Running Quarto on Windows and MacOS. How to overcome errors?

[sbacelar]

Description

I usually use Quarto with R. Now, I am trying to use it with Julia, and I am having some problems. I only tried to run the example on the web page [https://quarto.org/docs/computations/julia.html] using the Jupyter and Julia engines and Quarto version 1.5.37. Let me say first that I had no problems running it on Ubuntu (I had only to install rsvg-convert) and partially on WSL2. But I had problems running the same example on MacOS (GFK and Plots not found) and Windows 11 (I couldn't install rsvg-convert with Chocolatey, and I also had problems with Plots. I am including the error messages I received in each case:

MacOS 11.7.10 jupyter engine: quarto render --to pdf

Outputs pdf but inserts the following after the figure:

GKS: dlopen(/Users/sergiobacelar/.julia/artifacts/86a2153e203fb861d380988509048a2ffa8e3a9f/li
Referenced from: /Users/sergiobacelar/.julia/artifacts/86a2153e203fb861d380988509048a2ffa8e
Reason: Incompatible library version: cairoplugin.so requires version 11603.0.0 or later, b

MacOS 11.7.10 julia engine: quarto render --to pdf

(sbquarto_2) pkg> st
Status ~/Dropbox/JULIA/sbquarto_2/Project.toml
[91a5bcdd] Plots v1.40.4

shell> quarto render document.qmd --to pdf
Running [1/1] at line 16: using Plots
ERROR: Julia server returned error after receiving "run" command:
Failed to run notebook: /Users/sergiobacelar/Dropbox/JULIA/sbquarto_2/document.qmd
ERROR: EvaluationError: Encountered 1 error during evaluation

Error 1 of 1
@ /Users/sergiobacelar/Dropbox/JULIA/sbquarto_2/document.qmd:16
ArgumentError: Package Plots not found in current path.

• Run import Pkg; Pkg.add("Plots") to install the Plots package.

Windows 11 julia engine: quarto preview --to pdf

Julia server process started.
Running [1/1] at line 16: using Plots
ERROR: Julia server returned error after receiving "run" command:
Failed to run notebook: D:\Dropbox\JULIA\sbquarto_2\document.qmd
ERROR: EvaluationError: Encountered 1 error during evaluation

Error 1 of 1
@ D:\Dropbox\JULIA\sbquarto_2\document.qmd:16
Error showing value of type Plots.Plot{Plots.GRBackend}
only png or svg allowed. got: :pdf
Stacktrace:
[1] error(s::String)
@ Base .\error.jl:35
[2] _show(io::IOContext{IOBuffer}, ::MIME{Symbol("text/html")}, plt::Plots.Plot{Plots.GRBackend})
@ Plots C:\Users\sbacelar.julia\packages\Plots\ju9dp\src\output.jl:203
[3] #invokelatest#2
@ .\essentials.jl:892 [inlined]
[4] invokelatest
@ .\essentials.jl:889 [inlined]
[5] show(io::IOContext{IOBuffer}, m::MIME{Symbol("text/html")}, plt::Plots.Plot{Plots.GRBackend})
@ Plots C:\Users\sbacelar.julia\packages\Plots\ju9dp\src\output.jl:232
[6] show(io::IOContext{IOBuffer}, m::String, x::Plots.Plot{Plots.GRBackend})
@ Base.Multimedia .\multimedia.jl:123

ERROR: Internal julia server error

Stack trace:
at writeJuliaCommand (file:///C:/Users/sbacelar/AppData/Local/Programs/Quarto/bin/quarto.js:41672:19)
at eventLoopTick (ext:core/01_core.js:153:7)
at async executeJulia (file:///C:/Users/sbacelar/AppData/Local/Programs/Quarto/bin/quarto.js:41581:22)
at async Object.execute (file:///C:/Users/sbacelar/AppData/Local/Programs/Quarto/bin/quarto.js:41332:20)
at async renderExecute (file:///C:/Users/sbacelar/AppData/Local/Programs/Quarto/bin/quarto.js:77870:27)
at async renderFileInternal (file:///C:/Users/sbacelar/AppData/Local/Programs/Quarto/bin/quarto.js:78038:43)
at async renderFiles (file:///C:/Users/sbacelar/AppData/Local/Programs/Quarto/bin/quarto.js:77906:17)
at async render (file:///C:/Users/sbacelar/AppData/Local/Programs/Quarto/bin/quarto.js:82734:21)
at async Command.actionHandler (file:///C:/Users/sbacelar/AppData/Local/Programs/Quarto/bin/quarto.js:82882:32)
at async Command.execute (file:///C:/Users/sbacelar/AppData/Local/Programs/Quarto/bin/quarto.js:8015:13)

