Datasets:

hamel

/

quarto-issues

like 0

### Bug description - I am trying to publish a Quatro document to my personal space in Confluence. - When I provide the parent URL for my personal space, it returns "ERROR: Invalid Confluence parent URL:" My personal space key is "~brian.smith". - I tried removing the "." and using a parent url with the space "~briansmith" and the command gets to "[✓] Verifying...", but fails because of course that space doesn't actually exist. - macOS 13.2.1 (22D68) - RStudio IDE: Version 2023.03.0+386 The .qmd is just: ``` --- title: "Confluence Document Test" author: "Brian Smith" format: html-confluence --- ## Overview My text will go here. --- ``` quarto check: [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.25 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.1.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.1/Resources/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

For JS formats, e.g. HTML, the kbd shortcode sniffs the users OS and inserts icons for the shortcut keys, e.g. `{{< kbd mac=Shift-Command-O >}}` becomes ⇧ ⌘ 0. Replacing the words with icons is making things much worse for those using screen readers, e.g. (thanks @ateucher and @gtritchie ) for ⇧, ⌘, ⌃, ⌥ NVDA on Windows reads: "upwards hollow arrow", "Mac command key", and says nothing about the Ctrl or the option symbols.

Hi, we are looking at using Quarto but the ability to render Python variables into markdown text, using something similar to the `` `r variable` `` syntax is very important for us, as we have lots of titles and captions with auto-updating dates. Unfortunately, per [this recent comment](https://community.rstudio.com/t/how-can-i-use-inline-code-in-a-quarto-document/160575/3), it's not currently possible. Is this on the roadmap, or are there any recommended workarounds? (shortcodes don't seem to be a good option because the variables are computed at runtime)

We already do this for broken .qmd links, so it might make sense to make the behavior more uniform, especially since we are making .ipynb content more central to quarto.

There are many tools that can be implemented as a GHA workflow, such as https://github.com/stevenvachon/broken-link-checker. _Originally posted by @mcanouil in https://github.com/quarto-dev/quarto-cli/issues/5372#issuecomment-1533248112_

This came up in https://github.com/microsoft/winget-pkgs/pull/103701#discussion_r1183721670 where it seems our wix bundle still have RStudio as publisher. https://github.com/quarto-dev/quarto-cli/blob/4a4e9f1226df1f6f994ac084b226150966bc7aa5/package/src/windows/quarto.wxs#L4 This will show in the Windows install, and also prevent updating manifest for Windows bundle on winget Do think there is other places @dragonstyle to update ? Probably for other installer too https://github.com/quarto-dev/quarto-cli/blob/4a4e9f1226df1f6f994ac084b226150966bc7aa5/package/src/linux/installer.ts#L82 https://github.com/quarto-dev/quarto-cli/blob/4a4e9f1226df1f6f994ac084b226150966bc7aa5/package/src/linux/installer.ts#L108 Thanks to @dpprdan finding all this Too bad I did not knew about that before the release... 😞

From discussion in https://github.com/quarto-dev/quarto-cli/issues/5349, a project having both file will be silent and it seems we can improve that. I think this is the function that detects both file https://github.com/quarto-dev/quarto-cli/blob/4a4e9f1226df1f6f994ac084b226150966bc7aa5/src/project/project-shared.ts#L90-L94 We could either warn or even error if we detect both

I am talking about the news folder https://github.com/quarto-dev/quarto-cli/tree/main/news It would be good to have the release note file available in quarto.org to point to when we do releases, especially in bundle where we release only stable version. (like chocolatey or winget). Currently we only show the all news in https://quarto.org/docs/download/ but with no stable url to find that back after release. (no way to find the 1.2 release not in quarto.org now that we change to 1.3 for example) I think it would be good to have those pages live on our website somewhere (even if hidden and one must know the link). Something like `https://quarto.org/news/1.2.md` ?

I pressed the "Render" button in VSCode and the following error appears: ```powershell PS C:\Users\xxx\Code\demo> quarto preview c:/Users/xxx/Code/demo/quarto/walkthrough.qmd --no-browser --no-watch-inputs ERROR: NotFound: 系统找不到指定的文件。 (os error 2), remove 'C:\Users\xxx\AppData\Local\quarto\jt\f55fba9f67420280e4ee' NotFound: 系统找不到指定的文件。 (os error 2), remove 'C:\Users\xxx\AppData\Local\quarto\jt\f55fba9f67420280e4ee' at Object.removeSync (deno:runtime/js/30_fs.js:157:9) at connectToKernel (file:///C:/Users/xxx/scoop/apps/quarto/current/bin/quarto.js:54706:18) at async executeKernelKeepalive (file:///C:/Users/xxx/scoop/apps/quarto/current/bin/quarto.js:54500:31) at async Object.execute (file:///C:/Users/xxx/scoop/apps/quarto/current/bin/quarto.js:55305:17) at async renderExecute (file:///C:/Users/xxx/scoop/apps/quarto/current/bin/quarto.js:86465:27) at async renderFiles (file:///C:/Users/xxx/scoop/apps/quarto/current/bin/quarto.js:86588:51) at async render (file:///C:/Users/xxx/scoop/apps/quarto/current/bin/quarto.js:90675:21) at async renderForPreview (file:///C:/Users/xxx/scoop/apps/quarto/current/bin/quarto.js:102408:26) at async render (file:///C:/Users/xxx/scoop/apps/quarto/current/bin/quarto.js:102303:20) at async preview (file:///C:/Users/xxx/scoop/apps/quarto/current/bin/quarto.js:102309:21) ``` Note: It doesn't happen every time. If the error occurs in this run, the next time it will succeed, and the next time there will be an error again.

### Bug description I have an issue when setting the background colours of titles and sub-titles. It would appear that the specified colour is having some transparency applied. In the snippet provided I can match the colours by altering the transparency of the subtitle to that in the commented out line. ```` --- title: 'A title' subtitle: 'A subtitle' --- ```{=html} <style> h1.title { color:white; background-color: #1b3445; } h1.title + p.subtitle { color: white; background-color: #1b3445; /* background-color: #1b3445e6; */ margin-top: 0; } </style> ``` ```` <img width="285" alt="image" src="https://user-images.githubusercontent.com/43386915/235903690-f178226d-b4cc-4c22-9201-1bb3aa258b96.png"> --- title: 'A title' subtitle: 'A subtitle' --- ```{=html} <style> h1.title { color:white; background-color: #1b3445; } p.subtitle { color: white; background-color: #1b3445; /* background-color: #1b3445e6; */ margin-top: 0; } </style> ``` ************************ - MacOS - Ventura 13.3.1 - Rstudio - RStudio 2023.03.0+386 "Cherry Blossom" Release (3c53477afb13ab959aeb5b34df1f10c237b256c3, 2023-03-09) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.03.0+386 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36 - Quarto v `1.3.340` - Have also checked v `1.4.25` __Quarto check__ [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.25 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.13 (Conda) Path: /usr/local/anaconda3/bin/python Jupyter: 4.11.1 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.3.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description I was using quarto with a filter for pandoc, it was working great but it is not working anymore. I am working on a custom filter developed with [panflute](https://github.com/sergiocorreia/panflute) to render plantuml diagram in image. A library used to develop pandoc filter with python. A similar filter can be found [here](https://github.com/timofurrer/pandoc-plantuml-filter). I was trying to improve it. I got the same error with this filter too. I was using it with the `filters` parameter like this in a `index.qmd` file: ```yaml --- execute: echo: false pagination_next: null filters: - custom-filter editor: render-on-save: true --- # Welcome for fun ```plantuml @startuml actor "User" as user @enduml ``` ``` _This file is in a quarto project to render it in a docusaurus website._ The code block was rendered into image by my custom filter. I assume the filter was passed to pandoc directly because the filter is working great with `--filter` of pandoc cli. Now I got the following error: ```console > quarto preview /home/user/project/template_docs/docs/index.qmd --no-browser --no-watch-inputs pandoc to: >- markdown_strict+raw_html+all_symbols_escapable+backtick_code_blocks+fenced_code_blocks+space_in_atx_header+intraword_underscores+lists_without_preceding_blankline+shortcut_reference_links+autolink_bare_uris+emoji+footnotes+gfm_auto_identifiers+pipe_tables+strikeout+task_lists+tex_math_dollars+pipe_tables+tex_math_dollars+header_attributes+raw_html+all_symbols_escapable+backtick_code_blocks+fenced_code_blocks+space_in_atx_header+intraword_underscores+lists_without_preceding_blankline+shortcut_reference_links output-file: index.md standalone: true default-image-extension: png wrap: none html-math-method: webtex metadata pagination_next: null editor: render-on-save: true Error running filter /opt/quarto/share/filters/main.lua: Error running filter /home/user/project/template_docs/docs/custom-filter: Could not find executable /home/user/project/template_docs/docs/custom-filter stack traceback: /opt/quarto/share/filters/main.lua:4026: in function </opt/quarto/share/filters/main.lua:4005> [C]: in ? [C]: in method 'walk' /opt/quarto/share/filters/main.lua:171: in function 'run_emulated_filter' /opt/quarto/share/filters/main.lua:449: in local 'callback' /opt/quarto/share/filters/main.lua:454: in upvalue 'run_emulated_filter_chain' /opt/quarto/share/filters/main.lua:495: in function </opt/quarto/share/filters/main.lua:476> stack traceback: /opt/quarto/share/filters/main.lua:171: in function 'run_emulated_filter' /opt/quarto/share/filters/main.lua:449: in local 'callback' /opt/quarto/share/filters/main.lua:454: in upvalue 'run_emulated_filter_chain' /opt/quarto/share/filters/main.lua:495: in function </opt/quarto/share/filters/main.lua:476> ``` Operating system : WSL on Ubuntu 20.04.6 Quarto check: ``` > quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.3 Path: /home/user/.pyenv/versions/3.11.3/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

## Description Unlisted Vimeo videos produce a link that does not work with the Quarto shortcode {{ video }} ## Steps to Reproduce - Log in with a Standard Account. - select a video with privacy settings "unlisted" - click the share link button - The link copied to the clipboard is `https://vimeo.com/800138810/fdcc90d662?share=copy` - Use this link in the video short code `{{< video https://vimeo.com/800138810/fdcc90d662?share=copy >}}` ## Expected Result: A video snippet is created with the url. The video snippet can load the video. ## Actual Result: Using this link with the shortcode results in the error message "Invalid embedding-code" ### Workaround Replace the slash in the privacy hash with `"?h="` and delete `"?share=copy"` so `{{< video https://vimeo.com/800138810?h=fdcc90d662 >}}` Please note: the privacy setting "Hide from Vimeo", that creates links for embedding only, does not (!) contain a privacy hash and works well with the shortcode `{{< video https://vimeo.com/800139587?share=copy >}}` so no problem for "Hide-from-Vimeo" videos as of writing this post, but only for "Unlisted" videos.

