[SciPy-dev] scipy-weave unit tests fail on KeyError

Emmanuel Lambert Emmanuel.Lambert at intec.ugent.be
Thu Sep 24 02:57:41 EDT 2009 

Hi,

I compiled SciPy and Numpy on a machine with Scientific Linux (64bit).
We detected a problem with Weave and after
investigation, it turns out that some of the unit tests delivered
with Scipy-Weave also fail ! Below is a list of tests that fail in for
example the "test_c_spec" file. They all raise a KeyError.

This is with SciPy 0.7.1 on Python 2.6. I also downloaded the latest
Weave code again from the SVN repository (trunk), but the problem is not
resolved.

Any idea on how to tackle this problem? There are no posts that help
me further. 
It looks like the compilation done by Weave works fine (see sample
stdout also below), but afterwards, he cannot find the compiled code in
the list.

What could cause this? 

thanks for any help.
Emmanuel

******************* SAMPLE OF STDOUT ******************

-------------------- >> begin captured stdout << ---------------------
<weave: compiling>
running build_ext
running build_src
building extension "sc_d133102ab45193e072f8dbb5a1f6848513" sources
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'sc_d133102ab45193e072f8dbb5a1f6848513' extension
compiling C++ sources
C compiler: g++ -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -
Wall -fPIC

compile options: '-I/user/home/gent/vsc401/vsc40157/scipy-runtime/
scipy/weave -I/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/
weave/scxx -I/user/home/gent/vsc401/vsc40157/numpy-runtime/numpy/core/
include -I/apps/gent/gengar/harpertown/software/Python/2.6.2-
gimkl-0.5.0/include/python2.6 -c'
g++: /user/home/gent/vsc401/vsc40157/.python26_compiled/
sc_d133102ab45193e072f8dbb5a1f6848513.cpp
g++ -pthread -shared /tmp/vsc40157/python26_intermediate/
compiler_c1b5f1b73f1ce7d0c836cdad4c7c5ded/user/home/gent/vsc401/
vsc40157/.python26_compiled/sc_d133102ab45193e072f8dbb5a1f6848513.o /
tmp/vsc40157/python26_intermediate/
compiler_c1b5f1b73f1ce7d0c836cdad4c7c5ded/user/home/gent/vsc401/
vsc40157/scipy-runtime/scipy/weave/scxx/weave_imp.o -o /user/home/gent/
vsc401/vsc40157/.python26_compiled/
sc_d133102ab45193e072f8dbb5a1f6848513.so
running scons

--------------------- >> end captured stdout << ----------------------


********************** TESTS THAT FAIL ***********************

-bash-3.2$ python ./test_c_spec.py
E..........EE.................EEEE......E..........EE.................EEEE..............
======================================================================
ERROR: test_call_function (test_c_spec.CallableConverter)
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
tests/test_c_spec.py", line 296, in test_call_function
   compiler=self.compiler,force=1)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
inline_tools.py", line 301, in inline
   function_catalog.add_function(code,func,module_dir)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 648, in add_function
   self.cache[code] = self.get_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 615, in get_functions
   function_list = self.get_cataloged_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 529, in get_cataloged_functions
   if cat is not None and code in cat:
 File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/
lib/python2.6/shelve.py", line 110, in __contains__
   return key in self.dict
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/
dumbdbm_patched.py", line 73, in __getitem__
   pos, siz = self._index[key] # may raise KeyError
KeyError: 0

======================================================================
ERROR: test_file_to_py (test_c_spec.FileConverter)
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
tests/test_c_spec.py", line 262, in test_file_to_py
   force=1)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
inline_tools.py", line 301, in inline
   function_catalog.add_function(code,func,module_dir)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 648, in add_function
   self.cache[code] = self.get_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 615, in get_functions
   function_list = self.get_cataloged_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 529, in get_cataloged_functions
   if cat is not None and code in cat:
 File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/
lib/python2.6/shelve.py", line 110, in __contains__
   return key in self.dict
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/
dumbdbm_patched.py", line 73, in __getitem__
   pos, siz = self._index[key] # may raise KeyError
KeyError: 0

======================================================================
ERROR: test_py_to_file (test_c_spec.FileConverter)
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
tests/test_c_spec.py", line 246, in test_py_to_file
   inline_tools.inline(code,['file'],compiler=self.compiler,force=1)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
inline_tools.py", line 301, in inline
   function_catalog.add_function(code,func,module_dir)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 648, in add_function
   self.cache[code] = self.get_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 615, in get_functions
   function_list = self.get_cataloged_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 529, in get_cataloged_functions
   if cat is not None and code in cat:
 File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/
lib/python2.6/shelve.py", line 110, in __contains__
   return key in self.dict
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/
dumbdbm_patched.py", line 73, in __getitem__
   pos, siz = self._index[key] # may raise KeyError
KeyError: 0

