This analysis and synthesis error message may be seen in the UniPHY example project when the UniPHY IP has these combination of settings :
1) PHY Settings : Any of the PLL/DLL/OCT sharing mode options set to master or slave
2) Diagnostics : Enable EMIF On-Chip Debug Toolkit selected
The error is due to the file core_debug.sv being listed twice in the example design .qip file
The workaround is to comment out one of the files in the example design .qip file. For example :
#set_global_assignment -library "<IP_name>_example" -name SYSTEMVERILOG_FILE [file join $::quartus(qip_path) "<IP_name>_example/submodules/<IP_name>_example_if0_s0_software/core_debug.sv"]
This issue will be fixed in a future version of Quartus® II.