python - After Anaconda installation, conda command fails with "ImportError: no module named conda.cli"

45
votes

I installed 64 bit Linux version of Anaconda recently (1.8.0-Linux-x86_64). The installation seemed to work fine:

$ python 
Python 2.7.5 |Continuum Analytics, Inc.| (default, Nov  4 2013, 15:30:26)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-54)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>>
##No issues here

However if I try any of the conda commands, I get an error:

$ conda info
Traceback (most recent call last):
  File "~/anaconda/bin/conda", line 3, in <module>
    from conda.cli import main
ImportError: No module named conda.cli

Installation is under my user directory (~/anaconda). I have verified that $PATH contains ~/anaconda/bin. $PYTHONPATH is also set to ~/anaconda/lib.

Any thoughts on what is wrong with the 'conda' command? My searches do not appear to show any one else reporting this error.

6
pythonlinuxanaconda
What happens if you unset PYTHONPATH? – asmeurer
Thanks @asmeurer. unset PYTHONPATH by itself did not work. However, if I also unset PYTHONHOME, it works. Looks like PYTHONHOME was pointing to a different python installation which caused this error. – pk45059
Generally with Anaconda, you don't need to set those variables. Just $PATH. – asmeurer

6 Answers

17
votes

When you were installing it, you missed a section. When conda asked you if it can set your .bashrc file, you probably clicked NO. It's a simple fix: fire up your interpreter and add this line:

export PATH=/home/add your username here/anaconda/bin:$PATH

Now type python into the interpreter and you will see Anaconda 1.8.0 or whatever version you have. You will have to do this each time you start a new interpreter.

Enjoy!

43
votes

Note

If the accepted answer doesn't work, then this answer might help.

The Cause

According to the official thread on GitHub, this problem happens when there is a change in the python version. In my case, the original anaconda installation is anaconda 3 with python3.6. And I installed a new package which updated python topython3.7 along with some other packages. And this corrupts the anaconda base environment.

The solution

The solution that works for me is pretty simple... reinstall anaconda. I don't know if this is the optimal solution, but this what works for me.

  • First we need to delete the old installation: 
    rm -rf ~/anaconda3
rm -rf ~/.condarc ~/.conda ~/.continuum

  • Then, reinstall Anaconda.

  • Finally, update all packages (including conda itself) using:

    conda update --all

Now, your anaconda is up-to-date.

5
votes

If anaconda was installed by the root user, a permissions issue could produce the ImportError: No module named 'conda.cli' error.

Something like this

sudo chown -R [username] [anaconda_dir]

would help in that case.

Alternatively, the conda install could be cloned to another location, such as the user's home directory:

conda create -n [my_conda_root] --clone=[current_conda_dir]

But for this to work, you will need at least the read and traverse permissions.

4
votes

I ran into this problem while downgrading python in a Miniconda3 env. in my Dockerimage. With the Miniconda3-4.5.11-Linux-x86_64.sh installer the initial base python version is 3.7.0; I wanted to downgrade to 3.6.9 and got the "ImportError: no module named conda.cli" error (all in the same layer to reduce the image's size).

I fix this by using the Miniconda3-4.5.4-Linux-x86_64.sh installer instead (which will give you python==3.6.5) and called

conda install -y python==3.6.9
1
votes

I fixed it by reinstalling anaconda but keeping the envs folder.

So, I moved the old anaconda3 folder to anaconda3.old, I reinstalled anaconda3 at the same location and copied the content of the anaconda3.old/envs folder to anaconda3/envs. Then it worked.

0
votes

I am using Anaconda and I found this Solution from somewhere:

Change the content of: /opt/cloudera/parcels/Anaconda-5.2.0/bin/conda

#!/usr/bin/env python

# -*- coding: utf-8 -*-
import re
import sys

from conda.cli import main

if __name__ == '__main__':
    sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
    sys.exit(main())

to 

#!/opt/cloudera/parcels/Anaconda/bin/python
# -*- coding: utf-8 -*-
import sys
# Before any more imports, leave cwd out of sys.path for internal 'conda shell.*' commands.
# see https://github.com/conda/conda/issues/6549
if len(sys.argv) > 1 and sys.argv[1].startswith('shell.') and sys.path and sys.path[0] == '':
    # The standard first entry in sys.path is an empty string,
    # and os.path.abspath('') expands to os.getcwd().
    del sys.path[0]

if __name__ == '__main__':
    from conda.cli import main
    sys.exit(main())