Knitcitations gives pandoc-citeproc error

Question

I have the following document that I am trying to compile with Rstudio:

--- output: word_document: pandoc_args: [ "--biblio", "references.bib" ] --- ```{r} library("knitcitations") cleanbib() ``` This is a citation citet("10.1098/rspb.2013.1372"): ```{r} citet("10.1098/rspb.2013.1372") ``` ```{r} write.bibtex(file="references.bib") ``` ```{r} summary(cars) ``` 

When I run knit, it compiles the .md file, but pandoc gives an error:

 processing file: toy.Rmd |...................... | 33% ordinary text without R code |............................. | 44% label: unnamed-chunk-2 |.................................... | 56% ordinary text without R code |........................................... | 67% label: unnamed-chunk-3 |................................................... | 78% ordinary text without R code |.......................................................... | 89% label: unnamed-chunk-4 |.................................................................| 100% ordinary text without R code /Applications/RStudio.app/Contents/MacOS/pandoc/pandoc toy.utf8.md --to docx --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output toy.docx --highlight-style tango --biblio references.bib output file: toy.knit.md pandoc: Error running filter pandoc-citeproc pandoc-citeproc not found in path Error: pandoc document conversion failed with error 83 Execution halted 

The generated link file is reference.bib:

 @Article{Boettiger_2013, doi = {10.1098/rspb.2013.1372}, url = {http://dx.doi.org/10.1098/rspb.2013.1372}, year = {2013}, month = {Jul}, publisher = {The Royal Society}, volume = {280}, number = {1766}, pages = {20131372-20131372}, author = {C. Boettiger and A. Hastings}, title = {No early warning signals for stochastic transitions: insights from large deviation theory}, journal = {Proceedings of the Royal Society B: Biological Sciences}, } 

Answer 1

The error message indicates that pandoc-citeproc was not found in your $ PATH (i.e., / usr / bin / etc.). One way is to create a link from pandoc-citeproc built into Rstudio and put it in / usr / local / bin.

In terminal:

 sudo ln /Applications/RStudio.app/Contents/MacOS/pandoc/pandoc-citeproc /usr/local/bin/pandoc-citeproc cd /usr/local/bin chown root /usr/local/bin/pandoc-citeproc chgrp wheel /usr/local/bin/pandoc-citeproc 

Pandoc result: