[R] 4.5.0: Do NOT just copy library folder and update.packages()

[Matthew McCormack]

How about this:

lib_loc <- "/home/R/x86_64-pc-linux-gnu-library/4.4"
to_install <- unname(installed.packages(lib.loc = lib_loc)[, "Package"])
to_install
install.packages(pkgs = to_install)

      Copy the names of the packages, then install them in the new 
version of R.

Matthew

On 4/25/25 12:16 PM, Peter Dalgaard via R-help wrote:External Email - 
Use Caution
> A couple of people have gotten themselves in trouble by copying the contents of their 4.4 library folder into the 4.5 counterpart and running update.packages().
>
> That can be a really bad idea if the old library contains base packages like "tools" or "utils". They don't live on CRAN, so update.packages() just leaves them at the 4.4.x version.
>
> For instance,tools::md5sum has a new bytes= argument in 4.5.0 which gets used when loading other packages, but that cannot work anymore.
>
> So copying library folders was probably never a good idea, but this time it is a very, very bad idea.
>
> To avoid the problem, you can do something like this:
>
>> .libPaths()
> [1] "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library"
>> tbl <- installed.packages("/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library")
>> table(tbl[,"Priority"])
>         base recommended
>           14          15
>> pkglist <- rownames(tbl[is.na(tbl[,"Priority"]),])
> and then install.packages(pkglist) avoids touching the base/recommended ones.
>
> - pd
>
> PS: On MacOS, I have two systems upgraded 4.4.x to 4.5.0. One of them has tools in the 4.4 library and the other does not. I have no clue what the difference might be....
>
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