Hey,
So I ran into the same thing as well, and I installed the deprecated oldbookdown here:
However, I ended up with a pandoc error, which is definitely not something I'm good at fixing— this is an error I've encountered in other scenarios, and have been unable to fix, so I'm not sure that it's actually related to trying to make the ggplot2 book.
¯\(°_o)/¯
Rscript book/render-tex.R data-manip.rmd
--chapters has been removed. Use --top-level-division=chapter instead.
Try pandoc --help for more information.
Error: pandoc document conversion failed with error 2
Execution halted
make: *** [book/tex/data-manip.tex] Error 1