pdfcrop cannot be disabled?

[baptiste]

Referring to #2861 (which I can't reopen), I think pdf figures in knitr are always cropped,

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

Line 272 in 574396e

crop <- rmarkdown:::find_program("pdfcrop") != '' && tools::find_gs_cmd() != ''

The following MRE illustrates the problem:

---
title: "test"
format: pdf
---


```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, crop=FALSE)
```

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
```{r}
library(ggplot2)
ggplot() + theme(plot.margin = margin(t=2,b=2,unit='cm')) # wide margins to see the effect (or lack thereof)
```
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

As a workaround I can set knitr::knit_hooks$set(crop = function(...){}) to get the expected output

but one would expect opts_chunk(crop=FALSE) to prevent cropping without having to redefine the hook.

[mcanouil]

Do you mean like in the screenshot below (using Quarto v1.2.210)? (See https://quarto.org/docs/computations/r.html#knitr-options for details on how to set knitr options)

See Quarto document content

---
title: "test"
format: pdf
execute:
  echo: false
knitr:
  opts_chunk:
    crop: false
---

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

```{r}
library(ggplot2)
ggplot() + theme(plot.margin = margin(t=2,b=2,unit='cm')) # wide margins to see the effect (or lack thereof)
```

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

EDIT: I can't reproduce what you are seeing, even when setting crop to true.

---

PS: can you change the category from "general" to "Q&A"? (from the desktop version of GitHub website)

[baptiste]

If you don't get cropping with crop=TRUE, I'm guessing you don't have pdfcrop installed on your machine?

[baptiste]

Hmm, strange, I'm getting this

so I guess it's fixed in a different version of Quarto/Rstudio. I have Rstudio 2022.07.1 Build 554 and Quarto 1.1.251, on a Mac.

[mcanouil]

I'll have to double check, in theory I installed it, but since I changed a lot of things, I might have removed it recently.

[baptiste]

What do you get when you run rmarkdown:::find_program("pdfcrop") != '' && tools::find_gs_cmd() != '' ? If FALSE, you cannot reproduce the issue.

[baptiste]

... actually, I just installed the pre-release Quarto 1.2.226, and I get the same cropped output (plus an glitch with lua filters for the author field)

[mcanouil]

What's the results with rmarkdown instead of Quarto?
Also, could you try using the proper Quarto syntax (as per my code example)?
Are you using the lastest version of knitr?

[salim-b]

I can fully reproduce the issue (using Ubuntu 22.04 and Quarto 1.3.361). If the pdfcrop binary and Ghostscript are available on the system, Quarto crops PDF figures regardless of the relevant chunk option.

I've tried to disable cropping without success by

• setting the chunk option (in YAML format) crop: false
• setting the chunk option (in YAML format) fig-crop: false
• setting knitr.opts_chunk.crop: false in _quarto.yml.
• setting knitr.opts_chunk.fig_crop: false in _quarto.yml.
• setting format.pdf.crop: false in _quarto.yml.
• setting format.pdf.fig_crop: false in _quarto.yml.
• running knitr::opts_chunk$set(crop = FALSE) in a chunk before the figure chunks.
• running knitr::opts_chunk$set(fig_crop = FALSE) in a chunk before the figure chunks.

The only way that actually disabled PDF figure cropping was running knitr::knit_hooks$set(crop = function(...){}) in a chunk before the figure chunks.

Note that I'm a bit confused about the correct name of the cropping chunk option on the knitr side of things: While the R Markdown Cookbook mentions a crop chunk option (same what the Quarto sources seem to refer to), the R Markdown: The Definitive Guide mentions a fig_crop chunk option. Quarto seems to ignore both of them.

[cscheid]

Can you please open a new issue? Thanks.

[salim-b]

See #5981