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In the gcc-3 era the C++ timing performance were really poor, gcc-4 solved a lot such problem. I guess the situation is improved in the meantime but of course cygwin is slower than an equivalent native build as he try to replicate the UNIX/Posix enviroment in an unfriendly MS-Windows word.
My experience porting octave says that gcc-4 is much better but I have no idea of ROOT needs.
Ciao, Angelo.
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