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Solved!

While looking at the CMakeLists.txt I saw tf2_eigen was not in the find_package list. I don't know if it needs to be there but adding it solved my problem.

find_package(catkin REQUIRED COMPONENTS
  mavros
  roscpp
  mavros_msgs
  sensor_msgs
  geometry_msgs
  std_msgs
  visualization_msgs
  urdf
  tf
  tf2_eigen
)

Solved!

While looking at the CMakeLists.txt I saw tf2_eigen was not in the find_package list. I don't know if it needs to be there but adding it solved my problem.

find_package(catkin REQUIRED COMPONENTS
  mavros
  roscpp
  mavros_msgs
  sensor_msgs
  geometry_msgs
  std_msgs
  visualization_msgs
  urdf
  tf
  tf2_eigen
)

EDIT: Can't accept my own answer :(