Warren - thanks for your reply (again).

I must say that I'm a little bit confused about what I need to do. Your
explanations sounds like it will work, but here's what I understand:

1) I do have a Windows build of Graphviz, which includes dot, and I have
always been able to run dot under cygwin, even though it is not a native
cygwin build.
2) I have always used Doxygen and dot together like this, and it has worked
previously - I did get the diagrams built. 
3) I have used the same doxygen configuration file for quite a while,
without changes.
4) I get the executable of doxygen via "setup.exe" which is downloaded from
cygwin.com, and go through that installation process. I am currently using
doxygen v1.8.3.1

Are you suggesting that to use the version of dot that I currently have,
that I would need to:
1) provide a direction to doxygen to use relative paths? If so, how would I
do that?
2) build a new version of doxygen from the source code (which I have done
before and can do) that will understand relative paths.

I'm still uncertain what would have changed that would have caused things to
not work as expected anymore, but if I can get this to all work again, it's
a moot point.

Thanks again,

Jon


> -----Original Message-----
> From: Warren Young [mailto:war...@etr-usa.com]
> Sent: Friday, February 08, 2013 3:05 PM
> To: Doxygen-L
> Subject: Re: [Doxygen-users] Error: dot: can't find ###
> 
> On 2/8/2013 07:26, Jon S. Berndt wrote:
> >> Error: dot: can't open
> >> /home/jon/JSBSimCVSGit/JSBSim/documentation/html/inherit_graph_9.dot
> 
> I already told you why that doesn't work in my Dec 18 message, and
> proposed a way Doxygen could be changed to make it work.
> 
> To reiterate in brief:
> 
> /home/jon/... is an absolute POSIX path, and you have a native Windows
> version of dot.exe, which of course doesn't understand POSIX paths.
> (It wants a Windows path: c:\cygwin\home\jon\...)
> 
> The native Windows build of dot.exe *will* understand *relative* paths
> with forward slashes, though, so it is possible to use a Cygwin build
> of Doxygen (which will use POSIX paths) with a native version of
> dot.exe if Doxygen switches to relative paths.
> 
> The other solution is to use dot.exe as a filter, via popen().
> 
> Failing that, you have to get/make a Cygwin build of Graphviz, so its
> dot.exe will understand POSIX paths.
> 
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