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
> 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, ...)
>
> 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
>> ''
> 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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Re: [R] Packages sometimes don't update, but no error or warning is thrown
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 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
>> 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, ...)
>>
>
>> 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
>>> ''
>
>> 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
>
> __
> R-help@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.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk Priv: pda...@gmail.com
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Re: [R] Packages sometimes don't update, but no error or warning is thrown
Às 10:50 de 14/02/2024, Martin Maechler escreveu:
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
> 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, ...)
>
> 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
>> ''
> 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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and provide commented, minimal, self-contained, reproducible code.
Hello,
From within RStudio you can always run the qualified names
utils::install.packages()
utils::update.packages()
or run from the command line.
Hope this helps,
Rui Barradas
--
Este e-mail foi analisado pelo software antivírus AVG para verificar a presença
de vírus.
www.avg.com
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Packages sometimes don't update, but no error or warning is thrown
> 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
> 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, ...)
>
> 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
>> ''
> 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
__
R-help@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.
