Due to a problem in the Quartus® II software version 12.1 and later, this error message may appear when generating the example design for the DDR3 controller with UniPHY if the EMIF On-Chip Debug Toolkit interface type is set to Internal (JTAG).
The workaround is to change the on-chip debug setting from Internal (JTAG) to Shared. This generates an Avalon® slave interface, which does not need to be connected.
This issue has been fixed in Intel® Quartus® Prime Software version 13.0.