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

To the R-Help list,

I have also the same problem here. Most often when I attempt to update my packages, it seems that most of them, maybe all of them, are flagged as needing update, even when they were updated just the previous day.

I do not use RStudio, I only use R directly. Currently, I am using R version 4.6.0 Patched (2026-05-29 r90087 ucrt), on Windows 10 Professional.

Paulo Barata

Rio de Janeiro - Brazil

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> 
> Message: 1
> Date: Sun, 7 Jun 2026 16:30:34 +0200
> From: Karl Schilling <[email protected]>
> To: [email protected]
> Subject: Re: [R] issue with update.packages(), library 'utils'
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
> 
> 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 updated the day before were now identified as outdated.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 outdated, whereas they are clearly not...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.
> 
> ------------------------------
> 
> Message: 2
> Date: Sun, 7 Jun 2026 23:23:43 +0200
> From: Iago <[email protected]>
> To: [email protected]
> Subject: Re: [R] issue with update.packages(), library 'utils'
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset="utf-8"
> 
> 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
>