Earwaker's lists the following for Sir John's children:
(◾+ 1 st wife, Eleanor, daughter of Sir Thomas Gerard of Bryn, Lancashire. All the children are from this wife. There were six sons, Laurence, Richard, Nicholas, Jerome, Ralph and George. There was a daughter Cicely and possibly one whose Christian name is unknown who married a Legh of Lyme.)
East Cheshire Past and Present by J.P. Earwaker, London, 1877 (CRO, Knutsford). This is widely regarded as the best work on East Cheshire of the 19th century. It is useful for family trees of landed families. Now available from the Family History Society of Cheshire.
http://www.thornber.net/cheshire/htmlfiles/warren.html
No mention is made of a Robert. Is there a more contemporary resource for the children?
Re Robert, c.1485-c.1543 (seen in an LDS Family Search tree), I was surprised myself to see this individual (married Margaret Cornwallis) attached here (as son of Sir John Warren and Eleanor nee Gerard), as I already have him as son of William Warren and Bridget nee Oldham. Can anyone confirm this connection from their own resources?