Description
Due to a problem in the Quartus® II software version 12.0 and later, you may see above Fitter error when compiling a partial reconfiguration (PR) design if a HSSI refclk pin directly connects to a PR region.
Resolution
To work around this problem, insert an alt_clkctl module between the HSSI refclk pin and the PR region.
This problem is scheduled to be fixed in a future release of the Quartus II software.