[SciPy-user] Scipy.test() fails when building scipy-0.6 against numpy 1.1

LB berthe.loic@gmail....
Tue Jun 3 14:05:34 CDT 2008


     hi,

I'm trying to build scipy 0.6 with numpy 1.1 on a linux (32bits )and
I'm seeing errors when I run the test suite :

####################  ERROR MESSAGES
#####################################
.....................................................................................................
======================================================================
ERROR: check_string_add_speed (test_scxx_sequence.test_list)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/tests/test_scxx_sequence.py", line 405, in
check_string_add_speed
    inline_tools.inline(code,['a','b'])
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/inline_tools.py", line 339, in inline
    **kw)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/inline_tools.py", line 447, in compile_function
    verbose=verbose, **kw)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/ext_tools.py", line 365, in compile
    verbose = verbose, **kw)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/build_tools.py", line 269, in build_extension
    setup(name = module_name, ext_modules = [ext],verbose=verb)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/numpy/
distutils/core.py", line 184, in setup
    return old_setup(**new_attr)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/distutils/core.py",
line 168, in setup
    raise SystemExit, "error: " + str(msg)
CompileError: error: Command "g++ -pthread -fno-strict-aliasing -
DNDEBUG -g -O3 -Wall -fPIC -I/home/loic/tmp/bluelagoon/lib/python2.5/
site-packages/scipy/weave -I/home/loic/tmp/bluelagoon/lib/python2.5/
site-packages/scipy/weave/scxx -I/home/loic/tmp/bluelagoon/lib/
python2.5/site-packages/numpy/core/include -I/home/loic/tmp/bluelagoon/
include/python2.5 -c /home/loic/.python25_compiled/
sc_30bcdfe77c16ba01711b3f9b4f2d38df0.cpp -o /tmp/loic/
python25_intermediate/compiler_e0195f93cbce8aefbd6efe084f3c364b/home/
loic/.python25_compiled/sc_30bcdfe77c16ba01711b3f9b4f2d38df0.o" failed
with exit status 1

======================================================================
ERROR: check_false (test_scxx_object.test_object_is_true)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/tests/test_scxx_object.py", line 656, in check_false
    res = inline_tools.inline('return_val = a.mcall("not");',['a'])
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/inline_tools.py", line 342, in inline
    results = attempt_function_call(code,local_dict,global_dict)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/inline_tools.py", line 354, in attempt_function_call
    results = apply(func,(local_dict,global_dict))
AttributeError: foo instance has no attribute 'not'

======================================================================
ERROR: check_true (test_scxx_object.test_object_is_true)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/tests/test_scxx_object.py", line 660, in check_true
    res = inline_tools.inline('return_val = a.mcall("not");',['a'])
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/inline_tools.py", line 342, in inline
    results = attempt_function_call(code,local_dict,global_dict)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/inline_tools.py", line 354, in attempt_function_call
    results = apply(func,(local_dict,global_dict))
AttributeError: 'NoneType' object has no attribute 'not'

======================================================================
ERROR: check_set_from_member
(test_scxx_object.test_object_set_item_op_key)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/tests/test_scxx_object.py", line 820, in check_set_from_member
    inline_tools.inline('a["first"] = a["second"];',['a'])
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/inline_tools.py", line 339, in inline
    **kw)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/inline_tools.py", line 447, in compile_function
    verbose=verbose, **kw)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/ext_tools.py", line 365, in compile
    verbose = verbose, **kw)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/build_tools.py", line 269, in build_extension
    setup(name = module_name, ext_modules = [ext],verbose=verb)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/numpy/
distutils/core.py", line 184, in setup
    return old_setup(**new_attr)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/distutils/core.py",
line 168, in setup
    raise SystemExit, "error: " + str(msg)
CompileError: error: Command "g++ -pthread -fno-strict-aliasing -
DNDEBUG -g -O3 -Wall -fPIC -I/home/loic/tmp/bluelagoon/lib/python2.5/
site-packages/scipy/weave -I/home/loic/tmp/bluelagoon/lib/python2.5/
site-packages/scipy/weave/scxx -I/home/loic/tmp/bluelagoon/lib/
python2.5/site-packages/numpy/core/include -I/home/loic/tmp/bluelagoon/
include/python2.5 -c /home/loic/.python25_compiled/
sc_a35665b241c24d6c9d3fd21e957285660.cpp -o /tmp/loic/
python25_intermediate/compiler_e0195f93cbce8aefbd6efe084f3c364b/home/
loic/.python25_compiled/sc_a35665b241c24d6c9d3fd21e957285660.o" failed
with exit status 1

