[SciPy-User] Installing SciPy version 0.13.0b1: 1 test fail

Mon Oct 7 15:16:14 EDT 2013

On Mon, Oct 7, 2013 at 9:11 PM, Sergio Rojas <sergio_r at mail.com> wrote:

>
> Installing SciPy version 0.13.0b1 ended with a fail test message [1]
> which does not look too critical as the numerical values match
> close to single precision.
>

That test failure is fixed now in the 0.13.x branch.

>
> I am curious, however, about a deprecated message given at the
> beginning of the test:
>
> "
>  DeprecationWarning: `scipy.lib.lapack` is deprecated, use
> `scipy.linalg.lapack
> `" and a few others.
>
> How we are suppose to fix that in using scipy?
>

You're supposed to fix the warning, but if you have old code that imports
from scipy.lib you have to switch it over to scipy.linalg to avoid it
breaking with a future release.

Cheers,
Ralf

>
> Sergio
> [1]
>
> ======================================================================^M
> FAIL: test_qz_complex64 (test_decomp.TestQZ)^M
> ----------------------------------------------------------------------^M
> Traceback (most recent call last):^M
>   File
> "/home/myProg/Python273GNU/Linux64b/lib/python2.7/site-packages/scipy/li
> nalg/tests/test_decomp.py", line 1781, in test_qz_complex64^M
>     assert_array_almost_equal(dot(dot(Q,AA),Z.conjugate().T), A)^M
>   File
> "/home/myProg/Python273GNU/Linux64b/lib/python2.7/site-packages/numpy/te
> sting/utils.py", line 812, in assert_array_almost_equal^M
>     header=('Arrays are not almost equal to %d decimals' % decimal))^M
>   File
> "/home/myProg/Python273GNU/Linux64b/lib/python2.7/site-packages/numpy/te
> sting/utils.py", line 645, in assert_array_compare^M
>     raise AssertionError(msg)^M
> AssertionError: ^M
> Arrays are not almost equal to 6 decimals^M
> ^M
> (mismatch 4.0%)^M
>  x: array([[ 0.92961568+0.729689j  ,  0.31637624+0.99401343j,^M
>          0.18391913+0.67687303j,  0.20456031+0.79082209j,^M
>          0.56772494+0.17091393j],...^M
>  y: array([[ 0.92961609+0.72968906j,  0.31637555+0.99401456j,^M
>          0.18391882+0.67687368j,  0.20456028+0.79082251j,^M
>          0.56772500+0.17091426j],...^M
> ^M
> ----------------------------------------------------------------------^M
> Ran 9902 tests in 895.284s^M
> ^M
> FAILED (KNOWNFAIL=131, SKIP=324, failures=1)^M
> <nose.result.TextTestResult run=9902 errors=0 failures=1>^M
>
> Python 2.7.3 (default, Sep 30 2013, 13:55:58) ^M
> [GCC 4.6.3] on linux2^M
> Type "help", "copyright", "credits" or "license" for more information.^M
>
> Type "help", "copyright", "credits" or "license" for more information.^M
> >>> import scipy^M
> >>> scipy.show_config()^M
> amd_info:^M
>     libraries = ['amd']^M
>     library_dirs = ['/home/myProg/NumLibs64b/lib']^M
>     define_macros = [('SCIPY_AMD_H', None)]^M
>     swig_opts = ['-I/home/myProg/NumLibs64b/include']^M
>     include_dirs = ['/home/myProg/NumLibs64b/include']^M
> umfpack_info:^M
>     libraries = ['umfpack', 'amd']^M
>     library_dirs = ['/home/myProg/NumLibs64b/lib']^M
>     define_macros = [('SCIPY_UMFPACK_H', None), ('SCIPY_AMD_H', None)]^M
>     swig_opts = ['-I/home/myProg/NumLibs64b/include',
> '-I/home/myProg/NumLibs64
> b/include']^M
>     include_dirs = ['/home/myProg/NumLibs64b/include']^M
> atlas_threads_info:^M
>     libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']^M
