Different Rmarkdown to PDF compiler behavior with RMarkown and Bookdown

[cderv]

Hi @dkStevensNZed

Is this the same issues as in this other one ?

Issues with compilation to PDF

I had just updated R and RStudio to the latest versions a week or so before these issues and didn't see the problems until 6 days ago. I've since updated all the R libraries used and the issue remains, plus now there's a new issue where all the figures generated in the rmarkdown code have the axis scales and titles cut off and just the plot portion of the figure filling the page margins. Something is seriously wrong with my set up. I went to the C:\myDesktop\Data Analysis Book_bookdown_files_main_files\figure-latex folder where the generated figures' .png files are stored and the .png files also have the axis scales and titles missing, so that seems like an Rmarkdown/png generation issue. …

@dkStevensNZed

I think this is a red herring issue because without those 2 files, the book compiles and produces a pdf.

This seems to be related to some content in your Rmd file. Can you share the Rmd content related the tex output ? probably some missing escaping somehow maybe the & ?

@dkStevensNZed

This happens only when producing a tufte_handout or book .pdf.

I believe this could be related to cropping. By default, fig_crop = TRUE in tufte::tufte_book() and it seems it does not play well with some of your images. Can you try setting fig_crop = FALSE ?
Cropping only happens in PDF output not HTML. The default behavior may have changed some time ago on Windows, but it has been a while. Hopefully deactivating cropping will solve this issue.