======================================================================
ERROR: check_string_add_speed
(scipy.weave.tests.test_scxx_sequence.test_list)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/tests/test_scxx_sequence.py", line 405, in
check_string_add_speed
    inline_tools.inline(code,['a','b'])
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/inline_tools.py", line 339, in inline
    **kw)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/inline_tools.py", line 447, in compile_function
    verbose=verbose, **kw)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/ext_tools.py", line 365, in compile
    verbose = verbose, **kw)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/build_tools.py", line 269, in build_extension
    setup(name = module_name, ext_modules = [ext],verbose=verb)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/numpy/
distutils/core.py", line 184, in setup
    return old_setup(**new_attr)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/distutils/core.py",
line 168, in setup
    raise SystemExit, "error: " + str(msg)
CompileError: error: Command "g++ -pthread -fno-strict-aliasing -
DNDEBUG -g -O3 -Wall -fPIC -I/home/loic/tmp/bluelagoon/lib/python2.5/
site-packages/scipy/weave -I/home/loic/tmp/bluelagoon/lib/python2.5/
site-packages/scipy/weave/scxx -I/home/loic/tmp/bluelagoon/lib/
python2.5/site-packages/numpy/core/include -I/home/loic/tmp/bluelagoon/
include/python2.5 -c /home/loic/.python25_compiled/
sc_30bcdfe77c16ba01711b3f9b4f2d38df1.cpp -o /tmp/loic/
python25_intermediate/compiler_e0195f93cbce8aefbd6efe084f3c364b/home/
loic/.python25_compiled/sc_30bcdfe77c16ba01711b3f9b4f2d38df1.o" failed
with exit status 1

======================================================================
ERROR: check_false
(scipy.weave.tests.test_scxx_object.test_object_is_true)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/tests/test_scxx_object.py", line 656, in check_false
    res = inline_tools.inline('return_val = a.mcall("not");',['a'])
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/inline_tools.py", line 325, in inline
    results = attempt_function_call(code,local_dict,global_dict)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/inline_tools.py", line 354, in attempt_function_call
    results = apply(func,(local_dict,global_dict))
AttributeError: foo instance has no attribute 'not'

======================================================================
ERROR: check_true
(scipy.weave.tests.test_scxx_object.test_object_is_true)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/tests/test_scxx_object.py", line 660, in check_true
    res = inline_tools.inline('return_val = a.mcall("not");',['a'])
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/inline_tools.py", line 325, in inline
    results = attempt_function_call(code,local_dict,global_dict)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/inline_tools.py", line 354, in attempt_function_call
    results = apply(func,(local_dict,global_dict))
AttributeError: 'NoneType' object has no attribute 'not'

======================================================================
ERROR: check_set_from_member
(scipy.weave.tests.test_scxx_object.test_object_set_item_op_key)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/tests/test_scxx_object.py", line 820, in check_set_from_member
    inline_tools.inline('a["first"] = a["second"];',['a'])
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/inline_tools.py", line 339, in inline
    **kw)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/inline_tools.py", line 447, in compile_function
    verbose=verbose, **kw)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/ext_tools.py", line 365, in compile
    verbose = verbose, **kw)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/build_tools.py", line 269, in build_extension
    setup(name = module_name, ext_modules = [ext],verbose=verb)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/numpy/
distutils/core.py", line 184, in setup
    return old_setup(**new_attr)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/distutils/core.py",
line 168, in setup
    raise SystemExit, "error: " + str(msg)
CompileError: error: Command "g++ -pthread -fno-strict-aliasing -
DNDEBUG -g -O3 -Wall -fPIC -I/home/loic/tmp/bluelagoon/lib/python2.5/
site-packages/scipy/weave -I/home/loic/tmp/bluelagoon/lib/python2.5/
site-packages/scipy/weave/scxx -I/home/loic/tmp/bluelagoon/lib/
python2.5/site-packages/numpy/core/include -I/home/loic/tmp/bluelagoon/
include/python2.5 -c /home/loic/.python25_compiled/
sc_a35665b241c24d6c9d3fd21e957285661.cpp -o /tmp/loic/
python25_intermediate/compiler_e0195f93cbce8aefbd6efe084f3c364b/home/
loic/.python25_compiled/sc_a35665b241c24d6c9d3fd21e957285661.o" failed
with exit status 1

