I've got a Rmarkdown document that I recursively run over a set of input parameters. I would need to fetch a error description and where it has occured. Cannot manage to pull the chunk name (it is written in console on error though).
tryCatch({
render("my_Rmarkdown_doc.Rmd"),
output_file = paste0(print_path, "doc_", i, ".html"),
params = inpar[i, ])
},error = function(e) {
message <- conditionMessage(e)
new_message <- data.frame(message = message)
message_df <<- rbind(message_df , new_message)
})
Here's a description of the console
processing file: my_Rmarkdown_doc.Rmd
|........................................... | 14% [chunk_no2]
Quitting from lines 56-78 [chunk_no2] (my_Rmarkdown_doc.Rmd)
How can I pull the chunk name i.e. in this case "chunk_no2" and store it along with error message in message_df?
In a chunk, the chunk name is available as knitr::opts_current$get("label"). I think that is not available in your error handler, but you could write a hook function (see https://yihui.org/knitr/hooks/#chunk-hooks) that saved the label before trying to execute every chunk, and include the saved value in your message_df. In hook functions, the opts_current values are stored in the options argument.
For example, use this setup in your document:
```{r setup and data import, include=FALSE}
library(knitr)
hook_chunkname = function(before, options, envir, name, ...) {
if (before) {
saved_chunk <<- options$label
}
}
knit_hooks$set(chunkname = hook_chunkname)
opts_chunk$set(chunkname = TRUE)
```
and run the documents using code like this:
message_df <- data.frame(message=character(),
chunk=character())
saved_chunk <- "Initial value"
tryCatch({
rmarkdown::render("Untitled.Rmd")
},error = function(e) {
message <- conditionMessage(e)
new_message <- data.frame(message = message, chunk = saved_chunk)
message_df <<- rbind(message_df , new_message)
})