Reply To: ERROR: Option matching -s not found in command line top-level context

I have no experience with compiling Rosetta on Windows with or without cygwin, but I found a previous discussion on the forums which mentions the issue may be a spurious zlib at {rosetta_source}/external/lib/z.lib. Try removing the Rosetta-provided zlib, confirming that you have the appropriate zlib installed with your cygwin installation, and then redoing the building and installation.