Re: [R-pkg-devel] Writing to files without altering working directory in R package
On 07/05/2019 6:44 p.m., Uwe Ligges wrote: On 07.05.2019 19:57, Duncan Murdoch 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. Thank you, Duncan. Well, setwd(tempdir()) should be made local to the examples if used at all, as the user may not expect to have the working directory changed. Yes, I agree. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Writing to files without altering working directory in R package
On 07.05.2019 19:57, Duncan Murdoch 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.
Thank you, Duncan. Well, setwd(tempdir()) should be made local to the
examples if used at all, as the user may not expect to have the working
directory changed.
Best,
Uwe
Duncan Murdoch
On Fri, May 3, 2019 at 7:59 PM Duncan Murdoch
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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
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Re: [R-pkg-devel] Writing to files without altering working directory in R package
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 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
> > 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@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Writing to files without altering working directory in R package
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 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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
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https://stat.ethz.ch/mailman/listinfo/r-package-devel