>     library_dirs = ['/home/myProg/NumLibs64b/lib']^M
>     define_macros = [('NO_ATLAS_INFO', -1)]^M
>     language = f77^M
>     include_dirs = ['/home/myProg/NumLibs64b/include']^M
> blas_opt_info:^M
>     libraries = ['ptf77blas', 'ptcblas', 'atlas']^M
>     library_dirs = ['/home/myProg/NumLibs64b/lib']^M
>     define_macros = [('NO_ATLAS_INFO', -1)]^M
>     language = c^M
>     include_dirs = ['/home/myProg/NumLibs64b/include']^M
> atlas_blas_threads_info:^M
>     libraries = ['ptf77blas', 'ptcblas', 'atlas']^M
>     library_dirs = ['/home/myProg/NumLibs64b/lib']^M
>     define_macros = [('NO_ATLAS_INFO', -1)]^M
>     language = c^M
>     include_dirs = ['/home/myProg/NumLibs64b/include']^M
> lapack_opt_info:^M
>     libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']^M
>     library_dirs = ['/home/myProg/NumLibs64b/lib']^M
>     define_macros = [('NO_ATLAS_INFO', -1)]^M
>     language = f77^M
>     include_dirs = ['/home/myProg/NumLibs64b/include']^M
> lapack_mkl_info:^M
>   NOT AVAILABLE^M
> blas_mkl_info:^M
>   NOT AVAILABLE^M
> mkl_info:^M
>   NOT AVAILABLE^M
> >>> scipy.test('full', verbose=2)^M
> Running unit tests for scipy^M
> NumPy version 1.7.0^M
> NumPy is installed in
> /home/myProg/Python273GNU/Linux64b/lib/python2.7/site-pac
> kages/numpy^M
> SciPy version 0.13.0b1^M
> SciPy is installed in
> /home/myProg/Python273GNU/Linux64b/lib/python2.7/site-pac
> kages/scipy^M
> Python version 2.7.3 (default, Sep 30 2013, 13:55:58) [GCC 4.6.3]^M
> nose version 1.3.0^M
>
> /home/myProg/Python273GNU/Linux64b/lib/python2.7/site-packages/numpy/lib/utils.
> py:139: DeprecationWarning: `scipy.lib.blas` is deprecated, use
> `scipy.linalg.b
> las` instead!^M
>   warnings.warn(depdoc, DeprecationWarning)^M
>
> /home/myProg/Python273GNU/Linux64b/lib/python2.7/site-packages/numpy/lib/utils.
> py:139: DeprecationWarning: `scipy.lib.lapack` is deprecated, use
> `scipy.linalg
> .lapack` instead!^M
> ...
> ...
> ======================================================================
> FAIL: test_qz_complex64 (test_decomp.TestQZ)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File
> "/home/myProg/Python273GNU/Linux64b/lib/python2.7/site-packages/scipy/li
> nalg/tests/test_decomp.py", line 1781, in test_qz_complex64
>     assert_array_almost_equal(dot(dot(Q,AA),Z.conjugate().T), A)
>   File
> "/home/myProg/Python273GNU/Linux64b/lib/python2.7/site-packages/numpy/te
> sting/utils.py", line 812, in assert_array_almost_equal
>     header=('Arrays are not almost equal to %d decimals' % decimal))
>   File
> "/home/myProg/Python273GNU/Linux64b/lib/python2.7/site-packages/numpy/te
> sting/utils.py", line 645, in assert_array_compare
>     raise AssertionError(msg)
> AssertionError:
> Arrays are not almost equal to 6 decimals
>
> (mismatch 4.0%)
>  x: array([[ 0.92961568+0.729689j  ,  0.31637624+0.99401343j,
>          0.18391913+0.67687303j,  0.20456031+0.79082209j,
>          0.56772494+0.17091393j],...
>  y: array([[ 0.92961609+0.72968906j,  0.31637555+0.99401456j,
>          0.18391882+0.67687368j,  0.20456028+0.79082251j,
>          0.56772500+0.17091426j],...
>
> ----------------------------------------------------------------------
> Ran 9902 tests in 895.284s
>
> FAILED (KNOWNFAIL=131, SKIP=324, failures=1)
> <nose.result.TextTestResult run=9902 errors=0 failures=1>
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