Re: [R] Packages sometimes don't update, but no error or warning is thrown
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'
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"
An: "Martin Maechler" , "Berwin A Turlach"
Cc: "gernophil--- via R-help"
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
> > 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, ...)
> >
>
> > 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
Re: [R] Packages sometimes don't update, but no error or warning is thrown
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'
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'
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'
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'
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'
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"
An: "Martin Maechler" , "Berwin A Turlach"
Cc: "gernophil--- via R-help"
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
> > 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 =
[R] [Rd] R 4.3.3 scheduled for February 29
Full schedule available on developer.r-project.org in a short while. -- 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 ___ r-annou...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ 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.
Re: [R] VPAT OR Accessibility Conformance Report Request (Zachary Benner)
Dear Zachary,
People will rightly point you to:
this article: https://journal.r-project.org/archive/2013-1/godfrey.pdf
and this book chapter:
https://r-resources.massey.ac.nz/BrailleRInAction/WorkingBlind.html
There is additional information elsewhere, for example here:
https://www.google.com/search?q=using+r+as+a+blind+person=using+r+as+a+blind+person
though people with visual difficulties may not be your only concern.
"VPAT or Accessibility Conformance Information Report” is rather insider-ish
and evidently American; you’re kind-of on your own there. R is not our
software; it’s free open-source software.
-Richard
---
Richard Sherman
Associate Dean of Academic Affairs
Associate Professor of International Relations and Political Science
Director, Politics, Philosophy and Economics
Asian University for Women
https://asian-university.org/
> On Feb 16, 2024, at 5:00 PM, r-help-requ...@r-project.org wrote:
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> 1. VPAT OR Accessibility Conformance Report Request (Zachary Benner)
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> Message: 1
> Date: Thu, 15 Feb 2024 12:23:08 -0500
> From: Zachary Benner
> To: r-help@r-project.org, r-de...@r-project.org
> Subject: [R] VPAT OR Accessibility Conformance Report Request
> Message-ID:
>
> Content-Type: text/plain; charset="utf-8"
>
> To Whom It May Concern,
> My name is Zach Benner and I am the Accessibility (A.D.A.-Americans with
> Disabilities Act) Coordinator here at University of Maine at Machias. I am
> reaching out on the behalf of our science professors here at UMM. The
> professor is looking to utilize your software to implement within his
> courses however, due to possible accessibility concerns our IT department
> will not download the software onto school computers unless we have a copy
> of a VPAT or Accessibility Conformance Information Report. I was wondering
> if I could obtain this information to provide to the IT department?
> Thank you for your time on this matter and I look forward to hearing from
> you soon. Please let me know if you have any questions or concerns.
> Sincerely,
> Zach Benner
> Accessibility Coordinator & Student Success Liaison
> University of Maine Machias
> Office: 229A Torrey Hall
> 116 O'Brien Ave
> Machias, ME, 04654
> Office Number: 207-255-1228
>
> Confidentiality Notice: This e-mail and any attachments...{{dropped:12}}
>
>
>
>
> --
>
> Subject: Digest Footer
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R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] VPAT OR Accessibility Conformance Report Request
To Whom It May Concern,
My name is Zach Benner and I am the Accessibility (A.D.A.-Americans with
Disabilities Act) Coordinator here at University of Maine at Machias. I am
reaching out on the behalf of our science professors here at UMM. The
professor is looking to utilize your software to implement within his
courses however, due to possible accessibility concerns our IT department
will not download the software onto school computers unless we have a copy
of a VPAT or Accessibility Conformance Information Report. I was wondering
if I could obtain this information to provide to the IT department?
Thank you for your time on this matter and I look forward to hearing from
you soon. Please let me know if you have any questions or concerns.
Sincerely,
Zach Benner
Accessibility Coordinator & Student Success Liaison
University of Maine Machias
Office: 229A Torrey Hall
116 O'Brien Ave
Machias, ME, 04654
Office Number: 207-255-1228
Confidentiality Notice: This e-mail and any attachments...{{dropped:12}}
__
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.
