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