[SciPy-User] NumPy and SciPy test failures

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Mads M. Hansen

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Feb 1, 2012, 6:56:06 AM2/1/12
to scipy...@scipy.org
I have built NumPy 1.6.1 and SciPy 0.10.0 for Python 3.2 on a Fedora
16 system and I used gfortran, but when I run the tests I get the
following failures and errors

NumPy:

======================================================================
FAIL: test_kind.TestKind.test_all
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.2/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/usr/lib64/python3.2/site-packages/numpy/f2py/tests/test_kind.py",
line 30, in test_all
'selectedrealkind(%s): expected %r but got %r' % (i,
selected_real_kind(i), selectedrealkind(i)))
File "/usr/lib64/python3.2/site-packages/numpy/testing/utils.py",
line 34, in assert_
raise AssertionError(msg)
AssertionError: selectedrealkind(19): expected -1 but got 16

======================================================================
FAIL: test_doctests (test_polynomial.TestDocs)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib64/python3.2/site-packages/numpy/lib/tests/test_polynomial.py",
line 84, in test_doctests
return rundocs()
File "/usr/lib64/python3.2/site-packages/numpy/testing/utils.py",
line 988, in rundocs
raise AssertionError("Some doctests failed:\n%s" % "\n".join(msg))
AssertionError: Some doctests failed:
**********************************************************************
File "/usr/lib64/python3.2/site-packages/numpy/lib/tests/test_polynomial.py",
line 32, in test_polynomial
Failed example:
p / q
Expected:
(poly1d([ 0.33333333]), poly1d([ 1.33333333, 2.66666667]))
Got:
(poly1d([ 0.333]), poly1d([ 1.333, 2.667]))

**********************************************************************
File "/usr/lib64/python3.2/site-packages/numpy/lib/tests/test_polynomial.py",
line 54, in test_polynomial
Failed example:
p.integ()
Expected:
poly1d([ 0.33333333, 1. , 3. , 0. ])
Got:
poly1d([ 0.333, 1. , 3. , 0. ])

**********************************************************************
File "/usr/lib64/python3.2/site-packages/numpy/lib/tests/test_polynomial.py",
line 56, in test_polynomial
Failed example:
p.integ(1)
Expected:
poly1d([ 0.33333333, 1. , 3. , 0. ])
Got:
poly1d([ 0.333, 1. , 3. , 0. ])

**********************************************************************
File "/usr/lib64/python3.2/site-packages/numpy/lib/tests/test_polynomial.py",
line 58, in test_polynomial
Failed example:
p.integ(5)
Expected:
poly1d([ 0.00039683, 0.00277778, 0.025 , 0. , 0. ,
0. , 0. , 0. ])
Got:
poly1d([ 0. , 0.003, 0.025, 0. , 0. , 0. , 0. , 0. ])


----------------------------------------------------------------------:

And SciPy:

======================================================================
ERROR: Failure: ImportError (cannot import name _minimize_neldermead)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.2/site-packages/nose/failure.py", line 37, in runTest
raise self.exc_class(self.exc_val).with_traceback(self.tb)
File "/usr/lib/python3.2/site-packages/nose/loader.py", line 390, in
loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python3.2/site-packages/nose/importer.py", line 39,
in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python3.2/site-packages/nose/importer.py", line 86,
in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/usr/lib64/python3.2/site-packages/scipy/optimize/tests/test_anneal.py",
line 10, in <module>
from scipy.optimize import anneal, minimize
File "/usr/lib64/python3.2/site-packages/scipy/optimize/minimize.py",
line 16, in <module>
from .optimize import _minimize_neldermead, _minimize_powell, \
ImportError: cannot import name _minimize_neldermead

======================================================================
ERROR: Failure: ImportError (cannot import name cwt)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.2/site-packages/nose/failure.py", line 37, in runTest
raise self.exc_class(self.exc_val).with_traceback(self.tb)
File "/usr/lib/python3.2/site-packages/nose/loader.py", line 390, in
loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python3.2/site-packages/nose/importer.py", line 39,
in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python3.2/site-packages/nose/importer.py", line 86,
in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/usr/lib64/python3.2/site-packages/scipy/signal/tests/test_peak_finding.py",
line 7, in <module>
from scipy.signal._peak_finding import argrelmax, find_peaks_cwt,
_identify_ridge_lines
File "/usr/lib64/python3.2/site-packages/scipy/signal/_peak_finding.py",
line 7, in <module>
from scipy.signal.wavelets import cwt, ricker
ImportError: cannot import name cwt

