[SciPy-Dev] test output 0.7.2rc1

Ralf Gommers ralf.gommers@googlemail....
Thu Apr 1 09:24:21 CDT 2010


Hi all,

Here is the test output of the scipy 0.7.2rc1 for OS X. All tests pass with
numpy 1.3.0, two (harmless) failures with numpy 1.4.x branch. Outputs pasted
below. The questions I have are:
1. during compilation, is it normal for sparsetools to take forever and use
all available cpu cycles? I actually killed compilations before because I
thought I must have passed in the wrong flags, but it seems to work in the
end.
2. why am I warned about using fblas instead of cblas?
3. There seems to be a problem with the N_GSYM symbol, any idea what that
complaint is about (see partial build log at the bottom of this mail)?


Built with
$ export CC=/usr/bin/gcc-4.0
$ export CXX=/usr/bin/c++-4.0
$ paver dmg -p2.6

Cheers,
Ralf



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

In [2]: sp.test()
Running unit tests for scipy
NumPy version 1.3.0
NumPy is installed in /Users/rgommers/Code/numpy/numpy
SciPy version 0.7.2rc1
SciPy is installed in
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy
Python version 2.6.4 (r264:75821M, Oct 27 2009, 19:48:32) [GCC 4.0.1 (Apple
Inc. build 5493)]
nose version 0.11.1
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/linsolve/__init__.py:4:
DeprecationWarning: scipy.linsolve has moved to scipy.sparse.linalg.dsolve
  warn('scipy.linsolve has moved to scipy.sparse.linalg.dsolve',
DeprecationWarning)
............................................................................................................................................................................................................................./Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/interpolate/fitpack2.py:498:
UserWarning:
The coefficients of the spline returned have been computed as the
minimal norm least-squares solution of a (numerically) rank deficient
system (deficiency=7). If deficiency is large, the results may be
inaccurate. Deficiency may strongly depend on the value of eps.
  warnings.warn(message)
...../Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/interpolate/fitpack2.py:439:
UserWarning:
The required storage space exceeds the available storage space: nxest
or nyest too small, or s too small.
The weighted least-squares spline corresponds to the current set of
knots.
  warnings.warn(message)
...........................................K..K................................................................................................./Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/io/matlab/mio.py:111:
Warning: Unreadable variable "testfunc", because "Cannot read matlab
functions"
  matfile_dict = MR.get_variables()
........../Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/io/matlab/mio.py:165:
FutureWarning: Using oned_as default value ('column') This will change to
'row' in future versions
  oned_as=oned_as)
........................./Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/io/matlab/tests/test_mio.py:438:
FutureWarning: Using oned_as default value ('column') This will change to
'row' in future versions
  mfw = MatFile5Writer(StringIO())
......../Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/io/matlab/mio.py:84:
FutureWarning: Using struct_as_record default value (False) This will change
to True in future versions
  return MatFile5Reader(byte_stream, **kwargs)
...............................Warning: 1000000 bytes requested, 20 bytes
read.
./Users/rgommers/Code/numpy/numpy/lib/utils.py:108: DeprecationWarning:
write_array is deprecated
  warnings.warn(str1, DeprecationWarning)
/Users/rgommers/Code/numpy/numpy/lib/utils.py:108: DeprecationWarning:
read_array is deprecated
  warnings.warn(str1, DeprecationWarning)
......................./Users/rgommers/Code/numpy/numpy/lib/utils.py:108:
DeprecationWarning: npfile is deprecated
  warnings.warn(str1, DeprecationWarning)
.........................................................................................................................................................SSSSSS......SSSSSS......SSSS....NO
ATLAS INFO AVAILABLE
.........................................
****************************************************************
WARNING: cblas module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
  then scipy uses fblas instead of cblas.
****************************************************************

................S...................................................../Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/linalg/decomp.py:1177:
DeprecationWarning: qr econ argument will be removed after scipy 0.7. The
economy transform will then be available through the mode='economic'
argument.
  "the mode='economic' argument.", DeprecationWarning)
..........................................................................................................................................................................................................................................................................................
****************************************************************
WARNING: clapack module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
  then scipy uses flapack instead of clapack.
****************************************************************

...Result may be inaccurate, approximate err = 7.68933681286e-09
...Result may be inaccurate, approximate err = 7.27595761418e-12
.....SSS..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SSSSSSSSSSS...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K.K.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................../Users/rgommers/Code/numpy/numpy/lib/function_base.py:324:
Warning:
            The new semantics of histogram is now the default and the `new`
            keyword will be removed in NumPy 1.4.

