[Insight-users] All python tests fail
Gaëtan Lehmann
gaetan.lehmann at jouy.inra.fr
Thu Nov 29 08:38:37 EST 2007
Le 29 nov. 07 à 13:52, Marco Nolden a écrit :
> Gaëtan Lehmann wrote:
>>
>> Le 28 nov. 07 à 20:01, Marco Nolden a écrit :
>>
>>> nolden at mbi056:~$
>>> PYTHONPATH=/local/nolden/itk-bin-wo-cswig/Wrapping/WrapITK/
>>> Python/:/local/nolden/itk-bin-wo-cswig/bin/:$PYTHONPATH
>>>
>>> [...]
>> This one is nice.
>> Can you try to run one of the failed tests by hand, for example:
>>
>>
>> PYTHONPATH=/local/nolden/itk-bin-wo-cswig/Wrapping/WrapITK/
>> Python/:/local/nolden/itk-bin-wo-cswig/bin/:$PYTHONPATH
>> /usr/bin/python /usr/bin/python
>> /local/nolden/itk-3.4.0/InsightToolkit-3.4.0/Wrapping/WrapITK/
>> Python/Tests/template.py;
>> echo $?
>>
>> ? (There is no output log for this one in
>> http://www.itk.org/Testing/Sites/mbi056/Linux-c++/20071128-0957-
>> Experimental/Results/
>> __Wrapping_WrapITK_Python_Tests_PythonTemplate.html)
>>
>>
> Segmentation fault, see attached gdb output.
the result is weird: the segfault seems to be in the import of
pyexpat. I've checked on my system (with python 2.4): this module is
not loaded in that test.
Can you locate which python command makes the program segfault?
>
>> Also, can you check if the tests are always failing? I suspect a
>> problem
>> with itkTestDriver, rather than a problem in python layer.
>> I think you know how to use ctest, but just in case I'm wrong: you
>> can
>> choose to run only the python tests with the command "ctest -R
>> Python",
>> or even a single test with "ctest -R PythonTemplate" for example.
>>
> Same segfault for the MedianImageFilter test.
>
> Just for fun I tried executing it with python2.4 and at least got a
> python error (after lots of warnings abount mismatching API versions):
> Traceback (most recent call last):
> File
> "/local/nolden/itk-3.4.0/InsightToolkit-3.4.0/Wrapping/WrapITK/
> Python/Tests/MedianImageFilter.py",
> line 13, in ?
> filter = itk.MedianImageFilter[IType, IType].New( reader,
> Radius=eval( argv[3] ) )
> File
> "/local/nolden/itk-bin-wo-cswig/Wrapping/WrapITK/Python/
> itkTemplate.py",
> line 357, in New
> attrib(value)
> File "/local/nolden/itk-bin-wo-cswig/bin/itkMedianImageFilter.py",
> line 155, in SetRadius
> def SetRadius(*args): return
> _itkMedianImageFilter.itkMedianImageFilterIUS2IUS2_Pointer_SetRadius
> (*args)
> TypeError: Expected a pointer
>
> Don't know if this makes sense.
This one is much clear for me: it means that a typemap have failed.
Are you using cableswig CVS?
Cableswig cvs is currently not usable with WrapITK: it now reports
more complete type names which are breaking the typemaps.
>
> I did an additional test:
>
> 1. old wrapping method, same system:
> All tests fail, strangely no PYTHONPATH is set at all:
>
> http://www.itk.org/Testing/Sites/mbi056/Linux-c++/20071129-0907-
> Experimental/Test.html
>
> After manually setting the path I could execute the MedianImageFilter
> without errors but got a black result picture.
maybe because of the 16bits png? Have you checked the value of the
pixels?
>
> Right now I'm building ITK again with new wrapping and forced
> python2.4
> (on ubuntu 7.10) and also started testing a x86-64 Suse 10.2. Results
> should be available as an Experimental Build soon (Hostname eigg)
Great - thanks :-)
Gaëtan
>
>
>> Thanks for your patience,
>>
>> Gaëtan
>>
> Thanks for the support.
>
> Marco
>
>
> nolden at mbi056:/local/nolden/itk-bin-wo-cswig$ PYTHONPATH=/local/
> nolden/itk-bin-wo-cswig/Wrapping/WrapITK/Python/:/local/nolden/itk-
> bin-wo-cswig/bin/:$PYTHONPATH /usr/bin/python /local/nolden/
> itk-3.4.0/InsightToolkit-3.4.0/Wrapping/WrapITK/Python/Tests/
> template.py; echo $?
