Re: issue with update.packages(), library 'utils'

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updated the day before were now identified as outdated.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 outdated, whereas they are clearly not...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 
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