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the OpenCV Android native api is the same as the standard c++ api. I have a c++ class which is used to create panorama images in real-time. The class uses lots of OpenCV's functions and data structures and can be compiled for Android and my PC without any platform dependent code. Some OpenCV modules, e.g. the gpu module, are not supported on Android. Maybe you are using some of these unsupported modules in your code.

Best regards,