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

Martin Maechler m@ech|er @end|ng |rom @t@t@m@th@ethz@ch
Wed Feb 14 11:50:53 CET 2024

>>>>> 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),
    >> [...]

    >> 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...


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