I am not sure how well supported R is in general for this platform (R-admin
says: Cygwin has not been tested for R 3.0.0 or later). It seems this error
occurs because of file handling in this OS, related to memory mapping in
affxparser.  While Cygwin in general can be treated as a Unix OS it may be
that for this particular case it needs to be treated like Windows,
particular you could try setting _MSC_VER manually in src/Makevars.
 However, setting this also does other things so it may very well not work.
 You could try reading on on FILE handling in Cygwin vs. standard Unix.

Given that this platform is not really supported by R, you're on your own.
 This could prove pretty hard to fix.

Kasper

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