Atom preventing restart


I am using Atom on OSX 10.9.2, and the operating system just installed a security update, and then wanted to restart. But it fails to restart and says “Some updates could not be installed because the application Atom cancelled restart. Quit Atom and try again.”

I have tried quitting Atom using Cmd+Q and using kill -1, but it keeps restarting itself, which means the restart can’t proceed. Here is the process:

ps -fu david | grep atom
1426064955 11798   309   0  9:59am ??         0:00.02 /Applications/ com.github.atom.ShipIt