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I run Doxygen from the console, and get a lot of warnings and error messages for my project. For convenience, I want Doxygen to write this log output to a file. How do I specify a file for the log output?

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you need to edit the Doxyfile and search for

WARN_LOGFILE =

there you add the outputfile e.g. "DoxygenWarningLog.txt" and you are done

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