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

[Jim Lemon]

Please delete drjimlemon using gmail.com from your mailing list. He passed away a
month ago.
Regards,
Juel
Wife

On Tue, 17 Oct 2023, 01:15 John Fox <jfox using mcmaster.ca wrote:

> Dear list members,
>
> I believe that this issue has been discussed previously, but I'm not
> sure that I have the solution right.
>
> Georges Monette and I have developed a package that we intend to submit
> soon to CRAN which has a vignette including code that takes a long time
> to run. The sources for the package are available at
> <https://github.com/gmonette/cv>.
>
> We figure that we have to suppress running the code the vignette when
> CRAN checks the package or the check time will be excessive.
>
> The vignette is written as a .Rmd file to be compiled by knitr,
> producing an HTML vignette. The top of the .Rmd file looks like this:
>
> ------- snip -------
>
> ---
> title: "Cross-validation of regression models"
> author: "John Fox and Georges Monette"
> date: "`r Sys.Date()`"
> package: cv
> output:
>    rmarkdown::html_vignette:
>    fig_caption: yes
> bibliography: ["cv.bib"]
> csl: apa.csl
> vignette: >
>    %\VignetteIndexEntry{Cross-validation of regression models}
>    %\VignetteEngine{knitr::rmarkdown}
>    %\VignetteEncoding{UTF-8}
> ---
>
> ```{r setup, include = FALSE}
> knitr::opts_chunk$set(
>    collapse = TRUE,
>    message = TRUE,
>    warning = TRUE,
>    fig.align = "center",
>    fig.height = 6,
>    fig.width = 7,
>    fig.path = "fig/",
>    dev = "png",
>    comment = "#>",
>    eval = nzchar(Sys.getenv("REBUILD_CV_VIGNETTES"))
> )
>
> ### other irrelevant setup code not shown ###
>
> ```
>
> ------- snip -------
>
> So (near the bottom), if the environment variable REBUILD_CV_VIGNETTES
> isn't empty, the code blocks in the vignette are evaluated, otherwise
> not. To build the tarball for the package to be submitted to CRAN, we
> will set REBUILD_CV_VIGNETTES to "true". That works as intended.
>
> If we submit the tarball to CRAN, I believe that the package as
> distributed by CRAN will include the HTML vignette from our tarball,
> showing the evaluated code blocks, but when CRAN checks the package,
> these long-running code blocks will not be executed (because
> REBUILD_CV_VIGNETTES will not exist on the CRAN check machines).
>
> My questions:
>
> Is that correct?
>
> If not, how can we ensure that the complete vignette is distributed by
> CRAN without causing an overly long CRAN check time?
>
> In particular, we don't want CRAN to rebuild and distribute the
> vignette, because the resulting HTML file won't show the evaluated code.
>
> Any assistance would be appreciated.
>
> Thank you,
>   John
> --
> John Fox, Professor Emeritus
> McMaster University
> Hamilton, Ontario, Canada
> web: https://www.john-fox.ca/
>
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>

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