[R] install.packages() R vs RStudio

[Duncan Murdoch]

Hi John.

I suspect most good front ends do similar things.  For example, on 
MacOS, R.app messes up "history()".  I've never used ESS, but I imagine 
one could find examples where it acts differently than base R:  isn't 
that the point?

One hopes all differences are improvements, but sometimes they're not. 
If the modifications cause trouble (e.g. the ones you and I have never 
experienced with install.packages() in RStudio, or the one I experience 
every now and then with history() in R.app), then that may be a bug in 
the front-end.  It should be reported to the authors.

R is designed to be flexible, and to let people change its behaviour. 
Using that flexibility is what all users should do.  Improving the user 
experience is what front-end writers should do.  I don't find it 
inadvisable at all.  If it's the "silent" part that you object to, I 
think that's a matter of taste.  Personally, I've stopped reading the 
messages like

"Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

     as.Date, as.Date.numeric"

so they may as well be silent.

Duncan Murdoch


On 17/08/2020 10:02 a.m., John Fox wrote:
> Dear Duncan,
> 
> On 2020-08-17 9:03 a.m., Duncan Murdoch wrote:
>> On 17/08/2020 7:54 a.m., Ivan Calandra wrote:
>>> Dear useRs,
>>>
>>> Following the recent activity on the list, I have been made aware of
>>> this discussion:
>>> https://stat.ethz.ch/pipermail/r-help/2020-May/466788.html
>>>
>>> I used to install all packages in R, but for simplicity (I use RStudio
>>> for all purposes), I now do it in RStudio. Now I am left wondering
>>> whether I should continue installing packages directly from RStudio or
>>> whether I should revert to using R.
>>>
>>> My goal is not to flare a debate over whether RStudio is better or worse
>>> than R, but rather simply to understand whether there are differences
>>> and potential issues (that could lead to problems in code) about
>>> installing packages through RStudio.
>>>
>>> In general, it would be nice to have a list of the differences in
>>> behavior between R and RStudio, but I believe this should come from the
>>> RStudio side of things.
>>>
>>> Thank you all for the insights.
>>> Ivan
>>>
>>
>> To see the install.packages function that RStudio installs, just type
>> its name:
>>
>>   > install.packages
>> function (...)
>> .rs.callAs(name, hook, original, ...)
>> <environment: 0x7fe7dc5b65b0>
>>
>> You can debug it to see the other variables:
>>
>>   > debug(install.packages)
>>   > install.packages("abind")
>> debugging in: install.packages("abind")
>> debug: .rs.callAs(name, hook, original, ...)
>> Browse[2]> name
>> [1] "install.packages"
>> Browse[2]> hook
>> function (original, pkgs, lib, repos = getOption("repos"), ...)
>> {
>>       if (missing(pkgs))
>>           return(utils::install.packages())
>>       if (!.Call("rs_canInstallPackages", PACKAGE = "(embedding)")) {
>>           stop("Package installation is disabled in this version of
>> RStudio",
>>               call. = FALSE)
>>       }
>>       packratMode <- !is.na(Sys.getenv("R_PACKRAT_MODE", unset = NA))
>>       if (!is.null(repos) && !packratMode &&
>> .rs.loadedPackageUpdates(pkgs)) {
>>           installCmd <- NULL
>>           for (i in seq_along(sys.calls())) {
>>               if (identical(deparse(sys.call(i)[[1]]),
>> "install.packages")) {
>>                   installCmd <- gsub("\\s+", " ",
>> paste(deparse(sys.call(i)),
>>                     collapse = " "))
>>                   break
>>               }
>>           }
>>           .rs.enqueLoadedPackageUpdates(installCmd)
>>           stop("Updating loaded packages")
>>       }
>>       .rs.addRToolsToPath()
>>       on.exit({
>>           .rs.updatePackageEvents()
>>           .Call("rs_packageLibraryMutated", PACKAGE = "(embedding)")
>>           .rs.restorePreviousPath()
>>       })
>>       original(pkgs, lib, repos, ...)
>> }
>> <environment: 0x7fe7db925588>
>>
>> The .rs.callAs function just substitutes the call to "hook" for the call
>> to the original install.packages.  So you can see that they do the
>> following:
>>    - they allow a way to disable installing packages,
>>    - they support "packrat" (a system for installing particular versions
>> of packages, see https://github.com/rstudio/packrat),
>>    - they add RTools to the path (presumably only on Windows)
>>    - they call the original function, and at the end update internal
>> variables so they can show the library in the Packages pane.
>>
>> So there is no reason not to do it in R.
>>
>> By the way, saying that this is a "modified version of R" is like saying
>> every single user who defines a variable creates a modified version of
>> R.  If you type "x" in the plain R console, you see "Error: object 'x'
>> not found".  If you "modify" R by assigning a value to x, you'll see
>> something different.  Very scary!
> 
> I can't recall ever disagreeing with something you said on the R-help,
> but this seems to me to be off-base. While what you say is technically
> correct, silently masking a standard R function, in this case, I
> believe, by messing with the namespace of the utils package, seems
> inadvisable to me.
> 
> As has been noted, cryptic problems have arisen with install.packages()
> in RStudio -- BTW, I use it regularly and haven't personally experienced
> any issues. One could concoct truly scary examples, such as redefining
> isTRUE().
> 
> Best,
>    John
> 
>>
>> Duncan Murdoch
>>
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