Markdown to PDF: natbib citations are rendered as [?]

[pdehne]

Markdown to PDF: natbib citations are rendered as [?]

[pdehne]

Just like you suggested, this works perfectly:

pandoc example.md -s --natbib --pdf-engine=latexmk -o example.pdf

There is a strange error message from latexmk, but it can be ignored. The PDF is rendered correctly, including citations.

Latexmk: Missing bbl file '/tmp/tex2pdf.-d487ff2e850c87fc/input.bbl' in following:
 No file input.bbl.

[jgm]

Yes. Because when you go straight to pdf with --natbib, pandoc doesn't run bibtex for you.
If you use --natbib, you need to go to standalone latex and run the latex and bibtex commands yourself.

As the manual says:

--natbib
Use natbib for citations in LaTeX output. This option is not for use with the --citeproc option or with PDF output. It is intended for use in producing a LaTeX file that can be processed with bibtex.

[pdehne]

I see, I overlooked that it explicetely says natbib is not for PDF, sorry about that. Just as an idea, if the system already provides the latexmk command, using it would make it possible to render directly to PDF.

[jgm]

Yes, you can use --pdf-engine=latexmk, and then it might take care of the bibtex step for you. (You might need some additional --pdf-engine-opt)