quarto-dev / quarto-dev/quarto-cli

Computed Captions crash when rendering manuscript to HTML

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#11,117 9 comments 0 reactions 1 assignee View on GitHub

@cscheid is already working on this.

Since Oct 19, 2024.

bug crossref manuscript regression
Dominant language
JavaScript
Stars
6k
Forks
458
Avg merge
1d 9h
Merged PRs (30d)
41

Description

Bug description

Computed Captions don't work for HTML output of manuscript project.

Steps to reproduce

Minimal example based on documentation:

---
title: "Reproducible Computed Captions Document"
format: html
engine: jupyter
---

::: {#fig-box}

```{python}
x = [1, 2, 3, 4, 5, 10]
print(x)
```

This dataset has `{python} len(x)` observations.

:::

Reproduction repository: https://github.com/winniehell/quarto-playground/tree/1f3c6ecef794096655619ebd8238c3d98fc510fc

cd test-manuscript/
quarto render --to html
Expected behavior

Figure is rendered, similar to book:

screenshot of the rendered figure in test book project

Actual behavior

Rendering crashes:

⚠️  Import assertions are deprecated. Use `with` keyword, instead of 'assert' keyword.

    const resourceModule = (await import(toFileUrl2(resourcePath("editor/tools/yaml/yaml-intelligence-resources.json")).href, {

  at file:///nix/store/ps94d8icw9hbm9ky3jm3q2vwa672yfgz-quarto-1.5.57/bin/quarto.js:82360:119


Starting python3 kernel...Done

Executing 'index.quarto_ipynb'
  Cell 1/1: ''...Done

Rendering qmd embeds [index.qmd]
Error running filter /nix/store/ps94d8icw9hbm9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:
...9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:22378: attempt to index a nil value (field 'content')
stack traceback:
        ...9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:1233: in local 'filter_fn'
        ...9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:635: in function <...9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:625>
        (...tail calls...)
        [C]: in ?
        [C]: in method 'walk'
        ...9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:557: in function <...9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:546>
        (...tail calls...)
        ...9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:1334: in local 'callback'
        ...9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:1352: in upvalue 'run_emulated_filter_chain'
        ...9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:1388: in function <...9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:1385>
stack traceback:
        ...9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:557: in function <...9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:546>
        (...tail calls...)
        ...9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:1334: in local 'callback'
        ...9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:1352: in upvalue 'run_emulated_filter_chain'
        ...9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:1388: in function <...9ky3jm3q2vwa672yfgz-quarto-1.5.57/share/filters/main.lua:1385>
Your environment

NixOS 24.05.20241012.a3f9ad6 (Uakari)

Quarto check output

Quarto 1.5.57

output of quarto check 
[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.11: OK
      Dart Sass version 1.77.6: OK
      Deno version 1.46.3: OK
      Typst version 0.11.1: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.5.57
      Path: /nix/store/ps94d8icw9hbm9ky3jm3q2vwa672yfgz-quarto-1.5.57/bin

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

[✓] Checking LaTeX....................OK
      Using: Installation From Path
      Path: /run/current-system/sw/bin
      Version: undefined

⚠️  Import assertions are deprecated. Use `with` keyword, instead of 'assert' keyword.

    const resourceModule = (await import(toFileUrl2(resourcePath("editor/tools/yaml/yaml-intelligence-resources.json")).href, {

  at file:///nix/store/ps94d8icw9hbm9ky3jm3q2vwa672yfgz-quarto-1.5.57/bin/quarto.js:82360:119

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

[✓] Checking Python 3 installation....OK
      Version: 3.12.5
      Path: /nix/store/wqy1crq4yl12hjlcmvc8c7fsgmliyi4y-python3-3.12.5-env/bin/python3.12
      Jupyter: 5.7.2
      Kernels: python3

