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make sure that if builder configured with a non-standard (!= 3306) default TCP port that value actually gets used throughout. if they didn't configure a value, assume "use a sensible default", which will be read from /etc/services or, failing that, from the factory default. That makes the order of preference - command-line option - my.cnf, where applicable - $MYSQL_TCP_PORT environment variable - /etc/services (unless configured --with-tcp-port) - default port (--with-tcp-port=... or factory default)
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