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

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 availab=
le 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 sa=
me version as on the repository, yet it still is reported that an update fo=
r these packages is available. Of course I can re-install these (current) p=
ackages, 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 fun=
ction old.packages(). That is, old.packages() identifies also packages as o=
utdated, 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=3Dhttps://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=3Dhttps://cloud.r-project.org)
Warning message:
In .available.both(repos, method, ...) :
  Some listed binary packages have no source
> =

> head(old.pkgs)
               Package          LibPath                              Instal=
led
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" "0.3.1=
3" =

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; windo=
ws"
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; windo=
ws"
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"] =3D=3D old.pkgs[,"ReposVer"] )
[1] 519
> =

> sum( old.pkgs[,"Installed"] =3D=3D old.pkgs[,"ReposVer"] )
[1] 516
> =

> sum( old.pkgs[,"Installed"] !=3D old.pkgs[,"ReposVer"] )
[1] 3
> =

> old.pkgs[ old.pkgs[,"Installed"] !=3D 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=3DEnglish_United States.utf8 =

[2] LC_CTYPE=3DEnglish_United States.utf8   =

[3] LC_MONETARY=3DEnglish_United States.utf8
[4] LC_NUMERIC=3DC                          =

[5] LC_TIME=3DEnglish_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=3DqFHaMnoAAAAJ
http://www.scopus.com/authid/detail.url?authorId=3D6603101814