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? Thank you so much in advance, Karl Schilling
You say:> . I then copied my packages from my previous version (4.5) to the library of 4.6.This is extremely risky, especially when upgrading minor versions instead of patch versions of R. Delete the contents of your 4.6 library and install the desired packages using install.packages(). On May 27, 2026 9:01:09 AM PDT, Karl Schilling <karl.schilling at uni-bonn.de> 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? > >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]]
?s 17:01 de 27/05/2026, Karl Schilling escreveu:> 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? > > 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.Hello, I am also running R 4.6 on Windows 11. You can set a CRAN mirror in your etc/Profile.site file. If you edit, you will see # set a CRAN mirror # local({r <- getOption("repos") # r["CRAN"] <- "http://my.local.cran" # options(repos=r)}) Substitute your mirror for 'my.local.cran'. r["CRAN"] <- "https://cloud.r-project.org/" works everywhere. Then, uncomment the 'local' statement and restart R. Hope this helps, Rui Barradas
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.
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