The `og:image` tag doesn't show up in my website header tags if the only thing I do is set the following in `_quarto.yml` ```yaml website: title: "nbdev Tutorial: JupyterCon 2023" image: nbdev.png site-url: "https://fastai.github.io/jupytercon-2023/" open-graph: true ``` From [this file](https://github.com/fastai/jupytercon-2023/blob/main/_quarto.yml#L1C1-L23) According to the [docs](https://quarto.org/docs/reference/projects/websites.html#social) this should work. " By default, Quarto will use the image value from the format metadata." The reason I think this is a bug is then repeat this in a page front matter [like so](https://github.com/fastai/jupytercon-2023/blob/main/index.qmd), **then the image propagates to ALL pages on the site**. ```yaml --- title: "nbdev Tutorial" description: "An outline of the nbdev + Quarto tutorial for JupyterCon, 2023." image: nbdev.png --- ``` Here is a repo you can use to play with this https://github.com/fastai/jupytercon-2023 I tried this on both the bleeding edge `1.4.25` and stable `1.3.340` and happens in both places cc: @jjallaire @seem @mcanouil

### Bug description I've been working on a presentation at my job with a `http://myserver.local:8000/` being on the local network. The presentation includes Mermaid diagrams, and when the demo URL isn't available (whilst at home), the diagrams don't render. My workspace is a Docker container with Quarto cloned, in previewing mode, with Vim as editor (no plugin installed). **Environment**: * Host MacOS `13.3.1` (x86) * Docker `python:3.8` (Debian I believe) * `CMD ["quarto", "preview", "/Content", "--port", "8000", "--host", "0.0.0.0", "--timeout", "0", "--no-browser"]` * `jupyter matplotlib plotly` through pip **Quarto check**: ```bash $ docker exec keynote-presentation-1 quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Service/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.16 Path: /usr/local/bin/python3 Jupyter: 5.3.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` **Minimum working example**: `_quarto.yml`: ```yml project: output-dir: _output render: - index.qmd format: revealjs title: "Presentation" view-distance: 3 ``` `index.qmd`: ````md --- title: "foo" --- ## My Mermaid slide ```{mermaid} flowchart LR A --> B B --> A ``` ## My img slide <img src="http://myunreachableserver.local:8000/"> ```` Commenting out the `<img>` tag will render the diagram instead of it echoing its declaration. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description The language choice picked in YAML (`lang: it`)renders correctly in **html**, but fails in **docx** output for table caption (lang and crossreff). [docx_issues.docx](https://github.com/quarto-dev/quarto-cli/files/11372291/docx_issues.docx) ````qmd --- title: "docx_issues" lang: it toc: true format: html: toc-title: Indice embed-resources: true # external dependencies embedded (Not in ..._files/) docx: toc-title: Indice embed-resources: true # external dependencies embedded (Not in ..._files/) --- ## Issue Rendering in **html**: 1. crossreference of table (@tbl-test) works correctly 2. and shows the title in the required language picked in YAML `lang: it` (**"Tabella 1: table title"**) Rendering in **word** INSTEAD: 1. crossreference of table (@tbl-test) does **NOT** work 2. and shows the title **NOT** in the required language picked in YAML `lang: it`(**"Table 1: table title"**) ```{r} #| label: tbl-test #| echo: false #| warning: false #| output: true #| tbl-cap: "table title" library(quarto) library(flextable) library(magrittr) ft <- mtcars %>% head() %>% flextable() ft ``` + R version 4.2.2 (2022-10-31) + R Studio Version 2022.12.0+353 (2022.12.0+353) + Quarto Version ‘1.2.258’ ```` [✓] Checking Quarto installation......OK Version: 1.2.258 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.13 Path: /Library/Frameworks/Python.framework/Versions/3.9/bin/python3 Jupyter: 5.2.0 Kernels: python3, python2 (-) 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 16, in <module> import nbformat ModuleNotFoundError: No module named 'nbformat' [✓] Checking Jupyter engine render....OK ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

Currently, Quarto does not support Pandoc arguments that affect the reader format. This prevents the use of other markdown variants as input formats. As an example, these currently don't work: ``` reader: commonmark_x ``` ``` from: commonmark_x ``` ``` pandoc_args: ['-f commonmark_x+hard_line_breaks+lists_without_preceding_blankline'] ``` Would it be possible to change this in the future to allow the use of `commonmark_x`? _Originally posted by @bcdavasconcelos in https://github.com/quarto-dev/quarto-cli/issues/4905#issuecomment-1530001238_

Currently you must do the following to execute cells with Quarto. You either have to: 1. pass the `--execute` flag to `quarto preview` or `quarto render` 2. Set the `enabled: true` flag as specified [here](https://quarto.org/docs/computations/python.html#workflow) However, this is confusing for many reasons 1. `enabled` is not documented here under execution options https://quarto.org/docs/reference/formats/ipynb.html#execution 2. The [documentation suggests](https://quarto.org/docs/reference/cells/cells-jupyter.html#code-output) that setting `eval: true` should make quarto execute that cell (or notebook, if placed in the front matter). However, this is not the case. You have to additionally take the steps in number 1. 3. If you have a project where some notebooks are executed but others are not, this leads to **Quarto deleting all cell outputs** in notebooks where `eval: false` on cells (or for the whole notebook if in front matter). However, I don't think this is desirable for notebooks, because you may have long-running computations that generate some output that you don't want get clobbered by Quarto - and it looks like there isn't a way to "protect" those cells or notebooks? cc: @jjallaire @seem @cderv @mcanouil BTW I'm on `1.3.333`

### Bug description I was writing a blog post (<https://github.com/mcanouil/mickael.canouil.fr/pull/86>) when I realised at rendering time that you can't use code annotation in list (numbered and unnumbered) which is a bit unexpected and a bit annoying I must say 😅. Below a smaller version exhibiting the issue. <details><summary>See Quarto document.</summary> ````qmd --- format: html code-annotations: hover --- 1. Step 1 ```bash ARG QUARTO_VERSION="1.3.340" FROM ghcr.io/quarto-dev/quarto:${QUARTO_VERSION} AS builder # <1> ARG RIG_VERSION="latest" ARG R_VERSION="release" COPY install-rig.sh /tmp/install-rig.sh RUN bash /tmp/install-rig.sh "${RIG_VERSION}" # <2> RUN rig add ${R_VERSION} && Rscript -e 'pak::pkg_install("renv")' # <3> COPY mywebsite /app # <4> WORKDIR /app RUN Rscript -e "renv::restore()" RUN quarto render . # <5> FROM httpd:alpine # <6> COPY --from=builder /app/_site/ /usr/local/apache2/htdocs/ # <7> ``` 1. The base Docker image use to be the builder, here it is the Quarto image which is Ubuntu based image with Quarto pre-installed. The `builder` stage is used to install the `rig` and the specified R version, and to render the website. 2. The `install-rig.sh` script is used to install the `rig` software. 3. Using `rig`, we add the specified R version and install the `renv` package. 4. We copy the Quarto project into the `/app` directory of the builder. 5. We restore the `renv` environment and render the website. 6. The second and last stage is the `httpd:alpine` image which is a light image with Apache pre-installed. 7. We copy the rendered website from the `builder` to the `/usr/local/apache2/htdocs/` directory of the second stage. 2. Step 2 ```bash docker buildx build \ --platform "linux/amd64" \ # <1> --build-arg QUARTO_VERSION=1.3.340 \ # <2> --tag "mywebsite:1.0.0" \ # <3> . ``` 1. We specify the platform to build the image for. 2. We specify the Quarto version to use during the build. 3. We tag the image with the name `mywebsite` and the version `1.0.0`. This is useful to be able to identify the image later. 3. Step 3 ```bash docker container run \ --detach \ # <1> --platform "linux/amd64" \ # <2> --name mywebsite \ # <3> --publish 8080:80 \ # <4> mywebsite:1.0.0 # <5> ``` 1. We run the container in detached mode. 2. We specify the platform to define the architecture of the container, thus the image to use. 3. We name the container `mywebsite`, to ease identification. 4. We publish the port `8080` of the host to the port `80` of the container. This is useful to be able to access the website from the host. 5. We specify the image to use. ```` </details> <img width="608" alt="image" src="https://user-images.githubusercontent.com/8896044/235496953-699b2218-bc64-46f7-9369-0c66475e5acc.png"> --- Rendered via Quarto CLI in terminal on MacOS Apple Silicon using the latest dev version of Quarto. ```bash [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Users/mcanouil/Projects/quarto/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.3 Path: /Users/mcanouil/Projects/misc/quarto-playground/env/bin/python Jupyter: 5.3.0 Kernels: python3 (\) Checking Jupyter engine render....0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. [✓] Checking Jupyter engine render....OK (\) Checking R installation...........ℹ R version 4.3.0 (2023-04-21) ! Config '~/.Rprofile' was loaded! [✓] Checking R installation...........OK Version: 4.3.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/mcanouil/Projects/misc/quarto-playground/renv/library/R-4.3/aarch64-apple-darwin20 - /Users/mcanouil/Library/Caches/org.R-project.R/R/renv/sandbox/R-4.3/aarch64-apple-darwin20/84ba8b13 knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description When I add a figure before another figure which includes some math symbols, then math symbols is disappeared. The first figure. ```{r} # https://plotly.com/r/reference/scatter/ plotly::plot_ly(data = quakes, x = ~long, y = ~lat) |> plotly::add_markers() ``` Here is another figure. ```{r} x <- seq(from = -4, to = 8, length.out = 193) y1 <- dnorm(x, mean = 3, sd = 1) plotly::plot_ly( x = x, y = y1, type = "scatter", mode = "lines", fill = "tozeroy", fillcolor = "rgba(102, 102, 102, 0.2)", text = ~ paste0( "x：", x, "<br>", "y：", round(y1, 3), "<br>" ), hoverinfo = "text", name = plotly::TeX("\\mathcal{N}(3,1^2)"), line = list(shape = "spline", color = "#666666") ) |> plotly::layout( xaxis = list( showgrid = F, title = plotly::TeX("x") ), yaxis = list( showgrid = F, title = plotly::TeX("f(x)") ), legend = list(x = 0.8, y = 1, orientation = "v") ) |> plotly::config( mathjax = "cdn", displayModeBar = FALSE ) ``` ## The whole Qmd file ````md --- title: "Untitled" format: html: toc: true html-math-method: mathjax editor: visual --- ```{r} # https://plotly.com/r/reference/scatter/ plotly::plot_ly(data = quakes, x = ~long, y = ~lat) |> plotly::add_markers() ``` ```{r} x <- seq(from = -4, to = 8, length.out = 193) y1 <- dnorm(x, mean = 3, sd = 1) plotly::plot_ly( x = x, y = y1, type = "scatter", mode = "lines", fill = "tozeroy", fillcolor = "rgba(102, 102, 102, 0.2)", text = ~ paste0( "x：", x, "<br>", "y：", round(y1, 3), "<br>" ), hoverinfo = "text", name = plotly::TeX("\\mathcal{N}(3,1^2)"), line = list(shape = "spline", color = "#666666") ) |> plotly::layout( xaxis = list( showgrid = F, title = plotly::TeX("x") ), yaxis = list( showgrid = F, title = plotly::TeX("f(x)") ), legend = list(x = 0.8, y = 1, orientation = "v") ) |> plotly::config( mathjax = "cdn", displayModeBar = FALSE ) ``` ```` ## My Sessoninfo - Quarto 1.3.340 - plotly 4.10.1 RStudio 2023.03.0+386 "Cherry Blossom" Release (3c53477afb13ab959aeb5b34df1f10c237b256c3, 2023-03-09) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.03.0+386 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36 ```r sessionInfo() ``` ``` R version 4.3.0 (2023-04-21) Platform: x86_64-apple-darwin22.4.0 (64-bit) Running under: macOS Ventura 13.3.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /usr/local/Cellar/r/4.3.0/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 loaded via a namespace (and not attached): [1] gtable_0.3.3 jsonlite_1.8.4 dplyr_1.1.2 [4] compiler_4.3.0 tidyselect_1.2.0 Rcpp_1.0.10 [7] later_1.3.0 tidyr_1.3.0 scales_1.2.1 [10] yaml_2.3.7 fastmap_1.1.1 ggplot2_3.4.2 [13] R6_2.5.1 generics_0.1.3 knitr_1.42 [16] htmlwidgets_1.6.2 tibble_3.2.1 munsell_0.5.0 [19] pillar_1.9.0 rlang_1.1.0 utf8_1.2.3 [22] xfun_0.39 lazyeval_0.2.2 viridisLite_0.4.1 [25] plotly_4.10.1 cli_3.6.1 magrittr_2.0.3 [28] ps_1.7.5 digest_0.6.31 grid_4.3.0 [31] processx_3.8.1 rstudioapi_0.14 lifecycle_1.0.3 [34] vctrs_0.6.2 evaluate_0.20 glue_1.6.2 [37] data.table_1.14.8 fansi_1.0.4 colorspace_2.1-0 [40] rmarkdown_2.21 purrr_1.0.1 httr_1.4.5 [43] tools_4.3.0 pkgconfig_2.0.3 quarto_1.2 [46] htmltools_0.5.5 ``` ``` quarto check ``` ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.3 Path: /usr/local/opt/[email protected]/bin/python3.11 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.3.0 Path: /usr/local/Cellar/r/4.3.0/lib/R LibPaths: - /usr/local/lib/R/4.3/site-library - /usr/local/Cellar/r/4.3.0/lib/R/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

