get traceback from knitr on error

Question

How do I get better error reporting from knitr?

e.g. now knitr quits with:

Calls: knit ... lapply -> FUN -> lapply -> FUN -> rename -> <Anonymous>

When I run the same code interactively R quits with:

Calls: getSampleData ... lapply -> FUN -> lapply -> FUN -> rename -> <Anonymous>

Which is much better for understanding the problem - at least I know which function was throwing the error.

Ideally I would like also have the equivalent of traceback() appended.

Answer 1

You can set opts_chunk$set(error = FALSE), then you will be able to run traceback() when an error occurs. This requires you to run knitr in an interactive R session, though.

Answer 2

For the related problem where you actually want to display the error to the reader of your document, I wrote a wrapper function that computes and saves a traceback within a knitr document, and a replacement for traceback() that displays it. Here's the code:

saveTraceback <- local({
  savedTraceback <- NULL
  saver <- function(e) {
    calls <- sys.calls()
    deparsed <- lapply(calls, deparse)
    deparsed <- deparsed[-length(deparsed)+0:1] # leave off last 2
    lastjunk <- max(grep("withCallingHandlers", deparsed))
    deparsed <- deparsed[-seq_len(lastjunk)]
    savedTraceback <<- deparsed
  }
  function(expr)
    withCallingHandlers(expr, error = saver)
})

traceback <- function() {
  base::traceback(environment(saveTraceback)$savedTraceback)
}

You would use it like this. First display the code without executing it:

<<mycode,eval=FALSE>>=
f <- function() stop("this is an error")
g <- function() f()
g()
@

Then execute it in the saveTraceback() function without displaying:

<<echo=FALSE>>=
saveTraceback({
<<mycode>>
})
@

And finally call traceback(), which will display something like what the user would have seen in the console.