Today I was able to upgrade R to version 4.5, and was reminded in the process of a tedious "feature" of the upgrade.
R libraries are organized into two distinct groups. If you use RStudio, look at the "Packages" tab. You will see the heading "User Library" followed by whatever packages you have installed manually. Scroll down and you will get to another heading, "System Library", followed by another group of packages. These are the packages that were automatically installed when you installed R itself.
The upgrade from R 4.4 to R 4.5 was very easy, since it comes as a system package, at least on Ubuntu and Linux Mint (and presumably other Linux distributions). I'm not sure about Windows, macOS etc. The Mint update manager offered me updates to several system packages (r-base, r-base-core, r-base-html and r-recommended) among the morning's gaggle of updates. I just installed those and R 4.4.3 was replaced by R 4.5.0. That part could not be easier.
After the updates were done, I opened RStudio and looked to see if any packages there needed updates. The "System Library" group was there, and none of them needed updates (no shock since they had just been installed during the upgrade). The "User Library" did not exist. I should have known this was coming based on previous R upgrades, but I forgot.
You can of course reinstall all your previously installed libraries manually (if you can remember which ones they were), or you can just wait until something doesn't work due to a missing library and install it then. I prefer to reinstall them all at once, and I most definitely do not have the list memorized. The fix is easy if you know how to do it (and remember that you have to do it).
The first step is to open a file manager and navigate to the system directory where your libraries for the previous R version are stored. They will still be there. If you do not know where they are hiding, you can run the command .libPaths() and get a list of the directories in which R will look for libraries. One of them will contain the R version number. (It is consistently the first entry in the list when I do this, but I do not know if that will always be true.) In my case, the entry is "/home/paul/R/x86_64-pc-linux-gnu-library/4.5", which means I want to open "/home/paul/R/x86_64-pc-linux-gnu-library" in the file manager. There I find two directories, one for the previous version ( "/home/paul/R/x86_64-pc-linux-gnu-library/4.4") with lots of subdirectories and one for the new version ( "/home/paul/R/x86_64-pc-linux-gnu-library/4.5") that is empty. All it takes is copying or moving the contents of the older directory to the newer one. Once you have confirmed that the new R version can see the libraries (for instance, by observing that the "User Library" section has returned to the "Packages" tab in RStudio), you can delete the folder for the older version.
With that done, you will want to check for updates to the "User Library" packages. Several that I had installed needed updates today after moving to R 4.5. Updating them is done in the usual way.
I wonder if either R or RStudio has a "inherit libraries from previous version" function stashed away that would automate this? If so, I haven't found it.
