Rscript and Backticks

Question

I need to run knit2html on the command line using Rscript. I tried the following code and it works

Rscript -e "(knitr::knit2html(text = '## good', fragment.only = TRUE))"

However, when I introduce R code chunks (or anything involving backticks), the process hangs. So the following does NOT work

Rscript -e "(knitr::knit2html(text = '## good\n `r 1 + 1`',fragment.only = T))"

For the purpose of my use, I only have access to the contents and hence can NOT pass a file to knit2html, which I know will work.

My question is how do I make this work. I know the problem is the backticks and I have tried looking at escaping them, but nothing seems to be working.

Have you tried using a "here file" or "here document" construct (with `Rscript < — Josh O'Brien, Dec 10 '12 at 16:48

score 0 · Answer 1 · answered Dec 10 '12 at 15:11

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it is a shell issue.

On windows it works.

On linux You need to escape the backtick like \'

I think the reason , some shell interprets the double-quoted string once.

answered Dec 10 '12 at 15:11

agstudy

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@Ramnath I test it in windows and Ubuntu. Tell me if this works for Mac OS. – agstudy Dec 10 '12 at 15:18
Thanks for the heads up on what might be going wrong. However, I am unable to get it working on Mac OS. – Ramnath Dec 10 '12 at 15:40

score 0 · Answer 2 · answered Dec 11 '12 at 03:14

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A related issue has been reported once here. You have to use single quotes to avoid shell expansion. I'm not sure if that applies to Windows as well, though.

answered Dec 11 '12 at 03:14

Yihui Xie

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Tried this `Rscript -e '(knitr::knit2html(text = "## good\n `r 1 + 1`", fragment.only = TRUE))'` and got this. `ARGUMENT '~+~`r~+~1~+~+~+~1`",~+~fragment.only~+~=~+~TRUE))' __ignored__` – Ramnath Dec 11 '12 at 03:19
OK. It looks like an issue of your specific shell; this works for me: Rscript -e '(knitr::knit2html(text = "## good\n `r 1 + 1`", fragment.only = TRUE))' (backticks were eaten by SO). I'm under Ubuntu, and my `$SHELL` is `bash`. I do not know what is the default shell for Mac (is there such a thing `echo $SHELL`?) – Yihui Xie Dec 11 '12 at 04:24
I did `echo $SHELL` and it returned `bin/bash`. I need to dig deeper what the source of error is. – Ramnath Dec 11 '12 at 16:01

Rscript and Backticks

2 Answers2