revealjs does not work with knitr embed engine

[aronatkins]

Bug description

Using Quarto 1.2.335 (which is included in recent RStudio dailies, including 2023.03.0+385). This problem can be recreated without using the RStudio IDE when rendering using Quarto from the command-line.

Given a code.R file:

cat("this is code.R\n")

The following revealjs document does not show the embedded code:

---
title: embedding with reveal
format: revealjs
engine: knitr
---

## Embed!

```{embed, file = "code.R"}
```

The generated HTML contains a block, but no code:

<section id="embed" class="slide level2">
<h2>Embed!</h2>
<div class="cell" data-file="code.R">

</div>
<div class="footer footer-default">

</div>
</section>

In contrast, when we do not output to HTML, the embedded code is shown.

---
title: embedding without reveal
engine: knitr
---

## Embed!

```{embed, file = "code.R"}
```

Using the most recent version of knitr from CRAN and R 3.6.3 on macOS 12.6.3.

R -s -e "packageVersion('knitr')"
#> [1] ‘1.42’

Discovered while trying to apply the workaround from #1237

Checklist

• Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
• Please format your issue so it is easier for us to read the bug report.
• Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
• Please document the operating system you're running. If on Linux, please provide the specific distribution.

[aronatkins]

Have tried both embed and verbatim.

[cscheid]

The reason the report in #1237 isn't resolved for include specifically is that the include shortcode resolution happens in typescript, before Pandoc. Other shortcodes like meta, var, etc, happen in Lua.

We need to add include processing to Lua in one shape or another, but this is easier said than done. We need to be aware of a number of issues, and it's also going to be the case that a "Lua {{< include >}}" will behave differently than a typescript one out of necessity. This is going to be very confusing for users.

[cderv]

@aronatkins Did you try pre release yet ?

I can't reproduce with 1.3. From

---
title: embedding with reveal
format: revealjs
engine: knitr
---

## Embed!

```{embed, file = "code.R"}
```

I get

But I can reproduce with verbatim.

Using also knitr 1.42

Either some adjusments in quarto or something with knitr - I can have a look to this @cscheid

[cderv]

Oh I know - this is a side effect of a default we have for revealjs.
This is the default for revealjs format in Quarto.

execute:
  echo: false

We do that because minimal space on slides so by default we choose to hide code source. This is documented for this format.
https://quarto.org/docs/presentations/revealjs/#code-echo

For verbatim or embed to work, echo: true is needed. Add #| echo: true in your chunk (or echo = TRUE next to engine name)

We should probably handle specifically those engine with an option hook as they need to have echo = TRUE for knitr to output with source hook, and they have no output.

[cderv]

In fact there is something new now since #3429 - v1.3 has added internally a embed handler for this feature thttps://quarto.org/docs/prerelease/1.3/embed.html

For now we pass every cell handlers from quarto to knitr

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

Lines 54 to 68 in 5e38e1e

	# pass through all languages handled by cell handlers in quarto
	langs = lapply(
	setNames(handledLanguages, handledLanguages),
	function(lang) {
	function(options) {
	knitr:::one_string(c(
	paste0("```{", lang, "}"),
	options$yaml.code,
	options$code,
	"```"
	))
	}
	}
	)
	knitr::knit_engines$set(langs)

This creates a conflict (and why I get something with 1.3 using embed on cell with knitr - but wrong output when looking at HTML produced).

@cscheid @dragonstyle do all the language handler we have are supposed to pass to knitr ? Does setting

```{embed}

inside a document using knitr computation engine is supposed to be handled by our internal handler, or should we NOT overwrite knitr own embed engine ?

@cscheid @dragonstyle I need your input before doing more I have a fix already for verbatim engine, but embed knitr engine was not used as I would expect. I understand why now. I have some ideas on what to do, but need the full context to be sure.

[cderv]

What I think we should do : embed should be filtered out handledLanguages to support as knitr's engine for cells

I'll go with that, unless you think otherwise.

[aronatkins]

In case others find this issue, #1237 suggested using the https://github.com/quarto-ext/include-code-files extension.

This extension has worked and lets me include code from external files into a Quarto+revealjs presentation.

[cscheid]

This will be fixed by #4732