[R] issue with update.packages(), library 'utils'

Duncan Murdoch murdoch@dunc@n @end|ng |rom gm@||@com
Mon Jun 8 15:09:32 CEST 2026 

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
> guido.hooiveld using wur.nl, 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 <karl.schilling using uni-bonn.de>
>>>> To: r-help using r-project.org
>>>> Subject: Re: [R] issue with update.packages(), library 'utils'
>>>> Message-ID: <240738c2-9935-40a9-b461-c82776cd1a77 using uni-bonn.de>
>>>> 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:
>>>>> guido.hooiveld using wur.nl internet: http://www.humannutrition.nl
>>>>> http://scholar.google.com/citations?user=qFHaMnoAAAAJ
>>>>> http://www.scopus.com/authid/detail.url?authorId=6603101814
>>>>> ______________________________________________ R-help using r-project.org
>>>>> 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 <iagogv using disroot.org>
>>>> To: r-help using r-project.org
>>>> Subject: Re: [R] issue with update.packages(), library 'utils'
>>>> Message-ID: <bf1dc0c5-3a67-42c9-b5e9-05fada44e91f using disroot.org>
>>>> 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
>>>>
>>>
>>> ______________________________________________
>>> R-help using r-project.org 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.
>>
>> ______________________________________________
>> R-help using r-project.org 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.

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