numpy 1.9.2 and scipy 0.16.0 test errors - Python

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[ numpy 1.9.2 and scipy 0.16.0 test errors ]

Need help on resolving these errors on numpy 1.9.2 and scipy 0.16.0. The output is from numpy.test(verbose=10) and scipy.test(verbose=10) but I removed all lines with "ok".

numpy.test:

# python
Python 2.6.6 (r266:84292, Sep 27 2010, 18:07:46) 
[GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
&gt;&gt;&gt; import numpy
&gt;&gt;&gt; numpy.test(verbose=10)
Running unit tests for numpy
NumPy version 1.9.2
NumPy is installed in /data/python/base/lib/python2.6/site-packages/numpy-1.9.2-py2.6-linux-x86_64.egg/numpy
Python version 2.6.6 (r266:84292, Sep 27 2010, 18:07:46) [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)]
nose version 1.3.7
nose.config: INFO: Ignoring files matching ['^\\.', '^_', '^setup\\.py$']
nose.config: INFO: Excluding tests matching ['f2py_ext', 'f2py_f90_ext', 'gen_ext', 'pyrex_ext', 'swig_ext']
test_blasdot.test_blasdot_used ... SKIP: Skipping test: test_blasdot_used: Numpy is not compiled with _dotblas
test_blasdot.test_dot_override ... SKIP: Skipping test: test_dot_override: Test skipped due to test condition
Failure: SkipTest (Skipping test: test_ufunc_override_rop_precedence: Test skipped due to test condition) ... SKIP: Skipping test: test_ufunc_override_rop_precedence: Test skipped due to test condition
test_multiarray.TestBinop.test_ufunc_override_rop_simple ... SKIP: Skipping test: test_ufunc_override_rop_simple: Test skipped due to test condition
test_dot_override (test_multiarray.TestMethods) ... SKIP: Skipping test: test_dot_override: Test skipped due to test condition
test_field_names (test_multiarray.TestRecord) ... SKIP: non ascii unicode field indexing skipped; raises segfault on python 2.x
test_floating_exceptions (test_numeric.TestFloatExceptions) ... KNOWNFAIL: See ticket #2350
test_umath.TestComplexFunctions.test_branch_cuts_failing ... KNOWNFAIL: These branch cuts are known to fail
test_ufunc_override (test_umath.TestSpecialMethods) ... SKIP: Skipping test: test_ufunc_override: Test skipped due to test condition
test_ufunc_override_exception (test_umath.TestSpecialMethods) ... SKIP: Skipping test: test_ufunc_override_exception: Test skipped due to test condition
test_ufunc_override_methods (test_umath.TestSpecialMethods) ... SKIP: Skipping test: test_ufunc_override_methods: Test skipped due to test condition
test_ufunc_override_mro (test_umath.TestSpecialMethods) ... SKIP: Skipping test: test_ufunc_override_mro: Test skipped due to test condition
test_ufunc_override_out (test_umath.TestSpecialMethods) ... SKIP: Skipping test: test_ufunc_override_out: Test skipped due to test condition
test_umath_complex.TestCarg.test_zero ... KNOWNFAIL: Complex arithmetic with signed zero is buggy on most implementation
test_umath_complex.TestCexp.test_special_values2 ... KNOWNFAIL: cexp(nan + 0I) is wrong on most implementations
test_format.test_large_file_support ... SKIP: Could not create 5GB large file
Ticket 627. ... ERROR
test_simple (test_utils.TestArrayAlmostEqualNulp) ... KNOWNFAIL: Github issue #347

======================================================================
ERROR: Ticket 627.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/data/python/base/lib/python2.6/site-packages/numpy-1.9.2-py2.6-linux-x86_64.egg/numpy/linalg/tests/test_regression.py", line 51, in test_svd_build
    u, s, vh = linalg.svd(a)
  File "/data/python/base/lib/python2.6/site-packages/numpy-1.9.2-py2.6-linux-x86_64.egg/numpy/linalg/linalg.py", line 1327, in svd
    u, s, vt = gufunc(a, signature=signature, extobj=extobj)
ValueError: On entry to DGESDD parameter number 12 had an illegal value

----------------------------------------------------------------------
Ran 5593 tests in 53.953s

FAILED (KNOWNFAIL=5, SKIP=12, errors=1)
&lt;nose.result.TextTestResult run=5593 errors=1 failures=0&gt;

scipy.test:

