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

[John Fox]

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/