Thanks! That's actually super-helpful.
The Github repo lives on a cloud folder (box.com) that is synced to my various computers, so that may be the issue. If the problem re-emerges, I will experiment with moving the repo to my local machine.
I also read on an R forum somewhere (can't find the link now) that this is a known issue that sometimes appears and then mysteriously goes away.
After rebooting my machine several times, the issue went away, so I'll wait to see if it re-appears and try some of the suggested solutions.
Much appreciated.