troubleshooting a polyglot (Julia/R) document

[bbolker]

Description

I'm trying to write (and render) a Quarto document that includes and compares Julia and R computations. I'm using the newer julia engine, which (as I understand it) renders the Julia code natively and calls RCall to execute the R code.

Any advice on diagnostics, troubleshooting, etc. (including "take this to forum XXX instead") welcome.

My R installation is in a non-standard place, so I need to set LD_LIBRARY_PATH before trying to render/preview. However, despite setting that environment variable in the shell before calling quarto xxx, I get an error saying that RCall/quarto can't find the appropriate libraries. The full details are in the attached quarto file (which I attached rather than including directly because I was getting rendering errors, and renamed to .txt so GitHub would accept it), but here's the basic idea.

(in shell)

export LD_LIBRARY_PATH="/usr/local/lib/R/lib"
quarto render ...

The first chunk checks the load library path and finds it missing:

ld_library_path = get(ENV, "LD_LIBRARY_PATH", "missing")
println("LD_LIBRARY_PATH = $ld_library_path")

This returns LD_LIBRARY_PATH = missing (sigh).

The next chunk checks the contents of the library directory:

readdir("/usr/local/lib/R/lib")

3-element Vector{String}:
 "libR.so"
 "libRblas.so"
 "libRlapack.so"

I then get errors either when I try to load RCall or when I try to evaluate the first R chunk

(Julia)

using RCall

(R)

set.seed(101)
rnorm(10)

(I've tried a lot of different permutations. The attached .qmd file might have the chunks in a different order. Any chunks that fail prevent me from getting rendered output ...

The error is something like this:

EvaluationError: Encountered 1 error during evaluation

Error 1 of 1
@ /home/bolker/Documents/projects/SMLP2025/rcall.qmd:15
LoadError: could not load library "/usr/local/lib/R/lib/libR.so"
libRblas.so: cannot open shared object file: No such file or directory
in expression starting at /home/bolker/Documents/projects/SMLP2025/rcall.qmd:17

Quarto version 1.7.32, Julia 1.11.6, Ubuntu 24.04.3 LTS, R (unstable) (2025-08-10 r88559)

rcall.txt

[mcanouil]

I assume the attached text file is an example?
If so, using code block and plain text allows to easily access it and enable the copy button.

---

You can share a self-contained "working" (reproducible) Quarto document using the following syntax, i.e., using more backticks than you have in your document (usually four ````).
See https://quarto.org/bug-reports.html#small-is-beautiful-aim-for-a-single-document-with-10-lines.

If you have multiple files (and if it is absolutely required to have multiple files), please share as a Git repository.

R	Python
````qmd --- title: "Reproducible Quarto Document" format: html engine: knitr --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{r} x <- c(1, 2, 3, 4, 5) y <- c(1, 4, 9, 16, 25) plot(x, y) ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````	````qmd --- title: "Reproducible Quarto Document" format: html engine: jupyter --- This is a reproducible Quarto document. {{< lipsum 1 >}} ```{python} import matplotlib.pyplot as plt x = [1, 2, 3, 4, 5] y = [1, 4, 9, 16, 25] plt.plot(x, y) plt.show() ``` {#fig-placeholder} {{< lipsum 1 >}} The end after @fig-placeholder. ````

Additionally and if not already given, please share the output of quarto check within a code block (i.e., using three backticks ```txt), see https://quarto.org/bug-reports.html#check.

[bbolker]

Hmm, when I tried to include this in-line before I got a previewing error. Must have been doing something slightly wrong.

---
author: "Ben Bolker"
title: "R/Julia mixed model comparison"
engine: julia
execute:
  env:
    - "LD_LIBRARY_PATH=/usr/local/lib/R/lib"
---

'execute:env' was recommended by Claude but maybe that was a hallucination?

