Device Family: Stratix® V GX
Area: EMIF, Intellectual Property
IP Product: DDR3 SDRAM Controller supporting ALTMEMPHY
You may see this error in Quartus II software if you source <variation_name>_pin_assignments.tcl file when implementing UniPHY based IP in your system if your design has partitions.
To get around the error message run analysis & Synthesis (Processing -> Start Analysis & Synthesis) and partition merge (Processing -> Start Partition merge) before sourcing the tcl file.