The former U.S. commander of troops in Afghanistan will retire from the military instead of taking a new U.S. position in Europe.

President Obama said in a statement that he had met with Gen. John Allen on Tuesday and was accepting his request to retire so he could “address health issues within his family.”

Allen told the Washington Post that he was retiring to help his wife, Kathy, deal with chronic health issues, including an autoimmune disorder.

“Right now, I’ve just got to get her well,” Allen said. “It’s time to take care of my family.”

Allen had been nominated to become NATO Supreme Allied Commander, Europe, and head of U.S. European Command when he was ensnared in the scandal that led to the resignation of former CIA Director David Petraeus.

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In the investigation that uncovered Petraeus’s affair, the FBI also found tens of thousands of pages of emails between Allen and Jill Kelley, the woman who had first alerted the FBI about harassing emails.

The FBI turned over emails to the Pentagon, but a subsequent Defense Department Inspector General investigation cleared him. Allen maintained throughout that he had done no wrong.

Allen’s nomination was put on hold during the investigation, and when he was cleared the White House said he would be re-nominated to the NATO and European Command posts.

But Allen instead opted to retire. He would have required Senate confirmation, and the emails would have surely come up during his confirmation hearings.

Obama's statement about Allen did not mention the controversy.

“I told General Allen that he has my deep, personal appreciation for his extraordinary service over the last 19 months in Afghanistan, as well as his decades of service in the United States Marine Corps,” Obama said in the statement. “John Allen is one of America’s finest military leaders, a true patriot, and a man I have come to respect greatly. I wish him and his family the very best as they begin this new chapter, and we will carry forward the extraordinary work that General Allen led in Afghanistan.”

Allen finished his tour as the top commander in Afghanistan earlier this month, as Gen. Joseph Dunford succeeded him there.

Allen’s final major task in Afghanistan was to recommend drawdown plans for the president through 2014 and beyond, when NATO is scheduled to hand-off security control to Afghan forces. Obama announced in his State of the Union address that 34,000 troops would depart Afghanistan in the next year.

Defense Secretary Leon Panetta, who is also retiring soon, said in a statement that Allen proved himself in Afghanistan to be “one of the United States military's most outstanding battlefield leaders.”

“His leadership over the last 19 months will long be remembered as pivotal to this campaign,” Panetta said. “The strategy he developed and implemented has put us on the right path towards completing this mission, with Afghan forces now on track to step into the lead for security nationwide this spring and to assume full security responsibility by the end of next year.”

This story was updated at 2:47 p.m. and 5:15 p.m.