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I can't say for certain regarding ROS on windows, but on linux there are no problems if OpenCV was already installed while installing ROS. I guess it depends on what OpenCV and what ROS version you are trying to install. ROS Electric has OpenCV 2.3.1 I believe, so if you have 2.3.1 and are installing Electric there should be no problem at all. The same goes for ROS fuerte and OpenCV 2.4.0.

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