Non-manual solution to "cannot remove prior installation of package" when re-installing R-CodePudding

I recently began receiving warnings that prior installations of R packages cannot be removed when I try to re-install packages:

install.packages("gtools")
#> Warning: cannot remove prior installation of package ‘gtools’
#> Warning: restored ‘gtools’

I found solutions to this issue encouraging me to delete the packages manually from my library folder, which I could find with .libPaths(). However, (a) this seems like a way of addressing symptoms rather than the underlying issue (which remains unclear) and (b) there are two paths for seemingly different versions of R and I'm not sure which to delete from anyway:

.libPaths()           
#> [1] "C:/Users/foo/Documents/R/win-library/4.1"
#> [2] "C:/Program Files/R/R-4.1.2/library"

How can I fix the problem so I don't have to manually delete package folders every time I want to re-install a package? If there is no alternative, do I need to delete the subdirectories for the package from one of those folders or both? FWIW, I'm working in RStudio.

CodePudding user response：

The problem is that you have installed packages using different permissions. On Windows, you need elevated permissions to write to Program Files. At some point you (or an admin) probably used "Run as admin" to install gtools there, and now using regular permissions you can't delete that.

You should be able to delete the Users/foo copy, if you are running as user foo, but even that one may have had permissions changed. But I'd guess the issue is that gtools is in the Program files location.

The error message from R doesn't tell you which location it is trying to delete from, which is unfortunate. In fact, allowing installations of different versions in those two locations is a bad design feature in R that just leads to confusion, because you don't necessarily always use the same version each time you load packages. (The rule for which one you use is the first acceptable one found in the .libPaths list, but since you can change .libPaths, and since packages can load other packages, it's hard to predict which one you'll have loaded at any given time.)

To fix this, you can delete both copies (if you have two) and start over, but that's risky because other packages might be depending on gtools. If you are the only user on your computer, you could instead delete the entire "C:/Users/foo/Documents/R/win-library/4.1" library, and then do all your installs using "Run as admin", but that's also easy to mess up.

(On a Mac, that's effectively what happens, because most single user systems put the user in the "admin" group, so they can always install packages to the system location. It causes a lot less confusion, but some "purists" think the Windows way is better.)

So I don't have any good advice for you, but maybe this explains the situation, and you can work out for yourself the best way forward.