I am actually having a similar issue where I am building an python app on a 
Mac (current dev version of pyinstaller) that depends on pygraphviz and 
graphviz. Same issue as above with pygraphviz not finding the dot method. 
This occurs when I build with the option:

python pyinstaller.py [path] -w

But works just fine (runs graphviz) with:

python pyinstaller.py [path] -onefile

The main difference is that the first produces a Mac .app executable and 
the second produces a Unix Executable file. The reason I want to go with 
the first is that you can exclude the console window and have a custom 
.icns file (replace the default used in the pyinstaller/bootloader/images 
folder) which will show your program icon versus the feather icon. I know 
these issues are largely cosmetic but they definitely impact the user's 
ability to use the program.

Thanks a lot!

Nathan

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