======================================================================
ERROR: test_iv_cephes_vs_amos_mass_test (test_basic.TestBessel)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib64/python3.2/site-packages/scipy/special/tests/test_basic.py",
line 1642, in test_iv_cephes_vs_amos_mass_test
c1 = special.iv(v, x)
RuntimeWarning: divide by zero encountered in iv

======================================================================
ERROR: test_continuous_extra.test_cont_extra(<scipy.stats.distributions.loggamma_gen
object at 0x6b38f10>, (0.4141193182605212,), 'loggamma loc, scale
test')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.2/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/usr/lib64/python3.2/site-packages/scipy/stats/tests/test_continuous_extra.py",
line 78, in check_loc_scale
m,v = distfn.stats(*arg)
File "/usr/lib64/python3.2/site-packages/scipy/stats/distributions.py",
line 1632, in stats
mu = self._munp(1.0,*goodargs)
File "/usr/lib64/python3.2/site-packages/scipy/stats/distributions.py",
line 4120, in _munp
return self._mom0_sc(n,*args)
File "/usr/lib64/python3.2/site-packages/scipy/stats/distributions.py",
line 1166, in _mom0_sc
self.b, args=(m,)+args)[0]
File "/usr/lib64/python3.2/site-packages/scipy/integrate/quadpack.py",
line 247, in quad
retval = _quad(func,a,b,args,full_output,epsabs,epsrel,limit,points)
File "/usr/lib64/python3.2/site-packages/scipy/integrate/quadpack.py",
line 314, in _quad
return _quadpack._qagie(func,bound,infbounds,args,full_output,epsabs,epsrel,limit)
File "/usr/lib64/python3.2/site-packages/scipy/stats/distributions.py",
line 1163, in _mom_integ0
return x**m * self.pdf(x,*args)
File "/usr/lib64/python3.2/site-packages/scipy/stats/distributions.py",
line 1263, in pdf
place(output,cond,self._pdf(*goodargs) / scale)
File "/usr/lib64/python3.2/site-packages/scipy/stats/distributions.py",
line 4113, in _pdf
return exp(c*x-exp(x)-gamln(c))
RuntimeWarning: overflow encountered in exp

======================================================================
ERROR: test_continuous_extra.test_cont_extra(<scipy.stats.distributions.lomax_gen
object at 0x74ff610>, (1.8771398388773268,), 'lomax loc, scale test')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.2/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/usr/lib64/python3.2/site-packages/scipy/stats/tests/test_continuous_extra.py",
line 78, in check_loc_scale
m,v = distfn.stats(*arg)
File "/usr/lib64/python3.2/site-packages/scipy/stats/distributions.py",
line 1618, in stats
mu, mu2, g1, g2 = self._stats(*args)
File "/usr/lib64/python3.2/site-packages/scipy/stats/distributions.py",
line 4644, in _stats
mu, mu2, g1, g2 = pareto.stats(c, loc=-1.0, moments='mvsk')
File "/usr/lib64/python3.2/site-packages/scipy/stats/distributions.py",
line 1616, in stats
mu, mu2, g1, g2 = self._stats(*args,**{'moments':moments})
File "/usr/lib64/python3.2/site-packages/scipy/stats/distributions.py",
line 4595, in _stats
vals = 2*(bt+1.0)*sqrt(b-2.0)/((b-3.0)*sqrt(b))
RuntimeWarning: invalid value encountered in sqrt

======================================================================
ERROR: test_discrete_basic.test_discrete_extra(<scipy.stats.distributions.hypergeom_gen
object at 0x6c9f510>, (30, 12, 6), 'hypergeom entropy nan test')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.2/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/usr/lib64/python3.2/site-packages/scipy/stats/tests/test_discrete_basic.py",
line 199, in check_entropy
ent = distfn.entropy(*arg)
File "/usr/lib64/python3.2/site-packages/scipy/stats/distributions.py",
line 6315, in entropy
place(output,cond0,self.vecentropy(*goodargs))
File "/usr/lib64/python3.2/site-packages/numpy/lib/function_base.py",
line 1863, in __call__
theout = self.thefunc(*newargs)
File "/usr/lib64/python3.2/site-packages/scipy/stats/distributions.py",
line 6669, in _entropy
lvals = where(vals==0.0,0.0,log(vals))
RuntimeWarning: divide by zero encountered in log

