I had this problem too and I don’t use RStudio, so this is/was an R issue. Regarding the previous discussion on this issue, the curious thing is that it had never occurred before when updating from 4.4 to 4.5, from 4.3 to 4.4, etc., at least to me.
Iago On 07/06/2026 16:30, Karl Schilling wrote: > I have exactly the same problem as reported by Guido Hooiveld. > > I had previously attributed my problem with an inappropriate way of > updating my packages when I updated from R 4.5 to 4.6. I then > completely reinstalled R4.6 and all packages, which "solved" the > problem - at least when I run "update.packages2 the same day I > reinstalled everything (see my postings and related answers from > May27-29. > Alas, the next day the problem was back again, and ALL my packages > updated the day before were now identified as outdated. > > I have no idea about the background of this problem. But a cue may be > possibly come from the observation that when I use RStudio to check > for packages that need to be updated (RStudie >Tools > Check for > Package Updates ...), this does not happen. > > Karl Schilling > > > On 04.06.2026 13:49, Hooiveld, Guido via R-help wrote: >> Hi, I got confused by the recent behavior of update.packages() from >> the library utils. Since a while it reports that updates of ALL >> installed packages are available at the CRAN repository but turns out >> that this is not the case for MOST packages. In other words, most of >> the installed packages on my computer are of the same version as on >> the repository, yet it still is reported that an update for these >> packages is available. Of course I can re-install these (current) >> packages, but that is IMHO a waste of time/bandwidth. I had a look at >> it, and to me it seems this also somehow relates to the function >> old.packages(). That is, old.packages() identifies also packages as >> outdated, whereas they are clearly not... ?? See code below. Any >> suggestion on what may be causing this, and how to avoid it? Thanks, >> Guido >>> ## update.packages() identifies that updates for e.g. ## >>> 'ActivePathways' and 'alphavantager' are available for my >>> installation. ## Yet, the installed version is the same as on the >>> repository. ## (Note that after these 2 notifications I cancelled >>> update.packages() update.packages(repos=https://cloud.r-project.org) >> ActivePathways : Version 2.0.6 installed in C:/Program >> Files/R/R-4.6.0/library Version 2.0.6 available at >> https://cloud.r-project.org/bin/windows/contrib/4.6 alphavantager : >> Version 0.1.3 installed in C:/Program Files/R/R-4.6.0/library Version >> 0.1.3 available at >> https://cloud.r-project.org/bin/windows/contrib/4.6 cancelled by user >> Warning message: In .available.both(repos, method, ...) : Some listed >> binary packages have no source >>> ## check and compare the output of old.packages() old.pkgs <- >>> old.packages(repos=https://cloud.r-project.org) >> Warning message: In .available.both(repos, method, ...) : Some listed >> binary packages have no source >>> head(old.pkgs) >> Package LibPath Installed ActivePathways "ActivePathways" "C:/Program >> Files/R/R-4.6.0/library" "2.0.6" alphavantager "alphavantager" >> "C:/Program Files/R/R-4.6.0/library" "0.1.3" anytime "anytime" >> "C:/Program Files/R/R-4.6.0/library" "0.3.13" aod "aod" "C:/Program >> Files/R/R-4.6.0/library" "1.3.3" ape "ape" "C:/Program >> Files/R/R-4.6.0/library" "5.8-1" aplot "aplot" "C:/Program >> Files/R/R-4.6.0/library" "0.2.9" Built ActivePathways "R 4.6.0; ; >> 2026-05-30 02:41:50 