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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.
>>> import numpy
>>> 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)
<nose.result.TextTestResult run=5593 errors=1 failures=0>

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.
>>> import scipy
>>> 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
MarkTab www.marktab.net
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    How did you install those packages? – ali_m Sep 06 '15 at 02:02
  • @ali_m with easy_install-2.6 – MarkTab www.marktab.net Sep 06 '15 at 12:16
  • My guess is that something probably went wrong when compiling the extensions for numpy/scipy. The simplest thing to try would be to remove your currently installed versions of numpy and scipy and install them via RPM instead. Alternatively I would suggest you look for compilation errors in the output of `easy_install numpy` or `pip install -vvv numpy` (but you should really be using either `rpm` or `pip` rather than `easy_install`, which is deprecated). – ali_m Sep 06 '15 at 13:43
  • thanks -- tried pip install and did not work. I do not know how to do rpm method -- I put the newest errors into the original question (because I cannot put it here) – MarkTab www.marktab.net Sep 08 '15 at 00:20
  • Based on the output above, it looks as though you are running Red Hat linux, which uses RPM as a package manager. To be honest I'm not that familiar with Red Hat, but I think you could just use [YUM](https://en.wikipedia.org/wiki/Yellowdog_Updater,_Modified), which is a font-end for RPM (try `sudo yum install numpy`). You should remove the existing copy first. Regarding the SSL error you are getting with `pip`, it is probably related to this [issue](http://stackoverflow.com/q/19377045/1461210). – ali_m Sep 08 '15 at 00:44
  • Thanks @ali_m - I tried the yum method: install of numpy-1.2.1-2.el5.x86_64 conflicts with file from package python-numpy-1.0.1-1.el5.rf.x86_64 Looks like there is another python install linked to yum. yum check-update reported: python.x86_64 2.4.3-56.el5 -- to me means there are 2 python installs on this shared box -- please advise. – MarkTab www.marktab.net Sep 08 '15 at 01:04
  • Those are both extremely old versions of numpy anyway. I would uninstall the existing version with yum, then try to fix the SSL certification error with pip (see the link I posted above). If all else fails, you could manually compile it from source (see [here](http://stackoverflow.com/questions/11443302/compiling-numpy-with-openblas-integration/14391693#14391693) for some instructions). – ali_m Sep 08 '15 at 01:13
  • Thanks @ali_m -- I uninstalled and reinstalled numpy and scipy, and it came back with numpy 1.2.1-2.el5 and scipy 0.6.0-7.el5. I believe those versions may be limited by the python2.4, but using yum, I see that 300+ packages depend on this python, so I am not going to change it (other people on this shared box). I agree that the cert issue is the pip fail, and though I see where to maybe obtain pem info, I do not know where that corresponding location is on the box. With the build, I would experiment on my own system, but will need internal advice from our team before maybe proceeding. – MarkTab www.marktab.net Sep 08 '15 at 01:52
  • Moving forward: 1) yum is not in scope since that's connected to an old python install; 2) build is the path, but has been affected also by the cert issue -- for now, we are downloading to another machine and then ftp the software in (and the machine is schedule for a formal refresh); 3) discovered that we are out of disk space -- lol -- but we will work through that. thanks @ali_m – MarkTab www.marktab.net Sep 08 '15 at 15:38
  • Finally resolved: 1) build with OpenBLAS was the resolution path; 2) needed some disk space, but that was the easiest part; 3) cython was not installed, which may be related to the original issue of why easy_install did not do well. The numpy.test() and scipy.test() results are relatively clean, and more importantly, the needed import statement now works. – MarkTab www.marktab.net Sep 08 '15 at 18:38

1 Answers1

0

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.

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MarkTab www.marktab.net
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