Due to a problem in the Quartus® II software version 10.0 and later, you may see the error message in the ModelSim-Altera Edition software version 6.5e when you simulate an ALTDDIO_IN megafunction variation file generated in VHDL.
To work around the problem, comment out the following line in the VHDL variation file (.vhd) referenced in the error message generated by the ModelSim-Altera Edition software:implement_input_in_lcell => "ON"
This problem will be fixed in a future version of the Quartus II software.