[R] Problem with updating packages - SOLVED

[Karl Schilling]

Thank you everybody so much for your help.

I adjusted my CRAN mirror in my etc/Profile.site file as suggested by 
Rui Barradas - that solved the issue with the twice repeated question of 
which repository to use. It did not resolve, however, the issue that all 
packages were flagged as  not actual.

So I followed the advice of Jeff Newmiller - actually I went one step 
further and completely de-installed my R version, re-installed it, and 
then downloaded the packages I need. That solved the problem.


One point that I still do not understand is why AFTER updating my 
original R 4.5 packages to 4.6, those were still identified as not up-to 
date. So why I was in this "ndless" loop of ineffective (?) updating. 
But maybe I should be pragmatic and be satisfied that it now works again.

Again, thank you all for your help.

Best,

Karl Schillng

On 28.05.2026 00:33, Uwe Ligges wrote:
>
>
> On 28.05.2026 00:02, Jeff Newmiller wrote:
>> So can we interpret this to mean that update.packages() will fix 
>> (replace) old packages that were copied into the new library? What if 
>> one or more packages were dropped/archived or pulled from 
>> non-standard package sources?
>
> No, not if a package is archived from CRAN or downloaded from a 
> repository that is not declared. update.packages() won't find that the 
> update is needed in such a case
> I talked about active CRAN packages.
>
> Best,
> Uwe Ligges
>
>
>>
>>
>> On May 27, 2026 2:06:12 PM PDT, Uwe Ligges <ligges using statistik.tu- 
>> dortmund.de> wrote:
>>
>>
>>
>>     On 27.05.2026 18:01, 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.
>>
>>         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.
>>
>>         And when I run "old.packages()", it seems that all my packages
>>         are identified as being old.
>>
>>         Any suggestions what might be going on?
>>
>>
>>     For a major version change (as from 4.5.x to 4.6.y) we do not
>>     guarantee API compatibility, hence we cannot guarantee that a
>>     package built for 4.5.x will work under 4.6.y. As a consequence,
>>     update.packages() knows that everything has to be reinstalled.
>>
>>     Best,
>>     Uwe Ligges
>>
>>
>>
>>
>>
>>
>>         Thank you so much in advance,
>>
>>         Karl Schilling
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>> -- 
>> Sent from my phone. Please excuse my brevity.
>