Best way to run shell scripts

[rgaiacs]

When using R Markdown, I can convert the following minimal working example

---
title: "mwe"
author: "Raniere Silva"
date: "2022-07-20"
output: html_document
---

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

```{bash}
ls
```

and I will get

With Quarto, the following similar minimal working example

---
title: "mwe"
---

## Quarto

```{bash}
ls
```

raises the following error

Starting python3 kernel...Traceback (most recent call last):
  File "/usr/lib/rstudio/bin/quarto/share/jupyter/jupyter.py", line 21, in <module>
    from notebook import notebook_execute, RestartKernel
  File "/usr/lib/rstudio/bin/quarto/share/jupyter/notebook.py", line 16, in <module>
    import nbformat
ModuleNotFoundError: No module named 'nbformat'
Python 3 installation:
  Version: 3.10.5
  Path: /usr/bin/python3
  Jupyter: (None)

Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter

R Markdown was able to handle shell scripts using system2() as describe in https://bookdown.org/yihui/rmarkdown-cookbook/eng-bash.html. Do I need to install Jupyter and the Bash kernel? Or there is another solution?

system2() works with Quarto! The minimal working example

---
title: "mwe"
---

## Quarto

```{r}
system2("ls", stdout=TRUE)
```

produces

[jjallaire]

It's using the Jupyter engine by default b/c there are no R code cells. Just add engine: knitr to the front-matter and it will work as you expect.

[rgaiacs]

@jjallaire Thanks for the reply. Add engine: knitr to the front-matter worked. I tried to add it to _quarto.yml and it didn't work:

project:
  title: "mwe"

editor: visual

knitr: true

How do I define the engine globally?

[jjallaire]

Try this (not 100% sure if it will work though):

execute:
   engine: knitr

[rgaiacs]

Thanks for the answer. It did not work.

[salim-b]

Tracked in #3157.

[stschiff]

Yes, this also happened to me... I was adding a bash block and then it nonsensically switched to the Jupyter engine.

I then added engine: knitr to the frontmatter and it worked, but it's not documented anywhere. For what it's worth, I don't actually find a comprehensive API documentation of the frontmatter at all. There is lots of documentation for specific output documents, but as far as I can see no documentation for general options like this.

I was also surprised that there doesn't seem to be some kind of command line flag to choose between the two engines. I would have liked something like quarto render --engine knitr or so...

Great tool, anyway! But this part is a bit intransparent.

[jjallaire]

Docs on engine binding are in the article on execution options: https://quarto.org/docs/computations/execution-options.html#engine-binding

[stschiff]

Oh good, I overlooked this. Thanks for the pointer. But note that it doesn't seem exactly right. It looks like it's switching to Jupyter if a python block is discovered, and knitr if an r-block is discovered. But it doesn't say that Jupyter is also chosen with only bash blocks. Anyway, thanks!

[jjallaire]

Okay, thanks, I've updated the docs to be more clear about this.

[stschiff]

Perfect!