`embed` shortcode requires `knitr` engine cells to have `echo: true` (at cell level)

[mcanouil]

I have:

• searched the issue tracker for similar issues
• installed the latest version of Quarto CLI
• formatted my issue following the Bug Reports guide

Bug description

It appears one cannot set echo: false at code cell level and embed the corresponding cell.

Steps to reproduce

---
title: "Reproducible Quarto Document"
format: html
---

{{< embed cell.qmd#plot >}}

---
engine: knitr
---

```{r}
#| label: plot
#| echo: false
plot(1)
```

Actual behavior

Rendering qmd embeds
[1/1] cell.qmd
ℹ R version 4.5.2 (2025-10-31)
! Config '~/.Rprofile' was loaded!


processing file: cell.qmd
1/3       
2/3 [plot]
3/3       
output file: cell.knit.md

ERROR: The cell plot does not exist in notebook

Stack trace:
    at file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/core/jupyter/jupyter-embed.ts:446:15
    at Array.map (<anonymous>)
    at notebookMarkdown (file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/core/jupyter/jupyter-embed.ts:443:36)
    at eventLoopTick (ext:core/01_core.js:179:7)
    at async replaceNotebookPlaceholders (file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/core/jupyter/jupyter-embed.ts:326:26)
    at async renderPandoc (file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/command/render/render.ts:118:26)
    at async Object.onRender (file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/command/render/render-files.ts:731:30)
    at async renderFileInternal (file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/command/render/render-files.ts:693:9)
    at async renderFiles (file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/command/render/render-files.ts:331:9)
    at async render (file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/command/render/render-shared.ts:106:18)
    at async renderForPreview (file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/command/preview/preview.ts:422:24)
    at async render (file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/command/preview/preview.ts:169:22)
    at async preview (file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/command/preview/preview.ts:186:18)
    at async Command.actionHandler (file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/command/preview/cmd.ts:424:7)
    at async Command.execute (https://deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1948:7)
    at async Command.parseCommand (https://deno.land/x/cliffy@v1.0.0-rc.3/command/command.ts:1780:14)
    at async quarto (file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/quarto.ts:193:5)
    at async file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/quarto.ts:225:5
    at async file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/core/main.ts:45:14
    at async mainRunner (file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/core/main.ts:47:5)
    at async file:///Users/mcanouil/Projects/quarto-dev/quarto-cli/src/quarto.ts:215:3

Expected behavior

The embedding should work similarly to setting echo: false at document level.

---
engine: knitr
execute:
  echo: false
---

```{r}
#| label: plot
plot(1)
```

Your environment

• VSCode
• Latest macOS

Quarto check output

Quarto 99.9.9
[✓] Checking environment information...
      Quarto cache location: /Users/mcanouil/Library/Caches/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.6.3: OK
      Dart Sass version 1.87.0: OK
      NOTE: Deno version 2.4.5 does not strictly match 2.3.1 and strict checking is enabled. Please use 2.3.1.
      Typst version 0.13.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 99.9.9
      commit: 20d67b97dceb83c1d69034bf24bf47616100cc8d
      Path: /Users/mcanouil/Projects/quarto-dev/quarto-cli/package/dist/bin

[✓] Checking tools....................OK
      TinyTeX: v2025.11
      Chromium: (not installed)

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/mcanouil/Library/TinyTeX/bin/universal-darwin
      Version: 2025

[✓] Checking Chrome Headless....................OK
      Using: Chrome found on system
      Path: /Applications/Brave Browser.app/Contents/MacOS/Brave Browser
      Source: QUARTO_CHROMIUM

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

[✓] Checking Python 3 installation....OK
      Version: 3.14.0
      Path: /Users/mcanouil/Projects/quarto-dev/quarto-playground/.venv/bin/python
      Jupyter: 5.9.1
      Kernels: uv, julia-1.12, python3

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

(/) Checking R installation...........ℹ R version 4.5.2 (2025-10-31)
! Config '~/.Rprofile' was loaded!
[✓] Checking R installation...........OK
      Version: 4.5.2
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Users/mcanouil/Projects/quarto-dev/quarto-playground/renv/library/macos/R-4.5/aarch64-apple-darwin20
        - /Users/mcanouil/Library/Caches/org.R-project.R/R/renv/sandbox/macos/R-4.5/aarch64-apple-darwin20/4cd76b74
      knitr: 1.50
      rmarkdown: 2.30

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

[cderv]

Thanks for the report. Interesting use case.

