As long as you did a direct rollover (trustee to trustee), or if distributed to you, you deposited the funds into your IRA within 60 days, the transaction is not taxable. After you enter(ed) the 1099-R, there is a page that asks "What Did You Do With The Money From [Retirement Plan]"
Be sure you indicate first that you "...moved the money to another retirement account (or returned it to the same retirement account)." and that you "rolled over all of this money to another IRA or other retirement account (or returned it to the same account)."