Question: I'd like to create a PDF report with `knitr` with `LaTeX`-code in `RStudio` with `biblatex` for citations. However, the in-text-citations are always undefined and no bibliography is printed. The same bibliography works perfectly with a pure `.tex`-document stored in the same folder and containing the same citations, same path to the `.bib`-file etc. However, as for all references (also with `hyperref`) I have to compile twice. I thought this might be the problem with `knitr` (that the compilation is run only once), but the `hyperref`-references to figures work well. Any idea what might go wrong with the bibliography when using `knitr` and how I can solve the problem?

MWE:

```
\documentclass{article}

\usepackage[style=authoryear-comp, maxnames=1, bibencoding=utf8, backend=biber]{biblatex}
\bibliography{ZoteroOutput.bib}

\begin{document}

According to the literature \parencite{gonzalez2003} we can assume...

\printbibliography

\end{document}

```

From the `log`-file:

```
Package biblatex Warning: Please (re)run Biber on the file:
(biblatex)                mwe
(biblatex)                and rerun LaTeX afterwards.

```

Answer: 
RStudio allows you to use a [custom LaTeX program](http://www.rstudio.org/docs/authoring/latex_program?version=0.97.54&mode=desktop) with that

* you can set up a script that does the proper processing
* there are automatic solutions for this, e.g. [`latexmk`](http://ctan.tug.org/tex-archive/support/latexmk/), like so: `Sys.setenv(RSTUDIO_PDFLATEX = "/Library/TeX/texbin/latexmk")` (or whatever you path may be)

Another option is that RStudio allows to specify build tools for a project. This may be

* either a Makefile
* or again a custom script

In addition, you may want to tell the RStudio developers about the need to have a bibliography in Sweave documents. You can tell them that I'd need it, too :-)
This kinda works when I press the compile button twice. It is just an ugly system call to `biber`.

```
\documentclass{article}
\usepackage{filecontents}
\begin{filecontents}{\jobname.bib}
@misc{Doe,author={John Doe},title={Title}}
\end{filecontents}
\usepackage[backend=biber]{biblatex}
\addbibresource{\jobname.bib}
\begin{document}

Test \cite{Doe}

\printbibliography
\end{document}

<<biber>>=
system(paste("biber", sub("\\.Rnw$", "", current_input())))
@

```