R Markdown in tab indented code block raises duplicated label error

[jeromyanglim]

I have a tutorial where R Markdown code blocks are displayed as formatted code blocks. I was using knitr 0.8 and the same problem seems to occur after updating to version 0.9.

Here is a minimal example

Here is some formatted code:

    ```{r foo}
    print('hello world!')
    ```
It displays 

```{r foo}
print('hello world!')
```

This yields the following error:

Error in parse_block(g) : duplicated label 'foo'
Calls: knit ... process_file -> split_file -> lapply -> FUN -> parse_block
Execution halted

knitr terminated with status 1

I assume that the parser is not realising that R markdown in code blocks is not a real R Markdown code block . When I originally wrote the tutorial, I didn't have this problem.

Update: I just noticed when I updated the code blocks to remove the labels, that tab indented code blocks are run as regular R code chunks. Is this just the new intended behaviour of knitr that R code chunks don't have to start and end at the start of a new line?

[ramnathv]

Yes. I believe it was modified in 0.80. @yihui has an example showing how to use hooks to print a code chunk verbatim especially useful in tutorials https://github.com/yihui/knitr-examples/blob/master/062-chunk-wrapper.Rmd
It is not perfect, as it still does not display the entire chunk in one block, but I believe it can be tweaked easily to get the result desired for tutorials.

[ramnathv]

Here is the relevant change from NEWS.md

leading spaces are allowed in chunk headers now, e.g. in the past <<>>= must appear in the beginning of a line, but now we can indent the chunk header by a number of white spaces; this amount of spaces will be stripped off the chunk if the whole chunk is indented (#236) (thanks, @jamiefolson and Vitalie Spinu)

[jeromyanglim]

Thanks for that. The behaviour certainly surprised me, but I suppose it only really affects people writing R Markdown tutorials. And as you say, there are alternatives.

[yihui]

The easiest solution is to destroy the code chunk by adding an empty string to the chunk header:

    `r ''````{r foo}
    print('hello world!')
    ```

This is what I use when writing tutorials. Sorry for the trouble, but I think it makes sense to allow indented code blocks.

[jmarshallnz]

@yihui Apologies for reviving a dead issue, but is there a similar trick for displaying the source for an inline r computation, i.e.

The average speed was `r mean(cars$speed)`.

?

[yihui]

@jmarshallnz Yes, the simplest solution is to insert a zero-width space between the first backtick and the little r. A slightly more trickier solution:

`` `r '\x60r mean(cars$speed)\x60'` ``

\x60 is the backtick character. Let me know if there is anything else that you need me to explain.

[jmarshallnz]

Thanks - that does the trick :)

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