Jupyroot in Jupyterhub CLING init can not extract standard include library paths

Cling
4

Hi @bellenot, @etejedor,

thank you for your replies. No, our students typically don’t have a CERN account.

However, I think I figured it out. Actually, the path to x86_64-conda-linux-gnu-c++ was missing in the PATH environment variable. I prefixed PATH with the proper pass to the conda environment’s bin directory in my kernel.json file which now reads:

{
 "argv": [
  "/opt/anaconda3/envs/root6/bin/python",
  "-m",
  "ipykernel_launcher",
  "-f",
  "{connection_file}"
 ],
 "display_name": "CERN ROOT",
 "language": "python",
 "metadata": {
  "debugger": true
 },
 "env": {
     "PATH": "/opt/anaconda3/envs/root6/bin:${PATH}"    
 }
}

Afterwards the warning message was gone.

Cheers,

w.w.

P.S.: In case someone is interested in how this kind of problem may be figured out:

  • Start your (python-based) notebook via your JupyterHub instance.
  • Check the PATH environment variable:
[] import sys
[] printenv
[] ! echo $PATH
  • This way I was able to compare the environment variables between using the conda environment directly from the command line and via the Jupyter kernel.