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With catkin (groovy/hydro) there are no separate packages for OpenCV and PCL anymore. However, apparently the package you mentioned still uses rosmake, which historically requires these packages, if applied.... I am not really sure what is the best way in this case, but I'd try to remove pcl and opencv2 from the dependencies in manifest.xml and add to CMakeLists.txt something like

find_package( PCL 1.2 REQUIRED segmentation filters visualization )

You might need to add further:

include_directories(  ${PCL_INCLUDE_DIRS} )

link_directories(${PCL_LIBRARY_DIRS})
add_definitions(${PCL_DEFINITIONS})

and link your targets accordingly:

target_link_libraries ( your_exec ${PCL_LIBRARIES}  )