[SciPy-User] Scipy test failure

John Reid j.reid@mail.cryst.bbk.ac...
Wed Apr 7 08:08:53 CDT 2010


Hi,

My scipy tests fail although I seem to have built numpy correctly using 
a similar configuration. I'm on OpenSuse with gcc 4.2.3 and I'm using 
the svn versions of numpy and scipy (2.0.0dev8324 and 0.8.0dev6310). I'm 
using UMFpack and GotoBlas. My python was compiled with a pre-release 
version of gcc 4.1.2

python2.5 -c "import numpy; numpy.test()"

gives me 4 known failures.


python2.5 -c "import scipy; scipy.test()"

gives me a lot of errors (see below) and then a segmentation fault. I've 
checked to see if I'm using different fortran compilers. As far as I can 
tell I'm just using gfortran.

What can I do to track down the problem?

Thanks in advance,
John.



Here's the scipy test output:
/usr/local/lib/python2.5/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)
/usr/local/lib/python2.5/site-packages/scipy/splinalg/__init__.py:3: 
DeprecationWarning: scipy.splinalg has moved to scipy.sparse.linalg
   warn('scipy.splinalg has moved to scipy.sparse.linalg', 
DeprecationWarning)
............................................................................................................................................................................................................................................................................../usr/local/lib/python2.5/site-packages/scipy/interpolate/fitpack2.py:512: 
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)
...../usr/local/lib/python2.5/site-packages/scipy/interpolate/fitpack2.py:453: 
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............................................................Warning: 
divide by zero encountered in log
Warning: invalid value encountered in multiply
Warning: divide by zero encountered in log
Warning: invalid value encountered in multiply
Warning: divide by zero encountered in log
Warning: invalid value encountered in multiply
.Warning: divide by zero encountered in log
Warning: invalid value encountered in multiply
Warning: divide by zero encountered in log
Warning: invalid value encountered in multiply
.Warning: divide by zero encountered in log
Warning: invalid value encountered in multiply
Warning: divide by zero encountered in log
Warning: invalid value encountered in multiply
.........Warning: divide by zero encountered in log
Warning: invalid value encountered in multiply
Warning: divide by zero encountered in log
Warning: invalid value encountered in multiply
.................................../usr/local/lib/python2.5/site-packages/scipy/io/matlab/mio.py:190: 
FutureWarning: Using oned_as default value ('column') This will change 
to 'row' in future versions
   oned_as=oned_as)
........................./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:435: 
FutureWarning: Using oned_as default value ('column') This will change 
to 'row' in future versions
   mfw = MatFile5Writer(StringIO())
....../usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:450: 
FutureWarning: Using oned_as default value ('column') This will change 
to 'row' in future versions
   wtr = MatFile5Writer(sio)
../usr/local/lib/python2.5/site-packages/scipy/io/matlab/mio.py:99: 
FutureWarning: Using struct_as_record default value (False) This will 
change to True in future versions
   return MatFile5Reader(byte_stream, **kwargs)
.............................../usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:633: 
FutureWarning: Using struct_as_record default value (False) This will 
change to True in future versions
   rdr = MatFile5Reader(stream)
./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:637: 
FutureWarning: Using struct_as_record default value (False) This will 
change to True in future versions
   rdr = MatFile5Reader(stream, squeeze_me=True)
../usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:641: 
FutureWarning: Using struct_as_record default value (False) This will 
change to True in future versions
   rdr = MatFile5Reader(stream, byte_order=boc.native_code)
./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:645: 
FutureWarning: Using struct_as_record default value (False) This will 
change to True in future versions
   rdr = MatFile5Reader(stream, byte_order=boc.swapped_code)
../usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:652: 
FutureWarning: Using struct_as_record default value (False) This will 
change to True in future versions
   rdr = MatFile5Reader(stream)
./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:654: 
FutureWarning: Using struct_as_record default value (False) This will 
change to True in future versions
   rdr = MatFile5Reader(stream, chars_as_strings=False)
../usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:664: 
FutureWarning: Using struct_as_record default value (False) This will 
change to True in future versions
   rdr = MatFile5Reader(file(estring_fname))
./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:674: 
FutureWarning: Using struct_as_record default value (False) This will 
change to True in future versions
   rdr = MatFile5Reader(stream)
./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:679: 
FutureWarning: Using struct_as_record default value (False) This will 
change to True in future versions
   rdr = MatFile5Reader(stream)
../usr/local/lib/python2.5/site-packages/scipy/io/matlab/mio4.py:338: 
DeprecationWarning: Matlab 4 files only support <=2 dimensions; future 
versions of scipy will raise an error when trying to write >2D arrays to 
matlab 4 format files
   DeprecationWarning,
./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:699: 
FutureWarning: Using struct_as_record default value (False) This will 
change to True in future versions
   rdr = MatFile5Reader(file(func_eg))
./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:703: 
FutureWarning: Using oned_as default value ('column') This will change 
to 'row' in future versions
   wtr = MatFile5Writer(stream)
./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:709: 
FutureWarning: Using struct_as_record default value (False) This will 
change to True in future versions
   rdr = MatFile5Reader(file(double_eg), mat_dtype=False)
./usr/local/lib/python2.5/site-packages/scipy/io/matlab/tests/test_mio.py:712: 
FutureWarning: Using struct_as_record default value (False) This will 
change to True in future versions
   rdr = MatFile5Reader(file(double_eg), mat_dtype=True)
..............................................................................................................................Warning: 
1000000 bytes requested, 20 bytes read.
./usr/local/lib/python2.5/site-packages/numpy/lib/utils.py:139: 
DeprecationWarning: `write_array` is deprecated!

