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The problem is most likely due to you using rosmake, as per the ardrone_autonomy documentation, you should install it using catkin_make:

$ cd ~/catkin_ws/src
$ git clone https://github.com/AutonomyLab/ardrone_autonomy.git -b indigo-devel
$ cd ~/catkin_ws
$ rosdep install --from-paths src -i
$ catkin_make