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After installing Skype 4.0 on Ubuntu Precise, I see its indicator in top bar, but there is no running application icon on the left, thus I can't focus into it and pin to the Launcher.

I had 2.2 version before, but purged it as described in Skype 4.0 still looks like 2.2 beta, so I believe this can be considered clean install.

Related question is whether it's possible to have overlay with new/unread messages in the unity launcher icon similar to indicator?

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Try to start a chat from the menu that opens clicking the icon in unity panel. Doing this, I see the icon in the launcher. – jasmines Jun 15 '12 at 9:05
There was no icon at all, but appeared after I rebooted. In combination with skype-wrapper it works as expected. – Igor Semenko Jun 15 '12 at 17:50

You have to install sni-qt Install sni-qt package:

If your Ubuntu is 32 bits:

sudo apt-get install sni-qt

Or, if you are using 64 bits:

sudo apt-get install sni-qt:i386

I'm not sure if you need to logout / login afterwards, but Skype will then appear together with other indicators.

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This solves the problem even in Gnome fallback mode (non-Unity). – pts Mar 7 '13 at 10:07

Consider the missing launcher a benefit and install skype-wrapper, which integrates Skype nicely into Unity:

sudo add-apt-repository ppa:skype-wrapper/ppa
sudo apt-get update && sudo apt-get install skype-wrapper

See this article for further details:

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I have equal behavior with skype icon. But, after using "apt-get install" from command line to install skype, this problem was resolved.

You should try to install skype using "apt-get install", if it's not that.

More over, this installation method is recomended instead of skype website.

sudo add-apt-repository "deb $(lsb_release -sc) partner"
sudo apt-get update && sudo apt-get install skype

I've found it here:

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It's actually back to what it used to be (in early versions of Ubuntu), so you need to 'whitelist' the notification icon.

Take a look at (or google 'skype whitelist ubuntu'.

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