[R-pkg-devel] Writing to files without altering working directory in R package

[Henrik Bengtsson]

I agree that setwd(), tempdir(), etc. clutter up examples.  At the
same time, I respect the CRAN policy - it's conservative approach has
helped us avoid a wild-west working environment. One approach that
might help bring some standardization, instead of each package
developer rolls their own, and avoid having to have that tempdir code
in there is to have example() handle this.  For example, add a
workdir=tempdir() argument to example() and have example() change to
that directory temporarily, and report on the working directory at the
end.

> example(foo)
...
Any output files produced by this example may be found in the
temporary working directory '/tmp/alice/Rtmp4faDCv'.

This could be a message or a warning.  One could also imagine using
workdir=getOption("example.workdir", tempdir()) as the default.  If
properly done, this would allow the user to set
options(example.workdir = quote(getwd())) if they'd like to write to
the current directory.

What it does not solve is when a user cut'n'paste code, but maybe that
could be considered acceptable because in that case the user is not
running/source code, but calling it themself.

My $.02

/Henrik




These messages can be skipped if called with example(..., workdir=getwd()).

On Tue, May 7, 2019 at 10:57 AM Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>
> On 06/05/2019 12:16 p.m., Jim Hester wrote:
> > For what it's worth, the recommendation to use `tempfile()` is very
> > confusing to R users.
> >
> > Often users (particularly new users) jump directly to examples when
> > reading documentation and when you have these more complicated
> > examples they do not realize they can just use a simple string
> > literal.
> >
> > See https://github.com/tidyverse/readr/issues/635 for an issue where
> > multiple users explicitly request examples which do _not_ use
> > `tempfile()`.
>
> I think beginners rarely like the help pages, and that's really to be
> expected:  help pages need to be complete and correct, and beginners
> really need a small subset of possibilities.  Beginners need tutorials.
>
> In the Github issue, you mentioned pollution of the working directory,
> but I think a bigger problem is destruction of user data, e.g. if a user
> has a file "wine.csv", and the example writes to that file.
>
> So you need to do something to protect users.  I think making examples a
> little complicated by using setwd(tempdir()) with a literal filename, or
> writing to tempfile() is worth it.
>
> Duncan Murdoch
>
> >
> > On Fri, May 3, 2019 at 7:59 PM Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
> >>
> >> On 03/05/2019 6:33 p.m., Jarrett Phillips wrote:
> >>> Hello,
> >>>
> >>> My R package has a function with an argument to specify whether numerical
> >>> results should be outputted to a CSV file.
> >>>
> >>> CRAN policy stipulates verbatim that
> >>>
> >>> Packages should not write in the user’s home filespace (including
> >>> clipboards), nor anywhere else on the file system apart from the R
> >>> session’s temporary directory (or during installation in the location
> >>> pointed to by TMPDIR: and such usage should be cleaned up). Installing into
> >>> the system’s R installation (e.g., scripts to its bin directory) is not
> >>> allowed.
> >>>
> >>> I know I should use tempdir() within my package function, but I've not seen
> >>> any examples on how this is best done within existing R packages.
> >>>
> >>> Within my package documentation examples for my function, I have the lines:
> >>>
> >>>    \dontshow{.oldwd <- setwd(tempdir())}
> >>>
> >>> ... some R code ...
> >>>
> >>> \dontshow{setwd(.oldwd)}
> >>>
> >>> but I have been informed that this is not the accepted way.
> >>>
> >>> Any ideas from the community on how do do this properly?
> >>
> >> Use the tempfile() function to generate a filename in the temporary
> >> directory.  You might want to use the "pattern" or "fileext" arguments,
> >> but don't change the "tmpdir" argument.
> >>
> >> Then write to that file.
> >>
> >> For example,
> >>
> >> filename <- tempfile(fileext = ".csv")
> >> write.csv(df, filename)
> >>
> >> It's a good idea to clean up afterwards using
> >>
> >> unlink(filename)
> >>
> >> ______________________________________________
> >> R-package-devel using r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
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