Multiple pdf format fail with generated figures

[Nenuial]

Bug description

When you have multiple pdf formats in a Quarto document that contains figures (generated by R for example), the process cleans up those figures after rendering the first PDF and the second PDF fails to render.

Steps to reproduce

---
title: "Test"
format: 
  pdf: default
  pdf+option: default
---

```{r}
cars |> 
  ggplot2::ggplot(ggplot2::aes(x = speed, y = dist)) +
  ggplot2::geom_line()
```

Expected behavior

The figures should be kept until all formats are rendered.

Actual behavior

The figures are deleted after the first PDF is rendered.

Your environment

• IDE: RStudio Version 2023.12.0+369 (2023.12.0+369)
• MacOS Sonoma 14.2.1

Quarto check output

Quarto 1.4.545
[✓] Checking versions of quarto binary dependencies...
Pandoc version 3.1.11: OK
Dart Sass version 1.69.5: OK
Deno version 1.37.2: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
Version: 1.4.545
Path: /Applications/quarto/bin

[✓] Checking tools....................OK
TinyTeX: v2023.12
Chromium: 869685

[✓] Checking LaTeX....................OK
Using: TinyTex
Path: /Users/admin/Library/TinyTeX/bin/universal-darwin
Version: 2023

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
Version: 3.11.4 (Conda)
Path: /opt/homebrew/Caskroom/miniconda/base/bin/python
Jupyter: 5.3.1
Kernels: python3

[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
Version: 4.3.2
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
knitr: 1.45
rmarkdown: 2.25

[✓] Checking Knitr engine render......OK

[cderv]

This is related to other issues linked to

• Epic: Execution Planner #6518

We need to track input / output and intermediates totally to name them correctly and avoid overwrite

[andrewheiss]

There's a temporary workaround to this if you keep the intermediate markdown files around (see #8373 (comment)). This will work with Quarto 1.5.29 (and maybe earlier?):

---
title: "Test"
format: 
  pdf: default
  pdf+option: default
keep-md: true
---

```{r}
cars |> 
  ggplot2::ggplot(ggplot2::aes(x = speed, y = dist)) +
  ggplot2::geom_line()
```

[andrewheiss]

Though according to @cscheid it's likely an accident that it's working: #6705 (comment)

(but a happy accident that I'm (unwisely!) relying on!)

[Nenuial]

Thanks for this!
It will, as long as this accident works, offer a workaround that allows me to avoid manual renders.

[cderv]

I don't think this is an accident: when keep-md: true is set, the supporting files are kept. It is on purpose because in .md file, there will be linked to resources

quarto-cli/src/command/render/cleanup.ts

Lines 48 to 55 in 1ec0115

	// if we aren't keeping the markdown or text and we are instructed to
	// clean supporting files then do it
	if (
	!format.execute[kKeepMd] &&
	!format.render[kKeepTex] &&
	!format.render[kKeepTyp] &&
	supporting
	) {

So this works in this case, but you'll get leftovers at the end.

The "accident" is this example

---
title: "Test"
format: 
  pdf: default
  pdf+option:
    keep-md: true
---

```{r}
cars |> 
  ggplot2::ggplot(ggplot2::aes(x = speed, y = dist)) +
  ggplot2::geom_line()
```

Where compilation would work now, with no leftovers, but because we have an issue where keep-md: true is not really respected.

This will all be handled better with #6518

[Nenuial]

Ok, that good to know. Thanks for the explanation.

Looking forward to #6518 !!