I build Chromium from source on Linux (Ubuntu). I made it my default application for links, but I noticed that when clicking a link embedded in a PDF (using a reader like Evince), that it gave a permission problem.

The trick is to edit

/etc/apparmor.d/abstractions/ubuntu-browsers

and add a line like:

/opt/google/chromium/chrome PUx,

Then do:

sudo service apparmor reload