OK, I had a look into what this could be, and I think it’ll be either a syntax error in the code itself, or more likely some issue with the text encoding used on your computer (I assume this won’t be a plain ASCII US encoding…?).
Regardless, the reason we don’t get a more informative error message is due to the way we handle runtime errors. This is actually fixed in our development branch, but this hasn’t yet been released (coming soon though… 
). To at least let you investigate what the problem might be, I’ve back-ported those changes over to the master branch so you can run it and see what the actual error is. To use this, try the following (from within the MRtrix3 folder):
git fetch
git checkout configure_remove_naked_except
./configure
and hopefully that’ll give you a better idea. If you’re in any doubt, post the output of that last command, along with the contents of the configure.log file (as you did in your first post), and we’ll see if it makes any sense to us…