[R] Problem with updating packages

[Peter Dalgaard]

Also, it is WRONG to copy and then update.packages(). This _will_ overwrite packages from your freshly installed R with old ones which 1: might not work and 2: are not CRAN packages. I.e., you get stuck with a 4.6 install that contain pieces of 4.5, possibly broken ones. The only way out is to reinstall. 

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> Den 28. maj 2026 kl. 00.34 skrev Uwe Ligges <ligges using statistik.tu-dortmund.de>:
> 
> 
> 
>> 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.
> 
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