Crane announced that Astros would be parting ways with Click, declining to renew his contract for the 2023 season.
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"We are grateful for all of James' contributions," Crane said in a statement. "We have had great success in each of his three seasons, and James has been an important part of that success. I want to personally thank him and wish him and his family well moving forward."
Crane had tiptoed around questions regarding Click on Wednesday. Click's contract expired on Oct. 31.
Click was hired in Feb. 2020, succeeding Jeff Luhnow, who was fired in the wake of the Astros sign-stealing scandal.
Before coming to the Astros, Click had served as the Tampa Bay Rays vice president of baseball operations. He'd worked with the Rays for the last 14 seasons prior to his tenure in Houston.
Further announcements regarding the structure of the Baseball Operations department will come at a later time, the Astros said.
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Meanwhile, the Astros did strike a deal with manager Dusty Baker, who also took over in the wake of the scandal.
While Baker was without a deal amid leading the Astros to their second World Series title, there were no more questions about his future with the ball club after he was signed to a 1-year contract for the 2023 season.
"If I win one, I want to win two," Baker, 73, had said of a comeback.
ESPN contributed to this report.
The video above is previous report looking at the future of the top Astros' executives. It was taped before the decisions on Dusty Baker and James Click were announced.