CODEWITHSUNDEEP
rfiletextextractsweave
Joris Meys
Joris Meys

Reputation: 108533

How to extract all code chunks from a Rnw Sweave file?

I received a .Rnw file that gives errors when trying to build the package it belongs to. Problem is, when checking the package using the tools in RStudio, I get no useful error information whatsoever. So I need to figure out first on what code line the error occurs.

In order to figure this out, I wrote this 5-minute hack to get all code chunks in a separate file. I have the feeling though I'm missing something. What is the clean way of extracting all code in an Rnw file just like you run a script file? Is there a function to either extract all, or run all in such a way you can find out at which line the error occurs?

My hack:

ExtractChunks <- function(file.in,file.out,...){
  isRnw <- grepl(".Rnw$",file.in)
  if(!isRnw) stop("file.in should be an Rnw file")

  thelines <- readLines(file.in)

  startid <- grep("^[^%].+>>=$",thelines)
  nocode <- grep("^<<",thelines[startid+1]) # when using labels.
  codestart <- startid[-nocode]

  out <- sapply(codestart,function(i){
    tmp <- thelines[-seq_len(i)]
    endid <- grep("^@",tmp)[1]  # take into account trailing spaces / comments
    c("# Chunk",tmp[seq_len(endid-1)])
  })

  writeLines(unlist(out),file.out)

}

Upvotes: 4

Views: 4734

Answers (1)

Thomas
Thomas

Reputation: 44525

The two strategies are Stangle (for a Sweave variant) and purl for a knitr variant. My impression for .Rnw files is that they are more or less equivalent, but purl should work for other types of files, as well.

Some simple examples:

f <- 'somefile.Rnw'
knitr::purl(f)
Stangle(f)

Either way you can then run the created code file using source.

Note: This post describes an chunk option for knitr to selectively purl chunks, which may be helpful, too.

Upvotes: 14

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