[SciPy-User] scipy.test('full') (errors=8, failures=3)
josef.pktd at gmail.com
josef.pktd at gmail.com
Wed Dec 21 18:58:51 EST 2011
On Wed, Dec 21, 2011 at 6:47 PM, klo uo <klonuo at gmail.com> wrote:
>>>> scipy.test('full')
>
> Running unit tests for scipy
> NumPy version 1.6.1
> NumPy is installed in /usr/local/lib/python2.7/dist-packages/numpy
> SciPy version 0.10.0
> SciPy is installed in /usr/local/lib/python2.7/dist-packages/scipy
> Python version 2.7.1+ (r271:86832, Apr 11 2011, 18:05:24) [GCC 4.5.2]
> nose version 1.1.2
>
> {...}
>
> ======================================================================
> ERROR: test_iv_cephes_vs_amos_mass_test (test_basic.TestBessel)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/usr/local/lib/python2.7/dist-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_fdtri (test_basic.TestCephes)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/usr/local/lib/python2.7/dist-packages/scipy/special/tests/test_basic.py",
> line 153, in test_fdtri
> cephes.fdtri(1,1,0.5)
> RuntimeWarning: invalid value encountered in fdtri
>
> ======================================================================
> ERROR:
> test_continuous_extra.test_cont_extra(<scipy.stats.distributions.loggamma_gen
> object at 0x9c6232c>, (0.4141193182605212,), 'loggamma loc, scale test')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/local/lib/python2.7/dist-packages/nose/case.py", line 197, in
> runTest
> self.test(*self.arg)
> File
> "/usr/local/lib/python2.7/dist-packages/scipy/stats/tests/test_continuous_extra.py",
> line 78, in check_loc_scale
> m,v = distfn.stats(*arg)
> File "/usr/local/lib/python2.7/dist-packages/scipy/stats/distributions.py",
> line 1631, in stats
> mu = self._munp(1.0,*goodargs)
> File "/usr/local/lib/python2.7/dist-packages/scipy/stats/distributions.py",
> line 4119, in _munp
> return self._mom0_sc(n,*args)
> File "/usr/local/lib/python2.7/dist-packages/scipy/stats/distributions.py",
> line 1165, in _mom0_sc
> self.b, args=(m,)+args)[0]
> File "/usr/local/lib/python2.7/dist-packages/scipy/integrate/quadpack.py",
> line 247, in quad
> retval = _quad(func,a,b,args,full_output,epsabs,epsrel,limit,points)
> File "/usr/local/lib/python2.7/dist-packages/scipy/integrate/quadpack.py",
> line 314, in _quad
> return
> _quadpack._qagie(func,bound,infbounds,args,full_output,epsabs,epsrel,limit)
> File "/usr/local/lib/python2.7/dist-packages/scipy/stats/distributions.py",
> line 1162, in _mom_integ0
> return x**m * self.pdf(x,*args)
> File "/usr/local/lib/python2.7/dist-packages/scipy/stats/distributions.py",
> line 1262, in pdf
> place(output,cond,self._pdf(*goodargs) / scale)
> File "/usr/local/lib/python2.7/dist-packages/scipy/stats/distributions.py",
> line 4112, 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 0x9c62fec>, (1.8771398388773268,), 'lomax loc, scale test')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/local/lib/python2.7/dist-packages/nose/case.py", line 197, in
> runTest
> self.test(*self.arg)
> File
> "/usr/local/lib/python2.7/dist-packages/scipy/stats/tests/test_continuous_extra.py",
> line 78, in check_loc_scale
> m,v = distfn.stats(*arg)
> File "/usr/local/lib/python2.7/dist-packages/scipy/stats/distributions.py",
> line 1617, in stats
> mu, mu2, g1, g2 = self._stats(*args)
> File "/usr/local/lib/python2.7/dist-packages/scipy/stats/distributions.py",
> line 4643, in _stats
> mu, mu2, g1, g2 = pareto.stats(c, loc=-1.0, moments='mvsk')
> File "/usr/local/lib/python2.7/dist-packages/scipy/stats/distributions.py",
> line 1615, in stats
> mu, mu2, g1, g2 = self._stats(*args,**{'moments':moments})
> File "/usr/local/lib/python2.7/dist-packages/scipy/stats/distributions.py",
> line 4594, 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 0x9c7228c>, (30, 12, 6), 'hypergeom entropy nan test')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/local/lib/python2.7/dist-packages/nose/case.py", line 197, in
> runTest
> self.test(*self.arg)
> File
> "/usr/local/lib/python2.7/dist-packages/scipy/stats/tests/test_discrete_basic.py",
> line 199, in check_entropy
> ent = distfn.entropy(*arg)
> File "/usr/local/lib/python2.7/dist-packages/scipy/stats/distributions.py",
> line 6314, in entropy
> place(output,cond0,self.vecentropy(*goodargs))
> File "/usr/local/lib/python2.7/dist-packages/numpy/lib/function_base.py",
> line 1862, in __call__
> theout = self.thefunc(*newargs)
> File "/usr/local/lib/python2.7/dist-packages/scipy/stats/distributions.py",
