4/pymol copying modules/pymol/rpc.py -> build/lib.linux-i686-2.4/pymol creating build/lib.linux-i686-2.4/pymol/opengl copying modules/pymol/opengl/__init__.py -> build/lib.linux-i686-2.4/pymol/opengl creating build/lib.linux-i686-2.4/pymol/opengl/gl copying modules/pymol/opengl/gl/glconst.py -> build/lib.linux-i686-2.4/pymol/opengl/gl copying modules/pymol/opengl/gl/__init__.py -> build/lib.linux-i686-2.4/pymol/opengl/gl creating build/lib.linux-i686-2.4/pymol/opengl/glu copying modules/pymol/opengl/glu/gluconst.py -> build/lib.linux-i686-2.4/pymol/opengl/glu copying modules/pymol/opengl/glu/__init__.py -> build/lib.linux-i686-2.4/pymol/opengl/glu creating build/lib.linux-i686-2.4/pymol/opengl/glut copying modules/pymol/opengl/glut/glutconst.py -> build/lib.linux-i686-2.4/pymol/opengl/glut copying modules/pymol/opengl/glut/__init__.py -> build/lib.linux-i686-2.4/pymol/opengl/glut creating build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/renaming.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/appearance.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/stereodemo.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/fedora.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/demo.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/message.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/charge.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/annotation.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/security.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/distance.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/density.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/toggle.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/mutagenesis.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/box.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/cleanup.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/measurement.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/benchmark.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/label.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/pair_fit.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/__init__.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/sculpting.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/filter.py -> build/lib.linux-i686-2.4/pymol/wizard copying modules/pymol/wizard/dragging.py -> build/lib.linux-i686-2.4/pymol/wizard running build_ext building 'pymol._cmd' extension creating build/temp.linux-i686-2.4 creating build/temp.linux-i686-2.4/ov creating build/temp.linux-i686-2.4/ov/src creating build/temp.linux-i686-2.4/layer0 creating build/temp.linux-i686-2.4/layer1 creating build/temp.linux-i686-2.4/layer2 creating build/temp.linux-i686-2.4/layer3 creating build/temp.linux-i686-2.4/layer4 creating build/temp.linux-i686-2.4/layer5 gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_HAVE_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -I/usr/include/python2.4 -c ov/src/OVContext.c -o build/temp.linux-i686-2.4/ov/src/OVContext.o -ffast-math -funroll-loops -O3 gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_HAVE_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -I/usr/include/python2.4 -c ov/src/OVHeapArray.c -o build/temp.linux-i686-2.4/ov/src/OVHeapArray.o -ffast-math -funroll-loops -O3 gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_HAVE_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -I/usr/include/python2.4 -c ov/src/OVHeap.c -o build/temp.linux-i686-2.4/ov/src/OVHeap.o -ffast-math -funroll-loops -O3 gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_HAVE_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -I/usr/include/python2.4 -c ov/src/OVLexicon.c -o build/temp.linux-i686-2.4/ov/src/OVLexicon.o -ffast-math -funroll-loops -O3 ov/src/OVLexicon.c: In function âÂÂOVLexicon_GetFromCStringâÂÂ: ov/src/OVLexicon.c:290: warning: âÂÂresult.wordâ is used uninitialized in this function ov/src/OVLexicon.c:311: warning: âÂÂresult.wordâ is used uninitialized in this function gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_HAVE_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -I/usr/include/python2.4 -c ov/src/OVOneToOne.c -o build/temp.linux-i686-2.4/ov/src/OVOneToOne.o -ffast-math -funroll-loops -O3 gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_HAVE_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -I/usr/include/python2.4 -c ov/src/OVOneToAny.c -o build/temp.linux-i686-2.4/ov/src/OVOneToAny.o -ffast-math -funroll-loops -O3 gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_HAVE_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -I/usr/include/python2.4 -c ov/src/OVRandom.c -o build/temp.linux-i686-2.4/ov/src/OVRandom.o -ffast-math -funroll-loops -O3 gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_HAVE_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -I/usr/include/python2.4 -c ov/src/ov_utility.c -o build/temp.linux-i686-2.4/ov/src/ov_utility.o -ffast-math -funroll-loops -O3 gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_HAVE_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -I/usr/include/python2.4 -c layer0/Block.c -o build/temp.linux-i686-2.4/layer0/Block.o -ffast-math -funroll-loops -O3 gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_HAVE_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -I/usr/include/python2.4 -c layer0/Crystal.c -o build/temp.linux-i686-2.4/layer0/Crystal.o -ffast-math -funroll-loops -O3 layer0/Crystal.c:314:1: error: unterminated argument list invoking macro "sprintf" layer0/Crystal.c: In function âÂÂCrystalDumpâÂÂ: layer0/Crystal.c:201: warning: statement with no effect layer0/Crystal.c:201: error: expected âÂÂ;â at end of input layer0/Crystal.c:201: warning: unused variable âÂÂ_FBstrâ layer0/Crystal.c:199: warning: unused variable âÂÂiâ layer0/Crystal.c:198: warning: unused variable âÂÂGâ error: command 'gcc' failed with exit status 1