At the bottom of "notebook-views" section the link to the "live preview for the Penguins notebook" is broken (see <https://quarto.org/docs/authoring/notebook-embed.html#notebook-views>)[^1]. <img width="1508" alt="Screenshot 2023-05-01 at 15 08 18" src="https://user-images.githubusercontent.com/8896044/235455841-b0e6f57e-7360-4d2f-b800-60aa6817d41c.png"> [^1]: There is no notebooks in <https://github.com/quarto-dev/quarto-web/tree/main/docs/prerelease/1.3> and no idea where the notebook might be or what it should be.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5369 <div type='discussions-op-text'> ^{Originally posted by **DayuanJiang** May 1, 2023} My first paragraph is quite lengthy in my post, but when the description is generated on the index page, it only displays the first few words. How can I control the behavior of the description generation? My blog site is here: [blog](https://www.jiang.jp/) **post page**  **index page**  </div>

### Bug description When I compile a beamer document with `lualatex`, the total frame number would be fixed at 1. For example, when I rendered the following `.qmd` file with three slides, the total frame number was fixed at 1, and each frame number became 1/1, 2/1, 3/1, such as shown below:  When I set `pdf-engine` to `xelatex` instead, the issue disappeared. When I used `latexmk` on my device to compile the generated `.tex` file, the issue would also disappear. I am running Quarto 1.3.340 on macOS 13.3.1. My device is the 2020 MacBook Pro with the Apple M1 chip. Below is the output of `quarto check`: ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.3 Path: /opt/homebrew/opt/[email protected]/bin/python3.11 Jupyter: 5.3.0 Kernels: ir, julia-1.8 NOTE: No Jupyter kernel for Python found [✓] Checking R installation...........OK Version: 4.3.0 Path: /opt/homebrew/Cellar/r/4.3.0/lib/R LibPaths: - /opt/homebrew/lib/R/4.3/site-library - /opt/homebrew/Cellar/r/4.3.0/lib/R/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ``` Below the `.qmd` source code of a minimal example: ```qmd --- format: beamer: pdf-engine: lualatex theme: CambridgeUS keep-tex: true --- ## First page first sentence ## Second page second sentence ## Third page third sentence ``` Below is the source code of the generated `.tex` file: ```tex % Options for packages loaded elsewhere \PassOptionsToPackage{unicode}{hyperref} \PassOptionsToPackage{hyphens}{url} % \documentclass[ ignorenonframetext, ]{beamer} \usepackage{pgfpages} \setbeamertemplate{caption}[numbered] \setbeamertemplate{caption label separator}{: } \setbeamercolor{caption name}{fg=normal text.fg} \beamertemplatenavigationsymbolsempty % Prevent slide breaks in the middle of a paragraph \widowpenalties 1 10000 \raggedbottom \setbeamertemplate{part page}{ \centering \begin{beamercolorbox}[sep=16pt,center]{part title} \usebeamerfont{part title}\insertpart\par \end{beamercolorbox} } \setbeamertemplate{section page}{ \centering \begin{beamercolorbox}[sep=12pt,center]{part title} \usebeamerfont{section title}\insertsection\par \end{beamercolorbox} } \setbeamertemplate{subsection page}{ \centering \begin{beamercolorbox}[sep=8pt,center]{part title} \usebeamerfont{subsection title}\insertsubsection\par \end{beamercolorbox} } \AtBeginPart{ \frame{\partpage} } \AtBeginSection{ \ifbibliography \else \frame{\sectionpage} \fi } \AtBeginSubsection{ \frame{\subsectionpage} } \usepackage{amsmath,amssymb} \usepackage{iftex} \ifPDFTeX \usepackage[T1]{fontenc} \usepackage[utf8]{inputenc} \usepackage{textcomp} % provide euro and other symbols \else % if luatex or xetex \usepackage{unicode-math} \defaultfontfeatures{Scale=MatchLowercase} \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1} \fi \usepackage{lmodern} \usetheme[]{CambridgeUS} \ifPDFTeX\else % xetex/luatex font selection \fi % Use upquote if available, for straight quotes in verbatim environments \IfFileExists{upquote.sty}{\usepackage{upquote}}{} \IfFileExists{microtype.sty}{% use microtype if available \usepackage[]{microtype} \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts }{} \makeatletter \@ifundefined{KOMAClassName}{% if non-KOMA class \IfFileExists{parskip.sty}{% \usepackage{parskip} }{% else \setlength{\parindent}{0pt} \setlength{\parskip}{6pt plus 2pt minus 1pt}} }{% if KOMA class \KOMAoptions{parskip=half}} \makeatother \usepackage{xcolor} \newif\ifbibliography \setlength{\emergencystretch}{3em} % prevent overfull lines \setcounter{secnumdepth}{-\maxdimen} % remove section numbering \providecommand{\tightlist}{% \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}\usepackage{longtable,booktabs,array} \usepackage{calc} % for calculating minipage widths \usepackage{caption} % Make caption package work with longtable \makeatletter \def\fnum@table{\tablename~\thetable} \makeatother \usepackage{graphicx} \makeatletter \def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi} \def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi} \makeatother % Scale images if necessary, so that they will not overflow the page % margins by default, and it is still possible to overwrite the defaults % using explicit options in \includegraphics[width, height, ...]{} \setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio} % Set default figure placement to htbp \makeatletter \def\fps@figure{htbp} \makeatother \makeatletter \makeatother \makeatletter \makeatother \makeatletter \@ifpackageloaded{caption}{}{\usepackage{caption}} \AtBeginDocument{% \ifdefined\contentsname \renewcommand*\contentsname{Table of contents} \else \newcommand\contentsname{Table of contents} \fi \ifdefined\listfigurename \renewcommand*\listfigurename{List of Figures} \else \newcommand\listfigurename{List of Figures} \fi \ifdefined\listtablename \renewcommand*\listtablename{List of Tables} \else \newcommand\listtablename{List of Tables} \fi \ifdefined\figurename \renewcommand*\figurename{Figure} \else \newcommand\figurename{Figure} \fi \ifdefined\tablename \renewcommand*\tablename{Table} \else \newcommand\tablename{Table} \fi } \@ifpackageloaded{float}{}{\usepackage{float}} \floatstyle{ruled} \@ifundefined{c@chapter}{\newfloat{codelisting}{h}{lop}}{\newfloat{codelisting}{h}{lop}[chapter]} \floatname{codelisting}{Listing} \newcommand*\listoflistings{\listof{codelisting}{List of Listings}} \makeatother \makeatletter \@ifpackageloaded{caption}{}{\usepackage{caption}} \@ifpackageloaded{subcaption}{}{\usepackage{subcaption}} \makeatother \makeatletter \@ifpackageloaded{tcolorbox}{}{\usepackage[skins,breakable]{tcolorbox}} \makeatother \makeatletter \@ifundefined{shadecolor}{\definecolor{shadecolor}{rgb}{.97, .97, .97}} \makeatother \makeatletter \makeatother \makeatletter \makeatother \ifLuaTeX \usepackage{selnolig} % disable illegal ligatures \fi \IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}} \IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available \urlstyle{same} % disable monospaced font for URLs \hypersetup{ hidelinks, pdfcreator={LaTeX via pandoc}} \author{} \date{} \begin{document} \ifdefined\Shaded\renewenvironment{Shaded}{\begin{tcolorbox}[borderline west={3pt}{0pt}{shadecolor}, frame hidden, boxrule=0pt, sharp corners, breakable, enhanced, interior hidden]}{\end{tcolorbox}}\fi \begin{frame}{First page} \protect\hypertarget{first-page}{} first sentence \end{frame} \begin{frame}{Second page} \protect\hypertarget{second-page}{} second sentence \end{frame} \begin{frame}{Third page} \protect\hypertarget{third-page}{} third sentence \end{frame} \end{document} ``` Below is the terminal message from `quarto render` with `lualatex`: ``` pandoc to: beamer output-file: new.tex standalone: true pdf-engine: lualatex variables: graphics: true tables: true default-image-extension: pdf metadata block-headings: true theme: CambridgeUS running lualatex - 1 This is LuaHBTeX, Version 1.16.0 (TeX Live 2023) restricted system commands enabled. Output created: new.pdf ``` Below is the terminal message of the same command with `xelatex`: ``` pandoc to: beamer output-file: new.tex standalone: true pdf-engine: xelatex variables: graphics: true tables: true default-image-extension: pdf metadata block-headings: true theme: CambridgeUS running xelatex - 1 This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode running xelatex - 2 This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode Output created: new.pdf ``` Somehow for `lualatex`, the LaTeX command was run only once. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

I was able to reproduce a regression (in 1.4) for `number-sections` YAML option for websites and books[^1]. ```bash quarto create-project --type website:blog website echo " number-sections: true" >> website/_quarto.yml echo -e "\n\n## Heading 1\n\n### Heading 2\n\n## Heading 3" >> website/about.qmd quarto preview website ``` | 1.3 | 1.4 | |:---:|:---:| | <img width="1507" alt="image" src="https://user-images.githubusercontent.com/8896044/235436763-3044c512-6fe4-4ee7-872b-e2fd1d690185.png"> | <img width="1505" alt="image" src="https://user-images.githubusercontent.com/8896044/235436815-0084bed1-1a10-4d2c-8813-9b010c59e7a7.png"> | [^1]: Discussed in <https://github.com/quarto-dev/quarto-cli/discussions/5364>

