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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