Windows 11 jupyter engine: quarto preview --to pdf

FATAL (C:/Users/sbacelar/AppData/Local/Programs/Quarto/share/filters/main.lua:7144) An error occurred:
Could not convert a SVG to a PDF for output. Please ensure that rsvg-convert is available on the path.
Error running filter C:/Users/sbacelar/AppData/Local/Programs/Quarto/share/filters/main.lua:
...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:2617: attempt to call a nil value (global 'crash_with_stack_trace')
stack traceback:
...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:2196: in function 'fail'
...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:7144: in upvalue 'call_rsvg_convert'
...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:7168: in function <...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:7150>
(...tail calls...)
...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:2925: in function <...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:2919>
[C]: in ?
[C]: in method 'walk'
...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:535: in function <...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:524>
(...tail calls...)
...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:1312: in local 'callback'
...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:1330: in upvalue 'run_emulated_filter_chain'
...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:1366: in function <...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:1363>
stack traceback:
...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:535: in function <...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:524>
(...tail calls...)
...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:1312: in local 'callback'
...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:1330: in upvalue 'run_emulated_filter_chain'
...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:1366: in function <...lar/AppData/Local/Programs/Quarto/share/filters/main.lua:1363>

WSL2 with Julia engine: quarto preview --to pdf

ERROR: Julia server returned error after receiving "run" command:
Failed to run notebook: /home/sbacelar/JULIA/sbquarto/document2.qmd
ERROR: EvaluationError: Encountered 1 error during evaluation

Error 1 of 1
@ /home/sbacelar/JULIA/sbquarto/document2.qmd:16
Error showing value of type Plots.Plot{Plots.GRBackend}
only png or svg allowed. got: :pdf
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] _show(io::IOContext{IOBuffer}, ::MIME{Symbol("text/html")}, plt::Plots.Plot{Plots.GRBackend})
@ Plots ~/.julia/packages/Plots/ju9dp/src/output.jl:203
[3] #invokelatest#2
@ ./essentials.jl:892 [inlined]
[4] invokelatest
@ ./essentials.jl:889 [inlined]
[5] show(io::IOContext{IOBuffer}, m::MIME{Symbol("text/html")}, plt::Plots.Plot{Plots.GRBackend})
@ Plots ~/.julia/packages/Plots/ju9dp/src/output.jl:232
[6] show(io::IOContext{IOBuffer}, m::String, x::Plots.Plot{Plots.GRBackend})
@ Base.Multimedia ./multimedia.jl:123

ERROR: Internal julia server error

Stack trace:
at writeJuliaCommand (file:///opt/quarto/bin/quarto.js:41672:19)
at eventLoopTick (ext:core/01_core.js:153:7)
at async executeJulia (file:///opt/quarto/bin/quarto.js:41581:22)
at async Object.execute (file:///opt/quarto/bin/quarto.js:41332:20)
at async renderExecute (file:///opt/quarto/bin/quarto.js:77870:27)
at async renderFileInternal (file:///opt/quarto/bin/quarto.js:78038:43)
at async renderFiles (file:///opt/quarto/bin/quarto.js:77906:17)
at async render (file:///opt/quarto/bin/quarto.js:82734:21)
at async renderForPreview (file:///opt/quarto/bin/quarto.js:83760:26)
at async render (file:///opt/quarto/bin/quarto.js:83643:29)

[cscheid]

Different engines operate differently.

With the jupyter engine, you're likely running into a problem where the Julia kernel doesn't match the installed version of Julia you have: https://quarto.org/docs/troubleshooting/index.html#jupyter-appears-to-find-wrong-ijulia-kernel. That's not something Quarto can do anything about, but you can investigate further by typing jupyter kernelspec list.

With the julia engine, you have to install dependencies explicitly. go to the directory where the .qmd file resides and type

julia

julia> using Pkg
julia> Pkg.activate(".")
julia> Pkg.add("Plots")

[cscheid]

@ D:\Dropbox\JULIA\sbquarto_2\document.qmd:16
Error showing value of type Plots.Plot{Plots.GRBackend}
only png or svg allowed. got: :pdf

Can you provide a minimal document where this happens?

[mcanouil]

May I suggest to perform the tests outside of a synced directory? Or to at least disable syncing to ensure there is no issue from that which are known to exist.

[sbacelar]

Sorry I couldn't find the space to reply. I tried the same process out of Dropbox bu I got the same result. This the document I have used. I don't know if this is an answer to the need of a minimal document:

---
title: "Plots Demo"
engine: julia
author: "Norah Jones"
date: "5/22/2021"
format:
  html:
    code-fold: true
---

### Parametric Plots

Plot function pair (x(u), y(u)).
See @fig-parametric for an example.

```{julia}
#| label: fig-parametric
#| fig-cap: "Parametric Plots"

using Plots

plot(sin,
     x->sin(2x),
     0,
     2π,
     leg=false,
     fill=(0,:lavender))
```

[cscheid]

Thanks, I can repro this. I'll open an issue.

[mcanouil]

Tracking on:

• engine: julia fails with PDF rendering #9748