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 <[email protected]> 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 <[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
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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
______________________________________________ [email protected]
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provide commented, minimal, self-contained, reproducible code.
______________________________________________ [email protected]
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-- Sent from my phone. Please excuse my brevity. [[alternative HTML
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