On 2026-06-08 8:54 a.m., Karl Schilling wrote:
Dear Duncan Murdoch:I did just what you recommended. I have only one library. > lp <- .libPaths() > lp [1] "C:/Program Files/R/R-4.6.0patched/library" > length(lp) [1] 1
That looks suspicious to me. I haven't used Windows in a long time, but when I did, that directory would have been write protected. When I would try to install a package there it would fail, and R would add a user library and install there instead. The .libPaths() vector would be changed for the rest of that session, but could revert to just one entry if I started a new session.
But maybe the post by Jinsong ZZhao is relevent here:
Yes, that could explain everything. If the date when a binary package is built changes, that could mean that different C libraries were linked into it, and you should use the newer one. Or it might just mean that CRAN rebuilt it unnecessarily, but there's no way for R to know that.
Duncan Murdoch
The root of the problem is that old.packages have updated the internal function needs.install, which compares the built date of repo and the installed packages. And it seems that repo packages have newer built date, though I do not know why. So reinstallation R and all packages could not solve the problem. Best, Jinsong PS: the internal function need.install: .ts <- function(x) if (isTRUE(!is.na(x))) as.POSIXlt(x, optional = TRUE, tz = "UTC") else NA needs.install <- function(repo, inst) ((package_version(repo["Version"]) > package_version(inst["Version"])) || (package_version(repo["Version"]) == package_version(inst["Version"]) && (isTRUE(.builtDate(repo["Built"]) > .builtDate(inst["Built"])) || isTRUE(.ts(repo["Published"]) > .ts(inst["Published"])))))I reinstalled r 4.6patched and all packages on May 28. Later that day, then, "update.packages" did result in only three packages highlighted for updating. A couple of days later, ALL my packages were again in the list to be updated. And just as documented in the post by [email protected], my installed packages had the same version numbers as those in the repository. Looking at the repository https://cloud.r-project.org/bin/windows/contrib/4.6, I realized that the "Last modified" date was more recent (mostly June 7) - though the version numbers of my installed packages were identical to those in the repository. So does "Last modified" reflect / affect the .builtDate in the above function? And do different dates for "Last modified" imply changes even if the version numbers are unchanged? Thank you so much for your help, Karl Schilling On 08.06.2026 14:01, Duncan Murdoch 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 sourcehead(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] 519sum( old.pkgs[,"Installed"] == old.pkgs[,"ReposVer"] )[1] 516sum( old.pkgs[,"Installed"] != old.pkgs[,"ReposVer"] )[1] 3old.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______________________________________________ [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.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.html and provide commented, minimal, self-contained, reproducible code.
