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I was thinking of calling GKSu but I understand it's deprecated. How else can I do this?

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Rethink your application. It shouldn't be running the GUI as root. It should just get root for the things it needs to do as root. This is what gksudo is for. You should run as non-root, but launch gksudo blah blah in a subprocess when you need to do blah blah as root.

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