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There is a CERN application, ROOT, that when it is built with current Cygwin GCC 3.4.4-1, has problems at runtime (hang, stackdump...).
But following this http://cygwin.com/ml/cygwin/2006-04/msg00634.html, I have made a build of GCC-3.4.4 that includes --enable-fully-dynamic-string.
This new GCC build seems to have solved those problems!
It would be desirable to see this fixed in Cygwin as promised in http://cygwin.com/ml/cygwin/2005-10/msg00085.html.
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