I followed all of Yihui's debugging steps here: . I am knitting a Rmarkdown file from within an R script (as I have some variables that change value every time I want to knit). I create a folder to put all files in first, then call:

rmarkdown::render('reports.Rmd', output_file = "XXX.pdf"))

The first time it stops knitting halfway through, complaining that it can't find the pdf figures in the temp figure-latex folder. I check the folder, and it is indeed empty. The second time I run the code, all the figures are in the temp figure-latex folder, and it does knit to the end, but fails when trying to convert the .tex file to pdf with the following error (YYY and XXX redacted):

tlmgr search --file --global "/YYY/figure-latex/percentage-categories-1.pdf" ! Package pdftex.def Error: File `/YYY/figure-latex/percentage-categories-1.pdf' not found: using draft setting.

Error: LaTeX failed to compile ../XXX.tex.

Sorry, I can't think of a way to post a reproducible example, as I think it has to do with the latest update of tlmgr or pdftex.def?