Jim Hester

Should there be a helper to upgrade all installed packages, equivalent to `upgrade.packages()`? Or maybe a `lib_upgrade()` to upgrade all the packages in a library?

There isn't really anything that needs to be done for pak here. Bioconductor system requirements are already supported by the RStudio Package Manager, the Bioconductor specific system requirements would just...

Maybe as an option, but I don't think it would be a good idea to have non-failure be the default.

Probably only for interactive sessions as well?

I guess maybe none, but I was thinking about if people have a task running R on a server and would get worried if there was a warning showing up...

Have you ever encountered this style in code in the wild? I never have...

remotes now installs these packages anyway, which I think we should probably do in pak / pkgdepends as well

Since there are new features and linters in this release I think it should probably be 3.1.0

FWIW if you install ccache with homebrew it sets up symlinks for all the compiler aliases during installation, so you can set your `PATH` so that `$BREWPREFIX/opt/ccache/libexec` comes first and...

Yeah definitely true, we have not ported that remotes feature over to pak as of yet.