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Annotated code cell is dropped when the next annotated cell comes before any list #15215
Description
Bug description
When two executable code cells with annotations follow each other and no ordered list sits between them, the first cell is dropped from the output.
Its code, its annotation markers and its output are all missing.
Only the second cell, with the list that follows it, is rendered.
I found this while working on Typst code annotations in #14170.
It happens on main for HTML, so it is not specific to Typst.
Steps to reproduce
---
title: Two annotated cells in a row
format: html
code-annotations: true
---
```{r}
first_cell <- 1 # <1>
first_cell
```
```{r}
second_cell <- 2 # <1>
second_cell
```
1. A note.Actual behavior
The page shows only the second cell.
first_cell does not appear anywhere in the HTML.
Expected behavior
Both cells are rendered.
The note links to the annotation of the second cell, which is the one it sits under.
main (first cell missing) |
main with the one-line fix below |
|---|---|
![]() |
![]() |
Cause
In src/resources/filters/quarto-pre/code-annotation.lua, the branch that handles executable cells keeps an annotated cell in pendingCodeCell until the ordered list arrives.
When another annotated cell comes first, the new cell overwrites pendingCodeCell and the first one is never emitted.
The other branches, such as the one for plain code blocks, call flushPending() before they output a block.
A possible fix is to call flushPending() at the top of the if found then branch.
With that line, both cells are rendered, as in the right-hand screenshot.
I have not run the whole test suite with it.
Your environment
- OS: macOS
- Quarto: dev build, run with the
src/resourcesofmainat 210691f (set withQUARTO_SHARE_PATH), so the Lua filters are those ofmain. - R 4.6.1 with knitr 1.51.
Quarto check output
quarto checkQuarto 99.9.9
[✓] Checking environment information...
Quarto cache location: /Users/mcanouil/Library/Caches/quarto
Project: none found (single-file mode)
[✓] Checking versions of quarto binary dependencies...
Pandoc version 3.10.0: OK
Dart Sass version 1.101.0: OK
Deno version 2.7.14: OK
Typst version 0.15.1: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
Version: 99.9.9
[✓] Checking tools....................OK
TinyTeX: v2026.07
Chrome Headless Shell: (not installed)
VeraPDF: (not installed)
[✓] Checking LaTeX....................OK
[✓] Checking Chrome Headless....................OK
[✓] Checking basic markdown render....OK
[✓] Checking R installation...........OK
Version: 4.6.1
knitr: 1.51
rmarkdown: 2.31
[✓] Checking Knitr engine render......OK
[✓] Checking Python 3 installation....OK
Version: 3.9.6
Jupyter: (None)
[✓] Checking Julia installation...


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