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@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@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@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.
______________________________________________
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.
