Before_chapter_script doesn't work?

[hadley]

In _bookdown.yaml I have:

before_chapter_script: "_common.R"

and in _common.R I have:

knitr::opts_chunk$set(
  comment = "#>",
  collapse = TRUE,
  cache = TRUE
)

but the chunk options don't seem to have any affect. What am I missing?

[yihui]

You didn't miss anything. I just didn't implement it for the case new_session = TRUE. Done now.

[hadley]

After this change I'm getting:

Error in insert_chapter_script(config, "before") : 
  object 'config' not found
Calls: <Anonymous> -> render_new_session -> insert_chapter_script
Execution halted

[yihui]

Ah, fixed now

[dereckmezquita]

I know this is an old post; but I'm having this same issue. My before chapter script is not executing. I have the following set up:

• _bookdown.yml

new_session: yes
language:
  ui:
    chapter_name: "Chapter "
delete_merged_file: true
before_chapter_script: "_common.R"

• _common.R

knitr::opts_chunk$set(echo = TRUE, fig.width = 7, fig.height = 7, fig.align = "center")

I've tried everything to fix it to no avail. I would appreciate any help you may extend.

Might it possibly be the fact that I am using a "new_session: yes" for a K-M build mode? I saw that it was an issue when "new_session = TRUE"? I tried setting to TRUE/true in the yml and nothing.

[cderv]

Hi @dereckdemezquita,

I can't reproduced. This is working fine for me using the demo book.
I added a _common.R file with

knitr::opts_chunk$set(echo = FALSE)

and after building the book, all chunk source are correctly not shown.

Can you try that too ?

Also can you ask on the RStudio community or in a new issue, instead of an old issue ? It will be easier to continue discussion. Thank you.

[hadley]

@dereckdemezquita I don't recommend using before_chapter_script — because it literally inserts that code into your .Rmd file, it messes up line numbers making debugging very painful. It's easier to just copy and paste a standard block at the front of every chapter.

[cderv]

it literally inserts that code into your .Rmd file

I think this will only do that if new_session: no, i.e Merge and Knit approach. For new_session: yes, i.e Knit and Merge approach, it will the source the script before calling render() on each file.

It's easier to just copy and paste a standard block at the front of every chapter.

If one wants to follow this way, I would advice to use a child document, or import the _common.R file as chunk content to avoid copy pasting the same pieces of code and keep it all in the same place. Example:

```{r, include=FALSE, echo=FALSE, code = xfun::read_utf8('_common.R')}
```

or

```{r, child="_common.Rmd"}
```

it messes up line numbers making debugging very painful.

Easier debug of Rmarkdown project seems a topic to invest in.

[yihui]

@hadley That's no longer true, and @cderv was correct. The scripts will be source()d instead of being inserted into Rmd. This change was made in bookdown 0.18: https://github.com/rstudio/bookdown/releases/tag/v0.18.

Re: debugging, the issue is tracked in #620. That's something I definitely want to improve, and I'm pretty sure it can be improved (e.g. when an error occurs, it can automatically navigate to the relevant lines in the original Rmd file).

[hadley]

@yihui I didn't know that because you don't blog about it 😄 Regardless, I've now been burned by that behaviour, so I'm unlikely to use before_chapter_script again in the future.

[yihui]

@hadley Sorry, but I didn't know you were burned. Claus and Bob reported that this issue bothered them, so I made the change for them, but I had no idea how many more users were burned...

[github-actions]

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