Clara realises that as Cass refused to allow Lunn into the ship, he has not seem the writing on the wall, and therefore the message is not encoded in his brain meaning the ghosts won't attack him.
He has not seem the writing on the wall. Cass refused to allow Lunn into the ship. Clara realises this. Therefore the message is not encoded in his brain. The ghosts won't attack him. This was what the message was meaning.