#52 fails to build on SuSE 10.0 x86_64

open
nobody
None
5
2 days ago
2006-04-27
Anonymous
No

Here's what happens:

$ python setup.py install
running install
running build
running build_py
creating build/lib.linux-x86_64-2.4
creating build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/protein.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/io.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/brick.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/protein_amber99.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/charge.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/mass.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/protein_residues.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/arc.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/cc1.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/water_residues.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/models.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/cex.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/cpv.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/water_amber.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/gms.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/solvate.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/mae.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/map.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/lst.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/mmd.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/mol.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/pdb.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/pkl.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/protein_mmff.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/sdf.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/place.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/bond_mmff.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/xyz.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/protein_amber.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/dictdb.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/neighbor.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/gamess1.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/bonds.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/__init__.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/hetatm.py ->
build/lib.linux-x86_64-2.4/chempy
copying modules/chempy/bond_amber.py ->
build/lib.linux-x86_64-2.4/chempy
creating build/lib.linux-x86_64-2.4/chempy/bmin
copying modules/chempy/bmin/commands.py ->
build/lib.linux-x86_64-2.4/chempy/bmin
copying modules/chempy/bmin/state.py ->
build/lib.linux-x86_64-2.4/chempy/bmin
copying modules/chempy/bmin/util.py ->
build/lib.linux-x86_64-2.4/chempy/bmin
copying modules/chempy/bmin/__init__.py ->
build/lib.linux-x86_64-2.4/chempy/bmin
copying modules/chempy/bmin/realtime.py ->
build/lib.linux-x86_64-2.4/chempy/bmin
creating build/lib.linux-x86_64-2.4/chempy/champ
copying modules/chempy/champ/assign.py ->
build/lib.linux-x86_64-2.4/chempy/champ
copying modules/chempy/champ/amber99.py ->
build/lib.linux-x86_64-2.4/chempy/champ
copying modules/chempy/champ/formal_charges.py ->
build/lib.linux-x86_64-2.4/chempy/champ
copying modules/chempy/champ/__init__.py ->
build/lib.linux-x86_64-2.4/chempy/champ
creating build/lib.linux-x86_64-2.4/chempy/fast
copying modules/chempy/fast/__init__.py ->
build/lib.linux-x86_64-2.4/chempy/fast
creating build/lib.linux-x86_64-2.4/chempy/fragments
copying modules/chempy/fragments/__init__.py ->
build/lib.linux-x86_64-2.4/chempy/fragments
creating build/lib.linux-x86_64-2.4/chempy/tinker
copying modules/chempy/tinker/state.py ->
build/lib.linux-x86_64-2.4/chempy/tinker
copying modules/chempy/tinker/amber.py ->
build/lib.linux-x86_64-2.4/chempy/tinker
copying modules/chempy/tinker/__init__.py ->
build/lib.linux-x86_64-2.4/chempy/tinker
copying modules/chempy/tinker/realtime.py ->
build/lib.linux-x86_64-2.4/chempy/tinker
copying modules/chempy/tinker/keyword.py ->
build/lib.linux-x86_64-2.4/chempy/tinker
creating build/lib.linux-x86_64-2.4/pmg_tk
copying modules/pmg_tk/Demo.py ->
build/lib.linux-x86_64-2.4/pmg_tk
copying modules/pmg_tk/Setting.py ->
build/lib.linux-x86_64-2.4/pmg_tk
copying modules/pmg_tk/SetEditor.py ->
build/lib.linux-x86_64-2.4/pmg_tk
copying modules/pmg_tk/ColorEditor.py ->
build/lib.linux-x86_64-2.4/pmg_tk
copying modules/pmg_tk/PMGApp.py ->
build/lib.linux-x86_64-2.4/pmg_tk
copying modules/pmg_tk/__init__.py ->
build/lib.linux-x86_64-2.4/pmg_tk
creating build/lib.linux-x86_64-2.4/pmg_tk/startup
copying modules/pmg_tk/startup/apbs_tools.py ->
build/lib.linux-x86_64-2.4/pmg_tk/startup
copying modules/pmg_tk/startup/remote_pdb_load.py ->
build/lib.linux-x86_64-2.4/pmg_tk/startup
copying modules/pmg_tk/startup/__init__.py ->
build/lib.linux-x86_64-2.4/pmg_tk/startup
creating build/lib.linux-x86_64-2.4/pmg_tk/skins
copying modules/pmg_tk/skins/__init__.py ->
build/lib.linux-x86_64-2.4/pmg_tk/skins
creating
build/lib.linux-x86_64-2.4/pmg_tk/skins/normal
copying modules/pmg_tk/skins/normal/builder.py ->
build/lib.linux-x86_64-2.4/pmg_tk/skins/normal
copying modules/pmg_tk/skins/normal/__init__.py ->
build/lib.linux-x86_64-2.4/pmg_tk/skins/normal
creating build/lib.linux-x86_64-2.4/pmg_wx
copying modules/pmg_wx/__init__.py ->
build/lib.linux-x86_64-2.4/pmg_wx
creating build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/creating.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/povray.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/experimenting.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/parser.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/moving.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/xray.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/parsing.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/xwin.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/editor.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/helping.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/selecting.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/menu.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/externing.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/selector.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/importing.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/cgo.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/cmd.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/preset.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/fitting.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/callback.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/commanding.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/m4x.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/setting.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/movie.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/contrib.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/invocation.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/vfont.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/rpc.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/wizarding.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/util.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/editing.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/controlling.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/__init__.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/querying.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/viewing.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/exporting.py ->
