Embedded tables are not rendering in parent quarto document

[atsyplenkov]

Bug description

I am attempting to embed a table from one .qmd file into another .qmd file (parent document). However, regardless of how the table is rendered (using kable, gt, or hux), the embedding process causes the rendering to fail with the following errors. Individually, each quarto document renders successfully to .html.

processing file: index.qmd
                                                                                                    
output file: index.knit.md

Rendering qmd embeds
[1/1] notebooks/inset-table.qmd


processing file: inset-table.qmd
                                                                                                    
output file: inset-table.knit.md

ERROR: The notebook notebooks/inset-table.qmd doesn't contain output to embed with the cell id, tag, or label 'tbl-two'. Please be sure to have executed any cells that you are embedding.

Stack trace:
    at file:///C:/Users/TSYPLE~1/AppData/Local/Programs/Quarto/bin/quarto.js:69578:23
    at Array.map (<anonymous>)
    at notebookMarkdown (file:///C:/Users/TSYPLE~1/AppData/Local/Programs/Quarto/bin/quarto.js:69573:40)
    at eventLoopTick (ext:core/01_core.js:181:11)
    at async replaceNotebookPlaceholders (file:///C:/Users/TSYPLE~1/AppData/Local/Programs/Quarto/bin/quarto.js:69517:32)
    at async renderPandoc (file:///C:/Users/TSYPLE~1/AppData/Local/Programs/Quarto/bin/quarto.js:69873:28)
    at async Object.onRender (file:///C:/Users/TSYPLE~1/AppData/Local/Programs/Quarto/bin/quarto.js:76312:36)
    at async renderFileInternal (file:///C:/Users/TSYPLE~1/AppData/Local/Programs/Quarto/bin/quarto.js:76289:17)
    at async renderFiles (file:///C:/Users/TSYPLE~1/AppData/Local/Programs/Quarto/bin/quarto.js:76084:17)
    at async render (file:///C:/Users/TSYPLE~1/AppData/Local/Programs/Quarto/bin/quarto.js:81071:21)

Steps to reproduce

There are two documents. One is the parent document, the second is the supplementary document (named inset-table.qmd).

Parent document

---
title: "Test of embedding tables"
format:
  html:
    toc: true
---

Hello world

```{r}
#| label: tbl-one
#| tbl-cap: This is normal gt table

gt::gt(head(mtcars))

```

{{< embed inset-table.qmd#tbl-two >}}

Supporting document (inset-table.qmd)

---
title: "Notebook"
---

```{r}
#| label: tbl-two
#| tbl-cap: THis is embed example

gt::gt(head(mtcars))

```

Expected behavior

There should be two tables printed using the gt package in the parent document.

Actual behavior

Quarto crashes with the following error

processing file: index.qmd
                                                                                                    
output file: index.knit.md

Rendering qmd embeds
[1/1] notebooks/inset-table.qmd


processing file: inset-table.qmd
                                                                                                    
output file: inset-table.knit.md

ERROR: The notebook notebooks/inset-table.qmd doesn't contain output to embed with the cell id, tag, or label 'tbl-two'. Please be sure to have executed any cells that you are embedding.

Stack trace:
    at file:///C:/Users/TSYPLE~1/AppData/Local/Programs/Quarto/bin/quarto.js:69578:23
    at Array.map (<anonymous>)
    at notebookMarkdown (file:///C:/Users/TSYPLE~1/AppData/Local/Programs/Quarto/bin/quarto.js:69573:40)
    at eventLoopTick (ext:core/01_core.js:181:11)
    at async replaceNotebookPlaceholders (file:///C:/Users/TSYPLE~1/AppData/Local/Programs/Quarto/bin/quarto.js:69517:32)
    at async renderPandoc (file:///C:/Users/TSYPLE~1/AppData/Local/Programs/Quarto/bin/quarto.js:69873:28)
    at async Object.onRender (file:///C:/Users/TSYPLE~1/AppData/Local/Programs/Quarto/bin/quarto.js:76312:36)
    at async renderFileInternal (file:///C:/Users/TSYPLE~1/AppData/Local/Programs/Quarto/bin/quarto.js:76289:17)
    at async renderFiles (file:///C:/Users/TSYPLE~1/AppData/Local/Programs/Quarto/bin/quarto.js:76084:17)
    at async render (file:///C:/Users/TSYPLE~1/AppData/Local/Programs/Quarto/bin/quarto.js:81071:21)

Your environment

• IDE: RStudio 2023.09.1+470 "Desert Sunflower" Release (ecb7e65667c9e2f54fdec9e313f24df8c7b71adc, 2023-10-04) for windows
  Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.09.1+470 Chrome/116.0.5845.190 Electron/26.2.4 Safari/537.36

• OS: Windows 10 Enterprise, 22H2, OS build 19045.3570

• R:

R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: Pacific/Auckland
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] digest_0.6.33     utf8_1.2.3        R6_2.5.1          fastmap_1.1.1    
 [5] tidyselect_1.2.0  magrittr_2.0.3    glue_1.6.2        tibble_3.2.1     
 [9] htmltools_0.5.6   pkgconfig_2.0.3   gt_0.10.0         dplyr_1.1.3      
[13] generics_0.1.3    lifecycle_1.0.3   xml2_1.3.5        cli_3.6.1        
[17] fansi_1.0.4       vctrs_0.6.3       compiler_4.3.1    rstudioapi_0.15.0
[21] tools_4.3.1       pillar_1.9.0      rlang_1.1.1   