======================================================================
ERROR: test_discrete_basic.test_discrete_extra(<scipy.stats.distributions.hypergeom_gen
object at 0x6c9f510>, (21, 3, 12), 'hypergeom entropy nan test')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.2/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/usr/lib64/python3.2/site-packages/scipy/stats/tests/test_discrete_basic.py",
line 199, in check_entropy
ent = distfn.entropy(*arg)
File "/usr/lib64/python3.2/site-packages/scipy/stats/distributions.py",
line 6315, in entropy
place(output,cond0,self.vecentropy(*goodargs))
File "/usr/lib64/python3.2/site-packages/numpy/lib/function_base.py",
line 1863, in __call__
theout = self.thefunc(*newargs)
File "/usr/lib64/python3.2/site-packages/scipy/stats/distributions.py",
line 6669, in _entropy
lvals = where(vals==0.0,0.0,log(vals))
RuntimeWarning: divide by zero encountered in log

======================================================================
ERROR: test_fit (test_distributions.TestFitMethod)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib64/python3.2/site-packages/scipy/stats/tests/test_distributions.py",
line 439, in test_fit
vals2 = distfunc.fit(res, optimizer='powell')
File "/usr/lib64/python3.2/site-packages/scipy/stats/distributions.py",
line 1875, in fit
vals = optimizer(func,x0,args=(ravel(data),),disp=0)
File "/usr/lib64/python3.2/site-packages/scipy/optimize/optimize.py",
line 1622, in fmin_powell
fval, x, direc1 = _linesearch_powell(func, x, direc1, tol=xtol*100)
File "/usr/lib64/python3.2/site-packages/scipy/optimize/optimize.py",
line 1492, in _linesearch_powell
alpha_min, fret, iter, num = brent(myfunc, full_output=1, tol=tol)
File "/usr/lib64/python3.2/site-packages/scipy/optimize/optimize.py",
line 1313, in brent
brent.optimize()
File "/usr/lib64/python3.2/site-packages/scipy/optimize/optimize.py",
line 1214, in optimize
tmp2 = (x-v)*(fx-fw)
RuntimeWarning: invalid value encountered in double_scalars

======================================================================
ERROR: test_fix_fit (test_distributions.TestFitMethod)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib64/python3.2/site-packages/scipy/stats/tests/test_distributions.py",
line 460, in test_fix_fit
vals2 = distfunc.fit(res,fscale=1)
File "/usr/lib64/python3.2/site-packages/scipy/stats/distributions.py",
line 1875, in fit
vals = optimizer(func,x0,args=(ravel(data),),disp=0)
File "/usr/lib64/python3.2/site-packages/scipy/optimize/optimize.py",
line 302, in fmin
and max(abs(fsim[0]-fsim[1:])) <= ftol):
RuntimeWarning: invalid value encountered in subtract

======================================================================
ERROR: Failure: ImportError (cannot import name common_info)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.2/site-packages/nose/failure.py", line 37, in runTest
raise self.exc_class(self.exc_val).with_traceback(self.tb)
File "/usr/lib/python3.2/site-packages/nose/loader.py", line 390, in
loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python3.2/site-packages/nose/importer.py", line 39,
in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python3.2/site-packages/nose/importer.py", line 86,
in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/usr/lib64/python3.2/site-packages/scipy/weave/__init__.py",
line 26, in <module>
from .inline_tools import inline
File "/usr/lib64/python3.2/site-packages/scipy/weave/inline_tools.py",
line 5, in <module>
from . import ext_tools
File "/usr/lib64/python3.2/site-packages/scipy/weave/ext_tools.py",
line 7, in <module>
from . import converters
File "/usr/lib64/python3.2/site-packages/scipy/weave/converters.py",
line 4, in <module>
from . import common_info
ImportError: cannot import name common_info

======================================================================
FAIL: test_mio.test_mat4_3d
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.2/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/usr/lib64/python3.2/site-packages/scipy/io/matlab/tests/test_mio.py",
line 740, in test_mat4_3d
stream, {'a': arr}, True, '4')
File "/usr/lib64/python3.2/site-packages/numpy/testing/utils.py",
line 1008, in assert_raises
return nose.tools.assert_raises(*args,**kwargs)
AssertionError: DeprecationWarning not raised by
functools.partial(<function savemat at 0x9e482f8>, oned_as='row')

======================================================================
FAIL: Regression test for #651: better handling of badly conditioned
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib64/python3.2/site-packages/scipy/signal/tests/test_filter_design.py",
line 34, in test_bad_filter
assert_raises(BadCoefficients, tf2zpk, [1e-15], [1.0, 1.0])
File "/usr/lib64/python3.2/site-packages/numpy/testing/utils.py",
line 1008, in assert_raises
return nose.tools.assert_raises(*args,**kwargs)
AssertionError: BadCoefficients not raised by tf2zpk

----------------------------------------------------------------------

The NumPy errors seem to be mostly rounding errors, but it seems to
round quite aggressively. How siginificant are these errors?

