Although not related to the initial issue posted here, I got the same error when bringing up my own design. I just wanted to share my findings in case someone else gets stuck in the same way.
In my design we are using a different DDR standard to that on the GHRD. This error is clear, the EMIF does not complete configuration of the DDR.
In my case, I had configured the EMIF incorrectly for the chips that we had on the board. If you get this error double check your DDR structure and configuration with a DDR expert.
Note that if you have an engineering sample Silicon, this check is disabled, so you may need to take a deeper look if you fear you are having calibration issues.