R help - May 2026 - Problem with updating packages

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?

On May 27, 2026 2:06:12 PM PDT, Uwe Ligges <ligges at
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
>> 
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide https://www.R-project.org/posting-
guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
--
Sent from my phone. Please excuse my brevity.
	[[alternative HTML version deleted]]

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 at 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
>        
------------------------------------------------------------------------
>         R-help at r-project.org mailing list -- To UNSUBSCRIBE and more,
see
>         https://stat.ethz.ch/mailman/listinfo/r-help <https://
>         stat.ethz.ch/mailman/listinfo/r-help>
>         PLEASE do read the posting guide https://www.R-project.org/
>         posting- <https://www.R-project.org/posting-> guide.html
>         and provide commented, minimal, self-contained, reproducible code.
> 
> 
> --
> Sent from my phone. Please excuse my brevity.