On 2/10/2013 11:10, Jon S. Berndt wrote:
> 2) I have always used Doxygen and dot together like this, and it has worked
> previously - I did get the diagrams built.

I've been assuming Doxygen changed how it calls dot somehow, and that 
this change appeared in the Cygwin update in the normal course of things.

The Cygwin build of Doxygen is pretty much out-of-the-box, no special 
configuration.  I don't even recall there being any patches.

> 1) provide a direction to doxygen to use relative paths?

No, I'm saying (and keep saying) that this is a change that will happen 
to Doxygen itself.

> 2) build a new version of doxygen from the source code (which I have done
> before and can do) that will understand relative paths.

All that will do is get you another copy of the same problem 
doxygen.exe.  You wouldn't be building it any differently than I was 
when I maintained the Cygwin doxygen packages, or how David Stacey is 
now building them.

The DIY option is to build *graphviz* yourself, from source, under 
Cygwin.  Then you'll have a Cygwin build of dot.exe, which will 
understand the POSIX paths that the POSIX/Cygwin doxygen.exe is using.

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