conda, "Solving environment: failed" error on Linux CentOS 7

Question

I installed Conda through Miniconda on my laptop running Linux CentOS 7.

If I run the command conda update conda , I get the following error:

conda update conda
Solving environment: failed

NotWritableError: The current user does not have write permissions to a required path.
  path: /path/to/custom/dir/pkgs/urls.txt
  uid: 1000
  gid: 1000

If you feel that permissions on this path are set incorrectly, you can manually
change them by executing

  $ sudo chown 1000:1000 /path/to/custom/dir/pkgs/urls.txt

In general, it's not advisable to use 'sudo conda'.

I've no idea on how to solve this issue; I also asked on the Bioconda GitHub page but nobody replied.

Any suggestion on how to solve this problem? Thanks

Answer 1

This is discussed in conda issue #7267 ( https://github.com/conda/conda/issues/7267 ).

You may have logged in using sudo, perhaps as sudo -u davide bash ?

If so, then the following command will show SUDO_COMMAND as the command used to become the user, as well as SUDO_USER, SUDO_UID and SUDO_GID:

$ set | grep SUDO

You can instead use sudo su - davide to get a clean context with no SUDO definitions.

I encountered the same issue when administering a shared conda environment via ansible. My solution was to use the following to operate as the conda package owner:

- name: update conda environment
  command: conda update -y --all
  become: yes
  become_user: conda
  become_method: su

Whether or not it is a good idea to share an anaconda installation on a cluster is a separate question.