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We encounter this message sometimes when an user doesn't close it's X-Server correctly on a Windows Server 2008 Terminal Server (although I thing it will happen on other versions of Windows as well). It actually means there are locked files on the filesystem to ensure there are no two sessions at the same time on the same port. These files are found in the tmp directoy under the cygwin installation root, which is by default at C:\Cygwin:
C:\cygwin\tmp>dir
Volume in drive C has no label.
Volume Serial Number is 98D6-2DE4
Directory of C:\cygwin\tmp
16-02-2011 09:39 <DIR> .
16-02-2011 09:39 <DIR> ..
19-01-2011 12:42 11 .X0-lock
19-01-2011 12:42 <DIR> .X11-unix
1 File(s) 11 bytes
3 Dir(s) 21.463.330.816 bytes free
C:\cygwin\tmp>cd .X11-unix
C:\cygwin\tmp\.X11-unix>dir /a
Volume in drive C has no label.
Volume Serial Number is 98D6-2DE4
Directory of C:\cygwin\tmp\.X11-unix
19-01-2011 12:42 <DIR> .
19-01-2011 12:42 <DIR> ..
19-01-2011 12:42 54 X0
1 File(s) 54 bytes
2 Dir(s) 21.462.609.920 bytes free
If you try to delete the files you'll get a permissions error:
C:\cygwin\tmp>del .X0-lock C:\cygwin\tmp\.X0-lock Access is denied.
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