Julia code chunks with errors cause R Markdown/Quarto rendering to fail even with error=TRUE when rendering via knitr #249
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Description
I reported the problem as this issue to knitr. In a comment in that issue, @cderv identified the problem as occurring upstream (i.e., here) and asked that I post it here and indicated he could contribute.
Here is the issue:
In an R Markdown or qmd file, one can use error=TRUE with an R code chunk (or the Quarto style #| error: true), but rendering fails with a Julia code chunk:
---
title: test
engine: knitr
---
```{julia, error=TRUE}
y
```Here's the error (same thing if I do knit2html("test.qmd").
> rmarkdown::render("test.qmd")
processing file: test.qmd
|....................................................| 100% [unnamed-chunk-1]Error:
! Error happens in Julia.
UndefVarError: `y` not defined
Stacktrace:
[1] top-level scope
@ :0
[2] eval(m::Module, e::Any)
@ Core ./boot.jl:385
[3] macro expansion
@ /system/linux/lib/R-22.04/4.4.0/x86_64/site-library/JuliaCall/julia/RmdStd.jl:15 [inlined]
[4] top-level scope
@ ./none:14
[5] eval
@ ./boot.jl:385 [inlined]
[6] eval_string(x::String)
@ Main.JuliaCall /system/linux/lib/R-22.04/4.4.0/x86_64/site-library/JuliaCall/julia/setup.jl:203
[7] docall(call1::Ptr{Nothing})
@ Main.JuliaCall /system/linux/lib/R-22.04/4.4.0/x86_64/site-library/JuliaCall/julia/setup.jl:176
Backtrace:
1. rmarkdown::render("test.qmd")
2. knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
3. knitr:::process_file(text, output)
6. knitr:::process_group(group)
7. knitr:::call_block(x)
...
13. JuliaCall:::stdout_capture_command(buffer)
14. base::tryCatch(...)
15. base (local) tryCatchList(expr, classes, parentenv, handlers)
16. base (local) tryCatchOne(...)
17. value[[3L]](cond)
Quitting from lines 7-8 [unnamed-chunk-1] (test.qmd)Metadata
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