[SciPy-User] test issues with 0.10
Paul Anton Letnes
paul.anton.letnes at gmail.com
Tue Nov 15 05:04:23 EST 2011
I have now built netlib BLAS+LAPACK (liblapack.a and libblas.a), and linked against these when building. Most tests pass, but there are still 16 failures. I'm not sure whether this is known, so I am posting it here in case it is of any interest.
Paul
i-courant ~/src % python -c 'import scipy; scipy.test(verbose=1)'
Running unit tests for scipy
NumPy version 1.6.1
NumPy is installed in /usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy
SciPy version 0.10.0
SciPy is installed in /usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy
Python version 2.7.2 (default, Oct 9 2011, 18:03:13) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]
nose version 1.1.2
...................................................................................................................................................../usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/cluster/vq.py:588: UserWarning: One of the clusters is empty. Re-run kmean with a different initialization.
warnings.warn("One of the clusters is empty. "
.......................................................................K............................................................................................................/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/interpolate/fitpack2.py:674: 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/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/interpolate/fitpack2.py:605: 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....../usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/core/numeric.py:1920: RuntimeWarning: invalid value encountered in absolute
return all(less_equal(absolute(x-y), atol + rtol * absolute(y)))
............................................................................................................................................................................................................................................................................................................................................................................................................................................/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/io/wavfile.py:31: WavFileWarning: Unfamiliar format bytes
warnings.warn("Unfamiliar format bytes", WavFileWarning)
/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/io/wavfile.py:121: WavFileWarning: chunk not understood
warnings.warn("chunk not understood", WavFileWarning)
....................................................................................F..FF......................................................................................................................................SSSSSS......SSSSSS......SSSS.....................FFF.........................................F....FF.......S............................................................................................................................................................................................................................................................K......................................................................................................................................................................................................SSSSS............S........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................SSSSSSSSSSS.........../usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/arpack.py:63: UserWarning: Single-precision types in `eigs` and `eighs` are not supported on the OSX platform currently. Double precision routines are used instead.
warnings.warn("Single-precision types in `eigs` and `eighs` "
....F.F.....................F...........F.F..............................................................................................F........................F.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K...............................................................K...........................................................................................................................................................KK.............................................................................................................................................................................................................................................................................................................................................................................................................................................K.K.............................................................................................................................................................................................................................................................................................................................................................................................K........K..............SSSSSSS..........................................................................................................................................................S.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
======================================================================
FAIL: test_asum (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 58, in test_asum
assert_almost_equal(f([3,-4,5]),12)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
ACTUAL: 0.0
DESIRED: 12
======================================================================
FAIL: test_dot (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 67, in test_dot
assert_almost_equal(f([3,-4,5],[2,5,1]),-9)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
ACTUAL: 0.0
DESIRED: -9
======================================================================
FAIL: test_nrm2 (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/lib/blas/tests/test_blas.py", line 78, in test_nrm2
assert_almost_equal(f([3,-4,5]),math.sqrt(50))
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
ACTUAL: 0.0
DESIRED: 7.0710678118654755
======================================================================
FAIL: test_basic.TestNorm.test_overflow
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/linalg/tests/test_basic.py", line 581, in test_overflow
assert_almost_equal(norm(a), a)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 452, in assert_almost_equal
return assert_array_almost_equal(actual, desired, decimal, err_msg)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 800, in assert_array_almost_equal
header=('Arrays are not almost equal to %d decimals' % decimal))
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
(mismatch 100.0%)
x: array(-0.0)
y: array([ 1.00000002e+20], dtype=float32)
======================================================================
FAIL: test_basic.TestNorm.test_stable
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/linalg/tests/test_basic.py", line 586, in test_stable
assert_almost_equal(norm(a) - 1e4, 0.5)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
ACTUAL: -10000.0
DESIRED: 0.5
======================================================================
FAIL: test_basic.TestNorm.test_types
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/linalg/tests/test_basic.py", line 568, in test_types
assert_allclose(norm(x), np.sqrt(14), rtol=tol)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
verbose=verbose, header=header)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=2.38419e-06, atol=0
(mismatch 100.0%)
x: array(1.0842021724855044e-19)
y: array(3.7416573867739413)
======================================================================
FAIL: test_asum (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", line 99, in test_asum
assert_almost_equal(f([3,-4,5]),12)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
ACTUAL: 0.0
DESIRED: 12
======================================================================
FAIL: test_dot (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", line 109, in test_dot
assert_almost_equal(f([3,-4,5],[2,5,1]),-9)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
ACTUAL: 0.0
DESIRED: -9
======================================================================
FAIL: test_nrm2 (test_blas.TestFBLAS1Simple)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/linalg/tests/test_blas.py", line 127, in test_nrm2
assert_almost_equal(f([3,-4,5]),math.sqrt(50))
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 7 decimals
ACTUAL: 0.0
DESIRED: 7.0710678118654755
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM', None, 0.5, <function aslinearoperator at 0x1039b3230>, None, 'normal')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
verbose=verbose, header=header)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=normal
(mismatch 100.0%)
x: array([[ 0.23815642, 0.1763755 ],
[-0.10785346, -0.32103487],
[ 0.12468303, -0.11230416],...
