Correctly replace knitr options which had their name normalized from - to .

[cderv]

Example from

• How to specify tidy options? #5813
• Other occurence:
  • cache-lazy is an ignored cell option #6491

This below won't work

---
format: html
---

```{r}
#| tidy: true
#| tidy-opts: !expr list(width.cutoff = 50)
# a long expression
1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+
1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1+1
```

This is because

• knitr defines tidy.opts = NULL as a default
• knitr will parse the YAML chunk option and sees tidy-opts so it won't replace the default. Options have both now tidy-opts and tidy.opts
• Quarto will normalize - to . in an option hook step, but this will just rename. This means options in knitr have twice tidy.opts with two different value.
• Knitr will use only the first value, which will be the default one.

Our options hooks should make the replacement.

Longer term, knitr should probably do the normalization as the YAML chunk option parsing step

quarto-cli/src/resources/rmd/hooks.R

Lines 11 to 18 in 5df9451

	opts_hooks[["code"]] <- function(options) {
	lastYamlCode <<- options[["yaml.code"]]
	options <- knitr_options_hook(options)
	if (is.null(lastYamlCode)) {
	lastYamlCode <<- options[["yaml.code"]]
	}
	options
	}

quarto-cli/src/resources/rmd/hooks.R

Lines 631 to 634 in 5df9451

	} else {
	# convert any option with fig- into fig. and out- to out.
	options <- normalize_options(options)
	}

[cderv]

@yihui I would like your thoughts on this.

Currently in knitr we do not normalize all the dashed form option like tidy-opts or cache-lazy. Quarto does it currently but after knitr parsing.

quarto-cli/src/resources/rmd/hooks.R

Lines 631 to 634 in 5df9451

	} else {
	# convert any option with fig- into fig. and out- to out.
	options <- normalize_options(options)
	}

quarto-cli/src/resources/rmd/hooks.R

Lines 668 to 749 in 5df9451

	normalize_options <- function(options) {
	names(options) <- sapply(names(options), function(name) {
	if (name %in% c(
	# Text output
	"strip-white",
	"class-output",
	"class-message",
	"class-warning",
	"class-error",
	"attr-output",
	"attr-message",
	"attr-warning",
	"attr-error",
	# Paged tables
	"max-print",
	"sql-max-print",
	"paged-print",
	"rows-print",
	"cols-print",
	"cols-min-print",
	"pages-print",
	"paged-print",
	"rownames-print",
	# Code decoration
	"tidy-opts",
	"class-source",
	"attr-source",
	# Cache
	"cache-path",
	"cache-vars",
	"cache-globals",
	"cache-lazy",
	"cache-comments",
	"cache-rebuild",
	# Plots
	"fig-path",
	"fig-keep",
	"fig-show",
	"dev-args",
	"fig-ext",
	"fig-width",
	"fig-height",
	"fig-asp",
	"fig-dim",
	"out-width",
	"out-height",
	"out-extra",
	"fig-retina",
	"resize-width",
	"resize-height",
	"fig-align",
	"fig-link",
	"fig-env",
	"fig-cap",
	"fig-alt",
	"fig-scap",
	"fig-lp",
	"fig-pos",
	"fig-subcap",
	"fig-ncol",
	"fig-sep",
	"fig-process",
	"fig-showtext",
	# Animation
	"animation-hook",
	"ffmpeg-bitrate",
	"ffmpeg-format",
	# Code chunk
	"ref-label",
	# Language engines
	"engine-path",
	"engine-opts",
	"opts-label",
	# Other chunk options
	"R-options")) {
	sub("-", ".", name)
	} else {
	name
	}
	}, USE.NAMES = FALSE)
	options
	}

However, it is missing the merging step, meaning that if cache.lazy exist already in options (and it does because it has a default value), then renaming options$cache-lazy to options$cache.lazy just creates a duplicate.

Initially it was done by Quarto, but now this step is run only for old knitr

quarto-cli/src/resources/rmd/hooks.R

Lines 604 to 631 in 5df9451

	if (!knitr_has_yaml_chunk_options()) {
	# partition yaml options
	results <- partition_yaml_options(options$engine, options$code)
	if (!is.null(results$yaml)) {
	# convert any option with fig- into fig. and out- to out.
	# we need to do this to the yaml options prior to merging
	# so that the correctly interact with standard fig. and
	# out. options provided within knitr
	results$yaml <- normalize_options(results$yaml)
	# alias 'warning' explicitly set here to 'message'
	if (!is.null(results$yaml[["warning"]])) {
	options[["message"]] = results$yaml[["warning"]]
	}
	# merge with other options
	options <- knitr:::merge_list(options, results$yaml)
	# set code
	options$code <- results$code
	}
	options[["yaml.code"]] <- results$yamlSource
	# some aliases
	if (!is.null(options[["fig.format"]])) {
	options[["dev"]] <- options[["fig.format"]]
	}
	if (!is.null(options[["fig.dpi"]])) {
	options[["dpi"]] <- options[["fig.dpi"]]
	}
	} else {

In yihui/knitr@e24dcb4, only normalization for fig- and out- was added. But in fact, all dashed-version of knitr options should be transformed to the dot version.

If we do that in knitr directly, it would solve issue in Quarto.

Related issues is

• fig-dpi is not working on cell level for knitr #6576
  as Quarto has some alias like fig-dpi, normalized to fig-dpi but should assigned to dpi, and same for fig-dev.

Should we do that in knitr ?

Otherwise, I need to tweak options after knitr parsing to fix this, or maybe revert back to quarto parsing the YAML options using new exported knitr::partition_chunk() directly.

Thanks for your input.

[yihui]

I think we can normalize all option names inside knitr. I'll take a closer look today.

[cderv]

Ok great ! Here is the branch I had in case we wanted to fix both issues in Quarto
main...fix/knitr/option-normalization

It seems better to me to do it in knitr, even if this means that user's would have to update knitr.

[cderv]

This has been fixed on knitr - from next version 1.44 (and from current dev version 1.43.7), all dash option are changed to their dot version. This includes tidy-opts and cache-lazy