[R-pkg-devel] Suppressing long-running vignette code in CRAN submission

[Shu Fai Cheung]

Please pardon me if I suggest something unrelated below. Many experts
have made suggestions that I would also like to consider because I
also have a similar issue with some packages.

This is an approach I found, for Rmarkdown vignettes:

https://www.kloppenborg.ca/2021/06/long-running-vignettes/

This is similar to some of the suggestions. The vignette is rendered
locally. It uses the trick that, If we render the vignette by calling
knitr::knit() directly, the extension of the source file does not
matter. The output, although with the extension ".Rmd", actually
contains the results of the code, in chunks starting with "```r", not
"```{r}".

When this pre-buiult .Rmd file is built again, it will just convert
the file to an HTML file, with no need to rerun the code.

The method uses an extension for the source Rmd file (".orig" in the
post) to make sure the "real" source files are ignored when building
the vignettes.

Perhaps this is also a feasible solution for long running vignettes?

Regards,
Shu Fai

On Wed, Oct 18, 2023 at 6:51 AM John Fox <jfox using mcmaster.ca> wrote:
>
> Dear John,
>
> Unless I'm mistaken, the *installation* time of the package isn't really
> at issue. If a user installs a package from a tarball provided by CRAN,
> the vignettes aren't normally rebuilt.
>
> Best,
>   John
>
> On 2023-10-17 6:30 p.m., John Harrold wrote:
> > Caution: External email.
> >
> >
> > I ask myself the question: Who is the vignette for?  It does server two
> > purposes. One is testing but primarily it's for the users to learn how to
> > use a package. I think the testing is secondary, and if it slows down
> > installation or general usability I'd sacrifice the testing. If it's that
> > important, then the tests can be added explicitly in tests/.
> >
> > On Tue, Oct 17, 2023 at 3:04 PM Dirk Eddelbuettel <edd using debian.org> wrote:
> >
> >>
> >> On 18 October 2023 at 08:51, Simon Urbanek wrote:
> >> | John,
> >> |
> >> | the short answer is it won't work (it defeats the purpose of vignettes).
> >>
> >> Not exactly. Everything is under our (i.e. package author) control, and
> >> when
> >> we want to replace 'computed' values with cached values we can.
> >>
> >> All this is somewhat of a charade. "Of course" we want vignettes to run
> >> tests. But then we don't want to fall over random missing .sty files or
> >> fonts
> >> (macOS machines have been less forgiving than others), not to mention
> >> compile
> >> time.
> >>
> >> So for simplicity I often pre-make pdf vignettes that get included in other
> >> latex code as source. Works great, never fails, CRAN never complained --
> >> which is somewhat contrary to your statement.
> >>
> >> It is effectively the same with tests. We all want maximum test surfaces.
> >> But
> >> when tests fail, or when they run too long, or [insert many other reasons
> >> here] so many packages run tests conditionally.  Such is life.
> >>
> >> Dirk
> >>
> >>
> >> | However, this sounds like a purely hypothetical question - CRAN policies
> >> allow long-running vignettes if they declared.
> >> |
> >> | Cheers,
> >> | Simon
> >> |
> >> |
> >> | > On 18/10/2023, at 3:02 AM, John Fox <jfox using mcmaster.ca> wrote:
> >> | >
> >> | > Hello Dirk,
> >> | >
> >> | > Thank you (and Kevin and John) for addressing my questions.
> >> | >
> >> | > No one directly answered my first question, however, which was whether
> >> the approach that I suggested would work. I guess that the implication is
> >> that it won't, but it would be nice to confirm that before I try something
> >> else, specifically using R.rsp.
> >> | >
> >> | > Best,
> >> | > John
> >> | >
> >> | > On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote:
> >> | >> Caution: External email.
> >> | >> On 16 October 2023 at 10:42, Kevin R Coombes wrote:
> >> | >> | Produce a PDF file yourself, then use the "as.is" feature of the
> >> R.rsp
> >> | >> | package.
> >> | >> For completeness, that approach also works directly with Sweave.
> >> Described in
> >> | >> a blog post by Mark van der Loo in 2019, and used in a number of
> >> packages
> >> | >> including a few of mine.
> >> | >> That said, I also used the approach described by John Harrold and
> >> cached
> >> | >> results myself.
> >> | >> Dirk
> >> | >> --
> >> | >> dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
> >> | >> ______________________________________________
> >> | >> R-package-devel using 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
> >> | >
> >> |
> >> | ______________________________________________
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> >> | https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >> --
> >> dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
> >>
> >> ______________________________________________
> >> R-package-devel using r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >
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> >
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