Installation Errors

Hi! I’m trying to install AFNI, and when I evaluate the system, I get the following output:
========================= summary, please fix: =========================

  • login shell ‘bash’, trusting user to translate code examples from ‘tcsh’
  • shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile

I’ve been able to troubleshoot the other problems I got, but I can’t seem to figure out how to fix these problems, can anyone help?
thank you!!

Hi-

Those aren’t really errors, just suggestions.

The second one is probably the more useful one to do something about; the first is just a style choice (many AFNI scripts are written in tcsh, so if you use a bash terminal, you might have to alter some things like variable definition syntax-- but that is really not a major thing).

To deal with the second one, you can copy+paste this in a terminal:


echo ""
echo "source ~/.bashrc" >> ~/.bash_profile
echo ""

If you open up a new terminal and run


afni_system_check.py -check_all

there, then you should see that that 2nd message is gone (and every terminal opened thereafter should also have that property now).

–pt

Hello,

You do not necessarily need to do anything.

Those particular messages are not things that actually require fixing. They are more just along the lines of comments, but are left in the summary so they are likely to be seen.

The ‘trusting user to translate’ message is because most of our examples are given in tcsh syntax, but the user login shell is bash. So the user might have to alter some of the syntax to be able to run the commands in bash.

The ‘consider sourcing’ message is because, particularly on macs, some terminal programs process .bashrc, and some process .bash_profile. For that and similar reasons, it can be helpful if they both do the same things (so all the commands could go in one, and the other could source the first).

For a better understanding of these points, it might be good to review the Unix tutorial.

  • rick