### Bug description Hello, In the release 1.3, plots drawn using seaborn.objects (not seaborn) do not appear in HTML while they do in editors. It has been ok with the previous versions. MacOS 13.3.1 ```python import seaborn as sns import seaborn.objects as so tips = sns.load_dataset("tips") so.Plot(data=tips, x="total_bill", y="tip").add(so.Dot()) ``` The above code works perfectly in VS Code, but when quarto renders the ipynb file, the plot does not show up in the rendered HTML Thanks. ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Relationships are described with <span> tags in quarto with RStudio. I have checked same issues are occurred in VSCode. # qmd file ```` --- title: "Mermaid Diagram" format: html: theme: superhero self-contained: true mermaid: theme: dark --- ## Class Diagram ```{mermaid} %%| echo: true classDiagram Class01 <|-- AveryLongClass : Cool <<Interface>> Class01 Class09 --> C2 : Where am I? Class09 --* C3 Class09 --|> Class07 Class07 : equals() Class07 : Object[] elementData Class01 : size() Class01 : int chimp Class01 : int gorilla class Class10 { <<service>> int id size() } ``` ```` The output is as follows; <img width="811" alt="2023-05-01 9 45 35" src="https://user-images.githubusercontent.com/29029659/235384291-388fc23d-5921-4cab-94c8-6c1f6a0e60a8.png"> RStudio IDE version: * RStudio 2023.03.0+386 "Cherry Blossom" Release (3c53477afb13ab959aeb5b34df1f10c237b256c3, 2023-03-09) for macOS * Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.03.0+386 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36 OS: * Mac Monterey 12.2, Apple M1 Quarto check: [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /Applications/quarto/bin ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Hello dear quarto developers. When upgrading to quarto 1.3, quarto changed the way to transform may `qmd` files with python executable cells to `html`. This bug appeared after 1.3.146 that worked normally and current 1.3.340 where the first heading is moved to top of file as a title **when there is a notebook intermediate file**. Example: Some paragraph ## This is first heading and not the title The first heading is transformed in title and placed at the top of the document. ## Exécution ```{python} print("Hello") ``` Will be rendered with `This is first heading and not the title` as the title in the top of the document in the title block. **But**, if the python cell is converted to normal code block(not executed) `This is first heading and not the title` stays where it is as a h2 heading like this was rendered in previous quarto versions. It seems that the bug occurs when converting the `ipynb` file to `html` because in the notebook the first heading is preserved. Example runned on fresh archlinux. ``` [ben@archben ~]$ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.10 Path: /usr/bin/python3 Jupyter: 5.3.0 Kernels: lua, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

I have noticed that when I have made changes to a post that has to run Python or R code, the changes do not get published (`quarto publish`) or previewed (`quarto preview`) unless I delete first the folder in the `freeze` directory and repeat the process. I have set `freeze: true` in my `metadata` file Any help understanding and fixing this unexpected behaviour?

