I had this same problem, and I went to the Classic Timing Analyzer
Settings tab, clicked Individual Clocks, and added a new entry. The
name is arbitrary (refclk in my case) but "Applies to Node" must be
set to the clock giving the warning. So I clicked on the List button,
found my clock pin in the list (CPLD_REFCLK), added it, and clicked
OK. When I recompiled the warning went away. Perhaps you weren't
selecting the same "mclk" node that was triggering the warning? Do you
have other instances of "mclk" in your design? Mine was an external
pin so maybe it's different, but I can verify that this method does
work in Web Edition 7.0.
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