I installed R on Ubuntu without messing around with anything. Packages went wherever the default was. Then after the update to 4.4 it just doesn’t see my old packages and when I open up an R Markdown notebook it tells me a bunch of packages are not installed which I know I have installed (literally days before in some cases).

A bit of sleuthing reveals that all the packages I had installed are in "/home/user/R/x86_64-pc-linux-gnu-library/4.3".

But when I run .libPaths() I get:

[1] "/home/user/R/x86_64-pc-linux-gnu-library/4.4"
[2] "/usr/local/lib/R/site-library"                  
[3] "/usr/lib/R/site-library"                        
[4] "/usr/lib/R/library"  

I can use .libPaths(c("/home/user/R/x86_64-pc-linux-gnu-library/4.3", .libPaths())) to forcibly add the old repository back in and it works, but every time R restarts I have to rerun this command.

This has never happened to me before. How can I fix this long term?