Switching off file_scope in rmarkdown v23

Wouter1 · September 11, 2020, 4:28pm

My RMarkdown book contains sections with the same name (e.g., Questions) in several Chapters.

When I build this book with bookdown (0.20) and rmarkdown 2.3 to a gitbook (in RStudio 1.3.959), the pandoc command contains the --file-scope argument. As a consequence, the automatically generated HTML anchors of the sections only add sequence numbers (e.g., #questions-1, #questions-2) within a chapter (hmtl file), not across chapters. All entries in the table of contents to a Questions Section in a later chapter of the book refer to the first Questions Section in the first chapter. I guess this is an unintended side-effect of introducing the file_scope option in rmarkdown 2.3.

Note that this problem does not occur if I build the book with rmarkdown 2.2.

How can I turn the file_scope option off? I did not succeed in turning it off via file_scope: false in _output.yml, _bookdown.yml, or via the YAML of index.RMD.

cderv · September 11, 2020, 6:06pm

Hi !

You can update to current bookdown development version has now file scope is disabled by default.

github.com

rstudio/bookdown/blob/master/NEWS.md

# CHANGES IN bookdown VERSION 0.21

## NEW FEATURES

- Add the `number_sections` argument to `markdown_document2()` and its family. This allows to have now figure references numbered by chapters in these formats, like `word_document2()` or `odt_document2()` for example. This argument default to `TRUE` like `html_document2()` and  `pdf_document2()`. Set it to `number_sections = FALSE` to get the same output as previous version without numbered chapters (thanks, @atusy, #756). 

## BUG FIXES

- Correctly encode the document title when creating the twitter sharing link from a bookdown chapter (thanks, @maelle, #934).

- Make sure `search_index.json` contains valid characters for the JSON format (thanks, @wlandau, #913).

## MAJOR CHANGES

- The `--file-scope` behavior introduced in bookdown v0.20 is now disabled by default. This is due to broken TOC links for duplicate section names (e.g., "Exercises"; see #909) that have automatically generated identifiers.

- The `clean_envir` argument of `bookdown::render_book()` has been deprecated and will be removed in the future (thanks, @jenslaufer, #932).

# CHANGES IN bookdown VERSION 0.20

This file has been truncated. show original

You can also in 0.20 use

options(bookdown.render.file_scope = FALSE)

as stated in the NEWS file linked above. This should disable the file scope feature.

Wouter1 · September 12, 2020, 2:00pm

Thanks, cderv, for the quick response. Apologies for not checking out the bookdown development pages first.

With rmarkdown v2.3 and bookdown v0.20, I can't get options(bookdown.render.file_scope = FALSE) to work if I add it to the first R code chunk in index.Rmd. The --file-scope argument is still added to the pandoc command.

The bookdown development version (0.20.6) does not use the --file-scope argument, as intended. Great!

cderv · September 14, 2020, 7:23am

I think you need to set this option in your R session, before rendering. This is not read from you rmarkdown document when rendering - This is rather an option about bookdown rendering that needs to be set before using bookdown.

system · September 21, 2020, 7:23am

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