[scipion-users] Installation problems (WSL)

[Viktor B. <vik...@mm...>]

Dear all,
Before summer I could use Scipion without problem. However, after vacation (and possibly some change in environment) it would not start at all. Unfortunately I did not save the error message before trying to reinstall, and reinstallation does not seem to work at all.

The initial attempt was made on Ubuntu 16.04 installed through WSL on my work computer. I also tried installing on Ubuntu 18.04 installed on WSL on my home computer (where I have not used WSL at all previously, so no prior python installation). In all cases there have been a number of problems compiling python packages, and I can't start Scipion.

I followed the instructions found at https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install, both for "From Binaries" and "Sources from GitHub". The attached log files should include all input and all output.

Does anyone know what might be the problem?

Kind regards,
Viktor Bengtsson
PhD student
Stockholm University

PS. The final error I get when attempting to install from sources is :

/mnt/e/Linux_programs/scipion/scipion/software/bin/python /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip install requests==2.18.4
Traceback (most recent call last):
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py", line 16, in <module>
    from pip._internal import main as _main  # isort:skip # noqa
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py", line 19, in <module>
    from pip._vendor.urllib3.exceptions import DependencyWarning
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py", line 7, in <module>
    from .connectionpool import (
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py", line 45, in <module>
    from .util.queue import LifoQueue
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py", line 7, in <module>
    import Queue as _unused_module_Queue  # noqa: F401
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py", line 10, in <module>
    class LifoQueue(queue.Queue):
AttributeError: 'module' object has no attribute 'Queue'
Error: target '/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/requests' not built (after running '/mnt/e/Linux_programs/scipion/scipion/software/bin/python /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip install requests==2.18.4')

The original error (that reoccurred after installing from binaries) is:
user@WORKCOMPUTER:/mnt/e/Linux_programs/scipion/scipion$ scipion

Scipion v2.0 (2019-04-23) Diocletian

>>>>> python  /mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py
Traceback (most recent call last):
  File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py", line 32, in <module>
    from pyworkflow.gui.project import ProjectManagerWindow
  File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/__init__.py", line 27, in <module>
    from gui import *
  File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/gui.py", line 29, in <module>
    import Tkinter as tk
  File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/Tkinter/__init__.py", line 6, in <module>
    from Tkinter import (_cnfmerge, _default_root, _flatten,
ImportError: cannot import name _cnfmerge