References and bibliography with knitr, ESS and AUCTEX

Question

I'm trying to get references working in a knitr Rnw document using ESS, AUCTex, TeXLive, and natbib.

Here is a minimal example:

\documentclass{article}
\usepackage{natbib}

\begin{document}

<<setup, include=FALSE, cache=FALSE>>=
library(knitr)
@

<<normal-sample, echo=FALSE>>=
x <- rnorm(100)
plot(x)
@

The moon in June is like a big balloon \citep{smith2012}.

\bibliographystyle{apalike}
\bibliography{/path/to/my/references/refs}

\end{document}

When I run ess-swv-knit then ess-swv-PDF with M-n r then M-n P, I see errors like:

Package natbib Warning: Citation Smith2014 on page 23 undefined on input line 374

This is what I think is going on. Running ess-swv-PDF simply calls pdflatex, but to get the citations right, the correct number of bibtex and pdflatex commands need to be run.

Is there an way to do this by simply running M-n r then M-n P?

I have re-tagged the question, because it is about natbib and not biblatex. You can find information about Emacs and biblatex with Biber at Biblatex with Biber: Configuring my editor to avoid undefined citations maybe some of that is applicable to BIbTeX as well. — moewe, Sep 15 '15 at 05:30
Instead of writing I have this on this part of the document, can you provide a MWE? Will be easier to understand ;-) — Romain Picot, Sep 15 '15 at 06:40

jrm · Accepted Answer · 2015-09-18T17:37:05.517

0

Setting the variable ess-swv-pdflatex-commands to latexmk, so that running ess-swv.el (M-n P) calls latexmk instead of pdflatex seems to be working, although I haven't tested extensively.

Update: I've been using this for a few days now and latexmk is doing the right thing in that it only runs what is necessary to generate the final document.

edited Sep 18 '15 at 17:37

answered Sep 14 '15 at 21:29

jrm

121

score 0 · Answer 2 · answered Sep 15 '15 at 19:44

A solution not tested (I don't use ESS):

Write this in your init.el (or other emacs file of course):

(defun compile-ESS ()
  "compilation" 
  (ess-swv-PDF)
  (tex-bibtex-file)
  (ess-swv-PDF)
  (ess-swv-PDF)
)
(global-set-key "the shortcut you want to use" 'compile-ESS)

Replacing the shortcut you want to use by the one you want to use. Try to not use one that is already bind.

Then M-n r and the shortcut you want to use to do what you wanna perfom.

References and bibliography with knitr, ESS and AUCTEX

2 Answers2