[R] System("source activate condaenv")

[Ivan Krylov]

On Wed, 20 Mar 2019 09:59:21 +0100
Sandra Elisabeth Chaudron <sandra.chaudron using gmail.com> wrote:

> I am using the server version of RStudio and I have a script where I
> want to activate the conda environment that I set up for a
> bioinformatic tool called MinVar.
> For that I use in my script the command: system("source
> /home/ubuntu/miniconda3/bin/activate minvar").

Unfortunately, this is probably not going to work as is.

In *nix-like systems, child processes cannot alter the environment
variables of their parents, so when one wants a shell script to alter
environment variables in the current session, they use "source".

The reason your command returns an error message is probably because
"source" is a command specific to /bin/bash, while R calls /bin/sh,
which might be symlinked to /bin/dash instead of /bin/bash on Ubuntu.
The POSIX-correct form would be ". /home/ubuntu/miniconda3/bin/activate
minvar", that is, just a dot instead of the word "source".

But the underlying issue would stay the same: R system()
function launches a subprocess /bin/sh; the "source" or "." command
causes the environment of the *child* shell process to be changed;
environment of the *parent* R process stays unchanged.

Your best bet would be to read the activate script, understand the
changes to the environment it causes and use Sys.getenv() /
Sys.setenv() to make equivalent changes in R environment variables.

-- 
Best regards,
Ivan