Description
Yes, for Intel® Quartus® II software versions 11.1 and later, the UniPHY EMIF toolkit is incompatible with SOPC builder projects. This is due to a change in the debug architecture.
Resolution
If you require to use the UniPHY EMIF toolkit and have an SOPC builder project in Intel® Quartus® II 11.1 or later, some options are:
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Convert the project to use Qsys instead of SOPC builder
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As a starting point, debug the External Memory Interface using the standalone example design project that can be generated with the UniPHY IP using the Megawizard flow.
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Not recommended, but you could generate the SOPC builder project in an earlier Intel® Quartus® II release than 11.1 and use the EMIF toolkit for that Quartus® II software version.