Errors in render-book workflows (en and fr)

[katherinehebert]

The render-book (Render the book for this workshop in bookdown) workflow (en, fr) encounters two problems when rendering the bookdown for this workshop.

Installation of plotly package

The plotly package installation does not seem to work, though it can be installed locally and loaded without an error.

This example is from this run:

Quitting from lines 127-145 (book-en.Rmd)
Error: Error in FUN(X[[i]], ...) : there is no package called 'plotly'
Calls: ... withCallingHandlers -> withVisible -> eval -> eval -> lapply -> FUN
In addition: There were 20 warnings (use warnings() to see them)

Execution halted
Error: Process completed with exit code 1.

To work around this issue, I have temporarily commented out the lines installing and loading plotly and some dependencies in book-fr in commit 8ebf452 and in book-en in commit ca6eff4, and set eval = FALSE on the plotly chunk in book-en/05-fine-tuning-plots.Rmd in commit 11150b9 and in book-fr/05-peaufinage.Rmd in commit 3f5c77c. These lines should be un-commented and chunks should be reverted to eval = TRUE in book-en and book-fr when this issue is resolved.

Error: unexpected ')'

When the plotly installation is commented out, the job still returns the following error for each book:

This example is from this run:

Quitting from lines 561-569 (book-fr.Rmd)

Error: Error in parse(text = x, srcfile = src) : :4:16: unexpected ')'
3: y = "log10") + # ce thème produit un rendu visuel plus attrayant y
4: y = "log10")
^
Calls: ... -> parse_all -> parse_all.character -> parse
In addition: There were 50 or more warnings (use warnings() to see the first 50)

This parenthesis is, however, not problematic when I build the book locally, or run this chunk locally.

To work around this issue, I have temporarily set eval = FALSE for the two chunks that were causing the error in book-fr/03-mecanique-ggplot2.Rmd in commit 68a9d9f and in book-en/03-ggplot2-mechanics.Rmd in commit 15df821. These chunks should be reverted to eval = TRUE in book-en and book-fr when this issue is resolved.