I_USB_ULPI_CLK of HPS atom "~GND" must be connected to a top-level pin

Never mind, just found the problem. I had an input of HPS_USB_CLKOUT input that was supposed to be connected to .hps_0_hps_io_hps_io_usb1_inst_CLK, but was not connected, whereas the hps_0_...CLK variable was instead connected to HPS_USB_CLK ... an undeclared variable that wasn't used elsewhere. Quartus assumed that, by the nature of my using it, that it needed to be declared as a wire--one that wasn't connected to anything.

This would have been found by using `default_nettype none, but I had to turn that off because it broke a PLL implementation. Please allow me to suggest and recommend that you test all of your IP with `default_nettype none set.

Thank you,

Dan