  """, Warning)
....................................................................................S................................................................................../Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/stats.py:420:
DeprecationWarning: scipy.stats.mean is deprecated; please update your code
to use numpy.mean.
Please note that:
    - numpy.mean axis argument defaults to None, not 0
    - numpy.mean has a ddof argument to replace bias in a more general
manner.
      scipy.stats.mean(a, bias=True) can be replaced by numpy.mean(x,
axis=0, ddof=1).
  axis=0, ddof=1).""", DeprecationWarning)
./Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/stats.py:1329:
DeprecationWarning: scipy.stats.std is deprecated; please update your code
to use numpy.std.
Please note that:
    - numpy.std axis argument defaults to None, not 0
    - numpy.std has a ddof argument to replace bias in a more general
manner.
      scipy.stats.std(a, bias=True) can be replaced by numpy.std(x,
      axis=0, ddof=0), scipy.stats.std(a, bias=False) by numpy.std(x,
axis=0,
      ddof=1).
  ddof=1).""", DeprecationWarning)
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/stats.py:1305:
DeprecationWarning: scipy.stats.var is deprecated; please update your code
to use numpy.var.
Please note that:
    - numpy.var axis argument defaults to None, not 0
    - numpy.var has a ddof argument to replace bias in a more general
manner.
      scipy.stats.var(a, bias=True) can be replaced by numpy.var(x,
      axis=0, ddof=0), scipy.stats.var(a, bias=False) by var(x, axis=0,
      ddof=1).
  ddof=1).""", DeprecationWarning)
./Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/morestats.py:603:
UserWarning: Ties preclude use of exact statistic.
  warnings.warn("Ties preclude use of exact statistic.")
....../Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/stats/stats.py:498:
DeprecationWarning: scipy.stats.median is deprecated; please update your
code to use numpy.median.
Please note that:
    - numpy.median axis argument defaults to None, not 0
    - numpy.median has a ddof argument to replace bias in a more general
manner.
      scipy.stats.median(a, bias=True) can be replaced by numpy.median(x,
axis=0, ddof=1).
  axis=0, ddof=1).""", DeprecationWarning)
....................................................................................................................................................................................................Warning:
friedmanchisquare test using Chisquared aproximation
...............warning: specified build_dir '_bad_path_' does not exist or
is not writable. Trying default locations
...warning: specified build_dir '..' 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
...warning: specified build_dir '..' does not exist or is not writable.
Trying default locations
............................building extensions here:
/Users/rgommers/.python26_compiled/m13
................................................................................................
----------------------------------------------------------------------
Ran 3488 tests in 55.516s

OK (KNOWNFAIL=4, SKIP=32)
Out[2]: <nose.result.TextTestResult run=3488 errors=0 failures=0>


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



In [6]: sp.test()
Running unit tests for scipy
NumPy version 1.4.0
NumPy is installed in
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy
SciPy version 0.7.2rc1
SciPy is installed in
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy
Python version 2.6.4 (r264:75821M, Oct 27 2009, 19:48:32) [GCC 4.0.1 (Apple
Inc. build 5493)]
nose version 0.11.1
.............................................................................................................................................................................................................................................................................K..K...........................................................................................................................F...............................................Warning:
1000000 bytes requested, 20 bytes read.
.................................................................................................................................................................................SSSSSS......SSSSSS......SSSS.............................................
****************************************************************
WARNING: cblas module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
  then scipy uses fblas instead of cblas.
****************************************************************

................S...............................................................................................................................................................................................................................................................................................................................................
****************************************************************
WARNING: clapack module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
  then scipy uses flapack instead of clapack.
****************************************************************

...Result may be inaccurate, approximate err = 7.68933681286e-09
...Result may be inaccurate, approximate err = 7.27595761418e-12
.....SSS..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SSSSSSSSSSS...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K.K.....................................................................................................................................F.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................S..............................................................................................................................................................................................................................................................................................Warning:
friedmanchisquare test using Chisquared aproximation
...............warning: specified build_dir '_bad_path_' does not exist or
is not writable. Trying default locations
...warning: specified build_dir '..' 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
...warning: specified build_dir '..' does not exist or is not writable.
Trying default locations
............................................................................................................................
======================================================================
FAIL: test_mio.test_warnings(<type 'exceptions.FutureWarning'>, <function
loadmat at 0x4c59e70>,
'/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/io/matlab/tests/data/testdouble_7.1_GLNX86.mat')
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/nose-0.11.1-py2.6.egg/nose/case.py",
line 183, in runTest
    self.test(*self.arg)
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/testing/utils.py",
line 973, in assert_raises
    return nose.tools.assert_raises(*args,**kwargs)
AssertionError: FutureWarning not raised