======================================================================
ERROR: test_convert_to_dict (test_c_spec.SequenceConverter)
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
tests/test_c_spec.py", line 305, in test_convert_to_dict
   inline_tools.inline("",['d'],compiler=self.compiler,force=1)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
inline_tools.py", line 301, in inline
   function_catalog.add_function(code,func,module_dir)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 648, in add_function
   self.cache[code] = self.get_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 615, in get_functions
   function_list = self.get_cataloged_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 529, in get_cataloged_functions
   if cat is not None and code in cat:
 File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/
lib/python2.6/shelve.py", line 110, in __contains__
   return key in self.dict
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/
dumbdbm_patched.py", line 73, in __getitem__
   pos, siz = self._index[key] # may raise KeyError
KeyError: 0

======================================================================
ERROR: test_convert_to_list (test_c_spec.SequenceConverter)
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
tests/test_c_spec.py", line 309, in test_convert_to_list
   inline_tools.inline("",['l'],compiler=self.compiler,force=1)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
inline_tools.py", line 301, in inline
   function_catalog.add_function(code,func,module_dir)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 648, in add_function
   self.cache[code] = self.get_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 615, in get_functions
   function_list = self.get_cataloged_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 529, in get_cataloged_functions
   if cat is not None and code in cat:
 File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/
lib/python2.6/shelve.py", line 110, in __contains__
   return key in self.dict
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/
dumbdbm_patched.py", line 73, in __getitem__
   pos, siz = self._index[key] # may raise KeyError
KeyError: 0

======================================================================
ERROR: test_convert_to_string (test_c_spec.SequenceConverter)
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
tests/test_c_spec.py", line 313, in test_convert_to_string
   inline_tools.inline("",['s'],compiler=self.compiler,force=1)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
inline_tools.py", line 301, in inline
   function_catalog.add_function(code,func,module_dir)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 648, in add_function
   self.cache[code] = self.get_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 615, in get_functions
   function_list = self.get_cataloged_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 529, in get_cataloged_functions
   if cat is not None and code in cat:
 File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/
lib/python2.6/shelve.py", line 110, in __contains__
   return key in self.dict
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/
dumbdbm_patched.py", line 73, in __getitem__
   pos, siz = self._index[key] # may raise KeyError
KeyError: 0

======================================================================
ERROR: test_convert_to_tuple (test_c_spec.SequenceConverter)
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
tests/test_c_spec.py", line 317, in test_convert_to_tuple
   inline_tools.inline("",['t'],compiler=self.compiler,force=1)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
inline_tools.py", line 301, in inline
   function_catalog.add_function(code,func,module_dir)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 648, in add_function
   self.cache[code] = self.get_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 615, in get_functions
   function_list = self.get_cataloged_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 529, in get_cataloged_functions
   if cat is not None and code in cat:
 File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/
lib/python2.6/shelve.py", line 110, in __contains__
   return key in self.dict
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/
dumbdbm_patched.py", line 73, in __getitem__
   pos, siz = self._index[key] # may raise KeyError
KeyError: 0

======================================================================
ERROR: test_call_function (test_c_spec.TestCallableConverterUnix)
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
tests/test_c_spec.py", line 296, in test_call_function
   compiler=self.compiler,force=1)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
inline_tools.py", line 301, in inline
   function_catalog.add_function(code,func,module_dir)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 648, in add_function
   self.cache[code] = self.get_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 615, in get_functions
   function_list = self.get_cataloged_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 529, in get_cataloged_functions
   if cat is not None and code in cat:
 File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/
lib/python2.6/shelve.py", line 110, in __contains__
   return key in self.dict
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/
dumbdbm_patched.py", line 73, in __getitem__
   pos, siz = self._index[key] # may raise KeyError
KeyError: 0

======================================================================
ERROR: test_file_to_py (test_c_spec.TestFileConverterUnix)
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
tests/test_c_spec.py", line 262, in test_file_to_py
   force=1)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
inline_tools.py", line 301, in inline
   function_catalog.add_function(code,func,module_dir)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 648, in add_function
   self.cache[code] = self.get_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 615, in get_functions
   function_list = self.get_cataloged_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 529, in get_cataloged_functions
   if cat is not None and code in cat:
 File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/
lib/python2.6/shelve.py", line 110, in __contains__
   return key in self.dict
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/
dumbdbm_patched.py", line 73, in __getitem__
   pos, siz = self._index[key] # may raise KeyError
KeyError: 0

