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bugSomething isn't workingSomething isn't workingcode-annotationluaIssues related to the lua codebase, filter chain, etcIssues related to the lua codebase, filter chain, etc
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Description
Bug description
A common tool for creating reproducible documents via R Markdown and Quarto is to include the following to auto generate a code appendix.
# Code Appendix
```{r, ref.label=knitr::all_labels(),echo=TRUE,eval=FALSE}
```
However, when you use even a single code annotation (e.g., # <1>) in any code block, the generation of the code appendix fails. There are no warnings or errors displayed but the code appendix is blank.
Steps to reproduce
---
title: "test"
date-modified: now
latex-tinytex: false
format: pdf
---
## Quarto
Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
## Running Code
When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this:
```{r}
1 + 1 # <1>
```
1. Test statement
You can add options to executable code like this
```{r}
#| echo: false
2 * 2
```
The `echo: false` option disables the printing of code (only output is displayed).
# Code Appendix
```{r, ref.label=knitr::all_labels(),echo=TRUE,eval=FALSE}
```
### Expected behavior
[annotationIssues_expected.pdf](https://github.com/quarto-dev/quarto-cli/files/12744758/annotationIssues_expected.pdf)
Actual behavior
Your environment
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6.9
Quarto check output
neilhatfield$ quarto check
[✓] Checking versions of quarto binary dependencies...
Pandoc version 3.1.1: OK
Dart Sass version 1.55.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
Version: 1.3.353
Path: /Applications/RStudio.app/Contents/Resources/app/quarto/bin
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....OK
Version: 3.11.1
Path: /Library/Frameworks/Python.framework/Versions/3.11/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[✓] Checking R installation...........OK
Version: 4.3.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library
knitr: 1.44
rmarkdown: 2.25
[✓] Checking Knitr engine render......OK
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bugSomething isn't workingSomething isn't workingcode-annotationluaIssues related to the lua codebase, filter chain, etcIssues related to the lua codebase, filter chain, etc