Longtime Boston-based actor-director Lewis Wheeler has left the Wellfleet theater company he cofounded two years ago, under what appear to be difficult circumstances. Wheeler, who has played a wide range of roles, from Walter Neff in “Double Indemnity” to Judge Brack in “Hedda Gabler,” sent out an e-mail Saturday lamenting his departure from the Harbor Stage Company. In the e-mail, Wheeler describes his time with Harbor as “an incredible journey” but adds, “. . . it has become clear that there are fundamental rifts within the company about the present and future operations of the organization.” Wheeler calls no one out by name, but writes that his problems went beyond administrative issues. “Sadly these differences became personal and could not be bridged nor negotiated,” he writes. In a joint e-mail response, Wheeler’s former colleagues at the Harbor Stage Company say that their feelings about Wheeler’s departure “are complicated,” but they were grateful for his “original contributions” to the company. Beyond that, they wrote that they’d rather not hash out their differences in public and instead “let the work speak for itself.” The company is being run by four of its cofounders: Jonathan Fielding, Stacy Fischer, Brenda Withers, and artistic director Robert Kropf.