Just ran into the same issue, but in a slightly different way, and with slightly different consequences. You can actually eliminate this failure by manually running compileall on the affected directory:

sudo python3 -m compileall /usr/local/lib/python3.6/site-packages

In other words, a test failure can come and go depending on the presence of other files on the system.

IMO the test should (a) restrict itself to directories within the build tree, and (b) call compile_path with force=True. That should make it more consistent. Something like the attached patch.