======================================================================
ERROR: test_py_to_file (test_c_spec.TestFileConverterUnix)
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
tests/test_c_spec.py", line 246, in test_py_to_file
   inline_tools.inline(code,['file'],compiler=self.compiler,force=1)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
inline_tools.py", line 301, in inline
   function_catalog.add_function(code,func,module_dir)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 648, in add_function
   self.cache[code] = self.get_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 615, in get_functions
   function_list = self.get_cataloged_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 529, in get_cataloged_functions
   if cat is not None and code in cat:
 File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/
lib/python2.6/shelve.py", line 110, in __contains__
   return key in self.dict
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/
dumbdbm_patched.py", line 73, in __getitem__
   pos, siz = self._index[key] # may raise KeyError
KeyError: 0

======================================================================
ERROR: test_convert_to_dict (test_c_spec.TestSequenceConverterUnix)
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
tests/test_c_spec.py", line 305, in test_convert_to_dict
   inline_tools.inline("",['d'],compiler=self.compiler,force=1)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
inline_tools.py", line 301, in inline
   function_catalog.add_function(code,func,module_dir)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 648, in add_function
   self.cache[code] = self.get_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 615, in get_functions
   function_list = self.get_cataloged_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 529, in get_cataloged_functions
   if cat is not None and code in cat:
 File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/
lib/python2.6/shelve.py", line 110, in __contains__
   return key in self.dict
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/
dumbdbm_patched.py", line 73, in __getitem__
   pos, siz = self._index[key] # may raise KeyError
KeyError: 0

======================================================================
ERROR: test_convert_to_list (test_c_spec.TestSequenceConverterUnix)
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
tests/test_c_spec.py", line 309, in test_convert_to_list
   inline_tools.inline("",['l'],compiler=self.compiler,force=1)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
inline_tools.py", line 301, in inline
   function_catalog.add_function(code,func,module_dir)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 648, in add_function
   self.cache[code] = self.get_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 615, in get_functions
   function_list = self.get_cataloged_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 529, in get_cataloged_functions
   if cat is not None and code in cat:
 File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/
lib/python2.6/shelve.py", line 110, in __contains__
   return key in self.dict
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/
dumbdbm_patched.py", line 73, in __getitem__
   pos, siz = self._index[key] # may raise KeyError
KeyError: 0

======================================================================
ERROR: test_convert_to_string (test_c_spec.TestSequenceConverterUnix)
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
tests/test_c_spec.py", line 313, in test_convert_to_string
   inline_tools.inline("",['s'],compiler=self.compiler,force=1)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
inline_tools.py", line 301, in inline
   function_catalog.add_function(code,func,module_dir)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 648, in add_function
   self.cache[code] = self.get_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 615, in get_functions
   function_list = self.get_cataloged_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 529, in get_cataloged_functions
   if cat is not None and code in cat:
 File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/
lib/python2.6/shelve.py", line 110, in __contains__
   return key in self.dict
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/
dumbdbm_patched.py", line 73, in __getitem__
   pos, siz = self._index[key] # may raise KeyError
KeyError: 0

======================================================================
ERROR: test_convert_to_tuple (test_c_spec.TestSequenceConverterUnix)
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
tests/test_c_spec.py", line 317, in test_convert_to_tuple
   inline_tools.inline("",['t'],compiler=self.compiler,force=1)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
inline_tools.py", line 301, in inline
   function_catalog.add_function(code,func,module_dir)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 648, in add_function
   self.cache[code] = self.get_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 615, in get_functions
   function_list = self.get_cataloged_functions(code)
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/weave/
catalog.py", line 529, in get_cataloged_functions
   if cat is not None and code in cat:
 File "/apps/gent/gengar/harpertown/software/Python/2.6.2-gimkl-0.5.0/
lib/python2.6/shelve.py", line 110, in __contains__
   return key in self.dict
 File "/user/home/gent/vsc401/vsc40157/scipy-runtime/scipy/io/
dumbdbm_patched.py", line 73, in __getitem__
   pos, siz = self._index[key] # may raise KeyError
KeyError: 0

----------------------------------------------------------------------
Ran 88 tests in 32.581s

FAILED (errors=14)

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