[R] Building Packages.
Ben Bolker
bbo|ker @end|ng |rom gm@||@com
Thu Mar 21 14:00:30 CET 2024
Is your Fedora machine using the bspm package with bspm::enable() in
the .Rprofile (to install binary packages from the r2u repository)?
bspm adds a hook by using trace() on install.packages, which makes it
look like this.
My guess is that if you start with --vanilla *or* run bspm::disable()
that you'll get back to the original-as-installed version.
Even if you have RStudio installed you could change the association
in your GUI file browser to open R files in emacs by default ...
cheers
Ben Bolker
On 2024-03-21 4:40 a.m., Martin Maechler wrote:
>>>>>> Ben Bolker
>>>>>> on Wed, 20 Mar 2024 13:25:33 -0400 writes:
>
> > Hmm, looks platform-specific. Under Linux both RStudio
> > and external R console return
>
> > a0b52513622c41c11e3ef57c7a485767
>
> > for digest::digest(install.packages)
>
> Well, platform-specific maybe, notably probably the *RStudio*-version
> matters (for once).
>
> One one of our public compute-machines running Linux Fedora 38
> (I don't have RStudio installed on my desktop as I loathe it
> badly to see RStudio start up when I click at an *R script in
> the OS gui file browser ... !:!P:!)(*&))
>
> I definitely see
>
>> R.version.string
> [1] "R version 4.3.3 Patched (2024-02-29 r86162)"
>> RStudio.Version()$version
> [1] ‘2023.12.1.402’
>> install.packages
> function (...)
> .rs.callAs(name, hook, original, ...)
> <environment: 0x55f4e5d82948>
>>
>
> No need for any hashes to see that install.packages is not the
> one from R.
>
> ---
> Concluding from your, Ben's, finding I'd guess that Posit
> finally decided to move away from this very unfriendly idea of
> sneakily replacing a base R function ?
>
> That would actually give raise to some applause..
>
> Martin
>
>
>
> > On 2024-03-20 1:20 p.m., Duncan Murdoch wrote:
> >> On 20/03/2024 1:07 p.m., Duncan Murdoch wrote:
> >>> On 20/03/2024 12:37 p.m., Ben Bolker wrote:
> >>>> Ivan, can you give more detail on this? I've heard
> >>>> this issue mentioned, but when I open RStudio and run
> >>>> find("install.packages") it returns
> >>>> "utils::install.packages", and running dump() from
> >>>> within RStudio console and from an external "R
> >>>> --vanilla" gives identical results.
> >>>>
> >>>> I thought at one point this might only refer to
> >>>> the GUI package-installation interface, but you seem to
> >>>> be saying it's the install.packages() function as well.
> >>>>
> >>>> Running an up-to-date RStudio on Linux, FWIW --
> >>>> maybe weirdness only happens on other OSs?
> >>>
> >>> On MacOS, I see this:
> >>>
> >>> > install.packages function (...) .rs.callAs(name,
> >>> hook, original, ...) <environment: 0x7fa7c72a6268>
> >>>
> >>> I get the same results as you from find(). I'm not sure
> >>> what RStudio is doing to give a different value for the
> >>> function than what find() sees.
> >>
> >> Turns out that RStudio replaces the install.packages
> >> object in the utils package.
> >>
> >> Duncan Murdoch
> >>
> >>>
> >>> Duncan Murdoch
> >>>
> >>>>
> >>>> Ben Bolker
> >>>>
> >>>> On 2024-03-20 12:13 p.m., Ivan Krylov via R-help wrote:
> >>>>> В Wed, 20 Mar 2024 16:02:27 +0000 Jorgen Harmse via
> >>>>> R-help <r-help using r-project.org> пишет:
> >>>>>
> >>>>>>> install.packages(tar,type='source',repos=NULL)
> >>>>>>
>>>>>> Error in library(jhBase) : there is no package called
> >>>>>> ‘jhBase’
> >>>>>>
>>>>>> Execution halted
> >>>>>>
>>>>>> Warning in install.packages(tar, type = "source", repos =
> >>>>>> NULL) :
> >>>>>>
>>>>>> installation of package
>>>>>>
> >>>>>> ‘/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz’
>>>>>> had non-zero exit status
> >>>>>
> >>>>> Using RStudio? It happens to override install.packages
> >>>>> with a function that doesn't quite handle file
> >>>>> paths. Try utils::install.packages(tar, type =
> >>>>> "source", repos = NULL).
> >>>>>
> >>>>
> >>>> ______________________________________________
> >>>> R-help using 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.
> >>>
> >>
>
> > ______________________________________________
> > R-help using 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.
--
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
(Acting) Graduate chair, Mathematics & Statistics
> E-mail is sent at my convenience; I don't expect replies outside of
working hours.
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