# python
Python 2.6.6 (r266:84292, Sep 27 2010, 18:07:46) 
[GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
&gt;&gt;&gt; import scipy
&gt;&gt;&gt; scipy.test(verbose=10)
Running unit tests for scipy
NumPy version 1.9.2
NumPy is installed in /data/python/base/lib/python2.6/site-packages/numpy-1.9.2-py2.6-linux-x86_64.egg/numpy
SciPy version 0.16.0
SciPy is installed in /data/python/base/lib/python2.6/site-packages/scipy-0.16.0-py2.6-linux-x86_64.egg/scipy
Python version 2.6.6 (r266:84292, Sep 27 2010, 18:07:46) [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)]
nose version 1.3.7
nose.config: INFO: Ignoring files matching ['^\\.', '^_', '^setup\\.py$']
nose.config: INFO: Excluding tests matching ['f2py_ext', 'f2py_f90_ext', 'gen_ext', 'pyrex_ext', 'swig_ext']
/data/python/base/lib/python2.6/site-packages/numpy-1.9.2-py2.6-linux-x86_64.egg/numpy/lib/utils.py:95: DeprecationWarning: `scipy.weave` is deprecated, use `weave` instead!
  warnings.warn(depdoc, DeprecationWarning)
Failure: ImportError (/data/python/base/lib/python2.6/site-packages/scipy-0.16.0-py2.6-linux-x86_64.egg/scipy/linalg/cython_lapack.so: undefined symbol: zlacn2_) ... ERROR
test_notice (test_basic.TestSingleFFT) ... KNOWNFAIL: single-precision FFT implementation is partially disabled, until accuracy issues with large prime powers are resolved
test_improvement (test_quadpack.TestCtypesQuad) ... KNOWNFAIL: Unreliable test, see ticket 1684.
Failure: AttributeError ('module' object has no attribute 'qhull') ... ERROR
test_interpolate.TestInterp1D.test_bounds ... ERROR
test_interpolate.TestInterp1D.test_complex ... ERROR
test_interpolate.TestInterp1D.test_cubic ... ERROR
test_interpolate.TestInterp1D.test_nd ... ERROR
test_interpolate.TestInterp1D.test_nd_zero_spline ... KNOWNFAIL: zero-order splines fail for the last point
test_interpolate.TestInterp1D.test_validation ... ERROR
test_interpolate.TestInterp1D.test_zero ... KNOWNFAIL: zero-order splines fail for the last point
test_ndgriddata.TestGriddata.test_1d ... ERROR
test_ndgriddata.TestGriddata.test_1d_unsorted ... ERROR
/data/python/base/lib/python2.6/site-packages/numpy-1.9.2-py2.6-linux-x86_64.egg/numpy/core/arrayprint.py:641: DeprecationWarning: elementwise comparison failed; this will raise the error in the future.
  max_str_len = max(len(str(maximum.reduce(data))),
/data/python/base/lib/python2.6/site-packages/numpy-1.9.2-py2.6-linux-x86_64.egg/numpy/core/arrayprint.py:641: DeprecationWarning: elementwise comparison failed; this will raise the error in the future.
  max_str_len = max(len(str(maximum.reduce(data))),
/data/python/base/lib/python2.6/site-packages/numpy-1.9.2-py2.6-linux-x86_64.egg/numpy/core/arrayprint.py:641: DeprecationWarning: elementwise comparison failed; this will raise the error in the future.
  max_str_len = max(len(str(maximum.reduce(data))),
/data/python/base/lib/python2.6/site-packages/numpy-1.9.2-py2.6-linux-x86_64.egg/numpy/core/arrayprint.py:641: DeprecationWarning: elementwise comparison failed; this will raise the error in the future.
  max_str_len = max(len(str(maximum.reduce(data))),
/data/python/base/lib/python2.6/site-packages/numpy-1.9.2-py2.6-linux-x86_64.egg/numpy/core/arrayprint.py:641: DeprecationWarning: elementwise comparison failed; this will raise the error in the future.
  max_str_len = max(len(str(maximum.reduce(data))),
/data/python/base/lib/python2.6/site-packages/numpy-1.9.2-py2.6-linux-x86_64.egg/numpy/core/arrayprint.py:641: DeprecationWarning: elementwise comparison failed; this will raise the error in the future.
  max_str_len = max(len(str(maximum.reduce(data))),
/data/python/base/lib/python2.6/site-packages/numpy-1.9.2-py2.6-linux-x86_64.egg/numpy/core/arrayprint.py:641: DeprecationWarning: elementwise comparison failed; this will raise the error in the future.
  max_str_len = max(len(str(maximum.reduce(data))),
/data/python/base/lib/python2.6/site-packages/numpy-1.9.2-py2.6-linux-x86_64.egg/numpy/core/arrayprint.py:641: DeprecationWarning: elementwise comparison failed; this will raise the error in the future.
  max_str_len = max(len(str(maximum.reduce(data))),
Failure: ImportError (cannot import name _fblas) ... ERROR
Failure: ImportError (cannot import name _flapack) ... ERROR
Failure: AttributeError ('module' object has no attribute 'cython_blas') ... ERROR
Failure: ImportError (/data/python/base/lib/python2.6/site-packages/scipy-0.16.0-py2.6-linux-x86_64.egg/scipy/linalg/cython_lapack.so: undefined symbol: zlacn2_) ... ERROR
test_decomp.TestEig.test_singular ... KNOWNFAIL: See gh-2254.
test_crash_1580 (test_decomp.TestSVD) ... ERROR
test_random (test_decomp.TestSVD) ... ERROR
test_simple_overdet (test_decomp.TestSVD) ... ERROR
test_simple_underdet (test_decomp.TestSVD) ... ERROR
test_decomp.test_lapack_misaligned ... KNOWNFAIL: Ticket #1152, triggers a segfault in rare cases.
Failure: AttributeError ('module' object has no attribute '_decomp_update') ... ERROR
Failure: ImportError (cannot import name _fblas) ... ERROR
test_interpolative.TestInterpolativeDecomposition.test_rand ... Segmentation fault

Please advise on whether I need to check other packages, thanks

new: I tried pip install -vvv but was not successful -- I do not know how to try the rpm method.

