[SciPy-user] Scipy.test() fails when building scipy-0.6 against numpy 1.1
LB
berthe.loic at gmail.com
Tue Jun 3 15:05:34 EDT 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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