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I'm not sure what you're referring to in that log. It looks like the docs built successfully, minus one possibly spurious warning.

Upon re-reading your original post I think you're confused about the use of SAGE_KEEP_BUILT_SPKGS=yes. Your confusion is understandable--it shouldn't be outputting that message. That's just a generic message for some make target failures, but it's not applicable to the Sage documentation build.