Please can you try this diff for your next attempt? https://gist.github.com/jperkin/b9b84a178c1cc6ac56be26eab265def9Apply it to latest pkgsrc pkgin and use it directly for the upgrade. It should hopefully work correctly, though now the initial pkgtools-only upgrade may pull in a lot more packages, which kinda renders it pointless on such systems. I'd be interested in the output for both the initial run and the subsequent catch-all run.
It passes the test I've added for this based on your output: https://github.com/TritonDataCenter/pkgin-test-suite/commit/cd92ef2fb203f785f094844a7a1bc1a90505f62b Thanks, -- Jonathan Perkin pkgsrc.smartos.org Open Source Complete Cloud www.tritondatacenter.com