How to enable LaTeX shell-escape in bookdown

Question

I am writing a bookdown project using the LaTeX minted package to do code formatting. The minted package requires invoking pdflatex with the -shell-escape option.

See the related question Latex shell-escape options in YAML header don't use

I can do this in individual .Rmd files by putting options(tinytex.engine_args = "-shell-escape") in a startup chunk at the beginning of the document, but this doesn't seem to work when I invoke bookdown::render_book("Index.Rmd", output_format = "bookdown::pdf_book").

I have tried setting pandoc_args: "--pdf-engine-opt=-shell-escape" in output settings the _bookdown.yml file

output:
  bookdown::pdf_book:
    pandoc_args: "--pdf-engine-opt=-shell-escape"

but this doesn't work.

I can get the book to knit properly if I manually set options(tinytex.engine_args="-shell_escape") from the R console before running bookdown::render_book

library(bookdown)
options(tinytex.engine_args="-shell-escape")
render_book("Index.Rmd", output_format = "bookdown::pdf_book")

but I am wondering whether there is a way to set the tinytex.engine_args option programmatically from _bookdown.yml or one of my .Rmd files or something similar every time I run bookdown::render_book.

Answer 1

Indeed, the relevant statement to be executed is:

options(tinytex.engine_args="-shell-escape")

The only solution to automate this seems to be including that line in an .Rprofile config file, that should be located in the root directory of your RStudio project. Hence:

1. Create a plain text file named .Rprofile in your project directory and insert the line of code mentioned above.
2. Close your project and reopen it with RStudio, to load global options in .Rprofile.
3. Build your book that includes some LaTeX package requiring that option (e.g. minted). Now, the book should compile without errors.

Other alternatives, like including the same line of code in a chunk inside the index.Rmd file do not work.