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

[Gabor Grothendieck]

I used to copy and update but I found that over time my library gets
filled with packages that I don't use
so now every time a new version of R encounters a package it does not
know about I just reinstall it.
That keeps my library cleaner.

On Fri, Apr 25, 2025 at 12:17 PM Peter Dalgaard via R-help
<r-help using r-project.org> wrote:
>
> 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....
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd.mes using cbs.dk  Priv: PDalgd using gmail.com
>
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