[R] Execution halted when I use knitr and Rscript with opts_chunk

[Duncan Murdoch]

On 26/03/2013 12:26 PM, Marcus Nunes wrote:
> Hello all,
>
> 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?

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.)

Duncan Murdoch