Is it possible to have a small indicator showing that updates are available (red for security updates) instead of having the update manager pop up?
12.04 onwards
Newer Ubuntu users can find the settings in dconf-editor. Install dconf-tools
if necessary.
Then, launch dconf-editor, then go to com > ubuntu > update-notifier and uncheck auto-launch.
Older versions of Ubuntu
Open Configuration Editor , then go to apps > update-notifier, then uncheck auto-launch.
You'll still be able to see
Updates Available
from System menu accessible from the top-right corner of the screen.
