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With both Qt4 and Qt5, when using a click-to-focus policy, the first attempt to paste a selection by middle mouse in an external application which has no focus may fail. It is not clear why this succeeds for some applications and fails for others, but refreshing the timestamp of the selection request cures the issue. The cmake part is by Kornel. See also this thread: http://thread.gmane.org/gmane.editors.lyx.devel/162491