Re: Problem with updating packages

Thank you for these comments, which indeed do clarify what I had done 
wrong. "my packages" indeed should read "all packages".  So the next 
tome I certainly will t save the names of all contributed packages, and 
reinstall those.

I really appreciate the support and patience  that helped me to fix what 
I messed up by bein  too naive.

Best,

Karl Schilling

On 28.05.2026 18:31, Duncan Murdoch wrote:
> On 2026-05-27 12:01 p.m., Karl Schilling wrote:
>> I am running R under Windows 11. recently updated R to the 4.6patchhed
>> version. I then copied my packages from my previous version (4.5) to the
>> library of 4.6. Then I updated all packages.
>
> You don't say exactly what you mean by "my packages".  If you copy 
> *all* R 4.5 packages to the default R 4.6 library directory, you will 
> probably damage R beyond repair.  You need to remember that packages 
> with priority "base" contain code that implements R internals.  Trying 
> to use R 4.5 internals in R 4.6 will cause a lot of problems.
>
> If you only copy contributed packages (i.e. ones that you installed 
> which get priority NA, or recommended packages) then what you did 
> might work, but it's safest to just save the names of all contributed 
> packages, and reinstall those.>
>> Since then, I see the following behavior:
>>
>> Each time I run "update.packages(ask='graphics',checkBuilt=TRUE)" I am
>> asked TWICE
>>
>> "--- Please select a CRAN mirror for use in this session ---".
>>
>> And, more embarrassingly, all my Cran and Bioconductor are said to
>> require an update. That also happens when I run "update.packages", say,
>> one hour after my last update.
>
> I think others have pointed out that every contributed package *does* 
> need an update when going from R 4.5.* to R 4.6.*.  You can only get 
> away with keeping installed copies of packages when you stay within 
> the same minor version number, e.g. 4.6.1 to 4.6.2.
>
> Duncan Murdoch