> Segmentation fault (core dumped)
> 139
> nolden at mbi056:/local/nolden/itk-bin-wo-cswig$ export PYTHONPATH=/
> local/nolden/itk-bin-wo-cswig/Wrapping/WrapITK/Python/:/local/
> nolden/itk-bin-wo-cswig/bin/:$PYTHONPATH
> nolden at mbi056:/local/nolden/itk-bin-wo-cswig$ gdb /usr/bin/python
> GNU gdb 6.6-debian
> Copyright (C) 2006 Free Software Foundation, Inc.
> GDB is free software, covered by the GNU General Public License,
> and you are
> welcome to change it and/or distribute copies of it under certain
> conditions.
> Type "show copying" to see the conditions.
> There is absolutely no warranty for GDB. Type "show warranty" for
> details.
> This GDB was configured as "i486-linux-gnu"...
> Using host libthread_db library "/lib/tls/i686/cmov/libthread_db.so.
> 1".
> (gdb) run /local/nolden/itk-3.4.0/InsightToolkit-3.4.0/Wrapping/
> WrapITK/Python/Tests/template.py
> Starting program: /usr/bin/python /local/nolden/itk-3.4.0/
> InsightToolkit-3.4.0/Wrapping/WrapITK/Python/Tests/template.py
> [Thread debugging using libthread_db enabled]
> [New Thread -1210189632 (LWP 11538)]
>
> Program received signal SIGSEGV, Segmentation fault.
> [Switching to Thread -1210189632 (LWP 11538)]
> 0xb7e50583 in strlen () from /lib/tls/i686/cmov/libc.so.6
> (gdb) bt
> #0 0xb7e50583 in strlen () from /lib/tls/i686/cmov/libc.so.6
> #1 0x080944ea in PyString_FromString (str=0x0) at ../Objects/
> stringobject.c:108
> #2 0x080e5dad in PyModule_AddStringConstant (m=0x97612b4,
> name=0xb34aed50 "XML_ERROR_ENTITY_DECLARED_IN_PE", value=0x0)
> at ../Python/modsupport.c:630
> #3 0xb34985bf in initpyexpat () from /usr/lib/python2.5/site-
> packages/_xmlplus/parsers/pyexpat.so
> #4 0x080e1a34 in _PyImport_LoadDynamicModule (name=0xbfdc7e17
> "xml.parsers.pyexpat",
> pathname=0xbfdc6da7 "/usr/lib/python2.5/site-packages/_xmlplus/
> parsers/pyexpat.so", fp=0x9db6488)
> at ../Python/importdl.c:53
> #5 0x080df6d5 in load_module (name=0xbfdc7e17
> "xml.parsers.pyexpat", fp=0x0,
> buf=0xbfdc6da7 "/usr/lib/python2.5/site-packages/_xmlplus/
> parsers/pyexpat.so", type=3, loader=0x0)
> at ../Python/import.c:1758
> #6 0x080df98b in import_submodule (mod=0x9761c44,
> subname=0xbfdc7e23 "pyexpat", fullname=0xbfdc7e17
> "xml.parsers.pyexpat")
> at ../Python/import.c:2400
> #7 0x080dfe3e in load_next (mod=0x9761c44, altmod=0x81466b8,
> p_name=<value optimized out>,
> buf=0xbfdc7e17 "xml.parsers.pyexpat", p_buflen=0xbfdc7e10)
> at ../Python/import.c:2220
> #8 0x080e0068 in import_module_level (name=0x0, globals=0x816a170,
> locals=<value optimized out>, fromlist=0x9d4250c,
> level=-1) at ../Python/import.c:2001
> #9 0x080e04f7 in PyImport_ImportModuleLevel (name=0x9d9c6d4
> "pyexpat", globals=0x9d8cf0c, locals=0x9d8cf0c,
> fromlist=0x9d4250c, level=-1) at ../Python/import.c:2072
> #10 0x080c1db4 in builtin___import__ (self=0x0, args=0x9d2984c,
> kwds=0x0) at ../Python/bltinmodule.c:47
> #11 0x0805c9e7 in PyObject_Call (func=0x0, arg=0x9d2984c, kw=0x0)
> at ../Objects/abstract.c:1860
> #12 0x080c232c in PyEval_CallObjectWithKeywords (func=0xb7da7e6c,
> arg=0x9d2984c, kw=0x0) at ../Python/ceval.c:3433
> #13 0x080c4a9d in PyEval_EvalFrameEx (f=0x97a50d4, throwflag=0)
> at ../Python/ceval.c:2063
> #14 0x080ca115 in PyEval_EvalCodeEx (co=0x9d460f8,
> globals=0x9d8cf0c, locals=0x9d8cf0c, args=0x0, argcount=0, kws=0x0,
> kwcount=0, defs=0x0, defcount=0, closure=0x0) at ../Python/
