Re: issue with update.packages(), library 'utils'
Karl Schilling <[email protected]> Mon, 8 Jun 2026 16:39:04 +0200
| Newsgroups | gmane.comp.lang.r.general |
|---|---|
| Message-ID | <[email protected]> |
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 >>>>> 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.