SystemError: initialization of _heapq did not return an extension module

I’m experiencing the same error mentioned by @sirgogo in #88 .

oliver@oliver-arch:~ % ipython
Python 3.5.5 |Anaconda, Inc.| (default, Mar 12 2018, 23:12:44) 
Type 'copyright', 'credits' or 'license' for more information
IPython 6.2.1 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import julia

In [2]: j = julia.Julia()
Error processing line 1 of /home/oliver/local/miniconda3/lib/python3.5/site-packages/PyUtilib-5.4.1-py2.7-nspkg.pth:

Failed to import the site module
Traceback (most recent call last):
  File "/home/oliver/local/miniconda3/lib/python3.5/site.py", line 167, in addpackage
    exec(line)
  File "<string>", line 1, in <module>
  File "/home/oliver/local/miniconda3/lib/python3.5/types.py", line 166, in <module>
    import functools as _functools
  File "/home/oliver/local/miniconda3/lib/python3.5/functools.py", line 21, in <module>
    from collections import namedtuple
  File "/home/oliver/local/miniconda3/lib/python3.5/collections/__init__.py", line 29, in <module>
    import heapq as _heapq
  File "/home/oliver/local/miniconda3/lib/python3.5/heapq.py", line 587, in <module>
    from _heapq import *
SystemError: initialization of _heapq did not return an extension module

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/oliver/local/miniconda3/lib/python3.5/site.py", line 559, in <module>
    main()
  File "/home/oliver/local/miniconda3/lib/python3.5/site.py", line 541, in main
    known_paths = addsitepackages(known_paths)
  File "/home/oliver/local/miniconda3/lib/python3.5/site.py", line 318, in addsitepackages
    addsitedir(sitedir, known_paths)
  File "/home/oliver/local/miniconda3/lib/python3.5/site.py", line 206, in addsitedir
    addpackage(sitedir, name, known_paths)
  File "/home/oliver/local/miniconda3/lib/python3.5/site.py", line 177, in addpackage
    import traceback
  File "/home/oliver/local/miniconda3/lib/python3.5/traceback.py", line 3, in <module>
    import collections
  File "/home/oliver/local/miniconda3/lib/python3.5/collections/__init__.py", line 29, in <module>
    import heapq as _heapq
  File "/home/oliver/local/miniconda3/lib/python3.5/heapq.py", line 587, in <module>
    from _heapq import *
SystemError: initialization of _heapq did not return an extension module

I’m running Arch Linux and using the following versions:

Package	Version
python	3.5.5 :: Anaconda, Inc.
julia	0.6.2
PyJulia	0.1.5
PyCall	1.15.0

Any advice is appreciated!

Thanks, Oliver

[randy3k]

I have a similar issue on my conda python, but not the homebrew python.

It may be because JuliaCall fails to detect if (anaconda/miniconda) python has been initialized.

I got the following from my miniconda python

In [1]: import ctypes

In [2]: libpython = ctypes.PyDLL("/Users/Randy/miniconda3/lib/libpython3.6m.dylib")

In [3]: libpython.Py_IsInitialized()
Out[3]: 0

I got the following from my homebrew python

In [1]: import ctypes

In [2]: libpython = ctypes.PyDLL("/usr/local/Cellar/python3/3.6.5/Frameworks/Python.framework/Versions/3.6/lib/libpython3.6.dylib")

In [3]: libpython.Py_IsInitialized()
Out[4]: 1

UPDATE:

The following code works in miniconda python

In [1]: import ctypes

In [2]: libpython = ctypes.CDLL(None)

In [3]: libpython.Py_IsInitialized()
Out[3]: 1

And it seems that PyCall already loads in process symbols https://github.com/JuliaPy/PyCall.jl/pull/293 Not sure the reason now.

[sblinz-zz]

Removing ~/.julia/lib/v0.6/PyCall.jl worked for me. System info below:

OS: Ubuntu 16.04 (running inside a Docker container) Julia: 0.6 Python: 3.5.2 Virtual Environment: Conda (rllab, https://github.com/rll/rllab/blob/master/environment.yml)