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This might origin from some old/wrong setup instructions. Can you say how you setup/installed ROS, especially rosdep. Maybe there are still leftovers to be corrected somewhere.

To fix it, hard delete the .ros/rosdep directory (as root). If .ros also has root permissions, you should also delete that and then re-initialize rosdep as:

sudo rosdep init
rosdep update

Note: No sudo for the second call.

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