Execution halted when I use knitr and Rscript with opts_chunk

4
votes

I wrote a bash script in Mac OS that takes my .rnw file, knit it and then makes a .pdf. To knit my file, I'm using the command

Rscript -e "library(knitr); knit('file.rnw', encoding='utf8')"

and everything works fine. However, I don't want the ## characters in my final document. I tested, using R prompt, the following commands

library(knitr)
opts_chunk$set(comment=NA)
knit('file.rnw', encoding='utf8')

and they give me exactly what I want: the document without comments in the R commands output. But if I try to run

Rscript -e "library(knitr); opts_chunk$set(comment=NA); knit('livro.rnw', encoding='utf8')"

I get 

Error: could not find function "opts_chunk"
Execution halted

as result. What am I doing wrong? How can I ask for options for my chunk in knitr using the command line?

1
rbashknitrrscript
cross-posted in R-help and answered there; I hope someone can move the answer here. – Yihui Xie
You can instead put the following in your RMD file for example... knitr::opts_chunk$set(echo=TRUE) inside an r chunk. – agent18

1 Answers

2
votes

I'm not sure what Yihui meant when he said "move the answer here" but here is Duncan Murdoch's R-help answer that Yihui ratified:

That looks like a bash problem: it appears to be replacing $set with a blank string. Use appropriate quoting or escaping to tell it not to do that. (I think using single quotes around the command will work; you'll need double quotes within it.)

And Yihui added:

Yes I believe that was the problem. Same question asked here: https://github.com/yihui/knitr/issues/162#issuecomment-9017997