My problem is not related to the RFE.  It is an issue with the Cygwin inserting 
the current path to pre-defined values.

For example if I set
PLANTUML_JAR_PATH = $(PLANTUML_HOME)   where PLANTUML_HOME is an environment 
variable with the appropriate location.

Under Linux, OSX and Windows,  PLANTUML_HOME will be kept the same value.   
Under Cygwin the value is automatically overwritten to be 
$(PWD)/$(PLANTUML_HOME)

So if I set the $(PLANTUML_HOME) to C:/COTS/PlantUML,  the Cygwin version will 
convert it to /cygdrive/c/Development/MyProject/C:/COTS/PlantUML

If I set it to a cygpath (ie:, /cygdrive/c/COTS/PlantUML ), it will still 
override it to 
/cygdrive/c/Development/MyProject/cygdrive/c/COTS/PlantUML/plantuml.jar

No matter what value is or format is use, the Cygwin version of doxygen will 
always prepend $(PWD)/ to it.

Hope this helps.

-  Luis




From: Mark [mailto:doxygen-us...@erewhon0.net]
Sent: Monday, August 7, 2017 5:37 PM
To: Vega, Luis A (US) <luis.a.v...@lmco.com>
Cc: doxygen-users@lists.sourceforge.net
Subject: EXTERNAL: Re: [Doxygen-users] Doxygen on Cygwin overwrites user 
defined paths

I filed a bug about relative paths in a doxyfile being relative to where 
doxygen is executed eons ago. See 
https://bugzilla.gnome.org/show_bug.cgi?id=756161. There has been no action. 
However I encountered the problem on macOS and I thought on other platforms 
too. Not sure why your results are different.

As for the cygwin path issue, either make sure all tools, including doxygen, 
are cygwin tools or all are windows tools. You might be able to do some mixing 
by using scripts that use cygpath.

Regards

    -Mark

On Jul 31, 2017, at 14:51, Vega, Luis A 
<luis.a.v...@lmco.com<mailto:luis.a.v...@lmco.com>> wrote:

When setting up the PLANTUML_JAR_PATH (an others path based config option) 
within the Doxyfile configuration, the Cygwin version of doxygen will insert 
the current directory path to the front of the user specified path.   This 
behavior is very specific to the Cygwin version (not how the Linux, Win or OSX 
versions of doxygen behave) and is problematic in many ways.

The Cygwin version of doxygen is assuming that all paths are relative to the 
directory where doxygen is executed.   This is completely opposite to the norm. 
 Different users have different environments, which is the reason why the 
Doxyfile includes options to define this paths in the first place.  Also, under 
Cygwin, we have a problem when doxygen calls external tools that don't support 
the unix-like cygpath (i.e., anything none-cygwin).  For example, when 
executing Java to run PlantUML even if the plantuml.jar file is stored a 
matching relative path, the execution would fail because of the unsupported 
path format.

Don't know if this is the proper place to submit a bug related to the Cygwin 
version of doxygen.   If not, please let me know where I should submit a bug 
report.

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