```{julia}
readdir("/usr/local/lib/R/lib")
```

```{julia}
using RCall
```

```{julia}
print(1+1)
```


If I try to include an R chunk like this:

```{r}
set.seed(101)
rnorm(10)
```

I get this error:

```
EvaluationError: Encountered 1 error during evaluation

Error 1 of 1
@ /home/bolker/Documents/projects/SMLP2025/rcall.qmd:15
LoadError: could not load library "/usr/local/lib/R/lib/libR.so"
libRblas.so: cannot open shared object file: No such file or directory
in expression starting at /home/bolker/Documents/projects/SMLP2025/rcall.qmd:17
```

```{julia}
ld_library_path = get(ENV, "LD_LIBRARY_PATH", "missing")
println("LD_LIBRARY_PATH = $ld_library_path")
```

quarto check:

Quarto 1.7.32
[✓] Checking environment information...
      Quarto cache location: /home/bolker/.cache/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.6.3: OK
      Dart Sass version 1.85.1: OK
      Deno version 1.46.3: OK
      Typst version 0.13.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.7.32
      Path: /opt/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: (not installed)
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: Installation From Path
      Path: /usr/local/texlive/2024/bin/x86_64-linux
      Version: 2024

[✓] Checking Chrome Headless....................OK
      Using: Chrome found on system
      Path: /usr/bin/chromium-browser
      Source: PATH

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

[✓] Checking Python 3 installation....OK
      Version: 3.12.3
      Path: /usr/bin/python3
      Jupyter: 5.3.2
      Kernels: python3

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

[✓] Checking R installation...........OK
      Version: 4.6.0
      Path: /usr/local/lib/R
      LibPaths:
        - /usr/lib/R/site-library
        - /usr/local/lib/R/library
      knitr: 1.50
      rmarkdown: 2.29

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

[bbolker]

(my comment crossed with your answer)

I'm not surprised that it works for you, since it only fails because I have my R library in a non-standard location — that's why I need to set the environment variable in the first place. Thank you for confirming that the Julia engine doesn't have access to the same environment (i.e., I'm not losing my marbles). Should I close this discussion and open a related issue at the PumasAI repo ? (There are some apparently related discussions here and here ...)

[mcanouil]

A possible workaround, would be to go the other way around using knitr as the engine and JuliaCall to call Julia.

[bbolker]

(I will start by trying the various environments file to see if Quarto can read from there, but not from the shell environment ...)

[mcanouil]

The issue is not really Quarto.
For instance, if you set _quarto.yml to use _environment, the Julia engine still can't find any of the values in it while the two other engines and Quarto can.

[mcanouil]

Should I close this discussion and open a related issue at the PumasAI repo ?
We don't close discussion as the default GitHub search filter is is:open.

(There are some apparently related discussions here and here ...)

@bbolker
Accessibility: For better accessibility, please ensure link text is descriptive and meaningful rather than using generic terms such as "here". This helps all users understand the link's destination. See Writing meaningful link text (WCAG).

Small tip, if you make reference to issues/pull requests/discussions as a list, the title is automatically set as the link text.

- https://github.com/PumasAI/QuartoNotebookRunner.jl/issues/217
- https://github.com/PumasAI/QuartoNotebookRunner.jl/issues/278

• Take environment variables directly from the _environment file PumasAI/QuartoNotebookRunner.jl#217
• Cannot use env vars to point to other Conda env with running workers PumasAI/QuartoNotebookRunner.jl#278

[bbolker]

I've got a solution for now (see below) but have followed up the discussion (i.e., hoping for more documentation) at PumasAI/QuartoNotebookRunner.jl#331

Thanks for the help.

---

The solution as mentioned in PumasAI/QuartoNotebookRunner.jl#217 seems to be to include the environment variables in the YAML front matter as follows:

engine: julia
julia:
    env: ["LD_LIBRARY_PATH=/usr/local/lib/R/lib"]

This works in the (much simpler) test case:

---
author: "Ben Bolker"
title: "julia environment test"
engine: julia
julia:
    env: ["LD_LIBRARY_PATH=/usr/local/lib/R/lib"]
---

```{julia}
ld_library_path = get(ENV, "LD_LIBRARY_PATH", "missing")
println("LD_LIBRARY_PATH = $ld_library_path")
```

That thread suggested that variables defined in _environment should have been picked up by the Quarto notebook runner, but it didn't work for me (even after issuing quarto call engine close env.qmd to make sure I was restarting the runner): my _environment file is simply

LD_LIBRARY_PATH=/usr/local/lib/R/lib