Hi, Gerard-
OK, well, glad the first part is all set, then.
Re those two messages:
+ * login shell 'bash', trusting user to translate code examples from 'tcsh'
Nothing for you to change at all. This is not something to fix.
When we do shell scripting, we mostly use tcsh; those can be run from any shell, but if you were, say, to copy+paste from one into to a terminal, then you would want to be a 'tcsh' shell.
+ * shell bash: consider sourcing (non-login) .bashrc from (login) .profile
This is a minor thing, but can you please copy+paste this into a terminal:
echo "" >> ~/.profile
echo "source ~/.bashrc" >> ~/.profile
echo "" >> ~/.profile
Then, can you open a new terminal and verify that that message is gone from running "afni_system_check.py -check_all"? (It should be from all further terminals.)
And then that looks like you are all set.
--pt