quarto-dev / quarto-dev/quarto-cli

custom table label conflict with `gt` table

Open
#11,653 9 comments 0 reactions 1 assignee View on GitHub

@rich-iannone is already working on this.

Since Dec 11, 2024.

bug tables upstream
Dominant language
JavaScript
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Avg merge
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Merged PRs (30d)
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Description

Bug description

I can not generate pdf format with custom table table using gt table.

Steps to reproduce
```qmd
---
crossref:
  custom:
    - kind: float
      key: stb
      reference-prefix: "Table S"
      space-before-numbering: false
      caption-prefix: "Table S"
      latex-env: stb
      latex-list-of-file-extension: lost
      latex-list-of-description: Supplementary Table
format: pdf
---

::: {#stb-demo}

```{r}
data.frame(x = 1:3, y = 1:3) |>
gt::gt()

```

Caption

:::
```
Expected behavior

No response

Actual behavior
r$> nvim.interlace.rmd("demo.qmd", rmddir = "/Users/ming", envir = .GlobalEnv)


processing file: demo.qmd
1/3                  
2/3 [unnamed-chunk-1]
3/3                  
output file: demo.knit.md

pandoc 
  to: latex
  output-file: demo.tex
  standalone: true
  pdf-engine: xelatex
  variables:
    graphics: true
    tables: true
  default-image-extension: pdf
  
metadata
  documentclass: scrartcl
  classoption:
    - DIV=11
    - numbers=noendperiod
  papersize: letter
  header-includes:
    - \KOMAoption{captions}{tableheading}
  block-headings: true
  crossref:
    custom:
      - kind: float
        key: stb
        reference-prefix: Table S
        space-before-numbering: false
        caption-prefix: Table S
        latex-env: stb
        latex-list-of-file-extension: lost
        latex-list-of-description: Supplementary Table
  

Rendering PDF
running xelatex - 1
  This is XeTeX, Version 3.141592653-2.6-0.999996 (TeX Live 2024) (preloaded format=xelatex)
   restricted \write18 enabled.
  entering extended mode
  
updating tlmgr

updating existing packages
ERROR: 
compilation failed- error
LaTeX Error: Not in outer par mode.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.229 \fontsize
               {12.0pt}{14.4pt}\selectfont 

see demo.log for more information.
Error in `quarto::quarto_render()`:
✖ Error running quarto cli.
Caused by error:
! System command 'quarto' failed
Run `rlang::last_trace()` to see where the error occurred.

r$>
Your environment

MacOS:

  • chip Apple M1 Max
  • Sequoia 15.2 (24C98)
    IDE: NVim
nvim --version
NVIM v0.10.0
Build type: Release
LuaJIT 2.1.1713484068
Run "nvim -V1 -v" for more info
r$> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin23.2.0 (64-bit)
Running under: macOS 15.2

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions
/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /opt/homebrew/Cellar/r/4.3.3/lib/R/lib/libRlapack.dylib;
  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-
8

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] quarto_1.4.4   rmarkdown_2.29 nvimcom_0.9.58

loaded via a namespace (and not attached):
 [1] digest_0.6.37     R6_2.5.1          later_1.4.1      
 [4] fastmap_1.2.0     xfun_0.49         knitr_1.49       
 [7] htmltools_0.5.8.1 ps_1.8.0          cli_3.6.3        
[10] processx_3.8.4    compiler_4.3.3    rstudioapi_0.17.1
[13] tools_4.3.3       evaluate_1.0.1    yaml_2.3.10      
[16] Rcpp_1.0.13-1     rlang_1.1.4       jsonlite_1.8.9   
[19] colorout_1.3-0.2 

r$>
Quarto check output
> quarto check
Quarto 1.7.1
[✓] Checking environment information...
      Quarto cache location: /Users/ming/Library/Caches/quarto
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.4.0: OK
      Dart Sass version 1.70.0: OK
      Deno version 1.46.3: OK
      Typst version 0.11.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.7.1
      Path: /Applications/quarto/bin

[✓] Checking tools....................OK
      TinyTeX: v2024.10
      Chromium: 869685

[✓] Checking LaTeX....................OK
      Using: TinyTex
      Path: /Users/ming/Library/TinyTeX/bin/universal-darwin
      Version: 2024

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

[✓] Checking Python 3 installation....OK
      Version: 3.12.4 (Conda)
      Path: /Users/ming/.config/miniconda3/bin/python
      Jupyter: 5.7.2
      Kernels: python3

(|) Checking Jupyter engine render....Traceback (most recent call last):
  File "/Applications/quarto/share/jupyter/jupyter.py", line 21, in <module>
    from notebook import notebook_execute, RestartKernel
  File "/Applications/quarto/share/jupyter/notebook.py", line 20, in <module>
    from nbclient import NotebookClient
ModuleNotFoundError: No module named 'nbclient'
[✓] Checking Jupyter engine render....OK


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