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 >>>> 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. -- Sent from my phone. Please excuse my brevity. [[alternative HTML version deleted]] ______________________________________________ [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.
