When building flightgear from a fresh checkout (I mean the whole shebang) and 
trying either

  ./autogen.sh

 - or -

  rm config.cache
  make distclean
  aclocal -I .
  automake -a
  autoconf
  CFLAGS="" CXXFLAGS="" ./configure --with-logging
  make

I get to the ./configure line and this happens:

..
..
checking host system type... i386-pc-cygwin32
Simgear not specified
Building with Oliver's multi-pilot network support
Building with new experimental weather subsystem
checking for windows.h... yes
./configure: 2969: Syntax error: word unexpected (expecting ")")


Does anyone know what this is?

Jon



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