R help - Apr 2025 - 4.5.0: Do NOT just copy library folder and update.packages()

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 at cbs.dk  Priv: PDalgd at gmail.com

What about if there is only one folder for packages under 4.X... where 
any version of R $.X... would load from there the packages?

Thanks

Fer

On 4/25/25 11:16, Peter Dalgaard via R-help 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....
>
	[[alternative HTML version deleted]]

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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	[[alternative HTML version deleted]]

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 at 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 at cbs.dk  Priv: PDalgd at gmail.com
>
> ______________________________________________
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