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I suspect you're going about this the right way by manually specifying include and library directories. It won't be portable or installable elsewhere, but it should get you off the ground and allow you to experiment with OpenCV3 on your own system.

My best guess is that the search paths are getting passed to the compiler in the wrong order, and it's searching the ROS include path before the opencv paths that you're specifying.

Try moving your include_directories() and link_directories() statements as far up your CMakeLists.txt as you can; preferably before your find_package(catkin ...)

It may also be worth running catkin_make with VERBOSE=1 so that you can examine the exact arguments that are being passed to the compiler and the linker.