Tackling knitting errors in R Markdown

2021 R

When knitting an R Markdown document after the first time, errors may sometimes appear. Three tips are recommended below.

1. Close PDF reader window

When the document is knitted through the ‘Knit’ button, a PDF reader window opens to present the result. Closing this window can help resolve errors.

2. Delete service files

Every time the Rmd is knitted, some service files are created. Some of these files have the ‘.tex’ extension (e.g., index.tex, Appendix-B.tex), whereas others do not (e.g., index.log, ZHJhZnQtYXBhLlJtZA==.Rmd, index.synctex.gz). Deleting these files can help resolve errors (see a possible function).

3. Delete code chunks related to the appendices

When knitting papaja documents containing any appendices, some code chunks related to the appendices will automatically appear at the end of the primary Rmd file—e.g.:

```{r echo = FALSE, results = 'asis', cache = FALSE}
papaja::render_appendix('Appendix-A.Rmd')
```

Normally, these code chunks are automatically removed as the knitting finishes. However, if the chunks remain in place, deleting them manually can help resolve errors.

s R R Markdown

Pablo Bernabeu

Postdoctoral fellow at UiT –
The Arctic University of Norway

After doing a research master's, I became a PhD student and graduate teaching assistant in Psychology at Lancaster University, where I investigated how conceptual processing—that is, the comprehension of the meaning of words—is supported by linguistic and sensorimotor brain systems, and how research on this topic is influenced by methodological aspects such as the operationalisation of variables and the sample size of experiments. Currently, I am a postdoctoral fellow at UiT The Arctic University of Norway, where I am investigating the behavioural and neural underpinnings of multilingualism. Throughout my research, I have used methods such as behavioural and electroencephalographic experiments, corpus analysis, statistics and programming. Research materials at https://osf.io/25u3x. CV available here.