# pip install -vvv numpy
Starting new HTTPS connection (1): pypi.python.org
There was an error checking the latest version of pip
Traceback (most recent call last):
  File "/data/python/base/lib/python2.6/site-packages/pip-6.0.8-py2.6.egg/pip/utils/outdated.py", line 126, in pip_version_check
    headers={"Accept": "application/json"},
  File "/data/python/base/lib/python2.6/site-packages/pip-6.0.8-py2.6.egg/pip/_vendor/requests/sessions.py", line 473, in get
    return self.request('GET', url, **kwargs)
  File "/data/python/base/lib/python2.6/site-packages/pip-6.0.8-py2.6.egg/pip/download.py", line 365, in request
    return super(PipSession, self).request(method, url, *args, **kwargs)
  File "/data/python/base/lib/python2.6/site-packages/pip-6.0.8-py2.6.egg/pip/_vendor/requests/sessions.py", line 461, in request
    resp = self.send(prep, **send_kwargs)
  File "/data/python/base/lib/python2.6/site-packages/pip-6.0.8-py2.6.egg/pip/_vendor/requests/sessions.py", line 573, in send
    r = adapter.send(request, **kwargs)
  File "/data/python/base/lib/python2.6/site-packages/pip-6.0.8-py2.6.egg/pip/_vendor/cachecontrol/adapter.py", line 43, in send
    resp = super(CacheControlAdapter, self).send(request, **kw)
  File "/data/python/base/lib/python2.6/site-packages/pip-6.0.8-py2.6.egg/pip/_vendor/requests/adapters.py", line 431, in send
    raise SSLError(e, request=request)
SSLError: [Errno 1] _ssl.c:490: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed
Collecting numpy
  Getting page https://pypi.python.org/simple/numpy/
  Starting new HTTPS connection (1): pypi.python.org
  Could not fetch URL https://pypi.python.org/simple/numpy/: connection error: [Errno 1] _ssl.c:490: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed
  Will skip URL https://pypi.python.org/simple/numpy/ when looking for download links for numpy
  URLs to search for versions for numpy:
  * https://pypi.python.org/simple/numpy/
  Getting page https://pypi.python.org/simple/numpy/
  Starting new HTTPS connection (2): pypi.python.org
  Could not fetch URL https://pypi.python.org/simple/numpy/: connection error: [Errno 1] _ssl.c:490: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed
  Will skip URL https://pypi.python.org/simple/numpy/ when looking for download links for numpy
  Could not find any downloads that satisfy the requirement numpy
  Cleaning up...
  No distributions at all found for numpy
  Exception information:
  Traceback (most recent call last):
    File "/data/python/base/lib/python2.6/site-packages/pip-6.0.8-py2.6.egg/pip/basecommand.py", line 232, in main
      status = self.run(options, args)
    File "/data/python/base/lib/python2.6/site-packages/pip-6.0.8-py2.6.egg/pip/commands/install.py", line 339, in run
      requirement_set.prepare_files(finder)
    File "/data/python/base/lib/python2.6/site-packages/pip-6.0.8-py2.6.egg/pip/req/req_set.py", line 333, in prepare_files
      upgrade=self.upgrade,
    File "/data/python/base/lib/python2.6/site-packages/pip-6.0.8-py2.6.egg/pip/index.py", line 397, in find_requirement
      'No distributions at all found for %s' % req
  DistributionNotFound: No distributions at all found for numpy

Answer 1

Finally resolved:

1) build with OpenBLAS was the resolution path -- per one of @ali_m solutions: used Compiling numpy with OpenBLAS integration

2) on the local system: the two issues were outdated cacerts (this machine is at least 5 years old), and minor issue of needing a bit more disk space (resolved through deleting known old files)

3) Cython had not been installed, which may be related to the original issue of why easy_install did not do well. Other discussions on numpy and scipy have mentioned that cython is a somewhat secret requirement for people downloading from github directly. Thus, Cython was needed to complete installation of both numpy and scipy.

Results: The numpy.test() and scipy.test() results are relatively clean, and more importantly, the needed import statement from scipy now works.

numpy 1.9.2 and scipy 0.16.0 test errors - Python

[ numpy 1.9.2 and scipy 0.16.0 test errors ]

Answer 1

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