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>>>>> "Tomohiro" == Tomohiro Shibata <tom@jsk.t.u-tokyo.ac.jp> writes:

Tomohiro> BSD has both stream.h and filio.h but Linux doesn't.

When I do a:

  configure --with-dynamic-ffi --with-newreadline --build linux

with 0623, autoconf makes the correct decision about the presence of 
stream.h and fileio.h.  The package builds from beginning to
test-suite without a problem.  gcc-2.6.3, libc-5.2.5, Linux 1.3.15.

Tomohiro> Is there anyway to get over this problem?

I can't see any problem.