This function is replaced by numpy.savetxt which allows the same 
functionality
through a different syntax.

   warnings.warn(depdoc, DeprecationWarning)
/usr/local/lib/python2.5/site-packages/numpy/lib/utils.py:139: 
DeprecationWarning: `read_array` is deprecated!

The functionality of read_array is in numpy.loadtxt which allows the same
functionality using different syntax.

   warnings.warn(depdoc, DeprecationWarning)
...........................................Exception 
exceptions.AttributeError: "'netcdf_file' object has no attribute 
'mode'" in <bound method netcdf_file.close of 
<scipy.io.netcdf.netcdf_file object at 0xb33ae4cc>> ignored
............/usr/local/lib/python2.5/site-packages/numpy/lib/utils.py:139: 
DeprecationWarning: `npfile` is deprecated!

You can achieve the same effect as using npfile using numpy.save and
numpy.load.

You can use memory-mapped arrays and data-types to map out a
file format for direct manipulation in NumPy.

   warnings.warn(depdoc, DeprecationWarning)
...../usr/local/lib/python2.5/warnings.py:41: ComplexWarning: Casting 
complex values to real discards the imaginary part
   lineno = caller.f_lineno
..../usr/local/lib/python2.5/site-packages/scipy/io/wavfile.py:20: 
WavFileWarning: Unfamiliar format bytes
   warnings.warn("Unfamiliar format bytes", WavFileWarning)
/usr/local/lib/python2.5/site-packages/scipy/io/wavfile.py:92: 
WavFileWarning: chunk not understood
   warnings.warn("chunk not understood", WavFileWarning)
................................Running unit tests for scipy
NumPy version 2.0.0.dev8324
NumPy is installed in /usr/local/lib/python2.5/site-packages/numpy
SciPy version 0.8.0.dev6310
SciPy is installed in /usr/local/lib/python2.5/site-packages/scipy
Python version 2.5.2 (r252:60911, May  9 2008, 15:14:37) [GCC 4.1.2 
20070115 (prerelease) (SUSE Linux)]
nose version 0.11.3
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[[ 
......................E.....FF................................................................................................................................SSSSSS......SSSSSS...FFFSSSS........................................................EE.......F.......Warning: 
invalid value encountered in divide
.....Warning: invalid value encountered in divide
Warning: invalid value encountered in divide
............................................/usr/local/lib/python2.5/site-packages/scipy/linalg/decomp.py:1180: 
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)
........................



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