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

OP should also beware that on Windows it is common to install only binary p=
ackages for speed, and it is just as common for the appearance of binary pa=
ckages 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 i=
nstallation from source vs. the faster install from binary. =


The more dependencies you typically resolve in your library the more amplif=
ied this problem gets. IMO the best approach for sanity is to track the ver=
sions you have installed and restore them in a project-specific-library if =
you need bit-for-but reproducibility and just upgrade between projects or w=
hen you know that some fault exists that is affecting your results for a kn=
own reason. Don't upgrade packages just because upgrade.packages says there=
 are new packages every day... that way leads to obsessive-compulsive disor=
der (OCD).

On June 8, 2026 5:01:26 AM PDT, Duncan Murdoch <[email protected]> w=
rote:
>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 pack=
ages 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) cont=
ains two or more library paths.  You have old packages in one of those path=
s, 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 place=
s.  On my system, the first entry is my user library, the second is the sys=
tem library.  You generally need admin permissions to modify the system lib=
rary, so if you sometimes run with admin permissions and sometimes don't, y=
ou can end up with different versions in those two places.
>
>3.   To find out if you have different versions, run packageVersion(pkgnam=
e, lp[1]) and compare to packageVersion(pkgname, lp[2]).  For example, I se=
e that I have "bslib" installed in both places, and I see
>
>  > packageVersion("bslib", lp[1])
>  [1] =E2=80=980.11.0=E2=80=99
>  > packageVersion("bslib", lp[2])
>  [1] =E2=80=980.10.0=E2=80=99
>
>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 m=
y packages, it seems that most of them, maybe all of them, are flagged as n=
eeding 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 ver=
sion 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 <[email protected]>
>>> To: [email protected]
>>> Subject: Re: [R] issue with update.packages(), library 'utils'
>>> Message-ID: <[email protected]>
>>> Content-Type: text/plain; charset=3D"utf-8"; Format=3D"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=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 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"] =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
>>>> ______________________________________________ [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=3D"utf-8"
>>> =

>>> I had this problem too and I don=E2=80=99t 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
>>> =

>> =

>> ______________________________________________
>> [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.
>
>______________________________________________
>[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.h=
tml
>and provide commented, minimal, self-contained, reproducible code.

--
Sent from my phone. Please excuse my brevity.
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