Quarto check output

Quarto 1.4.415
[>] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.8: OK
      Dart Sass version 1.55.0: OK
      Deno version 1.33.4: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
      Version: 1.4.415
      Path: C:\Users\%username%\AppData\Local\Programs\Quarto\bin
      CodePage: 1252

[>] Checking tools....................OK
      TinyTeX: (external install)
      Chromium: (not installed)

[>] Checking LaTeX....................OK
      Using: TinyTex
      Path: C:\Users\%username%\AppData\Roaming\TinyTeX\bin\windows\
      Version: 2023

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

[>] Checking Python 3 installation....OK
      Version: 3.9.5 (Conda)
      Path: C:/Users/%username%/Miniconda3/python.exe
      Jupyter: 5.3.0
      Kernels: python3

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

[>] Checking R installation...........OK
      Version: 4.3.1
      Path: C:/PROGRA~1/R/R-43~1.1
      LibPaths:
        - C:/Users/%username%/AppData/Local/R/win-library/4.3
        - C:/Program Files/R/R-4.3.1/library
      knitr: 1.44
      rmarkdown: 2.25

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

[cderv]

I believe you are trying to use a Jupyter Notebook only feature: https://quarto.org/docs/authoring/notebook-embed.html

So it won't work with engine: knitr. @dragonstyle as it change ? Otherwise we could maybe try to stop early when we detect engine knitr and embed shortcode usage ?

[atsyplenkov]

I believe you are trying to use a Jupyter Notebook only feature: https://quarto.org/docs/authoring/notebook-embed.html

So it won't work with engine: knitr. @dragonstyle as it change ? Otherwise we could maybe try to stop early when we detect engine knitr and embed shortcode usage ?

Thanks for the prompt response! I don't understand how than it works in manuscript projects. For example see — https://mine.quarto.pub/manuscripts-conf23/#/embedded-computations

Roughly speaking, the only difference between slides and mine reprex is that the project type wasn't specified. Could that be the reason?

[cderv]

Oh yes new manuscript format and features. Sorry - I missed that. 🤦 Thanks for additional content !

Recent work have support for .qmd embedding indeed using intermediary files. I see there was a bug with fig- at some point (#6959) so maybe there is one with tbl-.

@dragonstyle will known more.

[atsyplenkov]

Recent work have support for .qmd embedding indeed using intermediary files. I see there was a bug with fig- at some point (#6959) so maybe there is one with tbl-.

Sure it is! tbl-cap was the reason for the strange behavior. Moreover, it fully depends on the project type. For example, switching the project to the manuscript type will not throw an error, but it will not render tables (example 1). Removing tbl-cap in the manuscript type will result in rendering only the knitr::kable table (example 2). Removing the project type, i.e., reproducing my initial issue without tbl-cap options, will render only the kable table expanded to the full width (example 3). Note that the gt table failed to embed but did not throw any error, while the kable table embedded successfully but without the Table 3 heading!

It turns out that only knitr::kable tables could be embed, while kableExtra, gt and hux are not.

Example 1

original issue switched to manuscript type with tbl-cap

Example 2

original issue switched to manuscript type without tbl-cap

Example 3

original issue without tbl-cap options

[dragonstyle]

Thanks for the additional details - I am tracking down the issues and think I know how to fix... will update here soon...

[dragonstyle]

This is resolved in the current Quarto pre-release.

[DOH-FAA3303]

@dragonstyle I'm still unable to render gt tables using a manuscript project type using quarto version 1.5.22 or 1.4.358. are there plans to add gt and other tables for manuscripts in the future? Or are there ways around this problem you know of?

[mcanouil]

@DOH-FAA3303 please provide a reproducible example as plain text or a Git repository.
We can't work with "it does not work for me".

I suggest you open a new issue (possibly linking this one) with a reproducible example and all information requested in the template.
Thank you for your cooperation and bug report.

[DOH-FAA3303]

Recent work have support for .qmd embedding indeed using intermediary files. I see there was a bug with fig- at some point (#6959) so maybe there is one with tbl-.

Sure it is! tbl-cap was the reason for the strange behavior. Moreover, it fully depends on the project type. For example, switching the project to the manuscript type will not throw an error, but it will not render tables (example 1). Removing tbl-cap in the manuscript type will result in rendering only the knitr::kable table (example 2). Removing the project type, i.e., reproducing my initial issue without tbl-cap options, will render only the kable table expanded to the full width (example 3). Note that the gt table failed to embed but did not throw any error, while the kable table embedded successfully but without the Table 3 heading!

It turns out that only knitr::kable tables could be embed, while kableExtra, gt and hux are not.

Example 1

original issue switched to manuscript type with tbl-cap

Example 2

original issue switched to manuscript type without tbl-cap

Example 3

original issue without tbl-cap options

@mcanouil I meant i reproduced this example exactly and was unable to render the gt table. I will make a new issue

[mcanouil]

Thanks for the clarification.

[mcanouil]

Unfortunately, using screenshots is really a pain.
@DOH-FAA3303 since you tried somehow the examples, would you mind sharing a Git repository which could be use to reproduce the issue (and possibly reopen the GitHub issue)?

[DOH-FAA3303]

Unfortunately, using screenshots is really a pain. @DOH-FAA3303 since you tried somehow the examples, would you mind sharing a Git repository which could be use to reproduce the issue (and possibly reopen the GitHub issue)?

I just submitted a new issue with the example in markdown @mcanouil