[R] issue with update.packages(), library 'utils'
Karl Schilling
k@r|@@ch||||ng @end|ng |rom un|-bonn@de
Mon Jun 8 16:39:04 CEST 2026
Thank you all for these clarifying comments.
And I guess Jeff Newmiller got the correct diagnosis (OCD) - at least
for my R-Related behavioR.
Karl
On 08.06.2026 15:26, Jeff Newmiller via R-help wrote:
> OP should also beware that on Windows it is common to install only
> binary packages for speed, and it is just as common for the appearance
> of binary packages to lag behind source packages on any given repo.
> Ergo, you can get a different update experience if you have Rtools
> installed AND you ask for installation from source vs. the faster
> install from binary. The more dependencies you typically resolve in
> your library the more amplified this problem gets. IMO the best
> approach for sanity is to track the versions you have installed and
> restore them in a project-specific-library if you need bit-for-but
> reproducibility and just upgrade between projects or when you know
> that some fault exists that is affecting your results for a known
> reason. Don't upgrade packages just because upgrade.packages says
> there are new packages every day... that way leads to
> obsessive-compulsive disorder (OCD). On June 8, 2026 5:01:26 AM PDT,
> Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>> I think what needs to happen here is that someone who is experiencing
>> this needs to debug it. It sounds as though old.packages() is
>> identifying packages that you think don't need replacing. You need to
>> figure out why this is happening. A guess: - Your .libPaths() vector
>> (which is used as the default for lib.loc) contains two or more
>> library paths. You have old packages in one of those paths, and when
>> you install new ones, they go into the other path. You can diagnose
>> this as follows: 1. Print .libPaths(). How many entries does it have?
>> 2. If it has two (or more) entries, run the following: lp <-
>> .libPaths() both <- intersect(list.files(lp[1]), list.files(lp[2]))
>> print(both) (If you have more than two entries, do this for all
>> pairs.) This will list all the packages that you have installed in
>> both places. On my system, the first entry is my user library, the
>> second is the system library. You generally need admin permissions to
>> modify the system library, so if you sometimes run with admin
>> permissions and sometimes don't, you can end up with different
>> versions in those two places. 3. To find out if you have different
>> versions, run packageVersion(pkgname, lp[1]) and compare to
>> packageVersion(pkgname, lp[2]). For example, I see that I have
>> "bslib" installed in both places, and I see > packageVersion("bslib",
>> lp[1]) [1] ‘0.11.0’ > packageVersion("bslib", lp[2]) [1] ‘0.10.0’ So
>> it looks as though my system library has an obsolete version
>> installed. I should delete it. Duncan Murdoch On 2026-06-08 7:40
>> a.m., Paulo Barata wrote:
>>> 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
>>> -------------------------------------------------
>>>> Message: 1 Date: Sun, 7 Jun 2026 16:30:34 +0200 From: Karl
>>>> Schilling <karl.schilling using uni-bonn.de> To: r-help using r-project.org
>>>> Subject: Re: [R] issue with update.packages(), library 'utils'
>>>> Message-ID: <240738c2-9935-40a9-b461-c82776cd1a77 using uni-bonn.de>
>>>> 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: 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
>>>>> ______________________________________________
>>>>> R-help using r-project.org 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 <iagogv using disroot.org> To:
>>>> r-help using r-project.org Subject: Re: [R] issue with update.packages(),
>>>> library 'utils' Message-ID:
>>>> <bf1dc0c5-3a67-42c9-b5e9-05fada44e91f using disroot.org> 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
>>> ______________________________________________ R-help using r-project.org
>>> 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.
>> ______________________________________________ R-help using r-project.org
>> 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.
> -- Sent from my phone. Please excuse my brevity. [[alternative HTML
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> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
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