Trouble Cloning root env

[Charles Gagnon]

We have been using Anaconda deployments for years on our Linux servers and Windows workstations. Just recently, as complexity increases, we decided to leverage virtual environments more for various particular needs. I just recently ran into an issue on a system cloning the root environment in the user space.

My install was done with Anaconda2-4.0.0 and the root environment is pretty vanilla. As a user, I tried cloning the root environment with:

$ source /usr/anaconda/bin/activate root

$ conda create -n q1_tf --clone root

[...]

This worked fine, no errors reported but my environment is using the system python instead of the Anaconda one and nothing is working:

(q1_tf) (cgagnon@hcq1pl7): ~$ which python

~/.conda/envs/q1_tf/bin/python

(q1_tf) (cgagnon@hcq1pl7): ~$ python -V

Python 2.7.5

Of course, nothing I need imports properly. The Python version reported by 'conda info' does not even match. I'm very confused, what am I missing?

$ conda info

Current conda install:

             platform : linux-64

        conda version : 4.1.5

    conda-env version : 2.5.1

  conda-build version : 1.20.0

       python version : 2.7.11.final.0

     requests version : 2.9.1

     root environment : /usr/anaconda  (read only)

  default environment : /home/cgagnon/.conda/envs/q1_tf

     envs directories : /home/cgagnon/.conda/envs

                        /home/cgagnon/envs

                        /usr/anaconda/envs

        package cache : /home/cgagnon/.conda/envs/.pkgs

                        /home/cgagnon/envs/.pkgs

                        /usr/anaconda/pkgs

         channel URLs : https://repo.continuum.io/pkgs/free/linux-64/

                        https://repo.continuum.io/pkgs/free/noarch/

                        https://repo.continuum.io/pkgs/pro/linux-64/

                        https://repo.continuum.io/pkgs/pro/noarch/

          config file : None

         offline mode : False

    is foreign system : False

[Tim Butler]

You might run conda with the --debug option.
In my case, debug shows numerous errors attempting to create
hard links to the /usr/anaconda files that I don't have permission to hard link to.
This includes :

ERROR:conda.install:failed to link (src='/opt/anaconda/pkgs/openssl-1.0.2g-0/bin/.openssl-libcrypto-fix', dst='/home/username/.conda/envs/q3_ft/bin/.openssl-libcrypto-fix', type=1, error=OSError(1, 'Operation not permitted'))
E
...
and the python2.7 binary itself:
DEBUG:conda.install:pkgs_dir='/opt/anaconda/pkgs', prefix='/home/PRLSS/tbutler/.conda/envs/q3_ft', dist=u'python-2.7.12-0', linktype=1
ERROR:conda.install:failed to link (src='/opt/anaconda/pkgs/python-2.7.12-0/bin/python2.7', dst='/home/PRLSS/tbutler/.conda/envs/q3_ft/bin/python2.7', type=1, error=OSError(1, 'Operation not permitted'))

Because python2.7 didn't get installed your which command reverts to the system python.

But I don't understand how you activated your new environment,
because I don't get a bin/activate file in mine.

-tim

[Kale]

Can you try cloning root to a new env *without* an env being active?  That is, is there a difference in behavior when you try cloning root when an environment is active, and when no conda environment is active?