Good practice regarding multiple package management systems

I am not sure what is available for R (heard about REnv), but for Python I've decided on the pragmatic approach that every user is responsible for their own Python environment with pyenv (same is true for Perl with perlbrew and Ruby with RVM). That way, users can create their own optimal environment for every project without my assistance (pyenv manages Python installations and then you can use pip to install modules local to that specific Python installation).

System packages are only used for system needs.