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Hey Matt, have you gotten this worked out? The way I uninstall is to right
click on c:/cygwin and hit delete. :)
The only thing I can think of is to make sure you add cygwin/bin to your
path...

I just updated my cygwin to a new machine a few days ago and have not had
any troubles.

Albert is this building with --enable-cygwin or --disable?

My Box:
AMD Turion64 X2
XP current

$ ./fltk-config --version
1.1.8

$ autoconf --version
autoconf (GNU Autoconf) 2.61
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software.  You may redistribute copies of it under the terms
of
the GNU General Public License <http://www.gnu.org/licenses/gpl.html>.
There is NO WARRANTY, to the extent permitted by law.

Written by David J. MacKenzie and Akim Demaille.

$ gcc --version
gcc (GCC) 3.4.4 (cygming special, gdc 0.12, using dmd 0.125)
Copyright (C) 2004 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.

$ ld --version
GNU ld version 2.17.50 20060817
Copyright 2005 Free Software Foundation, Inc.
This program is free software; you may redistribute it under the terms of
the GNU General Public License.  This program has absolutely no warranty.

$ svn info
Path: .
URL: http://svn.easysw.com/public/fltk/fltk/branches/branch-1.1
Repository Root: http://svn.easysw.com/public/fltk/fltk
Repository UUID: ea41ed52-d2ee-0310-a9c1-e6b18d33e121
Revision: 5698
Node Kind: directory
Schedule: normal
Last Changed Author: matt
Last Changed Rev: 5697
Last Changed Date: 2007-02-13 09:38:43 -0500 (Tue, 13 Feb 2007)

Hope this is of some help.
Mark

Link: http://www.fltk.org/str.php?L1598
Version: 1.1-current