Manuscript figures not found (wrong path)

[andjar]

Bug description

After rendering a manuscript project with notebooks, the notebook figure files are not displayed in the output html file. There seems to be an issue with the paths

Steps to reproduce

Create an new Quarto manuscript project (quarto create project manuscript).

Create a folder notebooks, and within it a new file notebook.qmd containing:

---
title: "Notebook"
---

## A test

```{r}
x <- 1:4
y <- 1:4
plot(x,y)
```

Render the project (quarto render)

Actual behavior

>quarto render
[1/2] notebooks\notebook.qmd


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

[2/2] index.qmd

Output created: _manuscript\index.html

But when opening the notebook html file, the figure is not found. The image file path in the html is _manuscript/notebooks/notebook_files/figure-html/unnamed-chunk-1-1.png whereas the figure file itself is located in the folder \.quarto\_freeze\notebooks\notebook\figure-html. To get the image to show in the html file, I have to manually copy the folder into _manuscript\notebooks and change the name

Expected behavior

The output figure files should automatically be moved to the folder _manuscript/notebooks/notebook_files

Your environment

• IDE: Rstudio 2024.12.1, build 563
• OS: Windows 10

Quarto check output

quarto check
Quarto 1.6.42
[>] Checking environment information...
      Quarto cache location: C:\Users\anderhja\AppData\Local\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: 1.6.42
      Path: C:\Users\anderhja\AppData\Local\Programs\Quarto\bin
      CodePage: 1252

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

[>] Checking LaTeX....................OK
      Tex:  (not detected)

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

[>] Checking Python 3 installation....(None)

      Unable to locate an installed version of Python 3.
      Install Python 3 from https://www.python.org/downloads/

[>] Checking R installation...........OK
      Version: 4.4.3
      Path: C:/Users/anderhja/AppData/Local/Programs/R/R-4.4.3
      LibPaths:
        - C:/Users/anderhja/AppData/Local/R/win-library/4.4
        - C:/Users/anderhja/AppData/Local/Programs/R/R-4.4.3/library
      knitr: 1.50
      rmarkdown: 2.29

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

[mcanouil]

I cannot reproduce your issue using 1.6.42 or 1.7.* but I get another error using latest development version (2546027):

❯ quarto render
[1/2] notebooks/notebook.qmd
ℹ R version 4.4.3 (2025-02-28)
! Config '~/.Rprofile' was loaded!


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

Error adding css vars block TypeError: Cannot read private member #rid from an object whose class did not declare it
    at Kv.get (ext:deno_kv/01_db.ts:57:59)
    at ProjectCacheImpl.get (file:///Users/mcanouil/Projects/quarto/quarto-cli/src/core/cache/cache.ts:137:39)
    at ProjectCacheImpl._getAs (file:///Users/mcanouil/Projects/quarto/quarto-cli/src/core/cache/cache.ts:149:31)
    at ProjectCacheImpl.getString (file:///Users/mcanouil/Projects/quarto/quarto-cli/src/core/cache/cache.ts:192:17)
    at file:///Users/mcanouil/Projects/quarto/quarto-cli/src/core/cache/cache.ts:208:33
    at eventLoopTick (ext:core/01_core.js:175:7)
    at async handleVarsBlock (file:///Users/mcanouil/Projects/quarto/quarto-cli/src/core/sass.ts:384:22)
    at async file:///Users/mcanouil/Projects/quarto/quarto-cli/src/core/sass.ts:415:17
    at async SassCache.setFromHash (file:///Users/mcanouil/Projects/quarto/quarto-cli/src/core/sass/cache.ts:85:7)
    at async compileSass (file:///Users/mcanouil/Projects/quarto/quarto-cli/src/core/sass.ts:161:18)
The resulting CSS file will not have SCSS color variables exported as CSS.
This is likely a Quarto bug.
Please consider reporting it at https://github.com/quarto-dev/quarto-cli,
along with the _quarto_internal_scss_error.scss file that can be found in the current working directory.
ℹ R version 4.4.3 (2025-02-28)
! Config '~/.Rprofile' was loaded!


