[R] [External] Re: Building Packages. (fwd)

Thu Mar 21 12:44:00 CET 2024

[forgot to copy to R-help so re-sending]

---------- Forwarded message ----------
Date: Thu, 21 Mar 2024 11:41:52 +0000
From: luke-tierney using uiowa.edu
To: Duncan Murdoch <murdoch.duncan using gmail.com>
Subject: Re: [External] Re: [R] Building Packages.

At least on my installed version (which tells me it is out of date)
they appear to just be modifying the "package:utils" parent frame of
the global search path.

There seem to be a few others:

checkUtilsFun <- function(n)
     identical(get(n, "package:utils"), get(n, getNamespace("utils")))
names(which(! sapply(ls("package:utils", all = TRUE), checkUtilsFun)))
## [1] "bug.report"       "file.edit"        "help.request" ## [4] "history" 
"install.packages" "remove.packages" ## [7] "View"

I don't know why they don't put these overrides in the tools:rstudio frame.
At least that would make them more visible.

You can fix all of these with something like

local({
       up <- match("package:utils", search())
       detach("package:utils")
       library(utils, pos = up)
})

or just install.packages with

local({
     up <- match("package:utils", search())
     unlockBinding("install.packages", pos.to.env(up))
     assign("install.packages", utils::install.packages, "package:utils")
     lockBinding("install.packages", pos.to.env(up))
})

Best,

luke

On Thu, 21 Mar 2024, Duncan Murdoch wrote:

> Yes, you're right.  The version found in the search list entry for 
> "package:utils" is the RStudio one; the ones found with two or three colons 
> are the original.
> 
> Duncan Murdoch
> 
> On 21/03/2024 5:48 a.m., peter dalgaard wrote:
>> Um, what's with the triple colon? At least on my install, double seems to 
>> suffice:
>> 
>>> identical(utils:::install.packages, utils::install.packages)
>> [1] TRUE
>>> install.packages
>> function (...)
>> .rs.callAs(name, hook, original, ...)
>> <environment: 0x7f79e0019860>
>> 
>> -pd
>> 
>>> On 21 Mar 2024, at 09:58 , Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>>> 
>>> The good news for Jorgen (who may not be reading this thread any more) is 
>>> that one can still be sure of getting the original install.packages() by 
>>> using
>>>
>>>     utils:::install.packages( ... )
>>> 
>>> with *three* colons, to get the internal (namespace) version of the 
>>> function.
>>> 
>>> Duncan Murdoch
>>> 
>>> 
>>> On 21/03/2024 4:31 a.m., Martin Maechler wrote:
>>>>>>>>> "Duncan Murdoch on Wed, 20 Mar 2024 13:20:12 -0400 writes:
>>>>      > 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
>>>> Yes, and this has been the case for several years now, and I
>>>> have mentioned this several times, too  (though some of it
>>>> possibly not in a public R-* mailing list).
>>>> And yes, that they modify the package environment
>>>>    as.environment("package:utils")
>>>> but leave the
>>>>    namespace  asNamespace("utils")
>>>> unchanged, makes it harder to see what's
>>>> going on (but also has less severe consequences; if they kept to
>>>> the otherwise universal *rule* that the namespace and package must have 
>>>> the same objects
>>>> apart from those only in the namespace,
>>>> people would not even have access to R's true install.packages()
>>>> but only see the RStudio fake^Hsubstitute..
>>>> We are still not happy with their decision. Also
>>>> help(install.packages) goes to R's documentation of R's
>>>> install.packages, so there's even more misleading of useRs.
>>>> Martin
>>>> 
>>> 
>>> ______________________________________________
>>> 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.
>

-- 
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:   luke-tierney using uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu/