[SciPy-User] Lots of warnings, errors and a segmentation fault in scipy.test()

Gerrit Holl gerrit.holl@ltu...
Mon Nov 29 04:11:20 CST 2010


Hi,

I recently installed scipy from source ("bleeding edge"). When running
the test, I get a lot of warnings and errors, and finally fail with a
segmentation fault:

Paste from http://bpaste.net/show/11710/ repeated below. I didn't get
any relevant warnings during compilation. Should I be worried? What
can I run in addition to track this down?

$ python -c "import scipy; scipy.test()"
Running unit tests for scipy
NumPy version 2.0.0.dev-12d0200
NumPy is installed in
/storage4/home/gerrit/.local/lib/python2.6/site-packages/numpy
SciPy version 0.9.0.dev6975
SciPy is installed in
/storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy
Python version 2.6.6 (r266:84292, Sep 15 2010, 16:22:56) [GCC 4.4.5]
nose version 0.11.1
...................................................................................................................................................../storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/cluster/vq.py:582:
UserWarning: One of the clusters is empty. Re-run kmean with a
different initialization.
  warnings.warn("One of the clusters is empty. "
............................/storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/fftpack/tests/test_basic.py:420:
ComplexWarning: Casting complex values to real discards the imaginary
part
  y1 = fftn(x.astype(np.float32))
/storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/fftpack/tests/test_basic.py:421:
ComplexWarning: Casting complex values to real discards the imaginary
part
  y2 = fftn(x.astype(np.float64)).astype(np.complex64)
/storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/fftpack/tests/test_basic.py:429:
ComplexWarning: Casting complex values to real discards the imaginary
part
  y1 = fftn(x.astype(np.float32))
/storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/fftpack/tests/test_basic.py:430:
ComplexWarning: Casting complex values to real discards the imaginary
part
  y2 = fftn(x.astype(np.float64)).astype(np.complex64)
......................K.............................................................................../storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/interpolate/fitpack2.py:673:
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)
....../storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/interpolate/fitpack2.py:604:
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
.........................................................../storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/io/matlab/mio.py:232:
FutureWarning: Using oned_as default value ('column') This will change
to 'row' in future versions
  oned_as=oned_as)
............................................................................................................................................................................................................................................................................./storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/io/wavfile.py:31:
WavFileWarning: Unfamiliar format bytes
  warnings.warn("Unfamiliar format bytes", WavFileWarning)
/storage4/home/gerrit/.local/lib/python2.6/site-packages/scipy/io/wavfile.py:121:
WavFileWarning: chunk not understood
  warnings.warn("chunk not understood", WavFileWarning)
.................................................................................ESSSSSS......SSSSSS......SSSS.......................................................Segmentation
fault

regards,
Gerrit.

-- 
Gerrit Holl
PhD student at Department of Space Science, Luleå University of
Technology, Kiruna, Sweden
http://www.sat.ltu.se/members/gerrit/


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