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With the current layout you would need to #include "proto/transform.pb.h".

But your package should install all its headers into include/${PROJECT_NAME} to avoid potential collisions with other packages. I don't know how the header files generated by protobuf look like but this should be the CMake install call:

install( FILES ${HDR} DESTINATION include/${PROJECT_NAME}/${DIR} )

Then you will be able to #include "my_protobuf/proto/transform.pb.h".

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