[SciPy-user] Weave woes

[Paul-Michael Agapow]

I've got errors installing and using weave, that persist across  
different installations and Python versions.  My google-fu has failed  
me and an identical error reported on the mailing list some time ago  
went unanswered.

Symptoms: First I installed weave from svn into Python2.5 and ran  
weave.test():

      Found 1 tests for weave.ast_tools
      [...snip...]
      Found 26 tests for weave.catalog
    building extensions here: /Users/agapow/.python25_compiled/m3
      [...snip...]
      Found 3 tests for weave.standard_array_spec
    /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/ 
site-packages/weave/tests/test_wx_spec.py:16: DeprecationWarning: The  
wxPython compatibility package is no longer automatically generated  
or activly maintained.  Please switch to the wx package as soon as  
possible.
      import wxPython
      Found 0 tests for weave.wx_spec
      Found 0 tests for __main__
    ...warning: specified build_dir '_bad_path_' does not exist or is  
not writable. Trying default locations
    .....warning: specified build_dir '_bad_path_' does not exist or  
is not writable. Trying default locations
    ............................removing '/tmp/ 
tmptBN1Qxcat_test' (and everything under it)
    .removing '/tmp/tmpY2WiLfcat_test' (and everything under it)
    ..............................F..F.................................. 
...........................
     
======================================================================
    FAIL: check_1d_3  
(weave.tests.test_size_check.test_dummy_array_indexing)
     
----------------------------------------------------------------------
    Traceback (most recent call last):
      File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/weave/tests/test_size_check.py", line 168, in  
check_1d_3
        self.generic_1d('a[-11:]')
      File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/weave/tests/test_size_check.py", line 135, in  
generic_1d
        self.generic_wrap(a,expr)
      File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/weave/tests/test_size_check.py", line 127, in  
generic_wrap
        self.generic_test(a,expr,desired)
      File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/weave/tests/test_size_check.py", line 123, in  
generic_test
        assert_array_equal(actual,desired, expr)
      File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/numpy/testing/utils.py", line 223, in  
assert_array_equal
        verbose=verbose, header='Arrays are not equal')
      File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/numpy/testing/utils.py", line 215, in  
assert_array_compare
        assert cond, msg
    AssertionError:
    Arrays are not equal
    a[-11:]
    (mismatch 100.0%)
     x: array([1])
     y: array([10])

     
======================================================================
    FAIL: check_1d_6  
(weave.tests.test_size_check.test_dummy_array_indexing)
     
----------------------------------------------------------------------
    Traceback (most recent call last):
      File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/weave/tests/test_size_check.py", line 174, in  
check_1d_6
        self.generic_1d('a[:-11]')
      File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/weave/tests/test_size_check.py", line 135, in  
generic_1d
        self.generic_wrap(a,expr)
      File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/weave/tests/test_size_check.py", line 127, in  
generic_wrap
        self.generic_test(a,expr,desired)
      File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/weave/tests/test_size_check.py", line 123, in  
generic_test
        assert_array_equal(actual,desired, expr)
      File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/numpy/testing/utils.py", line 223, in  
assert_array_equal
        verbose=verbose, header='Arrays are not equal')
      File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/numpy/testing/utils.py", line 215, in  
assert_array_compare
        assert cond, msg
    AssertionError:
    Arrays are not equal
    a[:-11]
    (mismatch 100.0%)
     x: array([9])
     y: array([0])

I'm uncertain if the "__bad_path__" message is important, but the two  
errors may relfect issues with numpy (v1.0.1). I installed weave into  
Python2.4 for identical symptoms. I then installed the whole Scipy  
package just to be sure (weave 0.4.9, numpy 1.0.4.dev3882). No change.

Along the way - mindful that maybe the tests were broken - I tried  
out a simple line of weave::

    >>> a = 1; weave.inline('printf("%d\\n",a);',['a'])

which gave::

Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/weave/inline_tools.py", line 325, in inline
     results = attempt_function_call(code,local_dict,global_dict)
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/weave/inline_tools.py", line 375, in  
attempt_function_call
     function_list = function_catalog.get_functions(code,module_dir)
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/weave/catalog.py", line 611, in get_functions
     function_list = self.get_cataloged_functions(code)
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/weave/catalog.py", line 524, in  
get_cataloged_functions
     cat = get_catalog(path,mode)
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/site-packages/weave/catalog.py", line 294, in get_catalog
     or os.path.exists(catalog_file):
   File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python2.5/posixpath.py", line 171, in exists
     st = os.stat(path)
TypeError: coercing to Unicode: need string or buffer, NoneType found


Any ideas on what to try next? (Technical details: MacOSX 10.4.10  
Intel macBook,  gcc 4.0.1.)

--
Dr Paul-Michael Agapow: VieDigitale / Inst. for Animal Health
pma at viedigitale.com / paul-michael.agapow at bbsrc.ac.uk



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