upon upgrades on next.moodle.org as well as moodle.org we faced a apparently one time issue
// Cleanup messaging.
+ if (!empty($CFG->messagingdeletereadnotificationsdelay)) {
+ $notificationdeletetime = $timenow - $CFG->messagingdeletereadnotificationsdelay;
+ $params = array('notificationdeletetime' => $notificationdeletetime);
+ $DB

the query above took too long. This will mainly be an MDL issue i suppose but its here incase we need to optimise anything on moodle.org & out other sites