Package build/check removes htmlwidget-derived files

Question

I'm having trouble building a package that uses plotly figures as htmlwidgets. It appears that the supporting files containing the figures and related resources are either never created or are deleted at some point in the build/check process.

I have asked a related question here which used buildVignette to create just the vignette. While that question was resolved, using the solution there does not work when doing a full build and check.

I have created a minimal package for testing on Github. If one builds/checks/installs and then looks at the vignette, one sees:

and indeed none of that directory structure or files are present in the built package.

The odd thing is this worked fine around the beginning of February in the real context (i.e. not a test package, the documentation shows the working widgets here) suggesting something has changed, but I cannot figure out what changed.

I have looked carefully at combinations of recent versions of the dependent packages and that does not seem to be the problem. I have also looked at recent changes in r-source files build.R and check.R. The only relevant change is in this commit:

commit eed23bae244b17b9366bf7bf6863f6f51f17064d Author: smeyer <smeyer@00db46b3-68df-0310-9c12-caf00c1e9a41> Date: Sat Feb 19 01:10:34 2022 +0000

'R CMD Sweave --clean' no longer removes existing files (PR#18242)

but I don't think this is the problem. The build/check code is complex and I cannot figure out what is happening to these files.

Answer 1

To embed interactive graphics in a vignette we could build it using output rmarkdown::html_vignette, a lightweight version of html_document.

---
title:  "Test Vignette"
output:
  rmarkdown::html_vignette:
      toc: yes
vignette: >
    %\VignetteIndexEntry{Vignette}
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteEncoding{UTF-8}
---
```{r SetUp, echo = FALSE, eval = TRUE, results = "hide"}
set.seed(13)
suppressPackageStartupMessages(library("knitr"))
suppressPackageStartupMessages(library("plotly"))
opts_chunk$set(eval = TRUE, echo = FALSE)
```

**Test Vignette**
Problem solved?

```{r testFig, results = "show"}
if (!is_latex_output()) {
  DF <- data.frame(
  x <- rnorm(50),
  y <- rnorm(50),
  z <- rnorm(50))
  plot_ly(
    name = "data", DF, x = ~x, y = ~y, z = ~z,
    marker = list(size = 2.0)) %>%
    add_markers()
}
```

html_vignette presets are slightly different from html_document. Because of this the graphic can appear quite small, some manual adjustment might be needed. Other stylistic changes can be made using CSS. The default file can be found using

system.file("rmarkdown", "templates", "html_vignette", "resources", "vignette.css",  package = "rmarkdown")

While it passes R CMD checks, it may hurt some feelings if submitted to CRAN:

neither data nor documentation should exceed 5MB