Capture mid-chunk output from rmarkdown::render() on error?

[cderv]

@bbimber

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@bbimber

When running chunks of an rmarkdown interactively using RStudio, the console output is visible. Therefore if an error happens, it can be debugged. When run headlessly, the only console output is the progress meter that tells which chunks have run and finished. That is helpful to a point, but it doesnt show where in the crunk the error happened. Are there any mechanism to capture the output from the partially executed chunk, when rmarkdown::render() is used? I realize that it is possible to debug a markdown by splitting apart chunks, etc.; however, that's not always an option.

Compare to interactive running directly in the document, when you use rmarkdown::render, the output of chunk is captured to be printed in the resulting document. Errors are not capture by default so that the rendering stop in the R console. This is not perfect, but when you have an error, here are some tricks you can use to see the chunk content, including the error:

You can add error = TRUE only on the chunk that you want to "debug":

```{r chunk2, error = TRUE}
print('This worked')

# Code will stop here, but no information is printed to console when run headless using rmarkdown::render()
stop('error')

print('This will not run')
```

This will capture the error in the document, so rmarkdown::render will not error and you can see the chunk content, including the error in the resulting document.

You can also add at the top of the document before any other chunk to apply on all chunk

```{r}
knitr::opts_chunk$set(error = TRUE)
```

See

11.2 Do not stop on error | R Markdown Cookbook

If you want to stop rendering, right after the chunk with issue to be quicker at rendering when debuging, you can add knitr::knit_exit() call at the end of the chunk, in an inline chunk or another chunk.
See

14.3 Exit knitting early | R Markdown Cookbook

This is not ideal but that what exist for now.

Improving the error message at render for an Rmd is in our backlog. Thank you for your feedback !