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At the time of his death (April 6, 2014), Rooney was married to Jan Chamberlin Rooney, although they had separated in June 2012. He had nine children and two stepchildren, as well as 19 grandchildren and several great-grandchildren. Rooney had been addicted to sleeping pills and overcame the addiction in 2000 when he was in his late 70s. In 1997, he was arrested on suspicion of beating his wife, Jan, but the charges were dropped due to lack of evidence. In the late 1970s, Rooney became a born-again Christian and was a fan of Pat Robertson. Rooney in 2006
On February 16, 2011, Rooney was granted a temporary restraining order against his stepson Christopher Aber and Aber's wife Christina, and they were ordered to stay 100 yards from Rooney, his stepson Mark Rooney, and Mark's wife Charlene. Rooney claimed that he was a victim of elder abuse. On March 2, 2011, Rooney appeared before a special U.S. Senate committee that was considering legislation to curb elder abuse, testifying about the abuse he claimed to have suffered at the hands of family members. In 2011, all of Rooney's finances were permanently handed over to a conservator, who called Rooney "completely competent". In April 2011, the temporary restraining order that Rooney was previously granted was replaced by a confidential settlement between Rooney and Aber. Aber and Jan Rooney denied all the allegations. In May 2013, Rooney sold his home for many years, reportedly for $1.3 million, and split the proceeds with his wife, Jan.