======================================================================
FAIL: check_syevr
(scipy.lib.lapack.tests.test_lapack.test_flapack_float)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
lib/lapack/tests/esv_tests.py", line 41, in check_syevr
    assert_array_almost_equal(w,exact_w)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/numpy/
testing/utils.py", line 255, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/numpy/
testing/utils.py", line 240, in assert_array_compare
    assert cond, msg
AssertionError:
Arrays are not almost equal

(mismatch 33.3333333333%)
 x: array([-0.66992444,  0.48769444,  9.18222713], dtype=float32)
 y: array([-0.66992434,  0.48769389,  9.18223045])

======================================================================
FAIL: check_syevr_irange
(scipy.lib.lapack.tests.test_lapack.test_flapack_float)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
lib/lapack/tests/esv_tests.py", line 66, in check_syevr_irange
    assert_array_almost_equal(w,exact_w[rslice])
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/numpy/
testing/utils.py", line 255, in assert_array_almost_equal
    header='Arrays are not almost equal')
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/numpy/
testing/utils.py", line 240, in assert_array_compare
    assert cond, msg
AssertionError:
Arrays are not almost equal

(mismatch 33.3333333333%)
 x: array([-0.66992444,  0.48769444,  9.18222713], dtype=float32)
 y: array([-0.66992434,  0.48769389,  9.18223045])

======================================================================
FAIL: check_noargs (test_scxx_object.test_object_call)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/tests/test_scxx_object.py", line 485, in check_noargs
    assert_equal(sys.getrefcount(res),2)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/numpy/
testing/utils.py", line 145, in assert_equal
    assert desired == actual, msg
AssertionError:
Items are not equal:
 ACTUAL: 3
 DESIRED: 2

======================================================================
FAIL: check_set_complex (test_scxx_object.test_object_set_item_op_key)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/tests/test_scxx_object.py", line 789, in check_set_complex
    assert_equal(sys.getrefcount(key),3)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/numpy/
testing/utils.py", line 145, in assert_equal
    assert desired == actual, msg
AssertionError:
Items are not equal:
 ACTUAL: 4
 DESIRED: 3

======================================================================
FAIL: check_noargs
(scipy.weave.tests.test_scxx_object.test_object_call)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/tests/test_scxx_object.py", line 485, in check_noargs
    assert_equal(sys.getrefcount(res),2)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/numpy/
testing/utils.py", line 145, in assert_equal
    assert desired == actual, msg
AssertionError:
Items are not equal:
 ACTUAL: 3
 DESIRED: 2

======================================================================
FAIL: check_set_complex
(scipy.weave.tests.test_scxx_object.test_object_set_item_op_key)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/
weave/tests/test_scxx_object.py", line 789, in check_set_complex
    assert_equal(sys.getrefcount(key),3)
  File "/home/loic/tmp/bluelagoon/lib/python2.5/site-packages/numpy/
testing/utils.py", line 145, in assert_equal
    assert desired == actual, msg
AssertionError:
Items are not equal:
 ACTUAL: 4
 DESIRED: 3

----------------------------------------------------------------------
Ran 2248 tests in 335.652s

FAILED (failures=6, errors=8)

###################################################################################

I didn't have theses errors with numpy 0.6.
I didn't have any problem when compiling, installing or testing numpy
1.1.


Besides, I see a lot of lines like
"""
/home/loic/.python25_compiled/sc_2b6af25d0035555e6a7579be09c9693c0.cpp:
34: attention : deprecated conversion from string constant to a char*
"""
With theses lines, my installation log is 2.6Mo big.


 Is this related with scipy's ticket  #490 ?
Have you got any clue to fix this ?

Thanks,

--
LB




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