.. Mads
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Charles R Harris

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Feb 1, 2012, 9:01:11 AM2/1/12
to SciPy Users List
On Wed, Feb 1, 2012 at 4:56 AM, Mads M. Hansen <mad...@gmail.com> wrote:
I have built NumPy 1.6.1 and SciPy 0.10.0 for Python 3.2 on a Fedora
16 system and I used gfortran, but when I run the tests I get the
following failures and errors

NumPy:

======================================================================
FAIL: test_kind.TestKind.test_all
----------------------------------------------------------------------
Traceback (most recent call last):
 File "/usr/lib/python3.2/site-packages/nose/case.py", line 198, in runTest
   self.test(*self.arg)
 File "/usr/lib64/python3.2/site-packages/numpy/f2py/tests/test_kind.py",
line 30, in test_all
   'selectedrealkind(%s): expected %r but got %r' %  (i,
selected_real_kind(i), selectedrealkind(i)))
 File "/usr/lib64/python3.2/site-packages/numpy/testing/utils.py",
line 34, in assert_
   raise AssertionError(msg)
AssertionError: selectedrealkind(19): expected -1 but got 16


I think this is a bug in the test that comes from adding the float16 type.
 

Denis Laxalde

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Feb 1, 2012, 10:37:54 AM2/1/12
to SciPy Users List
Mads M. Hansen wrote:
> I have built NumPy 1.6.1 and SciPy 0.10.0 for Python 3.2 on a Fedora
> 16 system and I used gfortran, but when I run the tests I get the
> following failures and errors

It's probably not scipy 0.10.0. Could you specify the exact versions of
you have installed (e.g. from the header displayed by scipy tests)?

> And SciPy:
>
> ======================================================================
> ERROR: Failure: ImportError (cannot import name _minimize_neldermead)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python3.2/site-packages/nose/failure.py", line 37, in runTest
> raise self.exc_class(self.exc_val).with_traceback(self.tb)
> File "/usr/lib/python3.2/site-packages/nose/loader.py", line 390, in
> loadTestsFromName
> addr.filename, addr.module)
> File "/usr/lib/python3.2/site-packages/nose/importer.py", line 39,
> in importFromPath
> return self.importFromDir(dir_path, fqname)
> File "/usr/lib/python3.2/site-packages/nose/importer.py", line 86,
> in importFromDir
> mod = load_module(part_fqname, fh, filename, desc)
> File "/usr/lib64/python3.2/site-packages/scipy/optimize/tests/test_anneal.py",
> line 10, in <module>
> from scipy.optimize import anneal, minimize
> File "/usr/lib64/python3.2/site-packages/scipy/optimize/minimize.py",
> line 16, in <module>
> from .optimize import _minimize_neldermead, _minimize_powell, \
> ImportError: cannot import name _minimize_neldermead

I was interested by this one but cannot reproduce it with current
master on python 3.2.2.

--
Denis

Mads M. Hansen

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Feb 1, 2012, 11:17:43 AM2/1/12
to SciPy Users List
2012/2/1 Denis Laxalde <dlax...@gmail.com>:

> Mads M. Hansen wrote:
>> I have built NumPy 1.6.1 and SciPy 0.10.0 for Python 3.2 on a Fedora
>> 16 system and I used gfortran, but when I run the tests I get the
>> following failures and errors
>
> It's probably not scipy 0.10.0. Could you specify the exact versions of
> you have installed (e.g. from the header displayed by scipy tests)?
>
Here is the header

>>> scipy.test('full')
Running unit tests for scipy
NumPy version 1.6.1
NumPy is installed in /usr/lib64/python3.2/site-packages/numpy
SciPy version 0.10.0
SciPy is installed in /usr/lib64/python3.2/site-packages/scipy
Python version 3.2.1 (default, Jul 11 2011, 18:54:42) [GCC 4.6.1
20110627 (Red Hat 4.6.1-1)]
nose version 1.1.2

I checked out the v.0.10.0 tag from the Git repository.

.. Mads

Ralf Gommers

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Feb 1, 2012, 12:12:49 PM2/1/12
to SciPy Users List
On Wed, Feb 1, 2012 at 5:17 PM, Mads M. Hansen <mad...@gmail.com> wrote:
2012/2/1 Denis Laxalde <dlax...@gmail.com>:
> Mads M. Hansen wrote:
>> I have built NumPy 1.6.1 and SciPy 0.10.0 for Python 3.2 on a Fedora
>> 16 system and I used gfortran, but when I run the tests I get the
>> following failures and errors
>
> It's probably not scipy 0.10.0. Could you specify the exact versions of
> you have installed (e.g. from the header displayed by scipy tests)?
>
Here is the header

>>> scipy.test('full')
Running unit tests for scipy
NumPy version 1.6.1
NumPy is installed in /usr/lib64/python3.2/site-packages/numpy
SciPy version 0.10.0
SciPy is installed in /usr/lib64/python3.2/site-packages/scipy
Python version 3.2.1 (default, Jul 11 2011, 18:54:42) [GCC 4.6.1
20110627 (Red Hat 4.6.1-1)]
nose version 1.1.2

I checked out the v.0.10.0 tag from the Git repository.

