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 That is, old.packages() identifies also packages as outdated, whereas they are clearly not...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.
