"This package should not be accessible on Python 3" error

Question

I installed phenix (phenix-installer-1.17.1-3660-intel-linux-2.6-x86_64-centos6) on my CentOS 7 system according the installation guide ( https://www.phenix-online.org/documentation/install-setup-run.html ). The original python version (/usr/bin/python) in my system is 2.7.5, but I installed anaconda3, so the output of "which python" command is "~/software/build/anaconda3/bin/python".

I tried to study the p9-sad tutorial and run the command "phenix.run_example p9-sad", but it gave the following error information:

Examples to be run:  p9-sad

Running PHENIX example: p9-sad  Fri Jan 17 15:04:44 CST 2020

Working directory: /home/sunyp/Documents/tutorial/PHENIX/p9-sad
Starting run now ... please wait a moment
Error processing line 1 of /home/sunyp/software/build/anaconda3/lib/python3.7/site-packages/google_auth-1.7.1-py3.6-nspkg.pth:

Fatal Python error: initsite: Failed to import the site module
Traceback (most recent call last):
  File "/home/sunyp/software/build/anaconda3/lib/python3.7/site.py", line 168, in addpackage
    exec(line)
  File "<string>", line 1, in <module>
  File "/home/sunyp/software/build/anaconda3/lib/python3.7/importlib/util.py", line 14, in <module>
    from contextlib import contextmanager
  File "/home/sunyp/software/build/anaconda3/lib/python3.7/contextlib.py", line 5, in <module>
    from collections import deque
  File "/home/sunyp/software/build/anaconda3/lib/python3.7/collections/__init__.py", line 27, in <module>
    from reprlib import recursive_repr as _recursive_repr
  File "/home/sunyp/software/Phenix/phenix-1.17.1-install/phenix-1.17.1-3660/conda_base/lib/python2.7/site-packages/reprlib/__init__.py", line 7, in <module>
    raise ImportError('This package should not be accessible on Python 3. '
ImportError: This package should not be accessible on Python 3. Either you are trying to run from the python-future src folder or your installation of python-future is corrupted.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/sunyp/software/Phenix/phenix-1.17.1-install/phenix-1.17.1-3660/build/../conda_base/lib/python2.7/site-packages/site.py", line 73, in <module>
    __boot()
  File "/home/sunyp/software/Phenix/phenix-1.17.1-install/phenix-1.17.1-3660/build/../conda_base/lib/python2.7/site-packages/site.py", line 22, in __boot
    loader.load_module('site')
  File "/home/sunyp/software/build/anaconda3/lib/python3.7/site.py", line 570, in <module>
    main()
  File "/home/sunyp/software/build/anaconda3/lib/python3.7/site.py", line 557, in main
    known_paths = addsitepackages(known_paths)
  File "/home/sunyp/software/build/anaconda3/lib/python3.7/site.py", line 349, in addsitepackages
    addsitedir(sitedir, known_paths)
  File "/home/sunyp/software/build/anaconda3/lib/python3.7/site.py", line 207, in addsitedir
    addpackage(sitedir, name, known_paths)
  File "/home/sunyp/software/build/anaconda3/lib/python3.7/site.py", line 178, in addpackage
    import traceback
  File "/home/sunyp/software/build/anaconda3/lib/python3.7/traceback.py", line 3, in <module>
    import collections
  File "/home/sunyp/software/build/anaconda3/lib/python3.7/collections/__init__.py", line 27, in <module>
    from reprlib import recursive_repr as _recursive_repr
  File "/home/sunyp/software/Phenix/phenix-1.17.1-install/phenix-1.17.1-3660/conda_base/lib/python2.7/site-packages/reprlib/__init__.py", line 7, in <module>
    raise ImportError('This package should not be accessible on Python 3. '
ImportError: This package should not be accessible on Python 3. Either you are trying to run from the python-future src folder or your installation of python-future is corrupted.

Does it mean that phenix requires python2 rather python3, but there is python3 in my system, so the error came out? And how to solve the problem? Thank you in advance.

Regards,

Yeping Sun

Answer 1

Solely based on /home/sunyp/software/Phenix/phenix-1.17.1-install/phenix-1.17.1-3660/conda_base/lib/python2.7/site-packages/reprlib/__init__.py Phenix contains a Python 2.7 environment.

You could maybe try running your code with /home/sunyp/software/Phenix/phenix-1.17.1-install/phenix-1.17.1-3660/conda_base/bin/python or something to use that Python interpreter, but it's hard to tell since Phenix source is not openly available.

Answer 2

Your environment probably contains path to python2.7.5 Check your PYTHONPATH

This doesn't work with Python 3 for obvious reasons. To remove it:

unset PYTHONPATH