After some digging, it turns out subprocess.Popen (invoked around line 864 in afni_base) defaults to /bin/sh. (Is this new?) My login shell is /bin/tcsh. (Has been for years.) Accordingly, I specify modifications to PATH, including $AFNI_HOME, in ~/.tcshrc, which /bin/sh, of course, does not look at. The odd thing is that I have been running this set up for years without this error. The only thing different now is that I am on a fresh migration to a new machine running OS X 10.10.
I did a find and replace to afni_base, inserting the argument “executable='/bin/tcsh’” into the call to Popen. This solved the problem. I, however, anticipate this breaking as soon as I next update AFNI. Any thoughts on a more stable solution?
cheers
Iain