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

[✓] Checking R installation...........OK
      Version: 4.4.1
      Path: /nix/store/z70v7siag32vkpwapfzmj84nw6y43gh9-R-4.4.1/lib/R
      LibPaths:
        - /nix/store/daik4k1c0wn51l60crca0bg5rwwb9ic3-r-boot-1.3-30/library
        - /nix/store/lwvbgifsdz5lp04763cy7c5xi7ak4zf3-r-class-7.3-22/library
        - /nix/store/ywxgbh558frpsgdfrv3d84rqb4zz12n5-r-MASS-7.3-61/library
        - /nix/store/5gh44f15yfx1zglp5405v3xr9lzmns7r-r-cluster-2.1.6/library
        - /nix/store/a1hrni8rqgxwfck0r597flf1fg3jj486-r-codetools-0.2-20/library
        - /nix/store/w16lsd6irk7z007f5kz5y10wa7h64iv4-r-foreign-0.8-87/library
        - /nix/store/2icpxrlzfgiaq8xnnrs9jb9y4nyfnrjh-r-KernSmooth-2.23-24/library
        - /nix/store/2ab6xwyjga7fcyjj2f8bqna8r9m3c7rs-r-lattice-0.22-6/library
        - /nix/store/3xnygjx6918c3jy4j19pbadzrc1z9kvw-r-Matrix-1.7-0/library
        - /nix/store/z928qmv92cc69962g3ywah8bya6aca38-r-mgcv-1.9-1/library
        - /nix/store/0dzm06h1xbwa9vpdmzhmhyp5fw38lvgr-r-nlme-3.1-166/library
        - /nix/store/8w40bnvgyz1v3bd9pxn1spy0s4631szm-r-nnet-7.3-19/library
        - /nix/store/cdyvmkzhc4zbm3rc9l9shrbfyyrhknnd-r-rpart-4.1.23/library
        - /nix/store/aqb14s5f7m2g1b8im2qk4aka2lfxgpp2-r-spatial-7.3-17/library
        - /nix/store/plbrhygxk1l22rx09dz6k64fikrdylxm-r-survival-3.7-0/library
        - /nix/store/zmj4vzdb7wv45hrnwlq8iylkxz30k4dc-r-rmarkdown-2.28/library
        - /nix/store/msrlr9vdh4cbg0md58ip425i32sqiaxz-r-bslib-0.8.0/library
        - /nix/store/ivj01b8xi7xsw4dcqk8c9yc5yi9k3d8h-r-base64enc-0.1-3/library
        - /nix/store/wmi5wbcyb8dfy92dqxcmhsxbaijs035v-r-cachem-1.1.0/library
        - /nix/store/svjm71fi93h67bhznkqr95s0k8mfkgaz-r-fastmap-1.2.0/library
        - /nix/store/6ki030nl3r1zwicv1zx5ps5s67bl5hgz-r-rlang-1.1.4/library
        - /nix/store/ymrvw8ikv46cwyx80nkkgkvm151k1plm-r-htmltools-0.5.8.1/library
        - /nix/store/2c8blk9g5lm3f7pmcy1pm3xzwj42qjnk-r-digest-0.6.36/library
        - /nix/store/gqsj71kl85bwnmqzxiyvhzc2622rhb5g-r-jquerylib-0.1.4/library
        - /nix/store/l0a09sccsi1dkg63c29mkpyggvb08z79-r-jsonlite-1.8.8/library
        - /nix/store/wkmhssmavkcjc1dabvzil839gsjygg1j-r-lifecycle-1.0.4/library
        - /nix/store/bwg6lqnpnpiv0fsq8ixm1a5phfmw8hn1-r-cli-3.6.3/library
        - /nix/store/5056ych2577zb9gyfy4qpj7h5fdf9ad1-r-glue-1.7.0/library
        - /nix/store/zm6jfjg2ssxh203mx4kh45xhrhfkdn8x-r-memoise-2.0.1/library
        - /nix/store/q2rzc6dhg84mmny6xjz42v2ac9hbpywf-r-mime-0.12/library
        - /nix/store/vzbfrr622313zh776r0aqf7y78fbrh28-r-sass-0.4.9/library
        - /nix/store/fzmm775ppypmwxxygm2rdr9vrvxnmr02-r-R6-2.5.1/library
        - /nix/store/pha01w01l40dsycyfnnvagzvv65zhd59-r-fs-1.6.4/library
        - /nix/store/v4azfk4cdz5rk1l0255p40sfll3kqc90-r-rappdirs-0.3.3/library
        - /nix/store/pi2whxkrj13cyqysc34w8xlrmlr26ckn-r-evaluate-0.24.0/library
        - /nix/store/klfvbq1ga9dmzs0z28b0r7v2qvdxgf3w-r-fontawesome-0.5.2/library
        - /nix/store/2jz6wc7wm1ajvi9baqsx0jv7c999h8cj-r-knitr-1.48/library
        - /nix/store/d3d5w3sjlchd3hq8fm7bm33zh8xgmia2-r-highr-0.11/library
        - /nix/store/jnfjcr31zmy9nnzm2li43hhp6rq8mjas-r-xfun-0.47/library
        - /nix/store/69w2fsnbq4dkgzg2prkd69k4icmk8mqc-r-yaml-2.3.10/library
        - /nix/store/1hgvyfnqaaj7vy7jnnv27a3y6gja081q-r-tinytex-0.52/library
        - /nix/store/z70v7siag32vkpwapfzmj84nw6y43gh9-R-4.4.1/lib/R/library
      knitr: 1.48
      rmarkdown: 2.28

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

also reproduced on latest main (71945532e1fc1a5cf113117f6d5ff5bee3991797)

Contributor guide

Open the contributing guide

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