I found a fix for the update issue. When starting atom in the foreground, I see the following:
2014-04-24 09:25:48.397 Atom[2618:507] App load time: 257ms
[2620:0424/092548:INFO:renderer_main.cc(227)] Renderer process started
[2618:0424/092550:INFO:CONSOLE(18)] "Window load time: 1374ms", source: /Users/tim/Applications/Atom.app/Contents/Resources/app/src/window-bootstrap.js (18)
2014-04-24 09:26:16.763 Atom[2618:1372b] Download completed to: file:///Users/tim/Library/Application%20Support/com.github.atom.ShipIt/update.Nh9EA0Q/download
Error Downloading Update: Installation in progress
I took a look at the
~/Library/Application Support/com.github.atom.ShipIt directory and found a few files there. The stderr log file had some messages dated 3/10 (probably the first time the update failed) trying to install to the
/Applications folder. I quit Atom, renamed the
com.github.atom.ShipIt directory and restarted Atom. The update completed successfully and I was able to restart with the new version.
I hope this helps others who might still be experiencing this issue. It looks like a failure in the update kept the state around and Atom thought it was still trying to update, hence the “Installation in progress” error.
Thanks to @ProbablyCorey for the debug tip in "Check for update" disappears from Atom menu.