y: array([[ 0.23815642, 0.24814051],
[-0.10785347, -0.15634772],
[ 0.12468302, 0.05671416],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LM', None, 0.5, <function aslinearoperator at 0x1039b3230>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
verbose=verbose, header=header)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LM, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=cayley
(mismatch 100.0%)
x: array([[ 0.23815693, -0.33630507],
[-0.10785286, 0.02168 ],
[ 0.12468344, -0.11036437],...
y: array([[ 0.23815643, -0.2405392 ],
[-0.10785349, 0.14390968],
[ 0.12468311, -0.04574991],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'LA', None, 0.5, <function aslinearoperator at 0x1039b3230>, None, 'normal')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
verbose=verbose, header=header)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=LA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=normal
(mismatch 100.0%)
x: array([[ 28.80129188, -0.6379945 ],
[ 34.79312355, 0.27066791],
[-270.23255444, 0.4851834 ],...
y: array([[ 3.93467650e+03, -6.37994494e-01],
[ 3.90913859e+03, 2.70667916e-01],
[ -3.62176382e+04, 4.85183382e-01],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'SA', None, 0.5, <function aslinearoperator at 0x1039b3230>, None, 'normal')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
verbose=verbose, header=header)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=SA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=normal
(mismatch 100.0%)
x: array([[ 0.26260981, 0.23815559],
[-0.09760907, -0.10785484],
[ 0.06149647, 0.12468203],...
y: array([[ 0.23744165, 0.2381564 ],
[-0.13633069, -0.10785359],
[ 0.03132561, 0.12468301],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <std-symmetric>, 'f', 2, 'SA', None, 0.5, <function aslinearoperator at 0x1039b3230>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
verbose=verbose, header=header)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:standard, typ=f, which=SA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=cayley
(mismatch 100.0%)
x: array([[ 0.29524244, -0.2381569 ],
[-0.08169955, 0.10785299],
[ 0.06645597, -0.12468332],...
y: array([[ 0.24180251, -0.23815646],
[-0.14191195, 0.10785349],
[ 0.03568392, -0.12468307],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <gen-symmetric>, 'f', 2, 'SM', None, 0.5, <function aslinearoperator at 0x1039b3230>, None, 'buckling')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
verbose=verbose, header=header)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:general, typ=f, which=SM, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=buckling
(mismatch 100.0%)
x: array([[-0.10940548, 0.01676016],
[-0.07154097, 0.4628113 ],
[ 0.06895222, 0.49206394],...
y: array([[-0.10940547, 0.05459438],
[-0.07154103, 0.31407543],
[ 0.06895217, 0.37578294],...
======================================================================
FAIL: test_arpack.test_symmetric_modes(True, <gen-symmetric>, 'f', 2, 'SA', None, 0.5, <function aslinearoperator at 0x1039b3230>, None, 'cayley')
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py", line 235, in eval_evec
assert_allclose(LHS, RHS, rtol=rtol, atol=atol, err_msg=err)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 1168, in assert_allclose
verbose=verbose, header=header)
File "/usr/local/Cellar/python/2.7.2/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Not equal to tolerance rtol=0.00178814, atol=0.000357628
error for eigsh:general, typ=f, which=SA, sigma=0.5, mattype=aslinearoperator, OPpart=None, mode=cayley
(mismatch 100.0%)
x: array([[-0.4404992 , -0.01935683],
[-0.25650678, -0.11053132],
[-0.36893024, -0.13223556],...
y: array([[-0.44017013, -0.0193569 ],
[-0.25525379, -0.11053158],
[-0.36818443, -0.13223571],...
----------------------------------------------------------------------
Ran 5093 tests in 50.678s
FAILED (KNOWNFAIL=12, SKIP=42, failures=16)
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