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Thanks! Yes, as you noticed, upgrading everything is challenging, and a lot of times just won't work, especially if you installed packages from non-CRAN sources.I hope we'll be able to have a function for this soon.
I see from #168 and #639 that there's interest in a function to upgrade all installed packages. I've been working on a function to do this: https://github.com/rossellhayes/upgrade/blob/main/R/pkg_upgrade.R
I completely understand if it's not up to the standard of this package. But if it would be useful, I'd be happy to submit the code as a PR.
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