Re. the need for "conda deactivate": you probably have conda set to activate an environment in one of the files that is executed every time a terminal starts.

What is the output of:

conda env list

? It will display a list of conda environments on your computer, and the one with an asterisk by it will be the one activated at present.

Can you run this:

grep -h "conda activate" ~/.*rc

and post the output? I expect a specific file like ~/.bash_profile has a "conda activate ..." command in it. In that case, you can open whatever file has it and comment it out, so new terminals will not have that environment being activated by default.

Also, what is the output of:

cat ~/.condarc

? That will show some of your conda default settings.

I find it weird that the "gcc" message went away when you deactivated your conda environment... But I only use conda for managing my Python usage.

In a terminal where you have run "conda deactivate", can you run this:

sudo rPkgsInstall -pkgs ALL

(requires admin password to run). That will try to install all the necessary R libraries (afex, snow, etc.).

--pt