build/lib.linux-x86_64-2.4/pymol
copying modules/pymol/shortcut.py ->
build/lib.linux-x86_64-2.4/pymol
creating build/lib.linux-x86_64-2.4/pymol/opengl
copying modules/pymol/opengl/__init__.py ->
build/lib.linux-x86_64-2.4/pymol/opengl
creating build/lib.linux-x86_64-2.4/pymol/opengl/gl
copying modules/pymol/opengl/gl/glconst.py ->
build/lib.linux-x86_64-2.4/pymol/opengl/gl
copying modules/pymol/opengl/gl/__init__.py ->
build/lib.linux-x86_64-2.4/pymol/opengl/gl
creating build/lib.linux-x86_64-2.4/pymol/opengl/glu
copying modules/pymol/opengl/glu/gluconst.py ->
build/lib.linux-x86_64-2.4/pymol/opengl/glu
copying modules/pymol/opengl/glu/__init__.py ->
build/lib.linux-x86_64-2.4/pymol/opengl/glu
creating build/lib.linux-x86_64-2.4/pymol/opengl/glut
copying modules/pymol/opengl/glut/__init__.py ->
build/lib.linux-x86_64-2.4/pymol/opengl/glut
copying modules/pymol/opengl/glut/glutconst.py ->
build/lib.linux-x86_64-2.4/pymol/opengl/glut
creating build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/measurement.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/demo.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/message.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/benchmark.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/dragging.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/distance.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/filter.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/charge.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/box.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/pair_fit.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/annotation.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/fedora.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/stereodemo.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/label.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/cleanup.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/renaming.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/mutagenesis.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/appearance.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/__init__.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/density.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/sculpting.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/toggle.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
copying modules/pymol/wizard/security.py ->
build/lib.linux-x86_64-2.4/pymol/wizard
running build_ext
building 'pymol._cmd' extension
creating build/temp.linux-x86_64-2.4
creating build/temp.linux-x86_64-2.4/ov
creating build/temp.linux-x86_64-2.4/ov/src
creating build/temp.linux-x86_64-2.4/layer0
creating build/temp.linux-x86_64-2.4/layer1
creating build/temp.linux-x86_64-2.4/layer2
creating build/temp.linux-x86_64-2.4/layer3
creating build/temp.linux-x86_64-2.4/layer4
creating build/temp.linux-x86_64-2.4/layer5
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2
-fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -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-x86_64-2.4/ov/src/OVContext.o
-ffast-math -funroll-loops -O3
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2
-fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -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-x86_64-2.4/ov/src/OVHeapArray.o
-ffast-math -funroll-loops -O3
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2
-fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -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-x86_64-2.4/ov/src/OVHeap.o
-ffast-math -funroll-loops -O3
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2
-fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -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-x86_64-2.4/ov/src/OVLexicon.o
-ffast-math -funroll-loops -O3
ov/src/OVLexicon.c: In function
‘OVLexicon_GetFromCString’:
ov/src/OVLexicon.c:288: warning: ‘result.word’ may be
used uninitialized in this function
ov/src/OVLexicon.c:306: warning: ‘result.word’ may be
used uninitialized in this function
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2
-fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -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-x86_64-2.4/ov/src/OVOneToOne.o
-ffast-math -funroll-loops -O3
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2
-fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -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-x86_64-2.4/ov/src/OVOneToAny.o
-ffast-math -funroll-loops -O3
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2
-fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -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-x86_64-2.4/ov/src/OVRandom.o
-ffast-math -funroll-loops -O3
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2
-fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -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-x86_64-2.4/ov/src/ov_utility.o
-ffast-math -funroll-loops -O3
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2
-fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -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-x86_64-2.4/layer0/Block.o
-ffast-math -funroll-loops -O3
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2
-fmessage-length=0 -Wall -D_FORTIFY_SOURCE=2 -g -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-x86_64-2.4/layer0/Crystal.o
-ffast-math -funroll-loops -O3
In file included
from /usr/include/python2.4/Python.h:8,
from layer0/os_python.h:26,
from layer1/Setting.h:19,
from layer1/CGO.h:21,
from layer0/Crystal.c:21:
/usr/include/python2.4/pyconfig.h:835:1: warning:
"_POSIX_C_SOURCE" redefined
In file included from /usr/include/stdio.h:28,
from layer0/os_std.h:23,
from layer0/Crystal.c:18:
/usr/include/features.h:190:1: warning: this is the
location of the previous definition
layer0/Crystal.c:314:1: error: unterminated argument
list invoking macro "sprintf"
layer0/Crystal.c: In function ‘CrystalDump’:
layer0/Crystal.c:201: error: syntax error at end of
input
layer0/Crystal.c:201: warning: unused variable
‘_FBstr’
layer0/Crystal.c:199: warning: unused variable ‘i’
layer0/Crystal.c:198: warning: unused variable ‘G’
error: command 'gcc' failed with exit status 1
$

Is there anything else I should mention to help
debugging this?

Thanks!

Discussion

  • Logged In: YES
    user_id=17586

    I got the same error on Fedora Core 5 i386 arch.