> ceval.c:2831
> #15 0x080ca187 in PyEval_EvalCode (co=0x9d460f8, globals=0x9d8cf0c,
> locals=0x9d8cf0c) at ../Python/ceval.c:494
> #16 0x080de9ac in PyImport_ExecCodeModuleEx (name=0xbfdcb247
> "xml.parsers.expat", co=0x9d460f8,
> pathname=0xbfdc9197 "/usr/lib/python2.5/site-packages/_xmlplus/
> parsers/expat.pyc") at ../Python/import.c:675
> #17 0x080df306 in load_source_module (name=0xbfdcb247
> "xml.parsers.expat",
> pathname=0xbfdc9197 "/usr/lib/python2.5/site-packages/_xmlplus/
> parsers/expat.pyc", fp=<value optimized out>)
> at ../Python/import.c:959
> ---Type <return> to continue, or q <return> to quit---
> #18 0x080df98b in import_submodule (mod=0x9761c44,
> subname=0xbfdcb253 "expat", fullname=0xbfdcb247 "xml.parsers.expat")
> at ../Python/import.c:2400
> #19 0x080dfe3e in load_next (mod=0x9761c44, altmod=0x9761c44,
> p_name=<value optimized out>,
> buf=0xbfdcb247 "xml.parsers.expat", p_buflen=0xbfdcb240) at ../
> Python/import.c:2220
> #20 0x080e00b0 in import_module_level (name=0x0, globals=<value
> optimized out>, locals=<value optimized out>,
> fromlist=0x9cfa7ec, level=-1) at ../Python/import.c:2008
> #21 0x080e04f7 in PyImport_ImportModuleLevel (name=0x9d085a4
> "xml.parsers.expat", globals=0x9cfc79c, locals=0x9cfc79c,
> fromlist=0x9cfa7ec, level=-1) at ../Python/import.c:2072
> #22 0x080c1db4 in builtin___import__ (self=0x0, args=0x9d07b44,
> kwds=0x0) at ../Python/bltinmodule.c:47
> #23 0x0805c9e7 in PyObject_Call (func=0x0, arg=0x9d07b44, kw=0x0)
> at ../Objects/abstract.c:1860
> #24 0x080c232c in PyEval_CallObjectWithKeywords (func=0xb7da7e6c,
> arg=0x9d07b44, kw=0x0) at ../Python/ceval.c:3433
> #25 0x080c4a9d in PyEval_EvalFrameEx (f=0x9c440dc, throwflag=0)
> at ../Python/ceval.c:2063
> #26 0x080ca115 in PyEval_EvalCodeEx (co=0x9d0b3c8,
> globals=0x9cfc79c, locals=0x9cfc79c, args=0x0, argcount=0, kws=0x0,
> kwcount=0, defs=0x0, defcount=0, closure=0x0) at ../Python/
> ceval.c:2831
> #27 0x080ca187 in PyEval_EvalCode (co=0x9d0b3c8, globals=0x9cfc79c,
> locals=0x9cfc79c) at ../Python/ceval.c:494
> #28 0x080de9ac in PyImport_ExecCodeModuleEx (name=0xbfdce677
> "apport.report", co=0x9d0b3c8,
> pathname=0xbfdcc5c7 "/var/lib/python-support/python2.5/apport/
> report.pyc") at ../Python/import.c:675
> #29 0x080df306 in load_source_module (name=0xbfdce677 "apport.report",
> pathname=0xbfdcc5c7 "/var/lib/python-support/python2.5/apport/
> report.pyc", fp=<value optimized out>)
> at ../Python/import.c:959
> #30 0x080df98b in import_submodule (mod=0x976117c,
> subname=0xbfdce67e "report", fullname=0xbfdce677 "apport.report")
> at ../Python/import.c:2400
> #31 0x080dfe3e in load_next (mod=0x976117c, altmod=0x976117c,
> p_name=<value optimized out>, buf=0xbfdce677 "apport.report",
> p_buflen=0xbfdce670) at ../Python/import.c:2220
> #32 0x080e00b0 in import_module_level (name=0x0, globals=<value
> optimized out>, locals=<value optimized out>,
> fromlist=0x9cfa74c, level=-1) at ../Python/import.c:2008
> #33 0x080e04f7 in PyImport_ImportModuleLevel (name=0xb7d62d04
> "apport.report", globals=0x9cfc604, locals=0x9cfc604,
> fromlist=0x9cfa74c, level=-1) at ../Python/import.c:2072
> #34 0x080c1db4 in builtin___import__ (self=0x0, args=0x9cfdb94,
> kwds=0x0) at ../Python/bltinmodule.c:47
> #35 0x0805c9e7 in PyObject_Call (func=0x0, arg=0x9cfdb94, kw=0x0)
> at ../Objects/abstract.c:1860
> #36 0x080c232c in PyEval_CallObjectWithKeywords (func=0xb7da7e6c,