### Bug description I am using version 1.4 of quarto (pre-release) to build a website. I want to place different contents in the margin using the block : ::: {.column-margin} content ::: The content placed in the margin mixes with the menu of the page. Are the two compatible? If not, how do I deactivate the page menu (I don't see any indication in the documentation).  ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

```` --- title: "plotly plot" --- ```{python} import plotly.express as px import plotly.io as pio df = px.data.iris() fig = px.scatter(df, x="sepal_width", y="sepal_length", color="species", marginal_y="violin", marginal_x="box", trendline="ols", template="simple_white") fig.show() ``` ```` A user suggests that smooth-scroll is to blame. ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2920 <div type='discussions-op-text'> ^{Originally posted by **lukefullard** October 18, 2022} Hi all, Occasionally when I load a html page with inspect mode activated I see the following error in the console: ``` site_compare.html:3905 Uncaught Error: Mismatched anonymous define() module: [object Object] https://requirejs.org/docs/errors.html#mismatch at makeError (site_compare.html:3905:1803) at T (site_compare.html:3905:8685) at site_compare.html:3905:15076 ``` Also, sometimes Python generated figures don't show unless I refresh the page. Has anyone had this issue before? Thanks</div>

### Bug description Currently, it looks like the date is formatted by quarto, and then the pandoc variable date is set accordingly. Thus, using `$date$` in any template renders the formatted date. While I don't know how this would be implemented, is it possible to use multiple formats at different locations in the template? ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Taking the example from https://quarto.org/docs/prerelease/1.4/typst.html ````md --- title: "My document" format: typst --- Hello, typst! ```` when I run this on my Mac I get: ``` quarto render typst1.qmd pandoc to: typst output-file: typst1.typ standalone: true shift-heading-level-by: -1 default-image-extension: svg wrap: none metadata title: My document ERROR: You need to install the Typst CLI in order to render typst documents. Installing Typst: https://github.com/typst/typst#installation ``` typst is installed though (via home-brew) ``` $ which typst /opt/homebrew/bin/typst ``` ``` $ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.14 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.1 Path: /Users/stephen/.pyenv/versions/3.11.1/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.3 Path: /opt/homebrew/Cellar/r/4.2.3/lib/R LibPaths: - /Users/stephen/NOBACKUP/RLIB - /opt/homebrew/Cellar/r/4.2.3/lib/R/library knitr: 1.41 rmarkdown: 2.19 [✓] Checking Knitr engine render......OK $ uname -a Darwin blur.local 22.4.0 Darwin Kernel Version 22.4.0: Mon Mar 6 20:59:28 PST 2023; root:xnu-8796.101.5~3/RELEASE_ARM64_T6000 arm64 ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description [Here](https://quarto.org/docs/reference/formats/html.html#format-options) is an example of a webpage which is confusing to read. Once someone becomes more comfortable with Quarto, it's hard to tell if a command is specifically for _quarto.yml, specifically for index.qmd or about.qmd, a yaml (say in doc xxx.qmd), a subsection (in xxx.qmd), or _publish.yml. - For example, _I may want to set my figures in my HTML webpage xxx.qmd to centred_. The linked website + image make it hard to know if these are commands to use in the **\!\[\]()** or the **yaml.** This is more of a stylistic choice for simplifying communication, but it is such a barrier to using Quarto that it kind of is a bug. - For example, if the keys were even colour-coded rather than just purple, that might help users know which commands were for a yaml, for which doc type, or if they are feature-specific (in text only). Thanks so much! <img width="788" alt="Screenshot 2023-04-29 at 10 16 36 AM" src="https://user-images.githubusercontent.com/81820608/235307560-6f55879b-cd8e-4c96-ba5f-5af9098b519c.png"> **System Info** - Mac OS - R version 4.2.2 (2022-10-31) **Quarto Check** [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.326 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.13 (Conda) Path: /Applications/anaconda3/bin/python Jupyter: 4.11.2 Kernels: python3, ir [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

I recently switched to Quarto 1.3, so I can have the option to include other formats in my blog posts. Sadly, this option does not work for me. Here is the error I get: ``` ERROR: Error executing '/Users/safishajjouz/Library/TinyTeX/bin/universal-darwin/tlmgr': No such file or directory (os error 2) Error: Error executing '/Users/safishajjouz/Library/TinyTeX/bin/universal-darwin/tlmgr': No such file or directory (os error 2) at execProcess (file:///Applications/quarto/bin/quarto.js:5630:15) at execTlmgr (file:///Applications/quarto/bin/quarto.js:85261:16) at tlmgrCommand (file:///Applications/quarto/bin/quarto.js:85275:16) at findPackages (file:///Applications/quarto/bin/quarto.js:85119:35) at Object.searchPackages (file:///Applications/quarto/bin/quarto.js:85482:20) at runLatexCommand (file:///Applications/quarto/bin/quarto.js:85440:60) at async runPdfEngine (file:///Applications/quarto/bin/quarto.js:85346:21) at async initialCompileLatex (file:///Applications/quarto/bin/quarto.js:85780:26) at async generatePdf (file:///Applications/quarto/bin/quarto.js:85754:22) at async Object.complete (file:///Applications/quarto/bin/quarto.js:86026:27) ``` My posts configurations are: ``` --- title: "Fed's Forward Guidance" subtitle: "*Some Stylised Facts and recent performance*" date: "04/22/2023" draft: false categories: - Monetary Policy - Inflation execute: echo: false format: html: default ipynb: default pdf: default title-block-banner: false comments: hypothesis: theme: clean --- ``` In case this helps this is the post/file: https://github.com/msh855/TheQuantEconomist/tree/main/posts/Hawkish_Fed

### Bug description About this machine and it's version of R and RStudio: ```{r} > tibble::enframe(Sys.info()) |> + dplyr::filter(name %in% c('sysname','release','version','machine')) # A tibble: 4 × 2 name value <chr> <chr> 1 sysname Windows 2 release 10 x64 3 version build 22621 4 machine x86-64 > paste(R.version$major, R.version$minor, sep='.') [1] "4.3.0" > RStudio.Version()$long_version [1] "2023.03.0+386" > quarto::quarto_version() [1] ‘1.4.11’ ``` In the project's `_quarto.yaml` are: ```{r} engine: knitr project: type: book book: title: "fancy title" author: "me" date: today date-format: long reader-mode: true ``` Note that I have attempted to add in the `engine: knitr` option as suggested in [https://github.com/quarto-dev/quarto-cli/discussions/4855](https://github.com/quarto-dev/quarto-cli/discussions/4855) The `index.qmd` contains: ```{r} # Preface {.unnumbered} These notes have been developed with: - R version `r paste(R.version$major, R.version$minor, sep='.')` - RStudio version 2023.03.0+386 - Quarto version `r quarto::quarto_version()` R, RStudio, and Quarto are all free to download and use. You can learn more about both R and RStudio and download them both from <https://posit.co/download/rstudio-desktop/>. To learn more about Quarto books visit <https://quarto.org/docs/books>. ``` However, whenever I attempt to render this document individually, the preview still shows the code and not the results. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Import the subcaption package as ``` \usepackage[list=true]{subcaption} ``` to allow for subcaptions being included in the list of figures. ### Checklist - [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [x] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

Allow changing lofdepth to include subfigures in lof when using latex. The subfig package provides this functionality, but the captions package currently used does not (* I think).

### Bug description When rendering to a PDF, code that flows off the page is lost:  It would be nice if quarto would be able to use some kind of line wrap for the code when rendering to PDF. ```` --- title: Analysis --- Now that we have the data in a tidy format, let's clean the values: 1. Convert all `"-"` to `"0"` 2. Convert all `"x"` to `"0"` 3. Convert all the values in the `:Value` column to a Float64 and a `:Year` column to an Int ```{julia} df = transform(df, :Value => ByRow(x -> ifelse(x == "-", "0", x)) => :Value) df = transform(df, :Value => ByRow(x -> ifelse(x == "x", "0", x)) => :Value) df = transform(df, :Value => ByRow(x -> parse(Float64, x)) => :Value, :Year => ByRow(x -> parse(Int, x)) => :Year) first(df, 3) #| hide_line ``` ```` When I run `quarto render --to pdf` I get a PDF like in the screenshot above. ``` julia> versioninfo() Julia Version 1.8.5 Commit 17cfb8e65e (2023-01-08 06:45 UTC) Platform Info: OS: Windows (x86_64-w64-mingw32) CPU: 8 × 11th Gen Intel(R) Core(TM) i5-1145G7 @ 2.60GHz WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, tigerlake) Threads: 1 on 8 virtual cores Environment: JULIA_EDITOR = code.cmd -g ``` ``` $ quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.326 Path: C:\Users\USERNAME\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.12 (Conda) Path: C:/Users/USERNAME/Miniconda3/python.exe Jupyter: 5.1.0 Kernels: python3, julia-1.8 [>] Checking Jupyter engine render....OK [>] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description I render documents in multiple formats, particularly as Website and RevealJS presentation. That worked well until the update, with v.1.3x the RevealJS Pause marker `. . .` is also rendered in HTML ouput. Would be great if that could be filtered out again. Thanks in advance! ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description **Attached is my example .qmd file**: [test.qmd.zip](https://github.com/quarto-dev/quarto-cli/files/11348406/test.qmd.zip) **Problem**: - Notice the annotation comment does not fit/display correctly on the screen when hovering over it (using `code-annotations: select` instead of `hover` has the same problem): - Yes, a horizontal scroll-bar appears on the bottom, however, trying to click on this scroll bar causes the annotation comment to disappear.  **RStudio IDE version:**  **OS:**  **quarto check** ``` [✓] Checking Quarto installation......OK Version: 1.2.335 Path: /Applications/RStudio.app/Contents/Resources/app/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.12 (Conda) Path: /Users/jarbet/opt/anaconda3/bin/python Jupyter: 4.9.2 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK quarto check (base) RELMJCCADM27261:group-statistics jarbet$ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.12 (Conda) Path: /Users/jarbet/opt/anaconda3/bin/python Jupyter: 4.9.2 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library knitr: 1.41 rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Hi as I have written [here](https://github.com/quarto-dev/quarto-cli/issues/5289#issuecomment-1526507104), using quarto 1.4.11 and running `quarto render tmp-lite.qmd` ([tmp-lite.zip](https://github.com/quarto-dev/quarto-cli/files/11348285/tmp-lite.zip)) the footnotes are inside `.column-margin`. Am I doing something wrong? My OS is Debian 11.  ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

I have recently updated to Quarto 1.3 but it seems is creating problems when I am trying to deploy my blog. I am using Github pages and for deployment, I am just using the publish command in the terminal. I have found out that after I start using Quarto 1.3 the process for deployment [seems to be erasing the CNAME](https://github.com/msh855/TheQuantEconomist/commit/146e92b9f99ec3d80b45be67884e4d4511586830#diff-76b26edb75578663ca0fd6515ec7880ca04046bdbab298938981c9f0bd3907dd) file needed for the custom domain: This is causing Github to also revert back to the default url, and not my custom domain.

### Bug description I am writing a document with python code using PaddleOCR. When Quarto starts to render and executes notebook cells, a `FileNotFoundError` exception is raised. However, I could run the cell from the Jupyter Notebook generated by Quarto without any error, via the Jupyter Notebook extension in VS Code. The quarto code cauing the problem is as follows: ````quarto --- title: "Problem with PaddleOCR" jupyter: python3 --- ```{python} from paddleocr import PaddleOCR OCR = PaddleOCR(use_angle_cls=True, show_log=False) print("OK") ``` ```` The output from VS Code's terminal is as follows ```log ❯ quarto preview e:/Development/comprehensive/dipExp/tasks/homework/task2/issue.qmd --no-browser --no-watch-inputs Starting python3 kernel...Done Executing 'issue.ipynb' Cell 1/1...ERROR: An error occurred while executing the following cell: ------------------ from paddleocr import PaddleOCR OCR = PaddleOCR(use_angle_cls=True, show_log=False) print("OK") ------------------ --------------------------------------------------------------------------- FileNotFoundError Traceback (most recent call last) Cell In[1], line 1 ----> 1 from paddleocr import PaddleOCR 3 OCR = PaddleOCR(use_angle_cls=True, show_log=False) 5 print("OK") File e:\Development\comprehensive\dipExp\tasks\.venv\lib\site-packages\paddleocr\__init__.py:14 1 # Copyright (c) 2020 PaddlePaddle Authors. All Rights Reserved. 2 # 3 # Licensed under the Apache License, Version 2.0 (the "License"); (...) 12 # See the License for the specific language governing permissions and 13 # limitations under the License. ---> 14 from .paddleocr import * 16 __version__ = paddleocr.VERSION 17 __all__ = [ 18 'PaddleOCR', 'PPStructure', 'draw_ocr', 'draw_structure_result', 19 'save_structure_res', 'download_with_progressbar', 'sorted_layout_boxes', 20 'convert_info_docx', 'to_excel' 21 ] File e:\Development\comprehensive\dipExp\tasks\.venv\lib\site-packages\paddleocr\paddleocr.py:21 17 import importlib 19 __dir__ = os.path.dirname(__file__) ---> 21 import paddle 23 sys.path.append(os.path.join(__dir__, '')) 25 import cv2 File e:\Development\comprehensive\dipExp\tasks\.venv\lib\site-packages\paddle\__init__.py:76 74 import paddle.jit # noqa: F401 75 import paddle.amp # noqa: F401 ---> 76 import paddle.dataset # noqa: F401 77 import paddle.inference # noqa: F401 78 import paddle.io # noqa: F401 File e:\Development\comprehensive\dipExp\tasks\.venv\lib\site-packages\paddle\dataset\__init__.py:27 25 import paddle.dataset. ``` The `quarto check` command's output is as follows: ```log ❯ quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.340 Path: D:\Program Files\Quarto\bin CodePage: 936 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.10 Path: E:/Development/comprehensive/dipExp/tasks/.venv/Scripts/python.exe Jupyter: 5.3.0 Kernels: python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` In the same virtual environment (created by poetry), I can also run the python code via the python interpretor without any error. I am using Quarto's VS Code extension, I don't have RStudio installed. I am using Python 3.10.10 on Windows 11 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description When publishing a document which is located in a subdirectory, I get the following error with Quarto 1.3 (this worked with Quarto 1.2): ``` ERROR: NotFound: No such file or directory (os error 2), stat '08/08/08/08_files/libs' NotFound: No such file or directory (os error 2), stat '08/08/08/08_files/libs' at Object.statSync (deno:runtime/js/30_fs.js:322:9) at file:///Users/clemens/Applications/quarto/bin/quarto.js:121353:18 at Array.reduce (<anonymous>) at normalizePublishFiles (file:///Users/clemens/Applications/quarto/bin/quarto.js:121351:45) at renderForPublish (file:///Users/clemens/Applications/quarto/bin/quarto.js:121303:24) at async renderForPublish (file:///Users/clemens/Applications/quarto/bin/quarto.js:109082:24) at async handlePublish (file:///Users/clemens/Applications/quarto/bin/quarto.js:108988:26) at async publishDocument (file:///Users/clemens/Applications/quarto/bin/quarto.js:121342:38) at async publish5 (file:///Users/clemens/Applications/quarto/bin/quarto.js:121438:132) at async doPublish (file:///Users/clemens/Applications/quarto/bin/quarto.js:121394:13) ``` Here, I used ``` quarto publish 08/08.qmd ``` However, when running the command from the same folder as the document, everything works: ``` quarto publish 08.qmd ``` I've already reported such an issue for an older version (#2623), but it seems like something broke that fix. OS: macOS Ventura 13.3.1 #### Output of `quarto check`: <details> ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /Users/clemens/Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.10 Path: /Library/Frameworks/Python.framework/Versions/3.10/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.3.