R: plot_ly() works only once each session before: "verbose must be TRUE or FALSE"

Question

What I do

I'm translating "OpenIntro::Introduction to Modern Statistics Tutorials" into German. I use the downloaded .zip tutorials to do so: https://openintrostat.github.io/ims-tutorials/. The tutorials are learnr::tutorials written as .Rmd files. In tutorial 3 lesson 8 I'm facing an Error I'm unable to solve.

Problem

While doing the tutorial you face the plot_ly() function four times. But it only works one time as expected (in one session). Using the function a second, time an error message says: "verbose must be TRUE or FALSE". In the RStudio "Render"-pane: "Quitting from lines 11-44 [ex5-babies-plotly] (exercise.Rmd)". This points to the {r setup} but also makes me wonder because verbose = FALSE.

knitr::opts_chunk$set(fig.align = "center", 
                      fig.height = 3, 
                      fig.width = 5,
                      echo = FALSE, 
                      message = FALSE, 
                      warning = FALSE,
                      verbose = FALSE)

Things I tried an checked

Running plot_ly several times in RStudio is no problem.

Running plot_ly in the original on shinyapps several times works as well.

I tried knitr::opts_chunk$set(verbose = FALSE) as the first line in the chunk where the plot_ly()function is used. Didn't work!

Everything is up to date.

Questions

I don't get why it only works the first time. Do you have an explanation? Do you know a way to solve this problem?

Answer 1

I apologize for passing you bad information. I must have left a cache somewhere making me think that the solution was the package unloading when clearly it is not.

However, it did tell me that something I did did actually fix it... since you messaged me I've been trying to figure out what I did that did work.

The BLUF or more trendy TL;DR:

Call library(data.table) when you initially call the necessary libraries in your setup chunk.

Yes, that's it. (For real this time...)

How did I get there?

While Plotly apparently imports data.table. When Plotly imports it, neither the environments of RMD nor Shiny prerendered pull the default R options for data.table into your script.

If you recall, I mentioned that I found a verbosity error having to do with data.table and I dismissed it.... in my original answer. .

Before fixing the situation (without calling library(data.table)) & after allowing messages & warnings)

In the viewer/browser, I rendered any two of the Plotly plots (how you directed me to recreate the error about verbosity).

For example, chunk ex5-babies-plotly - 3D visualization, then chunk ex10-babies-plotly-two - Drawing parallel planes in 3D.

After attempting to render the second plot, so that the error occurs, I deleted plot_ly(...) and replaced it with rlang::last_trace() (If you don't delete plotly it errors again before giving you the output of last_trace)

This allows us to see the rest of the error message...reading beyond that isn't necessary. (What last_trace returns starts with ..alloccol... -- what was discussed in that link I included in my original answer)

Once the error is present, run options() in your R console, then in any interactive exercise, you'll see several datatable options in the console and none in your RMD.

For me, R returns 15.

(The code for that without the picture: length(options()[startsWith(names(options()), "datatable")]))

The exercise returns zero.

After you add library(data.table) to your setup chunk and run the document, you can check the options again. You'll see it now matches the R console at 15.

---

---

Originally I wrote....(doesn't work)

This does not address the actual problem, it's a workaround.

The only corresponding information regarding a fix placed the blame on the package data.table. (You can read about that here.) Obviously, data.table isn't the issue. Unfortunately, I am not entirely sure what the problem is.

The fix I offer is to unload the Plotly library between each call to plot. You can leave these chunks invisible, so the reader won't know they are there. I would encourage you to leave comments for yourself, so that you remember why these are here, though.

Here is an excerpt from the English version, along with the fix I offer.

```{r unsetter, include=F}
unloadNamespace("plotly")
```

```{r ex3-mariokart, exercise=TRUE}
# load plotly package
library(plotly) 

# draw the 3D scatterplot
p <- plot_ly(data = mariokart, z = ~ ____,x = ~____, y = ~____, opacity = 0.6) |>
  add_markers() 
  
# draw the plane
p |>
  add_surface(x = ~x, y = ~y, z = ~_____, showscale = FALSE)
```

Notice that I've set include=FALSE so that it isn't visible to the user. Additionally, I didn't call the library after unloading it again since it's called in the code visible to the user.