Fix failing tests

[cderv]

Since we merge #6620 I believe and also #6851 we have a few issues - possible an interaction between both of them:

• quarto render docs\smoke-all\crossrefs\float\jats\jats-knitr-table-captions-1.qmd --to jats failling on windows. @cscheid same reason as other tests when there is a warning as output of a chunk.

  intermediate md

   ---
   title: Knitr Table Test
   format: jats
   keep-md: true
   _quarto:
     tests:
       jats:
         ensureJatsXpath:
           - 
             - '//fig//fig[@id="tbl-cars"]//table'
             - '//fig//fig[@id="tbl-cars"]//caption'
             - '//fig//fig[@id="tbl-pressure"]//table'
             - '//fig//fig[@id="tbl-pressure"]//caption'
             - '//fig[@id="tbl-tables"]/caption'
           - []
   ---
   
   
   ::: {#tbl-tables .cell layout-ncol="2" tbl-cap='Tables'}
   
   ```{.r .cell-code}
   library(knitr)
   ```
   
   ::: {.cell-output .cell-output-stderr}
   
   ```
   Warning: le package 'knitr' a été compilé avec la version R 4.2.3
   ```
   
   
   :::
   
   ```{.r .cell-code}
   kable(head(cars), caption = "Cars {#tbl-cars}")
   ```
   
   ::: {.cell-output-display}
   
   
   Table: Cars {#tbl-cars}
   
   | speed| dist|
   |-----:|----:|
   |     4|    2|
   |     4|   10|
   |     7|    4|
   |     7|   22|
   |     8|   16|
   |     9|   10|
   
   
   :::
   
   ```{.r .cell-code}
   kable(head(pressure), caption = "Pressure {#tbl-pressure}")
   ```
   
   ::: {.cell-output-display}
   
   
   Table: Pressure {#tbl-pressure}
   
   | temperature| pressure|
   |-----------:|--------:|
   |           0|   0.0002|
   |          20|   0.0012|
   |          40|   0.0060|
   |          60|   0.0300|
   |          80|   0.0900|
   |         100|   0.2700|
   
   
   :::
   :::
   
   
   See @tbl-cars for more information.
   
   </details>
  

• quarto render docs\smoke-all\crossrefs\float\asciidoc\asciidoc-knitr-table-captions-1.qmd --to asciidoc. Same reason

  Intermediate markdown

   ---
   title: Knitr Table Test
   format: asciidoc
   keep-md: true
   _quarto:
     tests:
       asciidoc:
         ensureFileRegexMatches:
           # The checks here are looser than I'd like, because checking for asciidoc
           # nested structures in line-by-line regexes seems impossible, but this
           # is the only smoke-all test we can run in asciidoc.. 
           #
           # TODO this is a problem.
           - 
             - "\\[\\[tbl-cars\\]\\]"
             - "\\[\\[tbl-pressure\\]\\]"
             - "\\[#tbl-tables\\]" # TODO understand the difference between [[foo]] and [#foo]. From my reading of the asciidoc docs it seems ok but we should double-check.
             - "\\. Tables"
             - "\\. Cars"
             - "\\. Pressure"
           - []
   ---
   
   
   ::: {#tbl-tables .cell layout-ncol="2" tbl-cap='Tables'}
   
   ```{.r .cell-code}
   library(knitr)
   ```
   
   ::: {.cell-output .cell-output-stderr}
   
   ```
   Warning: le package 'knitr' a été compilé avec la version R 4.2.3
   ```
   
   
   :::
   
   ```{.r .cell-code}
   kable(head(cars), caption = "Cars {#tbl-cars}")
   ```
   
   ::: {.cell-output-display}
   
   
   Table: Cars {#tbl-cars}
   
   | speed| dist|
   |-----:|----:|
   |     4|    2|
   |     4|   10|
   |     7|    4|
   |     7|   22|
   |     8|   16|
   |     9|   10|
   
   
   :::
   
   ```{.r .cell-code}
   kable(head(pressure), caption = "Pressure {#tbl-pressure}")
   ```
   
   ::: {.cell-output-display}
   
   
   Table: Pressure {#tbl-pressure}
   
   | temperature| pressure|
   |-----------:|--------:|
   |           0|   0.0002|
   |          20|   0.0012|
   |          40|   0.0060|
   |          60|   0.0300|
   |          80|   0.0900|
   |         100|   0.2700|
   
   
   :::
   :::
   
   
   See @tbl-cars for more information.

