I have the following document, that I am trying to compile with Rstudio:
---
title:
shorttitle:
author:
bibliography:
- library.bib
output: papaja::apa6_pdf
---
```{r message = FALSE, warning = FALSE}
library("papaja")
apa_prepare_doc() # Prepare document for rendering
```
# Introduction
@Bakan1966
# References
```{r create_r-references}
r_refs(file = "r-references.bib")
```
When I run knit, it compiles the .md file, but pandoc gives an error:
pandoc-citeproc: "stdin" (line 232, column 2):
unexpected "a"
expecting "c", "C", "p", "P", "s" or "S"
pandoc: Error running filter /Applications/RStudio.app/Contents/MacOS/pandoc/pandoc-citeproc
Error: pandoc document conversion failed with error 83
In addition: Warning messages:
1: In yaml::yaml.load(enc2utf8(string), ...) :
NAs introduced by coercion: 1,2,3 is not an integer
2: In yaml::yaml.load(enc2utf8(string), ...) :
NAs introduced by coercion: 1,2,3 is not an integer
Execution halted
I have found similar problems on different topics around but none of the proposed solutions worked for me...
"Solved".
The problem comes from my library.bib file.
I have generated it using Mendeley, which has inserted a lot of special characters that are not supported by pandoc-citeproc...
This is likely to be pandoc-citeproc problem. To diagnose, run rmarkdown::render
manually, e.g.:
rmarkdown::render(output_format = "html_document", input = your_vignette, clean = FALSE)
In my case, I needed to add the .bib
to the bibliography: bibfile
rows in the YAML header of the vignette.
I faced the error 83 when knit a rmarkdown file which apply arules::apriori()
.
---
title: "[**Pattern Discovery in Data Mining** *Programming Assignment: Frequent Itemset Mining Using Apriori*](https://www.coursera.org/learn/data-patterns)"
subtitle: "[**Data Mining** *by University of Illinois at Urbana-Champaign*](https://www.coursera.org/specializations/data-mining)"
author: "[®γσ, Eng Lian Hu](http://englianhu.wordpress.com) <img src='figure/ShirotoNorimichi2.jpg' width='24'> 白戸則道®"
date: "`r Sys.Date()`"
output:
tufte::tufte_html:
toc: yes
tufte::tufte_handout:
citation_package: natbib
latex_engine: xelatex
tufte::tufte_book:
citation_package: natbib
latex_engine: xelatex
bibliography: skeleton.bib
link-citations: yes
---
Its working fine after I removed the line : bibliography: skeleton.bib
.
I faced the same error when rendering a HTML file but the solution to my problem was different:
I had specified csl: nature.csl
in the YAML header. What I didn't know was that I had to also download the nature.csl
file and specify the path to it in the YAML header. So instead of having:
bibliography: references/library.bib
csl: nature.csl
I downloaded the nature.csl
file and put in in the same folder as the library.bib
. The correct YAML header looks like this
bibliography: references/library.bib
csl: references/nature.csl
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