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ``` </details> ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

Dear maintainers, I was just recommended about Quarto in a course and it looks great! However, in that course we got distracted by a minor issue: the inconsistent coding style in the R examples at [https://quarto.org/docs/get-started/hello/rstudio.html](https://quarto.org/docs/get-started/hello/rstudio.html). It is a minor Issue, but hey, let's make the website even more awesome :-) In the text, within the `.qmd` document, it reads: ``` library(tidyverse) ``` Note that the library is loaded without double-quotes. In the text later, however, a library is loaded with double-quotes: ``` install.packages("quarto") ``` This caused a discussion in class about which way is better and what are the differences, which was a needless distraction. I suggest to use a consistent loading of libraries.

I just switched to Quarto 1.3 to be able to download multiple formats and this has broken everything on my website/blog. I am not sure what is causing the problem. But has broken all my processes. For example, I cannot preview my blog anymore. Here is the error that I get once I type `quarto preview` : ERROR: Project _quarto.yml validation failed. In file _quarto.yml (line 11, columns 3--10) property name listing is invalid 10: left: "Usual Disclaimer applies" 11: listing: ~~~~~~~~ 12: contents: posts ℹ The error happened in location website:listing. In file _quarto.yml (line 17, columns 3--21) property name title-block-banner is invalid 16: feed: true 17: title-block-banner: true ~~~~~~~~~~~~~~~~~~~ ℹ The error happened in location website:title-block-banner. In file _quarto.yml (line 41, columns 3--10) property name filters is invalid 40: cookie-consent: false 41: filters: ~~~~~~~~ 42: - code-filename ℹ The error happened in location website:filters. Error: Project _quarto.yml validation failed. In file _quarto.yml (line 11, columns 3--10) property name listing is invalid 10: left: "Usual Disclaimer applies" 11: listing: ~~~~~~~~ 12: contents: posts ℹ The error happened in location website:listing. In file _quarto.yml (line 17, columns 3--21) property name title-block-banner is invalid 16: feed: true 17: title-block-banner: true ~~~~~~~~~~~~~~~~~~~ ℹ The error happened in location website:title-block-banner. In file _quarto.yml (line 41, columns 3--10) property name filters is invalid 40: cookie-consent: false 41: filters: ~~~~~~~~ 42: - code-filename ℹ The error happened in location website:filters. at readAndValidateYamlFromFile (file:///Applications/quarto/bin/quarto.js:42120:15) at async file:///Applications/quarto/bin/quarto.js:82868:26 at async projectContext (file:///Applications/quarto/bin/quarto.js:82720:26) at async serveProject (file:///Applications/quarto/bin/quarto.js:103144:19) at async Command.fn (file:///Applications/quarto/bin/quarto.js:103742:13) at async Command.execute (file:///Applications/quarto/bin/quarto.js:8437:13) at async quarto (file:///Applications/quarto/bin/quarto.js:127535:5) at async file:///Applications/quarto/bin/quarto.js:127553:9

The release notes are currently on the downloads page, <https://quarto.org/docs/download/#download-section-news>, but it is hard to link to a specific version's notes. We could consider adding a static release notes page on quarto.org for major versions, e.g. links on blog posts about the release. Perhaps something like quarto.org/download/release-notes/1.3.340/ These are available on github as part of the releases, <https://github.com/quarto-dev/quarto-cli/releases/download/v1.3.340/changelog.md>, but a formatted version would be nice.

### Bug description The following mermaid class diagram is rendered wrong, as `<|--` is translated to `&lt;|--`. Contents of `file.qmd` ````md --- title: Test format: gfm --- ```{mermaid} classDiagram Foo <|-- Bar ``` ```` Is rendered as `file.md`: ````md # Test ``` mermaid classDiagram Foo &lt;|-- Bar ``` ```` This example uses quarto v1.3.340. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

# Steps To Reproduce Description: `quarto tools` with no args throws error Steps to Reproduce: Check help of `quarto tools` and see "Use 'quarto tools' with no arguments to show the status of all tools." ``` ❯ quarto tools help Check file:///Users/amanning/projects/github/quarto/quarto-cli/src/quarto.ts Usage: quarto tools <command> [tool] Version: 99.9.9 Description: Installation and update of ancillary tools. tools: tinytex chromium commands: install uninstall update Use 'quarto tools' with no arguments to show the status of all tools. ``` - Follow doc by running `quarto tools` ## Expected Result: The same results as `quarto tools all` or `quarto tools list` ## Actual Result: `ERROR: Missing argument(s): command`

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5304 <div type='discussions-op-text'> ^{Originally posted by **eitsupi** April 25, 2023} At this time, no Hugo or Docusaurus format testing is being done in this repository. I believe this was one of the reasons for the serious regression in the 1.3 Docusaurus format (#5079). I believe there has been discussion of adding tests for these formats (e.g., comment #5087), but it has not been possible due to additional dependencies (e.g., Docusaurus itself). However, for Hugo and Docusaurus formats, the `quarto render` command only does markdown output, and I believe the functionality used in tests is not actually dependent on Hugo or Docusaurus. So I think something like snapshot tests can be performed only with Quarto CLI itself, how about that? (I think it would be easier for less experienced people like myself to make contributions to the code base if something like snapshot tests were in place.)</div>

In a list block, figures lose their captions and crossrefs are not valid.

### Bug description The `about` page templates don't seem to allow for computation within the YAML header. Computation still works in outer blocks like `title`, but not inside anything in `about`. A reproducible example (from the Quarto page): ``` --- title: "Finley Malloc" about: template: jolla image: profile.jpg links: - icon: twitter text: twitter href: https://twitter.com - icon: github text: Github href: "`r Sys.Date()`" --- Finley Malloc is the Chief Data Scientist at Wengo Analytics. When not innovating on data platforms, Finley enjoys spending time unicycling and playing with her pet iguana. ``` The link for "GitHub" is the literal string `r Sys.Date()` rather than doing the computation. I've tried `!expr` as well but haven't managed to get that to work successfully. Quarto check: ``` ✓] Checking Quarto installation......OK Version: 1.0.38 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.2 Path: /opt/homebrew/opt/[email protected]/bin/python3.11 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter (\) Checking R installation...........Warning message: This project is configured to use R version '4.1.2', but '4.2.2' is currently being used. [✓] Checking R installation...........OK Version: 4.2.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/mlyd0001/projects/SPECTRUMSPARKWebsite/renv/library/R-4.2/aarch64-apple-darwin20 - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description If I create a book project and specify "number-sections: false" in _quarto.yml, then view the rendered project in a browser in mobile view mode, the visible label of the collapsed sidebar will still show a section number. To reproduce: Create a new book project: ``` $ quarto create-project mybook --type book $ quarto preview mybook ``` Add "number-sections: false" to _quarto.yml as below: ``` project: type: book book: title: "mybook" author: "Norah Jones" date: "4/25/2023" chapters: - index.qmd - intro.qmd - summary.qmd - references.qmd bibliography: references.bib format: html: theme: cosmo number-sections: false pdf: documentclass: scrreprt ``` Remove ".unnumbered" class from Preface header in index.qmd so it appears as below: ``` # Preface This is a Quarto book. To learn more about Quarto books visit <https://quarto.org/docs/books>. ``` After the site is re-rendered, navigate to index.html and switch to mobile view (e.g. ctrl-shift-m in Firefox). The label next to the collapsed sidebar icon at the top of the screen reads "1 Preface". OS: Kubuntu 20.04 Quarto version: 1.3.282 Firefox version: 112.0.1 Chromium version: 111.0.5563.146 (Official Build) snap (64-bit) quarto check output: ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.282 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.10 Path: /usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.1 Path: /usr/lib/R LibPaths: - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/lib/R/library knitr: 1.37 rmarkdown: 2.11 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Running the `quarto render` on a project folder with a .qmd file that includes a long code block inside a callout block, generates a odd-formatted pdf file, as the one in attachment [test.pdf](https://github.com/quarto-dev/quarto-cli/files/11321575/test.pdf) Here a sample .md (.qmd) that causes this issue [test.md](https://github.com/quarto-dev/quarto-cli/files/11321616/test.md) The YAML of the project is the following ``` project: title: "qproject" output-dir: output format: pdf: toc: true toc-depth: 2 number-sections: true code-line-numbers: true code-block-bg: "#f0f3f5" cap-location: top ``` I'm running quarto 1.2.335 ```bash > quarto --version 1.2.335 ``` on vscode 1.77.3 ```bash > code --version 1.77.3 704ed70d4fd1c6bd6342c436f1ede30d1cff4710 x64 ``` on Ubuntu 22.04 LTS ```bash > lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 22.04.2 LTS Release: 22.04 Codename: jammy ``` `quarto check` returns the following ```bash > quarto check [✓] Checking Quarto installation......OK Version: 1.2.335 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.16 (Conda) Path: /home/edoardo/miniconda3/envs/DABDPA/bin/python Jupyter: 5.3.0 Kernels: python3, bash [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

As highlighted in the discussion below, it would be great to allow users to use GitLab, BitBucket, Gitea, for the "GitHub Links", and not only GitHub. ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5281 <div type='discussions-op-text'> ^{Originally posted by **christophsax** April 23, 2023} In Quarto, there is the lovely feature that directly links to the edit page on GitHub. At first glance, this seems to work for other platforms, such as Gitea, as well. However, quarto points to `edit`, Gitea expects it at `_edit`. Is there any way the edit link can be tweaked? This is where Quarto links to: `.../edit/main/index.qmd` This is how a Gitea edit link looks like: `.../_edit/main/index.qmd` </div>

## Description When no delete rights, "quarto-permission-test" empty confluence pages dumped to root confluence space. ## Steps to Reproduce - Configure a Confluence space where the logged in publisher has no delete rights (only archive for example) - Publish a quarto document to this space ### Expected Result Document is published, no test documents are left behind. If the account doesn't have permissions to delete the test page we will: - Attempt to archive this test and fail gracefully if this too isn't supported - Using the [Deno WebStorageAPI](https://deno.com/[email protected]/runtime/web_storage_api) save a flag that will disable this test in the future for this installation. Set in `localStorage` to persist across sessions - essentially disable check after the first fail. ### Actual Result - It prompts you to re-authorize the account - After doing so, a test document is created but not deleted in the root of the space - It re-authorizes you again in a loop - The publish doesn't complete ### Workaround - Publish to personal space, then manually move to target space ---- - For the permissions test we could - Detect that the delete failed and if so, attempt an archive? Not ideal as there would be a growing list of test archive documents. - Create a flag or environment variable to prevent the test (this puts the burden on the publisher which isn't ideal) - Remove the test as we aren't sure if it will create problems (this removes the warning which isn't ideal) - Do nothing, just advise as to the less-than-ideal work-around (publish to your personal space then move). ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5295 <div type='discussions-op-text'> ^{Originally posted by **angelotrivelli** April 24, 2023} I found that when I tried to make quarto publish to a particular confluence space, it put empty pages in the root of that space. All the pages were titled like... `quarto-permission-test-71dc05b5-664b-4ac5-a0de-673c51bdbc03` Where the `71dc...