• quarto render docs\smoke-all\lightbox\lightbox-explicit.qmd --to html. Issue with Lightbox (671ad9c)

  Lua error

   Error running filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/main.lua:
   ...R/quarto-cli/src/resources/filters/./ast/customnodes.lua:38: bad argument #1 to 'for iterator' (table expected, got nil)
   stack traceback:
           ...R/quarto-cli/src/resources/filters/./ast/customnodes.lua:38: in function 'run_emulated_filter'
           ...R/quarto-cli/src/resources/filters/./layout/lightbox.lua:165: in function <...R/quarto-cli/src/resources/filters/./layout/lightbox.lua:159>
           (...tail calls...)
           [C]: in ?
           [C]: in method 'walk'
           ...R/quarto-cli/src/resources/filters/./ast/customnodes.lua:61: in function <...R/quarto-cli/src/resources/filters/./ast/customnodes.lua:51>
           (...tail calls...)
           .../quarto-cli/src/resources/filters/./ast/runemulation.lua:36: in local 'callback'
           .../quarto-cli/src/resources/filters/./ast/runemulation.lua:49: in upvalue 'run_emulated_filter_chain'
           .../quarto-cli/src/resources/filters/./ast/runemulation.lua:84: in function <.../quarto-cli/src/resources/filters/./ast/runemulation.lua:81>
   stack traceback:
           ...R/quarto-cli/src/resources/filters/./ast/customnodes.lua:61: in function <...R/quarto-cli/src/resources/filters/./ast/customnodes.lua:51>
           (...tail calls...)
           .../quarto-cli/src/resources/filters/./ast/runemulation.lua:36: in local 'callback'
           .../quarto-cli/src/resources/filters/./ast/runemulation.lua:49: in upvalue 'run_emulated_filter_chain'
           .../quarto-cli/src/resources/filters/./ast/runemulation.lua:84: in function <.../quarto-cli/src/resources/filters/./ast/runemulation.lua:81>
   ERROR: Error
       at renderFiles (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-files.ts:334:23)
       at eventLoopTick (ext:core/01_core.js:181:11)
       at async render (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-shared.ts:98:18)
       at async Command.fn (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/cmd.ts:212:26)
       at async Command.execute (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/vendor/deno.land/x/cliffy@v0.25.4/command/command.ts:1790:7)
       at async quarto (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/quarto.ts:135:3)
       at async file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/quarto.ts:167:5
   ```
   
   </details>
  
  

• quarto render docs\smoke-all\lightbox\options.qmd --to html. Same as above (bbb46a4)

  Lua error

   Error running filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/main.lua:
   ...R/quarto-cli/src/resources/filters/./ast/customnodes.lua:38: bad argument #1 to 'for iterator' (table expected, got nil)
   stack traceback:
           ...R/quarto-cli/src/resources/filters/./ast/customnodes.lua:38: in function 'run_emulated_filter'
           ...R/quarto-cli/src/resources/filters/./layout/lightbox.lua:165: in function <...R/quarto-cli/src/resources/filters/./layout/lightbox.lua:159>
           (...tail calls...)
           [C]: in ?
           [C]: in method 'walk'
           ...R/quarto-cli/src/resources/filters/./ast/customnodes.lua:61: in function <...R/quarto-cli/src/resources/filters/./ast/customnodes.lua:51>
           (...tail calls...)
           .../quarto-cli/src/resources/filters/./ast/runemulation.lua:36: in local 'callback'
           .../quarto-cli/src/resources/filters/./ast/runemulation.lua:49: in upvalue 'run_emulated_filter_chain'
           .../quarto-cli/src/resources/filters/./ast/runemulation.lua:84: in function <.../quarto-cli/src/resources/filters/./ast/runemulation.lua:81>
   stack traceback:
           ...R/quarto-cli/src/resources/filters/./ast/customnodes.lua:61: in function <...R/quarto-cli/src/resources/filters/./ast/customnodes.lua:51>
           (...tail calls...)
           .../quarto-cli/src/resources/filters/./ast/runemulation.lua:36: in local 'callback'
           .../quarto-cli/src/resources/filters/./ast/runemulation.lua:49: in upvalue 'run_emulated_filter_chain'
           .../quarto-cli/src/resources/filters/./ast/runemulation.lua:84: in function <.../quarto-cli/src/resources/filters/./ast/runemulation.lua:81>
   ERROR: Error
       at renderFiles (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-files.ts:334:23)
       at eventLoopTick (ext:core/01_core.js:181:11)
       at async render (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-shared.ts:98:18)
       at async Command.fn (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/cmd.ts:212:26)
       at async Command.execute (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/vendor/deno.land/x/cliffy@v0.25.4/command/command.ts:1790:7)
       at async quarto (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/quarto.ts:135:3)
       at async file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/quarto.ts:167:5
  

[cderv]

I have dealt with the lightbox related issues. Nothing to do with cross ref by the way.

@cscheid I let you deal with the crossref issues as I believe you already dealt with that with other formats probably

[xtimbeau]

It is probably related : after 1.4.358 (so since 1.4.366 and after), label: tbl-xxxx raises an error when rendered.

a qmd to reproduce the error:

---
title: "table"
format: html
---

```{r}
#| label: tbl-unetable

library(gt)
start_date <- "2010-06-07"
end_date <- "2010-06-14"
sp500 |>
  dplyr::filter(date >= start_date & date <= end_date) |>
  dplyr::select(-adj_close) |>
  gt() |>
  tab_header(
    title = "S&P 500",
    subtitle = glue::glue("{start_date} to {end_date}")
  ) |>
  fmt_currency() |>
  fmt_date(columns = date, date_style = "wd_m_day_year") |>
  fmt_number(columns = volume, suffixing = TRUE)
```

[cderv]

@xtimbeau please do open new issue - this is best than commenting in another thread. I did open #6878 based on your comment. We'll discuss there.

[cscheid]

Fixed by #6887.