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The R matrix transforms from Cam1 system, to Cam2 system. Its a 3D->3D transformation. The warpPerspective() expects an 2D Image -> 2D Image tranformation (in normalized space).
Luckily there is a function for that: http://docs.opencv.org/modules/calib3d/doc/camera_calibration_and_3d_reconstruction.html?highlight=findhomography#findhomography
