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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 developer.nvidia.com (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).