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

[2/2] index.qmd

Creating MECA Bundle
  3 article files
  5 source files
  1 notebook
  1 other file

Output created: _manuscript/index.html

[cderv]

Thanks @mcanouil I'll open a new issue for that one. This is new projectCache problem. I can reproduce it.

[cderv]

It seems to be a windows issue because unlike @mcanouil I can reproduce

Somehow, the HTML contains

<p class=""><a href="notebook_files/figure-html/unnamed-chunk-1-1.png"

but the notebook_files/ folder is not in _manuscript output dir. I'll investigate.

[mcanouil]

I forgot to link with the Git repository/directory: https://github.com/mcanouil/quarto-issues-experiments/tree/main/quarto-cli-12360

[cderv]

This is not working in previous 1.5 either nor 1.4... 🤔 So I wonder if this is some specificity in resource path to consider, or if there is a breakage knitr level 👀

[cderv]

Several observations:

• This is a knitr engine issue in notebooks. It does not happen with engine: jupyter notebook

• First quarto render of the project shows the problem. Here is the initial content

   ├── README.md
   ├── _quarto.yml
   ├── index.qmd
   ├── main.py
   ├── notebook
   │   ├── notebook.qmd
   │   └── notebook2.qmd
   ├── pyproject.toml
   ├── references.bib
   └── uv.lock
  

  after first render We don't see the notebook_files in the _manuscript folder but it is correctly saved in freeze. Here is the folder structure

   .
   ├── _freeze
   │   ├── notebook
   │   │   ├── notebook
   │   │   │   ├── execute─results
   │   │   │   ├── figure─html
   │   │   │   └── figure─jats
   │   │   └── notebook2
   │   │       ├── execute─results
   │   │       └── figure─html
   │   └── site_libs
   │       ├── bootstrap
   │       ├── clipboard
   │       ├── manuscript─notebook
   │       ├── quarto─contrib
   │       │   └── glightbox
   │       └── quarto─html
   │           └── tabsets
   ├── _manuscript
   │   ├── notebook
   │   │   └── notebook2_files
   │   │       └── figure─html
   │   └── site_libs
   │       ├── bootstrap
   │       ├── clipboard
   │       ├── manuscript─notebook
   │       ├── quarto─contrib
   │       │   └── glightbox
   │       └── quarto─html
   │           └── tabsets
   └── notebook
  

  we see that

  • _freeze gets everything.
  • _manuscript only get the _files folder for the notebook2 (which is Jupyter engine)
  • No notebook_files for the resource of engine knitr one

• Now second render

   .
   ├── _freeze
   │   ├── notebook
   │   │   ├── notebook
   │   │   │   ├── execute─results
   │   │   │   ├── figure─html
   │   │   │   └── figure─jats
   │   │   └── notebook2
   │   │       ├── execute─results
   │   │       └── figure─html
   │   └── site_libs
   │       ├── bootstrap
   │       ├── clipboard
   │       ├── manuscript─notebook
   │       ├── quarto─contrib
   │       │   └── glightbox
   │       └── quarto─html
   │           └── tabsets
   ├── _manuscript
   │   ├── notebook
   │   │   ├── notebook2_files
   │   │   │   └── figure─html
   │   │   └── notebook_files
   │   │       └── figure─html
   │   ├── notebook_files
   │   │   └── figure─jats
   │   └── site_libs
   │       ├── bootstrap
   │       ├── clipboard
   │       ├── manuscript─notebook
   │       ├── quarto─contrib
   │       │   └── glightbox
   │       └── quarto─html
   │           └── tabsets
   └── notebook
  

  This is probably working because folders have been moved from _freeze this time, and we see the folder in _manuscript

So there is a problem with freeze and knitr engine notebook in manuscript somehow.

[cderv]

This is not a freeze thing it seems as setting to false still shows the problem

execute:
  freeze: false

notebook_files directory is not there.

.
├── _manuscript
│   ├── notebooks
│   └── site_libs
│       ├── bootstrap
│       ├── clipboard
│       ├── manuscript─notebook
│       ├── quarto─contrib
│       │   └── glightbox
│       └── quarto─html
└── notebooks

So it is related to knitr and rendering to ipynb only, which is what happens in Manuscript 🤔