Installation error: No module named numpy.distutils.core

Install, Configure and Update
1

Hi,

I got following errors in installing cryosparc. I attempted to reinstall by forcing update(cryosparcm update --override), but still I get same errors. Could any help me trouble shooting this issue? Thank you.

  ------------------------------------------------------------------------
    Done.
    conda packages installation successful.
  ------------------------------------------------------------------------
  Preparing to install all pip packages...
  ------------------------------------------------------------------------
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgra                                                                                                                        de your Python as Python 2.7 won't be maintained after that date. A future version of pip                                                                                                                         will drop support for Python 2.7.
Processing ./deps_bundle/python/python_packages/pip_packages/Flask-JSONRPC-0.3.1.tar.gz
Processing ./deps_bundle/python/python_packages/pip_packages/Flask-PyMongo-0.5.1.tar.gz
Processing ./deps_bundle/python/python_packages/pip_packages/libtiff-0.4.2.tar.gz
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-req-build-qqH0TH/setup.py", line 77, in <module>
        from numpy.distutils.core import setup, Extension
    ImportError: No module named numpy.distutils.core

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-req-build-qqH0TH/
  ------------------------------------------------------------------------
    Done.
    pip packages installation successful.
  ------------------------------------------------------------------------
  Main dependency installation completed. Continuing...
  ------------------------------------------------------------------------
  Completed.
  Currently checking hash for mongodb
  Forcing reinstall for dependency mongodb...
  ------------------------------------------------------------------------
  mongodb 3.4.10 installation successful.
  ------------------------------------------------------------------------
  Completed.
  Completed dependency check.

===================================================
Successfully updated master from version v2.12.4 to version v2.12.4.
===================================================

Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: No module named pymongo
2

Hi @BAE,

Can you ensure there are no orphan processes of cryoSPARC running?

ps -ax | grep “supervisord” (kill only the process that is running from your cryosparc2 install)
ps -ax | grep “cryosparc2_command” (kill all the matching processes related to your cryosparc2 instance)
ps -ax | grep “mongod” (kill only the process running your cryosparc2 database)

e.g. kill 82681

Can you also ensure there are no anaconda or python paths in your user environment (e.g., check your ~/.bashrc)

3

Thank you very much for the feedback. I found that the issue was caused by 1) orphaned 39000 port 2)anaconda path in my .bashrc, which was added by SPHIRE.

The issue was resolved by killing 39000 port (fuser -k 39000/tcp) ,deleting anaconda path in .bashrc, and reinstalling cryosparc.

I’m not sure if I’ve done properly, but at least now cryosparc works fine in my workstation.

Thank you so much for the help!

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