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Perhaps you have an old python in your cygwin which is preferred by OpenCV. Solution is easy: remove it out. cd .../cygwin.../bin del python. Than ensure you have an up-to-date python installed (python is used for generation of java wrapper, therefore it is needed even when you do not need opencv python bindings) and (on windows with developer tools it is very important) that default program for opening .py is python.exe (not e.g. WebMatrix). And it will work fine.