> line 6668, 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 0x9c7228c>, (21, 3, 12), 'hypergeom entropy nan test')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/local/lib/python2.7/dist-packages/nose/case.py", line 197, in
> runTest
> self.test(*self.arg)
> File
> "/usr/local/lib/python2.7/dist-packages/scipy/stats/tests/test_discrete_basic.py",
> line 199, in check_entropy
> ent = distfn.entropy(*arg)
> File "/usr/local/lib/python2.7/dist-packages/scipy/stats/distributions.py",
> line 6314, in entropy
> place(output,cond0,self.vecentropy(*goodargs))
> File "/usr/local/lib/python2.7/dist-packages/numpy/lib/function_base.py",
> line 1862, in __call__
> theout = self.thefunc(*newargs)
> File "/usr/local/lib/python2.7/dist-packages/scipy/stats/distributions.py",
> line 6668, 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/local/lib/python2.7/dist-packages/scipy/stats/tests/test_distributions.py",
> line 439, in test_fit
> vals2 = distfunc.fit(res, optimizer='powell')
> File "/usr/local/lib/python2.7/dist-packages/scipy/stats/distributions.py",
> line 1874, in fit
> vals = optimizer(func,x0,args=(ravel(data),),disp=0)
> File "/usr/local/lib/python2.7/dist-packages/scipy/optimize/optimize.py",
> line 1621, in fmin_powell
> fval, x, direc1 = _linesearch_powell(func, x, direc1, tol=xtol*100)
> File "/usr/local/lib/python2.7/dist-packages/scipy/optimize/optimize.py",
> line 1491, in _linesearch_powell
> alpha_min, fret, iter, num = brent(myfunc, full_output=1, tol=tol)
> File "/usr/local/lib/python2.7/dist-packages/scipy/optimize/optimize.py",
> line 1312, in brent
> brent.optimize()
> File "/usr/local/lib/python2.7/dist-packages/scipy/optimize/optimize.py",
> line 1213, 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/local/lib/python2.7/dist-packages/scipy/stats/tests/test_distributions.py",
> line 460, in test_fix_fit
> vals2 = distfunc.fit(res,fscale=1)
> File "/usr/local/lib/python2.7/dist-packages/scipy/stats/distributions.py",
> line 1874, in fit
> vals = optimizer(func,x0,args=(ravel(data),),disp=0)
> File "/usr/local/lib/python2.7/dist-packages/scipy/optimize/optimize.py",
> line 301, in fmin
> and max(abs(fsim[0]-fsim[1:])) <= ftol):
> RuntimeWarning: invalid value encountered in subtract
>
> ======================================================================
> FAIL: test_mio.test_mat4_3d
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/local/lib/python2.7/dist-packages/nose/case.py", line 197, in
> runTest
> self.test(*self.arg)
> File
> "/usr/local/lib/python2.7/dist-packages/scipy/io/matlab/tests/test_mio.py",
> line 740, in test_mat4_3d
> stream, {'a': arr}, True, '4')
> File "/usr/local/lib/python2.7/dist-packages/numpy/testing/utils.py", line
> 1008, in assert_raises
> return nose.tools.assert_raises(*args,**kwargs)
> AssertionError: DeprecationWarning not raised
>
> ======================================================================
> FAIL: test_datatypes.test_uint64_max
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/local/lib/python2.7/dist-packages/nose/case.py", line 197, in
> runTest
> self.test(*self.arg)
> File
> "/usr/local/lib/python2.7/dist-packages/scipy/ndimage/tests/test_datatypes.py",
> line 57, in test_uint64_max
> assert_true(x[1] > (2**63))
> AssertionError: False is not true
>
> ======================================================================
> FAIL: Regression test for #651: better handling of badly conditioned
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/usr/local/lib/python2.7/dist-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/local/lib/python2.7/dist-packages/numpy/testing/utils.py", line
> 1008, in assert_raises
> return nose.tools.assert_raises(*args,**kwargs)
> AssertionError: BadCoefficients not raised
>
> ----------------------------------------------------------------------
> Ran 5830 tests in 1198.157s
>
> FAILED (KNOWNFAIL=14, SKIP=36, errors=8, failures=3)
>
>
> Any cause for concern?
>
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>
Did you set "raise on warnings"?
The distribution failures all look like RuntimeWarnings for floating
point calculations, that might be just a byproduct of some of the
calculations and doesn't say anything about the actual tested result.
most of them look familiar: 0log0, or optimizers trying invalid numbers.
the lomax Warning looks strange and might indicate some problems with
the test (not with lomax, I think)
Josef
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