> arg=0x9cfdb94, kw=0x0) at ../Python/ceval.c:3433
> ---Type <return> to continue, or q <return> to quit---
> #37 0x080c4a9d in PyEval_EvalFrameEx (f=0x9b4549c, throwflag=0)
> at ../Python/ceval.c:2063
> #38 0x080ca115 in PyEval_EvalCodeEx (co=0x9d01188,
> globals=0x9cfc604, locals=0x9cfc604, args=0x0, argcount=0, kws=0x0,
> kwcount=0, defs=0x0, defcount=0, closure=0x0) at ../Python/
> ceval.c:2831
> #39 0x080ca187 in PyEval_EvalCode (co=0x9d01188, globals=0x9cfc604,
> locals=0x9cfc604) at ../Python/ceval.c:494
> #40 0x080de9ac in PyImport_ExecCodeModuleEx (name=0xbfdd2ae7
> "apport", co=0x9d01188,
> pathname=0xbfdcf9f7 "/var/lib/python-support/python2.5/apport/
> __init__.pyc") at ../Python/import.c:675
> #41 0x080df306 in load_source_module (name=0xbfdd2ae7 "apport",
> pathname=0xbfdcf9f7 "/var/lib/python-support/python2.5/apport/
> __init__.pyc", fp=<value optimized out>)
> at ../Python/import.c:959
> #42 0x080e09ce in load_package (name=0xbfdd2ae7 "apport",
> pathname=<value optimized out>) at ../Python/import.c:1015
> #43 0x080df98b in import_submodule (mod=0x81466b8,
> subname=0xbfdd2ae7 "apport", fullname=0xbfdd2ae7 "apport")
> at ../Python/import.c:2400
> #44 0x080dfe3e in load_next (mod=0x81466b8, altmod=0x81466b8,
> p_name=<value optimized out>, buf=0xbfdd2ae7 "apport",
> p_buflen=0xbfdd2ae0) at ../Python/import.c:2220
> #45 0x080e0068 in import_module_level (name=0xb7d62dd3 "fileutils",
> globals=0xb7dd3e74, locals=<value optimized out>,
> fromlist=0xb7dc8c2c, level=-1) at ../Python/import.c:2001
> #46 0x080e04f7 in PyImport_ImportModuleLevel (name=0xb7d62dcc
> "apport.fileutils", globals=0xb7d60824, locals=0x81466b8,
> fromlist=0xb7dc8c2c, level=-1) at ../Python/import.c:2072
> #47 0x080c1db4 in builtin___import__ (self=0x0, args=0x93227ac,
> kwds=0x0) at ../Python/bltinmodule.c:47
> #48 0x0805c9e7 in PyObject_Call (func=0x0, arg=0x93227ac, kw=0x0)
> at ../Objects/abstract.c:1860
> #49 0x080c232c in PyEval_CallObjectWithKeywords (func=0xb7da7e6c,
> arg=0x93227ac, kw=0x0) at ../Python/ceval.c:3433
> #50 0x080c4a9d in PyEval_EvalFrameEx (f=0x99eea64, throwflag=0)
> at ../Python/ceval.c:2063
> #51 0x080ca115 in PyEval_EvalCodeEx (co=0xb7dc9380,
> globals=0xb7d60824, locals=0x0, args=0x962f830, argcount=3, kws=0x0,
> kwcount=0, defs=0x0, defcount=0, closure=0x0) at ../Python/
> ceval.c:2831
> #52 0x081123e1 in function_call (func=0xb7d6179c, arg=0x962f824,
> kw=0x0) at ../Objects/funcobject.c:517
> #53 0x0805c9e7 in PyObject_Call (func=0x0, arg=0x962f824, kw=0x0)
> at ../Objects/abstract.c:1860
> #54 0x080c232c in PyEval_CallObjectWithKeywords (func=0xb7d6179c,
> arg=0x962f824, kw=0x0) at ../Python/ceval.c:3433
> #55 0x080e8f8e in PyErr_PrintEx (set_sys_last_vars=1) at ../Python/
> pythonrun.c:1082
> #56 0x080e9883 in PyRun_SimpleFileExFlags (fp=0x816a008,
> filename=0xbfdd4429 "/local/nolden/itk-3.4.0/
> InsightToolkit-3.4.0/Wrapping/WrapITK/Python/Tests/template.py",
> closeit=1, flags=0xbfdd3fc8) at ../Python/pythonrun.c:978
> ---Type <return> to continue, or q <return> to quit---
> #57 0x08059390 in Py_Main (argc=1, argv=0xbfdd4094) at ../Modules/
> main.c:523
> #58 0x080588c2 in main (argc=Cannot access memory at address 0x0
> ) at ../Modules/python.c:23
> (gdb)
--
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
http://voxel.jouy.inra.fr
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