[R] issue with update.packages(), library 'utils'
Hooiveld, Guido
gu|do@hoo|ve|d @end|ng |rom wur@n|
Thu Jun 4 13:49:09 CEST 2026
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 That is, old.packages() identifies also packages as outdated, whereas they are clearly not...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: guido.hooiveld using wur.nl
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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