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 <[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
______________________________________________
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and provide commented, minimal, self-contained, reproducible code.
______________________________________________
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PLEASE do read the posting guide https://www.R-project.org/posting-guide.html
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