[R] Packages sometimes don't update, but no error or warning is thrown

[Rui Barradas]

Às 10:09 de 13/02/2024, gernophil--- via R-help escreveu:
> Yes you're right that it started as an Bioconductor issue. The reason I am writing it here, if because of one of the core members of the Bioconductor project stated this:
> "(...) But anyway, it's almost certainly an install.packages issue rather than BiocManager::install, so you might check over at r-help using r-project.org."
>   
> It's hard to give an explicit example here since it's always a bit time dependent, when and if this happens. And "unfortunately", right now all packages can be updated, but I'll come back to this as soon as I experience it again. It's more of a general feature request then a help request, but as you say "In my experience update.packages() asks whether you want the source or binary install and respects your choice." However, at least for me, it does not do this anymore, but simply silently fails to update those packages.
>   
> The Bioconductor thread is the most informative for this (https://support.bioconductor.org/p/9156283[https://support.bioconductor.org/p/9156283/#9156308]) in case anyone wants to check the situation in more detail.
> 
>   
> Philipp
>   
> 
> Gesendet: Dienstag, 13. Februar 2024 um 10:53 Uhr
> Von: "Duncan Murdoch" <murdoch.duncan using gmail.com>
> An: "R Project Help" <R-help using r-project.org>
> Betreff: [R] Packages sometimes don't update, but no error or warning is thrown
> Those three references are about RStudio and Bioconductor (or at least
> they start out that way, I didn't read through the long threads).
> Neither of those is relevant here, but from my quick scan it appears the
> issue is that those systems detect a package in source form is
> available, then install an older binary instead.
> 
> If you have an example where update.packages() does this, that would be
> on topic on this list. Please post just that here: your calls, and all
> the output you received. In my experience update.packages() asks
> whether you want the source or binary install and respects your choice.
> 
> Duncan Murdoch
> 
> On 13/02/2024 3:59 a.m., gernophil--- via R-help wrote:
>> Hey everyone,
>>
>> this question is related to this (https://community.rstudio.com/t/packages-are-not-updating/166214/3[https://community.rstudio.com/t/packages-are-not-updating/166214/3]), this (https://www.biostars.org/p/9586316/#9586323[https://www.biostars.org/p/9586316/#9586323]) and this (https://support.bioconductor.org/p/9156283/#9156308[https://support.bioconductor.org/p/9156283/#9156308]). The two latter ones are pots from myself.
>>
>> To sum it up: If I am updating packages (be it via Bioconductor or CRAN) some packages simply don’t update, but they also don’t throw any warning or error that they have not been updated. The reason behind this is most likely that there is an update, but it’s not yet available as a binary – in my case as a "mac.binary.big-sur-arm64", since I am on Apple Silicon. My pkgType is set to "both" (default), but my .Platform$pkgType is "mac.binary.big-sur-arm64" (also default).
>>
>> If the system shows an update is available and I click update (or update via install.packages()), but the package will not be updated, I would expect any kind of message that the package will not be updated, since no newer binary is available or a prompt, if I want to compile from source. However, the only message I get is:
>> ```
>> trying URL '<url_to_package>'
>> Content type 'application/x-gzip' length XXXXXXX bytes (X.X MB)
>> ==================================================
>> downloaded X.X MB
>>
>>
>> The downloaded binary packages are in
>>                  /var/folders/ws/XXX/T//YYY/downloaded_packages
>> ```
>> To see, if the package was actually updated, I have to check for updates again (or check the version of the installed package). Is this the expected behavior and if so, why? (Also, why is there a double slash in the path to the downloaded packages?)
>>
>> Thanks for your help.
>>
>> Best,
>> Philipp
>>
>> ______________________________________________
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>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html[http://www.R-project.org/posting-guide.html]
>> and provide commented, minimal, self-contained, reproducible code.
> 
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html[http://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 http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
Hello,

Not exactly an answer, just a thought:
Whenever I have problems updating or installing packages from whithin 
RStudio I close RStudio, write a script with the install.packages() call 
and run it from a command window.


R -q -f "instscript.R"


This many times works better and it also works with Bioconductor's 
BiocManager::install or with remotes'/devtools's install_github.

Hope this helps,

Rui Barradas


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