EACCES, permission denied
That was the error message that I received when I was trying to update my Atom packages (I think it was linter-php). Basically, the updater was failing because it didn’t have permission to remove an old config file. The fix was simple enough. All I had to do was resign the permissions to my user by running the following command:
sudo chown -R `whoami` ~/.atom
Easy as that the permissions were fixed and the updater could do its thing again.