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

Fri Feb 16 18:01:58 CET 2024

The normal way to update packages is to use update.packages() rather 
than install.packages().  Likely the problem you're having is from using 
install.packages() (or RStudio using it). I normally use 
update.packages(ask=FALSE), but if you want to pick and choose, you 
could use the default which will prompt you for each one.

Duncan Murdoch

On 16/02/2024 11:33 a.m., Philipp Schneider wrote:
> Hey everyone,
> 
> Thanks for all the input. It's happening again. This time for the 
> packages "DBI", "parallelly", "segmented", "survival", "V8". So, RStudio 
> shows updates for those and updating them via RStudio leads to this output:
> 
> ```
>  > install.packages(c("DBI", "parallelly", "segmented", "survival", "V8"))
> trying URL 
> 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.3/DBI_1.2.0.tgz' <https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.3/DBI_1.2.0.tgz'>
> Content type 'application/x-gzip' length 822755 bytes (803 KB)
> ==================================================
> downloaded 803 KB
> 
> trying URL 
> 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.3/parallelly_1.36.0.tgz' <https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.3/parallelly_1.36.0.tgz'>
> Content type 'application/x-gzip' length 349831 bytes (341 KB)
> ==================================================
> downloaded 341 KB
> 
> trying URL 
> 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.3/segmented_2.0-2.tgz' <https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.3/segmented_2.0-2.tgz'>
> Content type 'application/x-gzip' length 1210146 bytes (1.2 MB)
> ==================================================
> downloaded 1.2 MB
> 
> trying URL 
> 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.3/survival_3.5-7.tgz' <https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.3/survival_3.5-7.tgz'>
> Content type 'application/x-gzip' length 7101721 bytes (6.8 MB)
> ==================================================
> downloaded 6.8 MB
> 
> trying URL 
> 'https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.3/V8_4.4.1.tgz' <https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.3/V8_4.4.1.tgz'>
> Content type 'application/x-gzip' length 10093069 bytes (9.6 MB)
> ==================================================
> downloaded 9.6 MB
> 
> 
> The downloaded binary packages are in
> /var/folders/ws/XXX/T//YYY/downloaded_packages
> ```
> 
> After that, all the packages are still updatable. No warning, no error, 
> but also no updated packages. utils::install.packages(c("DBI", 
> "parallelly", "segmented", "survival", "V8")) leads to the exact same 
> output. The only difference, if I run it directly from command-line is, 
> that I have to select a mirror. After that it's again the same output. 
> The DBI package for example is installed with version 1.2.0, which is 
> the latest available macOS arm64 binary. However, there is an update 
> available for other binaries or source. So, I guess in the end, it's not 
> the install.packages() that is failing, but the check for updates from 
> RStudio. On the other hand, shouldn't there be at least a warning that 
> there are new updates available, just no new binaries.
> 
> Best,
> Philipp
> 
> 
> 
> 
> 
> Gesendet: Mittwoch, 14. Februar 2024 um 18:44 Uhr
> Von: "Duncan Murdoch" <murdoch.duncan using gmail.com>
> An: "Martin Maechler" <maechler using stat.math.ethz.ch>, "Berwin A Turlach" 
> <berwin.turlach using gmail.com>
> Cc: "gernophil--- via R-help" <r-help using r-project.org>
> Betreff: Re: [R] Packages sometimes don't update, but no error or 
> warning is thrown
> On 14/02/2024 5:50 a.m., Martin Maechler wrote:
>  >>>>>> Berwin A Turlach
>  >>>>>> on Wed, 14 Feb 2024 11:47:41 +0800 writes:
>  >>>>>> Berwin A Turlach
>  >>>>>> on Wed, 14 Feb 2024 11:47:41 +0800 writes:
>  >
>  > > G'day Philipp,
>  >
>  > > On Tue, 13 Feb 2024 09:59:17 +0100 gernophil--- via R-help
>  > > <r-help using r-project.org> wrote:
>  >
>  > >> 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>),
>  > >> [...]
>  >
>  > >> To sum it up: If I am updating packages (be it via
>  > >> Bioconductor or CRAN) some packages simply don’t update,
>  > >> [...]
>  >
>  > >> 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.
>  >
>  > > RStudio is doing its own thing for some task, including
>  > > 'install.packages()' (and for some reasons, at least on
>  > > the platforms on which I use RStudio, RStudio calls
>  > > 'install.packages()' and not 'update.packages()' when an
>  > > update is requested via the GUI). See:
>  >
>  > RStudio> install.packages
>  > > function (...) .rs.callAs(name, hook, original, ...)
>  > > <environment: 0x55bab9293998>
>  >
>  > > compared to:
>  >
>  > R> install.packages
>  > > function (pkgs, lib, repos = getOption("repos"),
>  > > contriburl = contrib.url(repos, type), method, available =
>  > > NULL, destdir = NULL, dependencies = NA, type =
>  > > getOption("pkgType"), configure.args =
>  > > getOption("configure.args"), configure.vars =
>  > > getOption("configure.vars"), clean = FALSE, Ncpus =
>  > > getOption("Ncpus", 1L), verbose = getOption("verbose"),
>  > > libs_only = FALSE, INSTALL_opts, quiet = FALSE,
>  > > keep_outputs = FALSE, ...) { [...]
>  >
>  >
>  > > So if you use Install/Update in the Packages tab of
>  > > RStudio and do not experience the behaviour you are
>  > > expecting, it is something that you need to discuss with
>  > > Posit, not with R. :)
>  >
>  > >> However, the only message I get is: ``` trying URL
>  > >> '<url_to_package>'
>  >
>  > > The package name has the version number encoded in it, so
>  > > theoretical you should be able to tell at this point
>  > > whether the package that is downloaded is the version that
>  > > is already installed, hence no update will happen.
>  >
>  > > Best wishes,
>  >
>  > > Berwin
>  >
>  >
>  > Yes, thank's a lot, Berwin.
>  >
>  > Indeed I've raised the fact that RStudio
>  > hides R's own install.packages() from the user and uses its
>  > own, undocumented one ... this has been the case for quite a few years.
>  > I found out during teaching --- one of the few times, I use
>  > RStudio to use R... in another case where RStudio's
>  > install.packages() behaved differently than R's.
>  >
>  > I'm pretty sure this is reason for quite a bit of confusion...
> 
> Did they ignore your bug report?
> 
> Duncan Murdoch
> 
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