R help - Feb 2024 - Packages sometimes don't update, but no error or warning is thrown

Hey everyone,
?
this question is related to this
(https://community.rstudio.com/t/packages-are-not-updating/166214/3), this
(https://www.biostars.org/p/9586316/#9586323) and this
(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

G'day Philipp,

On Tue, 13 Feb 2024 09:59:17 +0100
gernophil--- via R-help <r-help at 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