[R] install.packages() R vs RStudio

[Ivan Calandra]

Thank you Duncan for the very detailed and clear answer!

Best,
Ivan

--
Dr. Ivan Calandra
TraCEr, laboratory for Traceology and Controlled Experiments
MONREPOS Archaeological Research Centre and
Museum for Human Behavioural Evolution
Schloss Monrepos
56567 Neuwied, Germany
+49 (0) 2631 9772-243
https://www.researchgate.net/profile/Ivan_Calandra

On 17/08/2020 15:03, 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!
>
> Duncan Murdoch
>
>