pymc test failure

[bk801]

I have followed the instruction for installation and testing of pymc. This generates failure report . I have included the report here. Any ides what is causing the failure? Python 3.6.1 (v3.6.1:69c0db5, Mar 21 2017, 18:41:36) [MSC v.1900 64 bit (AMD64)] on win32 Type "copyright", "credits" or "license()" for more information.

import pymc
pymc.test()
Running unit tests for pymc.tests
NumPy version 1.12.1
NumPy relaxed strides checking option: True
NumPy is installed in C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\numpy
Python version 3.6.1 (v3.6.1:69c0db5, Mar 21 2017, 18:41:36) [MSC v.1900 64 bit (AMD64)]
nose version 1.3.7
Warning (from warnings module):
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\pymc\InstantiationDecorators.py", line 101
(args, varargs, varkw, defaults) = inspect.getargspec(func)
DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec()
Warning (from warnings module):
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\pymc\CommonDeterministics.py", line 77
parent_values) = inspect.getargspec(lam_fun)
DeprecationWarning: inspect.getargspec() is deprecated, use inspect.signature() or inspect.getfullargspec()
Warning (from warnings module):
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\importlib_bootstrap.py", line 205
return f(*args, **kwds)
ImportWarning: can't resolve package from spec or package, falling back on name and path
......Could not generate output statistics for early_mean
Could not generate output statistics for early_mean
Could not generate output statistics for switchpoint
Could not generate output statistics for rate
Could not generate output statistics for late_mean
.........S..S.............S.......
Warning (from warnings module):
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\pymc\tests\test_database.py", line 449
progress_bar=0)
ResourceWarning: unclosed file <_io.TextIOWrapper name='testresults/interactivesqlite.log' mode='w' encoding='cp1252'>
.............................................................................................
Warning (from warnings module):
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\pymc\CommonDeterministics.py", line 849
'b': lambda a, b: np.log(a) * a ** b}
RuntimeWarning: invalid value encountered in log
0 x
1 (x_pow_2)
dtype: object
.....SS.....
Warning (from warnings module):
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\pymc\tests\test_interactive.py", line 22
progress_bar=0)
ResourceWarning: unclosed file <_io.TextIOWrapper name='testresults/interactive.log' mode='w' encoding='cp1252'>
...............[-----------------68%----- ] 680 of 1000 complete in 0.5 sec
[-----------------100%-----------------] 1000 of 1000 complete in 0.8 sec
.[-----------------100%-----------------] 1000 of 1000 complete in 0.3 sec
.E............

ERROR: Failure: ValueError (size is not compatible with inputs)

Traceback (most recent call last):
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\pymc\distributions.py", line 111, in newfun
return np.reshape(randfun(size=shape, *args, **kwargs), shape)
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\pymc\distributions.py", line 869, in rbinomial
return np.random.binomial(np.ravel(n), np.ravel(p), size)
File "mtrand.pyx", line 3788, in mtrand.RandomState.binomial (numpy\random\mtrand\mtrand.c:32376)
File "mtrand.pyx", line 388, in mtrand.discnp_array (numpy\random\mtrand\mtrand.c:9960)
ValueError: size is not compatible with inputs

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\nose\failure.py", line 39, in runTest
raise self.exc_val.with_traceback(self.tb)
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\nose\loader.py", line 418, in loadTestsFromName
addr.filename, addr.module)
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\nose\importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\nose\importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\imp.py", line 234, in load_module
return load_source(name, filename, file)
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\imp.py", line 172, in load_source
module = _load(spec)
File "", line 675, in _load
File "", line 655, in _load_unlocked
File "", line 678, in exec_module
File "", line 205, in _call_with_frames_removed
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\pymc\tests\test_special_methods.py", line 27, in 
pm.Binomial('x3', 100, .4),
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\pymc\distributions.py", line 320, in init
**arg_dict_out)
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\pymc\PyMCObjects.py", line 764, in init
verbose=verbose)
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\pymc\Node.py", line 214, in init
Node.init(self, doc, name, parents, cache_depth, verbose=verbose)
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\pymc\Node.py", line 129, in init
self.parents = parents
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\pymc\Node.py", line 147, in _set_parents
self.gen_lazy_function()
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\pymc\PyMCObjects.py", line 794, in gen_lazy_function
self.value = self._random(**self._parents.value)
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\pymc\distributions.py", line 114, in newfun
return randfun(size=shape, *args, **kwargs)
File "C:\Users\Bahram\AppData\Local\Programs\Python\Python36\lib\site-packages\pymc\distributions.py", line 869, in rbinomial
return np.random.binomial(np.ravel(n), np.ravel(p), size)
File "mtrand.pyx", line 3788, in mtrand.RandomState.binomial (numpy\random\mtrand\mtrand.c:32376)
File "mtrand.pyx", line 388, in mtrand.discnp_array (numpy\random\mtrand\mtrand.c:9960)
ValueError: size is not compatible with inputs

Ran 177 tests in 28.535s

FAILED (SKIP=5, errors=1)
<nose.result.TextTestResult run=177 errors=1 failures=0>

[fonnesbeck]

Could you please reformat this report to use markdown properly. Its pretty hard to read as presented.

What version of PyMC did you install, and from where?

[bk801]

I can't get rid of bold type face when I cut and paste from Python environment. Sorry. other information you asked for are:

pymc was download from http://www.lfd.uci.edu/~gohlke/pythonlibs/ the version is pymc-2.3.6-cp36-cp36m-win_amd64.whl which was installed for Python 3.6.1

[fonnesbeck]

I've fixed it. You needed to use Markdown to make it work.

Did you mean to close this issue?

[fonnesbeck]

There may be a problem with that particular build. I am not familiar with those. I recommend using Anaconda and installing via:

conda install -c anaconda pymc=2.3.6

If that is not possible, try building PyMC from source:

pip install pymc

[bk801]

Thanks for fixing the test.I need to learn the Markdown. I have installed on Anaconda and it works fine and I get Zero error. My problem is with the native Python in Windows 10. I will try installing pymc on Raspberry Pi and Mint ( installed on Virtual Box) in the next few days. Thanks for your help and guidance.

[cgohlke]

I can't reproduce this with the binaries from http://www.lfd.uci.edu/~gohlke/pythonlibs/

>>> pymc.__version__
'2.3.6'
>>> pymc.test()
Running unit tests for pymc.tests
NumPy version 1.11.3
NumPy relaxed strides checking option: False
NumPy is installed in X:\Python36\lib\site-packages\numpy
Python version 3.6.1 (v3.6.1:69c0db5, Mar 21 2017, 18:41:36) [MSC v.1900 64 bit (AMD64)]
nose version 1.3.7
<snip>
----------------------------------------------------------------------
Ran 192 tests in 24.417s

OK (SKIP=3)
<nose.result.TextTestResult run=192 errors=0 failures=0>

The issue might be specific to numpy 1.12.x.