[SciPy-User] NumPy and SciPy test failures

Charles R Harris charlesr.harris@gmail....
Wed Feb 1 08:01:11 CST 2012


On Wed, Feb 1, 2012 at 4:56 AM, Mads M. Hansen <madsmh@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.


> ======================================================================
> 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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> SciPy-User@scipy.org
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>
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