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

[peter dalgaard]

What Martin says...

Also, it might help to know that the original, base-R functions are still there, as

utils::install.packages()
utils::update.packages()

(+ most likely, a restart of RStudio to make it adapt to the packages that you installed behind its back.)

- Peter D.

> On 14 Feb 2024, at 11:50 , Martin Maechler <maechler using stat.math.ethz.ch> 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),
>>> [...]
> 
>>> 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...
> 
> Martin
> 
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-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
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