The reason you're seeing the _minimize_neldermead failure, and probably some others, is likely that you didn't clean the install dir before installing 0.10.0. That test was only added after 0.10.0 came out.

Ralf

Mads M. Hansen

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Feb 1, 2012, 2:05:57 PM2/1/12
to SciPy Users List
2012/2/1 Ralf Gommers <ralf.g...@googlemail.com>:

Hm that's odd, I delete /usr/lib64/python3.2/site-packages/scipy (and
numpy/) prior to each reinstall - is scipy installed in
other places by defaultr?

Pauli Virtanen

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Feb 1, 2012, 2:17:08 PM2/1/12
to scipy...@scipy.org
01.02.2012 20:05, Mads M. Hansen kirjoitti:
> Hm that's odd, I delete /usr/lib64/python3.2/site-packages/scipy (and
> numpy/) prior to each reinstall - is scipy installed in
> other places by defaultr?

You'll also need to delete the build/ directory.

--
Pauli Virtanen

Mads M. Hansen

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Feb 1, 2012, 2:41:28 PM2/1/12
to SciPy Users List
Thanks, properly cleaning before building brought the errors down to
one which follows,

======================================================================
ERROR: Failure: AttributeError ('module' object has no attribute 'FileType')


----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.2/site-packages/nose/failure.py", line 37, in runTest
raise self.exc_class(self.exc_val).with_traceback(self.tb)
File "/usr/lib/python3.2/site-packages/nose/loader.py", line 390, in
loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python3.2/site-packages/nose/importer.py", line 39,
in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python3.2/site-packages/nose/importer.py", line 86,
in importFromDir
mod = load_module(part_fqname, fh, filename, desc)

File "/usr/lib64/python3.2/site-packages/scipy/weave/__init__.py",
line 22, in <module>
from .blitz_tools import blitz
File "/usr/lib64/python3.2/site-packages/scipy/weave/blitz_tools.py",
line 6, in <module>


from . import converters
File "/usr/lib64/python3.2/site-packages/scipy/weave/converters.py",

line 19, in <module>
c_spec.file_converter(),
File "/usr/lib64/python3.2/site-packages/scipy/weave/c_spec.py",
line 74, in __init__
self.init_info()
File "/usr/lib64/python3.2/site-packages/scipy/weave/c_spec.py",
line 264, in init_info
self.matching_types = [types.FileType]
AttributeError: 'module' object has no attribute 'FileType'

----------------------------------------------------------------------

2012/2/1 Pauli Virtanen <p...@iki.fi>:

Ralf Gommers

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Feb 1, 2012, 4:29:34 PM2/1/12
to SciPy Users List
This failure is caused by the weave module not being py3k compatible. Is known.

Ralf
 

Denis Laxalde

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Feb 1, 2012, 11:34:20 AM2/1/12
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Mads M. Hansen wrote:
> I checked out the v.0.10.0 tag from the Git repository.

But this file (quoting the first error in scipy's test from your
original message):
> > File "/usr/lib64/python3.2/site-packages/scipy/optimize/tests/test_anneal.py"

is not in 0.10.0. See
<https://github.com/scipy/scipy/tree/v0.10.0/scipy/optimize/tests>

Maybe your local repository was not clean when you built the package?

--
Denis

Mads M. Hansen

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Feb 3, 2012, 7:13:28 AM2/3/12
to SciPy Users List
2012/2/1 Denis Laxalde <denis....@mcgill.ca>:

> Mads M. Hansen wrote:
>> I checked out the v.0.10.0 tag from the Git repository.
>
> But this file (quoting the first error in scipy's test from your
> original message):
>> >   File "/usr/lib64/python3.2/site-packages/scipy/optimize/tests/test_anneal.py"
>
> is not in 0.10.0. See
> <https://github.com/scipy/scipy/tree/v0.10.0/scipy/optimize/tests>
>
> Maybe your local repository was not clean when you built the package?

Hi Dennis - that was indeed the case - I forgot to run git clean -xdf
in the repo.

.. Mads

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