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

[Yihui Xie]

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

BTW, for future reference, this question was cross-posted at
http://stackoverflow.com/questions/15640353/execution-halted-when-i-use-knitr-and-rscript-with-opts-chunk

Regards,
Yihui
--
Yihui Xie <xieyihui at gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA


On Tue, Mar 26, 2013 at 12:30 PM, Duncan Murdoch
<murdoch.duncan at gmail.com> wrote:
> 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