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LGTM.com performs its own checks by running queries over source code (all queries are open source on GitHub). It does not show alerts that are generated by Flake.
Unfortunately the provided Flake commands actually return an error, which means that LGTM's Python analysis fails:
(https://lgtm.com/projects/g/PowerDNS/pdns/logs/rev/3a0387f7429710a21af7abcc745c71d6932e14be/lang:python/stage:Build%20child%20(3a0387f))