When you set this in the embedded file

execute:
  echo: false

it does not seem to apply. See the ipynb html produce

And the intermediate

---
engine: knitr
execute: 
  echo: false
---


::: {.cell}

```{.r .cell-code}
#| label: plot
plot(1)
```

::: {.cell-output-display}
![](test_files/figure-ipynb/plot-1.png)
:::
:::

See also with python

---
execute:
  echo: false
---

```{python}
#| label: plot
import matplotlib.pyplot as plt
import numpy as np
x = np.linspace(0, 10, 100)
y = np.sin(x)
plt.plot(x, y)
plt.title("Sine Wave")
plt.xlabel("X-axis")
plt.ylabel("Y-axis")
plt.show()
```

You will have the echo is the .ipynb produce too

However, setting it per-cell for Jupyter engine does not fail

---
title: Notebook
---

```{python}
#| label: plot
#| echo: false
import matplotlib.pyplot as plt
import numpy as np
x = np.linspace(0, 10, 100)
y = np.sin(x)
plt.plot(x, y)
plt.title("Sine Wave")
plt.xlabel("X-axis")
plt.ylabel("Y-axis")
plt.show()
```

and produce notebook preview is with no source

Oddly some intermediate does have the source like the one from --to ipynb conversion (cell.ipynb.md)

---
title: Notebook
---

::: {#cell-plot .cell execution_count=1}
``` {}
#| label: plot
#| echo: false
import matplotlib.pyplot as plt
import numpy as np
x = np.linspace(0, 10, 100)
y = np.sin(x)
plt.plot(x, y)
plt.title("Sine Wave")
plt.xlabel("X-axis")
plt.ylabel("Y-axis")
plt.show()
```

::: {.cell-output .cell-output-display}
![](test_files/figure-ipynb/plot-output-1.png){#plot}
:::
:::


---
jupyter:
  kernelspec:
    display_name: Python 3 (ipykernel)
    language: python
    name: python3
    path: C:\Users\chris\Documents\DEV_OTHER\00-TESTS\test-quarto\.venv\share\jupyter\kernels\python3
---

but not the one from the preview ( cell.embed.html.md)

---
title: Notebook
---


:::{#f4ad92de-5d30-49ed-b244-a4272c01c41d .cell .markdown}

:::

::: {#cell-plot .cell execution_count=1}

::: {.cell-output .cell-output-display}
![](test.embed_files/figure-html/plot-output-1.png){#plot}
:::
:::

So something to look at more deeply.

We know using knitr wth embed is not ideal, because it was not design for that totally. (knitr is not aware of ipynb as output format).

And I don't know if an embed notebook without source is expected initially.

Anyhow, something to investigate.

[mcanouil]

For reference, this came up in:

• https://github.com/orgs/quarto-dev/discussions/13734

[cderv]

This is a tricky problem.

Basically, it confirms that embed has been designed with engine: jupyter in mind.
Most of the logic happens while handling the executed ipynb different in case of embed or direct rendering.

With knitr this works differently. Setting echo: false will be passed to knitr engine that will return no source cell in the output to quarto.

For jupyter, this is different. Jupyter does not care about echo or not. Execution still happens, and then quarto is the one handling the option echo depending on context.

So either knitr needs to be taught about the embed renderng case, or we need to find a way to exectute with echo: true and then filter output when needed.

Anyhow, this is not a bug fix really - this is another design problem to make embed work with knitr