feature lost: cross references do not pass to pdf

I'm writing a book in Rstudio using Bookdown. I had to take a break and suddenly none of my cross-references work in the pdf version of the document although they still work in HTML. Before, everything was okay, but now no bib or equation or figure references work. I looked for an explanation and it may be due to pandoc version. I don't know what to do :-( Can anyone help me?