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In an interview with Radar to promote his role in the upcoming Texas Chainsaw Massacre remake, R. Lee Ermey, Hollywood's go-to guy for scary, creatively profane authority figure parts, lets slip (i.e., probably doesn't give a shit whom he tells) that the director might not have had the best creative chemistry with star Tom Cruise on Eyes Wide Shut:

Did you and Kubrick become close while shooting Full Metal Jacket? Very close. Stanley called me up all the time. He'd call at three o'clock in the morning and say, "Oh, it's 10 o'clock over here." [Laughs] "Yeah, well, it's three o-fucking-clock in the morning here, Stanley. Oh well." He called me about two weeks before he died, as a matter of fact. We had a long conversation about Eyes Wide Shut. He told me it was a piece of shit and that he was disgusted with it and that the critics were going to have him for lunch. He said Cruise and Kidman had their way with him—exactly the words he used.

What did he mean?
He was kind of a shy little timid guy. He wasn't real forceful. That's why he didn't appreciate working with big, high-powered actors. They would have their way with him, he would lose control, and his movie would turn to shit.

This story makes Kubrick's death before the movie's release even more tragic for his fans. Had he lived through to the DVD release, not only might he have pushed to have those digital, penetration-blocking orgy-goers the studio inserted to get an R rating removed in an alternate cut of the film, we might also have been treated to a commentary track where the notoriously controlling director rants about how Tom Cruise's inability to realistically portray being stoned, even after four hundred takes, turned his movie to shit.