iuke-tier@ey m@iii@g oii uiow@@edu
2024-Mar-21 11:44 UTC
[R] [External] Re: Building Packages. (fwd)
[forgot to copy to R-help so re-sending]
---------- Forwarded message ----------
Date: Thu, 21 Mar 2024 11:41:52 +0000
From: luke-tierney at uiowa.edu
To: Duncan Murdoch <murdoch.duncan at 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At least on my installed version (which tells me it is out of date)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 at
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 at 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 at 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 at uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu/
If you are wondering why RStudio did this, you can see their substitute function using (parent.env(environment(install.packages)))$hook They appear to do these things: - Allow package installation to be disabled. - Check if a package to be installed is already loaded, so that RStudio can restart R for the install. - Add Rtools to the PATH if necessary. - Trigger an event to say that something is about to be changed about the installed packages, presumably so that they can mark a cached list of installed packages as stale. - Call the original function. I think all of these things could be done if install.packages() called a hook at the start, as library() does (via attachNamespace()) when a package is attached. It might be that putting the wrapper code into tools:rstudio would cause confusion for users when there were two objects of the same name on the search list, though I don't see how. Duncan Murdoch On 21/03/2024 7:44 a.m., luke-tierney--- via R-help wrote:> [forgot to copy to R-help so re-sending] > > ---------- Forwarded message ---------- > Date: Thu, 21 Mar 2024 11:41:52 +0000 > From: luke-tierney at uiowa.edu > To: Duncan Murdoch <murdoch.duncan at 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 at 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 at 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 at 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. >> >