[R] Building Packages.

[Ben Bolker]

   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.