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Any data being processed by the navigation stack needs to be able to be transformed using tf. The left arm is rarely in the critical path for that, but it will be a problem for doing things like self filtering data so you don't avoid your own arm.

You need to provide more information about what the errors actually are, but it is probably some of the safety systems on the PR2 which are preventing you from driving not an algorithmic need for all elements of the pr2's tf tree.