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Using Gnome Shell in F15, I don't see any more notifications when a new message is received. empathy-3.0.0-1.fc15.x86_64
Have you set the Me Menu to busy? That will stop all notifications (Empathy, PackageKit, Rhythmbox) to the desktop.
Yes I did, I thought that would only set my empathy status to busy.
(In reply to comment #2) > Yes I did, I thought that would only set my empathy status to busy. The GNOME Shell was designed so that when the user sets himself as busy from the Me Menu, all interruptions (i.e. notifications) are stopped, and the user is allowed to focus on the task at hand. There is documentation online that tells about this and other features of GNOME Shell, which is worthwhile reading since it is a change from the old style desktops. Marking as NOTABUG, since this is the desire behavior of the desktopk.