UTC; windows" alphavantager "R 4.6.0; ; >> 2026-05-30 03:56:11 UTC; windows" anytime "R 4.6.0; >> x86_64-w64-mingw32; 2026-05-30 01:03:29 UTC; windows" aod "R 4.6.0; ; >> 2026-05-30 01:07:09 UTC; windows" ape "R 4.6.0; x86_64-w64-mingw32; >> 2026-05-30 02:11:50 UTC; windows" aplot "R 4.6.0; ; 2026-05-30 >> 03:14:45 UTC; windows" ReposVer Repository ActivePathways "2.0.6" >> https://cloud.r-project.org/bin/windows/contrib/4.6 alphavantager >> "0.1.3" https://cloud.r-project.org/bin/windows/contrib/4.6 anytime >> "0.3.13" https://cloud.r-project.org/bin/windows/contrib/4.6 aod >> "1.3.3" https://cloud.r-project.org/bin/windows/contrib/4.6 ape >> "5.8-1" https://cloud.r-project.org/bin/windows/contrib/4.6 aplot >> "0.2.9" https://cloud.r-project.org/bin/windows/contrib/4.6 >>> ## Of the 519 packages on my system, only 3 are really outdated. ## >>> Note that these are NOT ActivePathways' and 'alphavantager' that >>> were identified ## by update.packages() above. length( >>> old.pkgs[,"Installed"] == old.pkgs[,"ReposVer"] ) >> [1] 519 >>> sum( old.pkgs[,"Installed"] == old.pkgs[,"ReposVer"] ) >> [1] 516 >>> sum( old.pkgs[,"Installed"] != old.pkgs[,"ReposVer"] ) >> [1] 3 >>> old.pkgs[ old.pkgs[,"Installed"] != old.pkgs[,"ReposVer"] ,] >> Package LibPath Installed limSolve "limSolve" "C:/Program >> Files/R/R-4.6.0/library" "2.0.1" RCurl "RCurl" "C:/Program >> Files/R/R-4.6.0/library" "1.98-1.18" rjsoncons "rjsoncons" >> "C:/Program Files/R/R-4.6.0/library" "1.3.2" Built limSolve "R 4.6.0; >> x86_64-w64-mingw32; 2026-05-30 01:01:26 UTC; windows" RCurl "R 4.6.0; >> x86_64-w64-mingw32; 2026-04-21 00:45:50 UTC; windows" rjsoncons "R >> 4.6.0; x86_64-w64-mingw32; 2026-05-30 03:10:49 UTC; windows" ReposVer >> Repository limSolve "2.0.2" >> https://cloud.r-project.org/bin/windows/contrib/4.6 RCurl "1.98-1.19" >> https://cloud.r-project.org/bin/windows/contrib/4.6 rjsoncons "1.3.3" >> https://cloud.r-project.org/bin/windows/contrib/4.6 >>> ## sessionInfo() sessionInfo() >> R version 4.6.0 (2026-04-24 ucrt) Platform: x86_64-w64-mingw32/x64 >> Running under: Windows 11 x64 (build 22631) Matrix products: default >> LAPACK version 3.12.1 locale: [1] LC_COLLATE=English_United >> States.utf8 [2] LC_CTYPE=English_United States.utf8 [3] >> LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C [5] >> LC_TIME=English_United States.utf8 time zone: Europe/Amsterdam tzcode >> source: internal attached base packages: [1] stats graphics grDevices >> utils datasets methods base loaded via a namespace (and not >> attached): [1] compiler_4.6.0 tools_4.6.0 >> --------------------------------------------------------- Guido >> Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of >> Human Nutrition & Health Wageningen University the Netherlands >> Visiting address: Mail address: HELIX (Building 124), room 2048 >> Stippeneng 4 PO Box 17 6708 WE Wageningen 6700 AA Wageningen the >> Netherlands the Netherlands tel: (+) 31 317 485788 fax: (+) 31 317 >> 483342 email: [email protected] internet: >> http://www.humannutrition.nl >> http://scholar.google.com/citations?user=qFHaMnoAAAAJ >> http://www.scopus.com/authid/detail.url?authorId=6603101814 >> ______________________________________________ [email protected] >> 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. > > ______________________________________________ > [email protected] 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. ​ [[alternative HTML version deleted]] ______________________________________________ [email protected] 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.
