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You can switch off gpu modules with CMake options:

WITH_CUDA=OFF
BUILD_opencv_gpu=OFF
BUILD_opencv_gpuarithm=OFF
BUILD_opencv_gpubgsegm=OFF
BUILD_opencv_gpucodec=OFF
BUILD_opencv_gpufeatures2d=OFF
BUILD_opencv_gpufilters=OFF
BUILD_opencv_gpuimgproc=OFF
BUILD_opencv_gpulegacy=OFF
BUILD_opencv_gpuoptflow=OFF
BUILD_opencv_gpustereo=OFF
BUILD_opencv_gpuwarping=OFF