Generating PDF from Doxygen?

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I am trying to generate a PDF file from the Doxygen output (html / LaTeX). As far as I could understand there's a batch file placed inside the LaTeX output folder that should generate the file. When I execute it I get repeated warnings of the following format:

LaTeX Warning: Reference `group___example' on page 1 undefined on input line 3.

Not sure what are these and what to do with them. If I ignore them the PDF file is not generated. Anyone has any experience with this?