SVG bounding box error when rendering Jupyter notebook with Julia code blocks

[rhwrhw]

I am using Quarto 1.2.207 and Jupyter Notebook (6.5.2), Python 3.9.6 (default, Aug 5 2022, 15:21:02)
[Clang 14.0.0 (clang-1400.0.29.102)].

I am using the elsevier template, invoked as "quarto use template quarto-journals/elsevier"

The kernel is Julia 1.8.2.

There is a code cell that creates and displays a VegaLite graphic, as follows:

#| label: fig-boxplots
#| fig-cap: "Boxplots comparing EVI2 to NBR distributions at each age."

u = tidybox |> @vlplot(:boxplot, y=:value, x=:year, column=:index)
display(u)

where tidybox is a dataframe read from a csv file.

when I render I get the error below. I have tried nearly everything, including changing pdf-engines, ensuring I have Inkscape in the path, etc.

"LaTeX Error: Cannot determine size of graphic in hpf_files/figure-pdf/fig-boxplots-output-1.svg (no BoundingBox).

See the LaTeX manual or LaTeX Companion for explanation.
Type H for immediate help.
...

l.370 ...les/figure-pdf/fig-boxplots-output-1.svg}"

The same thing also occurs if I render the qmd file.

Relevant YAML header options are as follows:

header-includes:

• '\usepackage[left]{lineno}'
• \linenumbers
  pdf-engine: xelatex
  pdf-engine-opt: '--shell-escape'
  jupyter: julia-1.8

Any help would be appreciated.

[cscheid]

We should first start by making sure you're using the latest v1.2 prerelease, which is v1.2.269. But I think the issue is ultimately coming the fact that the library you're using (whatever has the @vlplot macro) doesn't seem to be emitting width and height values with the SVG. I believe those are necessary for the PDF engine to determine the size of the figure.

I haven't used this library and I will need a fully reproducible example to test any of this on my side, but you could try to have your plotting library emit a high-resolution PNG, which isn't an ideal solution but would probably work.

[rhwrhw]

Hi, thanks for picking this up. I did just upgrade to v1.1.269, but that did not help. I failed to mention that this is on a Mac with the M1 Max and macOS Monterey v. 12.6. I just shared a repository with the fully reproducible example you requested.

[compleathorseplayer]

I have the same issue (older Mac). [I was going to recommend quarto to my students for use in class until I came across this (and will if I can find a resolution)]. Thanks for any insights.

[kjohnsen]

I'm actually having an issue including just any SVG in LaTeX output, even with height and width defined. I'm using Quarto 1.2.280 and just barely upgraded TinyTex to v2022.12.12.

test.svg:

<svg xmlns="http://www.w3.org/2000/svg" width="100" height="100">
  <circle cx="50" cy="50" r="40" stroke="green" stroke-width="4" fill="yellow" />
</svg>

test.qmd:

# hello there

![test SVG](test.svg)

Render, and for me it complains about the bounding box:

quarto render test.qmd --to pdf

LaTeX Error: Cannot determine size of graphic in test.svg (no BoundingBox).

See the LaTeX manual or LaTeX Companion for explanation.

[compleathorseplayer]

This is the only thing keeping me from using Quarto in my (200+ size) (university postgrad) classes - if this were fixed, I would require every student to install and use Quarto.

[kjohnsen]

@cscheid Maybe my example belongs more in issues than discussions. I'll post it there

[cderv]

See answer below #3283 (comment)

[hillyuan]

Same problem (LaTex no BoundingBox error) still exists in version 1.3.302 with tinytex v2023.04 in Windows 11.

[cderv]

See answer below #3283 (comment)

[hillyuan]

Thanks for your help. All my svg files could be transferred to PDF successfully following your instruction. However, when including gif animation file, I still git similar error like:

LaTeX Error: Cannot determine size of graphic in ./img/wave1D.gif (no BoundingBox)

[cderv]

Yes GIF are different than .svg. They can't be included easily in LaTeX. See discussion about potential solutions in #3551

There is no automatic conversion for that in Quarto.

[hillyuan]

I see! Thanks your for the notice.

[cderv]

Quarto should now handle SVG image in PDF output format, by converting the SVG file to PDF file for inclusion. This is a new feature of Quarto 1.3 and it requires rsvg-convert CLI tool.

This is documented for now a 1.3 release feature : https://quarto.org/docs/prerelease/1.3/pdf.html#svg-images with some indication on how to install rsvg-convert for each OS.

Taking the example from @kjohnsen at #3283 (comment)

---
title: Testing SVG
format: pdf
---

# hello there

![test SVG](test.svg)

with test.svg being

<svg xmlns="http://www.w3.org/2000/svg" width="100" height="100">
  <circle cx="50" cy="50" r="40" stroke="green" stroke-width="4" fill="yellow" />
</svg>

This should render without error now, the test.svg file will be converted on the fly to test.pdf to be included using \includegraphics

For context, this was done in #2575