Installation in existing anaconda environment

Install, Configure and Update
1

I tried to install cryosparc with my user account,
where an anaconda environment (python3) is always activated by .bashrc.

Then cryosparc installation went wrong, below are the error messages,

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-ZAKntj/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-ZAKntj/

************ CRYOSPARC SYSTEM: STANDALONE INSTALLER **************

The installer will now download, install and connect the worker
package on this machine. The worker package will allow cryoSPARC
to run compute jobs.

Starting cryoSPARC…

Starting cryoSPARC System master process…
CryoSPARC is not already running.
database: started
Traceback (most recent call last):
File “”, line 1, in
ImportError: No module named pymongo

and my anaconda base environment (originally python3) was turned into
a mysterious python 2.7.15 environment.

Is there anyone experienced similar situation?

Thanks,
Kotaro

2

I’ve had similar issues. I find I need to comment out any existing anaconda stuff from my bashrc before installing or upgrading cryosparc (and then put it back in afterwards).

Cheers
Oli

1 Like
3

Just to be sure…

conda deactivate
unset CONDA_SHLVL
unset CONDA_PROMPT_MODIFIER
unset _CE_CONDA
unset CONDA_EXE
unset CONDA_PREFIX
unset CONDA_PYTHON_EXE
unset CONDA_DEFAULT_ENV
unset PYTHONPATH
1 Like
4

Thank you for your reply. I’ll reinstall as you told.

I’m sad my anaconda environment broken.
I think it is better for cryoSPARC team to emphasize this issue in the installation instruction.

1 Like