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This post is kind of old, so I'm not sure if it's still relevant, but I was having the same problem installing OpenCV 2.4.4 on Ubuntu 12.10 after having installed the CUDA 5.0 toolkit from (though with the NVIDIA driver that was installed from the nvidia-current package when I installed Bumblebee from the bumblebee PPA, version 304.84, I believe). I was able to successfully compile OpenCV by running cmake -i, saying yes to see the advanced options, and adding -L/usr/lib/nvidia-current -lcuda each time I was asked for linker flags (/usr/lib/nvidia-current/ is where the NVIDIA libraries were installed from the nvidia-current package).