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updated the day before were now identified as outdated.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outdated, whereas they are clearly not...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
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