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Why do you need to compile from source at all? Why not simply run "sudo apt-get install ros-diamondback-pr2-mechanism"? If you follow the 3d_navigation instructions you should already have that package installed.
If you checked out pr2_mechanism from source, did you get the correct branch according to http://www.ros.org/wiki/pr2_mechanism/Releases? That should be pr2_mechanism-1.4.4.
When you don't check out the right version it will be newer than your installed packages and depend on versions that you don't have installed (or can't even install). This is likely the case with urdf_interface that is only available since electric.
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