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.
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 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. >
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. Sendt fra min iPhone> Den 28. maj 2026 kl. 00.34 skrev Uwe Ligges <ligges at 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 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. > > ______________________________________________ > 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.