` is obviously some GUID, different for every page. For whatever reason, I am not able to publish an actual page to that confluence space. Instead it just dumps one of those empty files into the root of the space. If I publish to my personal space, I found I can then manually move my page from the personal space into wherever I want it, but I can't do it directly from quarto publish. Unfortunately, I am not super proficient in confluence, nor quarto. Are there any pointers for troubleshooting what's going here? It's kind of embarrassing that quarto dumped a empty page like that (with my name on it) into a highly visible Confluence space. </div>

### Bug description Hi I am writing a large document using quarto book. When organizing my files in folders. Quarto is no longer able to solve cross-references. Not sure if I am doing something wrong or if it is a bug. I put a sample here: https://github.com/andlekbra/minimal-sample-quarto-cross-ref-issue I am using VS code on windows: ``` Version: 1.77.3 (user setup) Commit: 704ed70d4fd1c6bd6342c436f1ede30d1cff4710 Date: 2023-04-12T09:16:02.548Z Electron: 19.1.11 Chromium: 102.0.5005.196 Node.js: 16.14.2 V8: 10.2.154.26-electron.0 OS: Windows_NT x64 10.0.19044 Sandboxed: Yes ``` Result from `quarto check` ``` [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.299 Path: C:\Users\ALB\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.11.2 Path: C:/Users/ALB/AppData/Local/Programs/Python/Python311/python.exe Jupyter: 5.3.0 Kernels: python3 (-) Checking Jupyter engine render....0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. [>] Checking Jupyter engine render....OK [>] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

This is to track possible enhancement/fix when inline HTML such as SVG is included in a Figure Pandoc AST node (such as the one emitted by `diagram.lua` below). Note that the issue was raised in the discussion below when using a version of <https://github.com/pandoc-ext/diagram> under active development. A workaround has been found and is documented in the discussion. ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5266 <div type='discussions-op-text'> ^{Originally posted by **netw0rkf10w** April 21, 2023} Hello, I'm using [this filter](https://github.com/pandoc-ext/diagram/blob/main/diagram.lua) for converting TikZ code to SVG in Quarto. When using the filter as is, it works (an example can be found at https://raw.githubusercontent.com/pandoc-ext/diagram/main/test/input-tikz.md). However, when I changed the code to replace the SVG file with inline SVG, the caption is not showing (I checked the output HTML and the `figure` container was not even generated). More precisely, in the original code, an SVG image is created and store in `img`, then: ```lua -- Use the block's filename attribute or create a new name by hashing the image content. local basename, _extension = pandoc.path.split_extension( props.filename or pandoc.sha1(img) ) local fname = basename .. '.' .. extension_for_mimetype[imgtype] -- Store the data in the media bag: pandoc.mediabag.insert(fname, imgtype, img) -- Create a figure that contains just this image. local img_obj = pandoc.Image(props.alt, fname, "", props['image-attr']) return pandoc.Figure(pandoc.Plain{img_obj}, props.caption, props['fig-attr']) ``` What I did is, instead of creating a file in the media bag, I used directly the SVG as an inline HTML element: ```lua return pandoc.Figure(pandoc.RawInline('html', img), props.caption, props['fig-attr']) ``` (the above line replaces the entire previous code block) **Using Pandoc alone, it worked:** ``` quarto pandoc --lua-filter filters/diagram.lua -s tikz.qmd -o tikz.html ``` However, when rendering `tikz.qmd` containing ``` filters: - diagram.lua ``` with Quarto, the SVG is displayed but not in a figure container and thus there's no caption. Could you please help? Thank you very much in advance!</div>

Hi The above option is available for the github version of the plugin. However the version of the menu plugin which ships with Quarto does not allow this. I would really love to have this option. Currently, the menu inserts the first few words of each slide whenever there is no title text. This fills up the menu with a lot of text and makes it very difficult to read. Having the above option would solve this issue. (NB there is a general lack of documentation regarding the various options on the Quarto website).

### Bug description I created a listing page with a title block banner and categories set to true, with a sidebar defined in _quarto.yml. When each of those elements is specified and I view the page in my browser (Firefox or Chromium), the title banner displays. When I switch to mobile view (e.g. ctrl-shift-m in Firefox), the title banner disappears. To reproduce: Create a new website project: ``` $ quarto create-project mysite --type website $ quarto preview mysite ``` Edit _quarto.yml so its contents are as below. Note only the sidebar entry has been added: ``` project: type: website website: title: "mysite" navbar: left: - href: index.qmd text: Home - about.qmd sidebar: - id: sidebar_id format: html: theme: cosmo css: styles.css ``` Edit about.qmd as below: ``` --- title: "Listing Example" listing: type: default categories: true title-block-banner: true --- ``` After quarto preview has re-rendered the site with these edits, switch to mobile view. The title block with the text "Listing Example" is not displayed. If I remove the "title-block-banner", "categories" or "sidebar" entry, the title block is displayed in mobile view. It's the combination of the three features that causes the problem. OS: Kubuntu 20.04 Quarto version: 1.3.282 Firefox version: 112.0.1 Chromium version: 111.0.5563.146 (Official Build) snap (64-bit) ### Checklist - [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description By default, my computer uses the `pdflatex` engine, although `xelatex` also produces this bug. Removing any line other than `keep-tex: true` prevents the bug, but I need every line for my (more complex) file. Adding `echo: false` does not remove the entire bug, only the R code chunk. Other code chunks and pure latex code works wonderfully, I was proofreading my document when I noticed this problem. Here is the buggy .qmd file ````md --- format: pdf keep-tex: true --- - A ```B```{=latex} ```{r} Sys.sleep(1) ``` ```` which produces the following (truncated to the buggy part) .tex file ```tex \begin{document} \ifdefined\Shaded\renewenvironment{Shaded}{\begin{tcolorbox}[borderline west={3pt}{0pt}{shadecolor}, frame hidden, sharp corners, boxrule=0pt, breakable, interior hidden, enhanced]}{\end{tcolorbox}}\fi \begin{itemize} \tightlist \item A \end{itemize} \begin{Shaded} \begin{Highlighting}[] \NormalTok{::: \{.cell\}} \NormalTok{\textasciigrave{}\textasciigrave{}\textasciigrave{}\{.r .cell{-}code\}} \NormalTok{Sys.sleep(1)} \end{Highlighting} \end{Shaded} ::: \end{document} ``` which produces the PDF  ## Technical details RStudio version: 2023.03.0 Build 386 OS: Windows 10 ```cmd $ quarto.exe check [>] Checking Quarto installation......OK Version: 1.2.475 Path: C:\Users\xxxxx\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.11.2 Path: C:/Users/xxxxx/AppData/Local/Programs/Python/Python311/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with py -m pip install jupyter [>] Checking R installation...........OK Version: 4.2.2 Path: C:/PROGRA~1/R/R-42~1.2 LibPaths: - C:/Program Files/R/R-4.2.2/library rmarkdown: 2.21 [>] Checking Knitr engine render......OK ``` Is this something I did, or a proper bug? ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Hi, I have this "hello world" qmd file: https://gist.github.com/aborruso/a9a95b902b35e77b0042e66dd7714a8f It reads a CSV and an image. In [this zipped file](https://github.com/quarto-dev/quarto-cli/files/11311360/files.zip), the qmd file, the CSV, the image and the HTML output. The problem I have is that the column margin text is not aligned correctly, it is moved further down. I removed other output blocks from this example: in the original, the further I scroll down, the more this shift increases. And the column-margin content is no longer aligned to its reference section, but to the next one. If I remove the charts generated with altairs, everything realigns. What am I doing wrong? I'm using Debian 11 and quarto 1.3.253. Thank you very much  ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Hello I've noticed with the latest version that the code annotation doesn't work correctly for PDF, as in the `tikz` package is not included and the `\circled` command is not defined. I've tried following snippet: ````qmd # Parallelität ## Reentrancy ### Dis-/Enable Interrupts ::: callout-warning ## Nachteil ::: ### Critical Sections ``` c #define CriticalVariable() \ uint8_t cpuSR // <1> ``` 1. definiert lokale Variable `cpuSR` für Sicherung des aktuellen Interrupt-Zustandes ``` c #define EnterCritical() \ do { \ __asm ( \ "mrs r0, PRIMASK \n" \ // <1> "cpsid i \n" \ // <2> "strb r0, cpuSR \n" \ // <3> ); \ } while(0) ``` 1. `PRIMASK` wird in `R0` abgespeichert 2. Interrupts deaktivieren 3. `R0` in `cpuSR` abspeichern ``` c #define ExitCritical() \ do { \ __asm( \ "ldrb r0, cpuSR \n" \ // <1> "msr PRIMASK,r0 \n" \ // <2> ); \ } while(0) ``` 1. Inhalt von `cpuSR` in `R0` laden 2. `R0` nach `PRIMASK` kopieren. ```` I've also tried defining the `\circled`-command in the preamble of the document, which seems to produce the code annotation in the code block, but not the stylized list elements below it.  If you need anything else from me, just ask! Thank you for the help! --- ## `quarto check` ``` [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.336 Path: C:\Users\joelv\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.4 Path: C:/Users/joelv/AppData/Local/Programs/Python/Python310/python.exe Jupyter: 4.9.2 Kernels: python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.2.2 Path: C:/PROGRA~1/R/R-4.2.2 LibPaths: - C:/Users/joelv/AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.2/library knitr: 1.41 rmarkdown: 2.20 [>] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5276 <div type='discussions-op-text'> ^{Originally posted by **royfrancis** April 22, 2023} I have a quarto website which renders correctly except for the 404 page. When previewing, the 404 page looks fine. `quarto preview` [![enter image description here][1]][1] When rendered, the 404 page is missing css styling and image path is broken too. `quarto render` [![enter image description here][2]][2] This is the only page on the entire website that is misbehaving. And I don't think I am treating this page in any special way. I have uploaded the rendered files to github pages and it's broken there too. The same image path when on another page seems to work fine. My directory structure looks like: ``` . ├── 404.qmd ├── assets │   └── 404.png ├── index.qmd ├── _quarto.yml └── _site ├── 404.html ├── assets │   └── 404.png ├── index.html ├── search.json └── site_libs ``` **_quarto.yml** ``` project: type: website website: title: "Website" navbar: left: - text: Home href: "index.html" format: html ``` **404.qmd** ``` --- pagetitle: "404: Page not found" format: html ---  # 404: Page not found ``` **index.qmd** ``` --- format: html --- # Hello This is the index page. ``` `quarto 1.2.335` [1]: https://i.stack.imgur.com/jCCBV.png [2]: https://i.stack.imgur.com/xPnXE.png</div>

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5282 How can I prevent repo-action from always displaying in the footer on GitHub after updating Quarto from v1.2.475 to v1.3.336? I believe this is "GitHub Links" feature, see https://quarto.org/docs/websites/website-navigation.html#github-links. Note that the links only appear if you are logged in. Far as I know (from documentation), there is no option to avoid the links to appear in the footer while keeping them elsewhere, but maybe such option should exist.

### Bug description On every ePub I make in Quarto, the chapter numbers are generated automatically and then duplicated in the final output. Here's the ePub `toc.ncx` source in a book with three chapters. Note how each `<text>` label includes two instances of the chapter number. ```xml </docTitle> <navMap> <navPoint id="navPoint-0"> <navLabel> <text>This is a book</text> </navLabel> <content src="text/title_page.xhtml" /> </navPoint> <navPoint id="navPoint-1"> <navLabel> <text>1 1 Intro</text> </navLabel> <content src="text/ch001.xhtml" /> </navPoint> <navPoint id="navPoint-2"> <navLabel> <text>2 2 Sample Page</text> </navLabel> <content src="text/ch002.xhtml" /> </navPoint> <navPoint id="navPoint-3"> <navLabel> <text>3 3 Typical grid</text> </navLabel> <content src="text/ch003.xhtml" /> </navPoint> </navMap> </ncx> ``` Maybe this is by design? but I've tried setting `toc: true` to change the behavior and can't figure this out. Here's the ePub output viewed in the Calibre ebook viewer:  I have a simple working example on Github: [richardsprague/quartosample](https://github.com/richardsprague/quartosample) OSX 13, Quarto 1.3.333 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description If I added the following code ``` --- format: elsevier-pdf: fig-pos: 'H' --- ``` to position all the figures in document, in the output article.pdf file, only figure using format `![]()` is positioned as desired. Figure having subfigures using following code is not affected. ``` ::: {#asdf layout-ncol=2} ![]() ![]() ::: ``` I tried to add `fig.pos='H'` like ``` ::: {#asdf fig.pos='H' layout-ncol=2} ![]() ![]() ::: ``` . Still didn't work. I also checked the output article.tex file. It seems that single figure is converted to `\begin{figure}[H]` while the side-by-side figure is always `\begin{figure}`. I'm on Windows 10. The output of `quarto check` is: ``` [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.336 Path: E:\quarto\anzhuang\bin CodePage: 936 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.7.4 Path: E:/python/anzhuang/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with py -m pip install jupyter [>] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` At current situation, I could directly add `[H]` in the output article.tex file as a workaround. But I have no idea on how to process the tex file. I tried ``` quarto render article.tex --to elsevier-pdf ``` , but error occurs ``` ERROR: Unable to render article.tex ``` . ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

Context from https://community.rstudio.com/t/embed-sound-player-in-quarto-book/164739 ````markdown ```{r} html_tag_audio <- function(file, type = c("wav")) { type <- match.arg(type) htmltools::tags$audio( controls = "", htmltools::tags$source( src = file, type = glue::glue("audio/{type}", type = type) ) ) } ``` `r html_tag_audio("t-rex-roar.mp3", type = "wav")` ```` will create something like ````html <audio controls=""> <source src="t-rex-roar.mp3" type="audio/wav"/> </audio> ```` and [site-resources](https://quarto.org/docs/websites/website-tools.html#site-resources) is not detected and copied to `output-dir` https://github.com/quarto-dev/quarto-cli/blob/75736ef241aefcd1aaa55f116bf7c40ac18a932c/src/core/html.ts#L89-L97 We should probably also find `<source src=>` for local file

