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Empathy shows up in my window picker list and it appears to be started according to the indicator applet and the process manager but I can't see any of its windows! People were sending me messages and there was no empathy window to switch to!

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Did you try clicking "Chat" in the messaging menu (the little envelope icon next to the clock)? It should show the contacts list from where you can open any hidden message windows and change the settings concerning hiding and showing of windows.

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That's what I'm saying, I can't even see the contacts list window :S – omouse Jan 25 '11 at 15:27

To get empathy to properly exit by killing processes from the command line, you first need to kill telepathy and telepathy-butterfly processes, then kill the empathy process(es).

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Run killall empathy, or open the System Monitor and kill it from there.

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not good enough, I restarted empathy and it still didn't show any windows :S – omouse Dec 6 '10 at 14:53

Empathy shows that it is running in the indicator applet.

You can click the applet and select "Chat" to open empathy, or you can simply run the launcher (I tend to do this as I'm using Gnome Do). The shortcut to the indicator applet is meta-m (meta is the windows-key).

To close Empathy, either press ctrl-q while having the main window focused, or run killall empathy in a terminal.

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