======================================================================
FAIL: test_nrdtrisd (test_basic.TestCephes)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/special/tests/test_basic.py",
line 349, in test_nrdtrisd
    assert_equal(cephes.nrdtrisd(0.5,0.5,0.5),0.0)
  File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/testing/utils.py",
line 301, in assert_equal
    raise AssertionError(msg)
AssertionError:
Items are not equal:
 ACTUAL: -0
 DESIRED: 0.0

----------------------------------------------------------------------
Ran 3488 tests in 58.811s

FAILED (KNOWNFAIL=4, SKIP=32, failures=2)
Out[6]: <nose.result.TextTestResult run=3488 errors=0 failures=2>




######################### part of build log
######################################

building 'scipy.special._cephes' extension
compiling C sources
C compiler: /usr/bin/gcc-4.0 -arch ppc -arch i386 -isysroot
/Developer/SDKs/MacOSX10.4u.sdk -fno-strict-aliasing -fno-common -dynamic
-DNDEBUG -g -O3

compile options: '-I/Users/rgommers/Code/numpy/numpy/core/include
-I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c'
gcc-4.0: scipy/special/specfun_wrappers.c
gcc-4.0: scipy/special/toms_wrappers.c
gcc-4.0: scipy/special/ufunc_extras.c
gcc-4.0: scipy/special/cdf_wrappers.c
gcc-4.0: scipy/special/amos_wrappers.c
gcc-4.0: scipy/special/_cephesmodule.c
/usr/local/bin/gfortran -Wall -undefined dynamic_lookup -bundle -arch i386
-arch ppc -Wl,-search_paths_first -Lbuild
build/temp.macosx-10.3-fat-2.6/scipy/special/_cephesmodule.o
build/temp.macosx-10.3-fat-2.6/scipy/special/amos_wrappers.o
build/temp.macosx-10.3-fat-2.6/scipy/special/specfun_wrappers.o
build/temp.macosx-10.3-fat-2.6/scipy/special/toms_wrappers.o
build/temp.macosx-10.3-fat-2.6/scipy/special/cdf_wrappers.o
build/temp.macosx-10.3-fat-2.6/scipy/special/ufunc_extras.o
-Lbuild/temp.macosx-10.3-fat-2.6 -lsc_amos -lsc_toms -lsc_c_misc -lsc_cephes
-lsc_mach -lsc_cdf -lsc_specfun -lgfortran -o
build/lib.macosx-10.3-fat-2.6/scipy/special/_cephes.so
ld: warning: can't find atom for N_GSYM stabs max_offset:G(0,32) in
build/libgfortran.a(unit.o)
ld: warning: can't find atom for N_GSYM stabs unit_root:G(0,1) in
build/libgfortran.a(unit.o)
ld: warning: can't find atom for N_GSYM stabs unit_lock:G(0,37) in
build/libgfortran.a(unit.o)
ld: warning: can't find atom for N_GSYM stabs l8_to_l4_offset:G(0,2) in
build/libgfortran.a(main.o)
ld: warning: can't find atom for N_GSYM stabs
options:G(0,32)=(0,33)=s72stdin_unit:(0,8),0,32;stdout_unit:(0,8),32,32;stderr_unit:(0,8),64,32;optional_plus:(0,8),96,32;allocate_init_flag:(0,8),128,32;allocate_init_value:(0,8),160,32;locus:(0,8),192,32;separator_len:(0,8),224,32;separator:(0,5),256,32;mem_check:(0,8),288,32;use_stderr:(0,8),320,32;all_unbuffered:(0,8),352,32;default_recl:(0,8),384,32;fpu_round:(0,8),416,32;fpu_precision:(0,8),448,32;fpe:(0,8),480,32;sighup:(0,8),512,32;sigint:(0,8),544,32;;
in build/libgfortran.a(environ.o)
ld: warning: can't find atom for N_GSYM stabs
compile_options:G(0,5)=(0,6)=s24warn_std:(0,4),0,32;allow_std:(0,4),32,32;pedantic:(0,4),64,32;convert:(0,4),96,32;record_marker:(0,7)=(0,8)=r(0,8);0;037777777777;,128,32;max_subrecord_length:(0,4),160,32;;
in build/libgfortran.a(compile_options.o)
ld: warning: object file compiled with -mlong-branch which is no longer
needed. To remove this warning, recompile without -mlong-branch:
/usr/local/lib/gcc/powerpc-apple-darwin8/4.2.3/crt3.o
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