I see

#if (defined(Win32) || defined(Win64))/* R instance as a global */Rstart 
Rp;#endif
in src/rinterface/_rinterface.c.
That sounds fishy for Cygwin.


It looks like: http://trac.sagemath.org/ticket/16089
And that the cygwin patch was ill porte here: 
http://trac.sagemath.org/ticket/19638

Note sure why:
* the linking to readline was removed, maybe R does it properly now without 
handholding.
* this change in the patch is either not enough or too much:
-#if defined(Win32) || defined(Win64)
+#if defined(Win32) || defined(Win64) || defined(__CYGWIN__)
   Rp->R_Interactive = rtruefalse;
 #else
   R_Interactive = rtruefalse;

Try to remove it first.
If that's not sufficient the numerous try instead to perform the same 
change for all #if around R_Interactive stuff.

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