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I just upgraded from OS X Mavericks / XQuartz 2.7.6 / gnubg (dated Jul 28, 2013) to Yosemite 10.10.3 / XQuartz 2.7.7 / gnubg 1.04 (dated Oct 28, 2014). The problem appeared immediately after the upgrade. If I minimize the gnubg window, it correctly slides into the dock with the Genie effect. If I then unminimized it by clicking on the icon in the dock, it correctly reappears from the dock with the Genie effect, but no longer responds to clicks. X11 is shown in the OS X menu bar. If I type Command-1, the window disappears without any Genie effect, reappears by sliding in with the Genie effect from the top-left corner of the screen instead of from the dock, and becomes responsive to clicks.
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