I agree with Rulesman - the play by rule has ended in a TD. The R won't signal the confirmation, but everyone on the field needs to know that the runner has crossed the goal line. I've twice seen 4th down runs toward the pylon where there was an obvious holding call, the wing did not signal TD, just killed the clock, and everyone on the field (including the rest of the crew) thought there was a COP short of the goal line. Teams are changing personnel, coach is signaling to decline the penalty, etc.
Signal the TD, administer the penalty, and move on.