install.packages() R vs RStudio

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