No, provided 100% of the funds removed from one IRA, are deposited in the new IRA. If this was a trustee-to-trustee transfer where you never saw or touched the money, then no 1099-R will be issued.
But if a third party was involved, that will result in a 1099-R being issued for the withdrawal from the old account. For example, if a check was cut payable to you, then regardless of what you did with that check, you will be receiving a 1099-R. If it's an "early withdrawal" then that 1099-R will have a code 1 in box 7. When you enter it in the program it's important that you read the followup screens after the data entry screen. You'll be asked what you did with the money. Then when you tell the program you "rolled it" into another IRA, there will be no taxes or penalties assessed, and the amount rolled will not be included in your AGI.