Comments in the discussion referenced below mentioned a problem with URLs without trailing slash as opposed to with; to wit: "So when I go my website on the subdomain without a trailing / the site doesn't work. So for example I have this deployed to https://www.algebraicjulia.org/blog/ but if you go to https://www.algebraicjulia.org/blog the website does not function correctly." @cscheid responded "Can you open a new issue? We definitely want to fix this." Commenter apparently never did. I'm doing it now because behavior is still the same. ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3615 <div type='discussions-op-text'> ^{Originally posted by **michielvdmeulen** December 9, 2022} I'm trying to serve a blog on a non-root path, but despite following the instructions in the [documentation](https://quarto.org/docs/websites/website-navigation.html#non-root-site-paths) I can't get it to work. My situation is identical to that in the docs, apart from different url naming of course, so something like this: URL: https://example.com/mysite/ _quarto.yml: ``` website: title: "My Site" site-path: "/mysite/" ``` When I render the site with and without the `site-path` option and compare the generated `index.html` file in the `_site` folder, both are exactly identical - even when I have completely deleted and re-rendered the content. In fact, only the `_site\site_libs\quarto-nav\quarto-nav.js` file has one line difference:  Apparently, this is either not enough or is not picked up on the server side. I'm using the latest Quarto version (1.2.269). Does someone have an idea what could be wrong? Any help would be highly appreciated!</div>

Wrong Repo. With Quarto 1.3.333 on Windows 11, I get the same "[WARNING] Could not fetch resource" as the below posting but when running something like `quarto_render(input = "qmd/blah.qmd", output_file= "not-blah.qmd")`. Interestingly the warnings and lack of formatting don't show up if I simply move `blah.qmd` to the project root folder and set input to match. Similar posting by @bryanwhiting in https://github.com/quarto-dev/quarto-cli/discussions/4041_

### Bug description ## Description We are using the `twitter-card` option to include a "summary" Twitter card. The main issue here is that the card shows up, but the "description" is not showing up in the card. In particular, the `twitter:description` meta element is added, but the content is missing, so our HTML source has the following: ```html <meta name="twitter:description" content=""> ``` You can also see this by viewing the HTML source of our live website at https://datascijedi.org/. A second minor issue is that the "title" is not being pulled in automatically from the website settings, though this has an easy fix of adding the `title` key manually under the `twitter-card` setting. ## Reproducible Example Any Quarto config with the following `twitter-card` settings included within the `website` option should reproduce the issue: ```yaml website: twitter-card: card-style: summary site: "@datascijedi" title: "JEDI Outreach Group" description: "The Justice, Equity, Diversity, and Inclusion (JEDI) Outreach Group, a community of statisticians and data scientists, is committed to communication, programming, and professional development to advance and support a society that values all people." image: "images/jedi-logo-square.png" ``` To test, just build the Quarto website and you should see that the HTML source is not including the description in the `twitter:description` meta element. To test the second minor issue mentioned, remove `title` from the `twitter-card` setting and ensure a `title` setting is included immediately under the `website` key. After building, you should see in the HTML source that the title is not in the `twitter:title` meta element. ## Additional Information As a reference, our full Quarto config is below: https://github.com/datascijedi/website/blob/1960be6c6c5ccac8bd012f694f1dd80c9f5719eb/_quarto.yml Quarto Version: `quarto-1.3.298-linux-amd64` Operating System: Linux (the version being used on Netlify build servers) ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description When adding the metadata `title` and `title-block-banner` with an image path. The background image is rendered in the banner and the H1 in the banner.  This is caused by quarto adding following to the html page: ```html <style> .quarto-title-block .quarto-title-banner, .quarto-title-block .quarto-title-banner h1, .quarto-title-block .quarto-title-banner h2, .quarto-title-block .quarto-title-banner h3, .quarto-title-block .quarto-title-banner h4, .quarto-title-block .quarto-title-banner h5, .quarto-title-block .quarto-title-banner h6 { background-image: url(images/heros/home_hero.jpg); background-size: cover; } </style> ``` The background-image is added to `.quarto-title-block .quarto-title-banner` and `.quarto-title-block .quarto-title-banner h1`. This is rendered using RC quarto 1.3.333, fedora 37. You can find a small repo preview in https://github.com/KaiWaldrant/quarto-title-block. quarto check output: ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.333 Path: /home/kai/opt/quarto-1.3.333/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.9 (Conda) Path: /home/kai/anaconda3/bin/python Jupyter: 5.2.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.3 Path: /usr/lib64/R LibPaths: - /usr/lib64/R/library - /usr/share/R/library knitr: (None) rmarkdown: (None) The rmarkdown package is not available in this R installation. Install with install.packages("rmarkdown") ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Thank you for the fast fixing of https://github.com/quarto-dev/quarto-cli/issues/5239 ! I have the next problem. - fresh `git pull` of quarto, book project, pdf output - embedding of a notebook cell when the path to the notebook starts with dots: `{{< embed ../notebooks/nb1.ipynb#cell1 >}}` - `quarto render --to html` works - `quarto render --to pdf` fails ``` ERROR: Unable to embed content from notebook 'nb1.ipynb' The file /home/hellmund/Julia/23/notebooks/nb1.ipynb doesn't exist or cannot be read. Error: Unable to embed content from notebook 'nb1.ipynb' The file /home/hellmund/Julia/23/notebooks/nb1.ipynb doesn't exist or cannot be read. at notebookIncludes (file:///home/hellmund/W/quarto-cli/src/core/jupyter/jupyter-embed.ts:203:17) at replaceNotebookPlaceholders (file:///home/hellmund/W/quarto-cli/src/core/jupyter/jupyter-embed.ts:208:18) at async renderPandoc (file:///home/hellmund/W/quarto-cli/src/command/render/render.ts:112:26) at async renderSingleFileBook (file:///home/hellmund/W/quarto-cli/src/project/types/book/book-render.ts:341:30) at async Object.onComplete (file:///home/hellmund/W/quarto-cli/src/project/types/book/book-render.ts:283:17) at async renderFiles (file:///home/hellmund/W/quarto-cli/src/command/render/render-files.ts:534:12) at async renderProject (file:///home/hellmund/W/quarto-cli/src/command/render/project.ts:263:23) at async Command.fn (file:///home/hellmund/W/quarto-cli/src/command/render/cmd.ts:211:26) at async Command.execute (file:///home/hellmund/W/quarto-cli/src/vendor/deno.land/x/[email protected]/command/command.ts:1790:7) at async quarto (file:///home/hellmund/W/quarto-cli/src/quarto.ts:122:3) ``` (A path to the notebook cell that does not start with dots works since yesterday's patch!) Minimal example with both path variants attached. [test2.zip](https://github.com/quarto-dev/quarto-cli/files/11287728/test2.zip) ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

IIUC posts rendered as website pages have titles always in the format: `<website title> - <post title>`. I would like the option to customize this. E.g. for my personal website, social preview cards render like so: <img width="610" alt="image" src="https://user-images.githubusercontent.com/559360/233345684-da767bd9-c4d0-43d0-97a6-277018312cf8.png"> But I'd prefer if the `Wasim Lorgat - ` part weren't there, since the website URL already has my name 😄

### Bug description This line of code seems to be responsible: https://github.com/quarto-dev/quarto-cli/blob/5e255aaab9f091a66b4ab6da3d63f0812fe38f70/src/project/types/website/listing/website-listing-read.ts#L997 The listing renders just as `.qmd` files do, so perhaps the warning isn't needed? ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

Apologies if I'm missing something, but there doesn't seem to be a way to disable Quarto from setting the image of a post to the first image. I was thinking of something like setting `image: null` in the post metadata.

Tracking https://github.com/quarto-dev/quarto-cli/pull/5245

### Bug description Currently it doesn't appear to be possible (afaict) to use `page-navigation: true` with `sidebar: false`. I'm on MacOS ``` $ quarto --version 1.3.326 ``` I've had to set `sidebar: contents: auto` with the styles for `.sidebar-menu-container` set to `display: none` with `page-navigation: true` to get a somewhat desirable behavior. I'm also getting some inconsistent ordering for the page navigation. Sometimes it links to one page and other times it links to another. I'm not sure if this should be a separate issue or not, but it would be nice if I could add contents to the sidebar from the YAML inside a single page. ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

The JATS format currently expects keywords to provided as `tags`: https://github.com/quarto-dev/quarto-cli/blob/024bba6387fc0abe7de1deb2640bd387fc28a692/src/resources/schema/document-attributes.yml#L122-L130 But other formats (e.g. HTML) use `keywords`: https://github.com/quarto-dev/quarto-cli/blob/024bba6387fc0abe7de1deb2640bd387fc28a692/src/resources/schema/document-metadata.yml#L1-L6

Unfortunately, we don't support Confluence server which I think is why it isn't working for you. We made this decision early on in the development to only focus on Confluence Cloud as Atlassian is EoLing Confluence Server in favor of cloud. More information on this can be found here: https://www.atlassian.com/migration/assess/journey-to-cloud. Based on this, I'm going to close this as Won't Fix. @cwickham It may be wise for us to include a note about this in our Confluence docs to reduce potential confusion from existing Server users. _Originally posted by @allenmanning in https://github.com/quarto-dev/quarto-cli/issues/4846#issuecomment-1475792630_

I now know how to extract line numbers from lua calls - we can use it so that our warnings and error messages in Lua will have line numbers associated with them.

### Bug description I created a website locally on my Mac with Quarto, and I observed that when opening it in Safari, there are some `[Error] Failed to load resource: the server responded with a status of 404 ()`. It turns out that your official website https://quarto.org also has this issue: <img width="1440" alt="Screen Shot 2023-04-19 at 16 09 13" src="https://user-images.githubusercontent.com/8569515/233101431-bb5ef253-4c03-4588-a21a-06eec1d970a5.png"> This seems to cause some important page load speed on Safari compared to Chrome, so please consider fixing this. ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description - quarto 1.3.330 on Debian Linux - book project, HTML and pdf output, - quarto preview in VS Code works perfect - `quarto render --to html` works perfect - `quarto render --to pdf` fails index.qmd: ``` # index {{< embed notebooks/nb1.ipynb#cell1 >}} ``` `quarto render --to pdf` fails: ``` ERROR: Internal Error: named lifetime render-file not found Error: Internal Error: named lifetime render-file not found at getCachedNotebookInfo (file:///opt/quarto/bin/quarto.js:80750:15) at notebookMarkdown (file:///opt/quarto/bin/quarto.js:80700:32) at replaceNotebookPlaceholders (file:///opt/quarto/bin/quarto.js:80679:38) at renderPandoc (file:///opt/quarto/bin/quarto.js:80981:34) at renderSingleFileBook (file:///opt/quarto/bin/quarto.js:98912:36) at async Object.onComplete (file:///opt/quarto/bin/quarto.js:98890:48) at async renderFiles (file:///opt/quarto/bin/quarto.js:86640:16) at async renderProject (file:///opt/quarto/bin/quarto.js:86785:25) at async Command.fn (file:///opt/quarto/bin/quarto.js:90841:32) at async Command.execute (file:///opt/quarto/bin/quarto.js:8437:13) ``` all files attached in test.zip [test.zip](https://github.com/quarto-dev/quarto-cli/files/11273575/test.zip) ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description I have been struggling with this for a while now. I came to the understanding that there is a bug. Depending on the position at which the chapters are defined, a cross-referencing to them will work or not. Please have a look at the two following configuration, where one file has some text and tries to corss-ref to chapters which are defined in another file. By the way, up to now I only saw this behavior with chapters, i.e. one dash header, not sections two or more dash headers. ### First configuration _trial.qmd_ ``` Further check [@sec-chap_1_Intro] -- Unable to resolve crossref chapter [-@sec-chap_1_Abc] -- will be found ``` _other_File.qmd_ ``` # Introduction {#sec-chap_1_Intro} Here is some more text # Chap Test_4 {#sec-chap_1_Abc} Here is some more text ``` ### Second configuration Here only the order of chapter declaration has been changed, i.e., the chapter **Chap Test_4** is defined first and the chapter Introduction _trial.qmd_ ``` Further check [@sec-chap_1_Intro] -- is found now (able to resolve crossref) chapter [-@sec-chap_1_Abc] -- now this becomes the issue (will not be found anymore) ``` _other_File.qmd_ ``` # Chap Test_4 {#sec-chap_1_Abc} Here is some more text # Introduction {#sec-chap_1_Intro} Here is some more text ``` ``` quarto --version 1.3.330 ``` Operating system: Linux Manjaro ``` quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.330 Path: /home/jav/Progs/quarto/quarto-1.3.330/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.10 Path: /usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### Show me the full project The reason why the bug is important to me is because of a bigger project. I have some cross-refs which are not found. If you want to have a look at them, feel free to have a look at the bigger project: ``` git clone https://huggingface.co/spaces/JavedA/master_Thesis/ cd master_Thesis quarto preview ``` In case there is any issue with obtaining the bigger project, please let me know. Thank you for your time and effort ### Checklist - [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description I created an ePub version of my Quarto project, and although the ePub appears to work correctly, it fails a check on W3.org's [epubcheck](https://www.w3.org/publishing/epubcheck/) which is how Apple Books and others ensure that ePub is publishable. error: `Error while parsing file: element "figcaption" not allowed here; expected the element end-tag, text, element "a", "abbr", "area", "audio", "b", "bdi", "bdo", "br", "button", "canvas", "cite", "code", "data", "datalist", "del", "dfn", "em", "embed", "epub:switch", "i", "iframe", "img", "input", "ins", "kbd", "label", "link", "map", "mark", "meta", "meter", "ns1:math", "ns2:svg", "object", "output", "picture", "progress", "q", "ruby", "s", "samp", "script", "select", "small", "span", "strong", "sub", "sup", "template", "textarea", "time", "u", "var", "video" or "wbr" (with xmlns:ns1="http://www.w3.org/1998/Math/MathML" xmlns:ns2="http://www.w3.org/2000/svg") or an element from another namespace` This is the epub source that fails. ```xml <div class="quarto-figure quarto-figure-center"> <figure> <p><img src="../media/file0.jpg" /></p> <p><figcaption>Local Image</figcaption></p> </figure> </div> ``` which looks fine to me, but I'm reporting this in case it's a known issue, or in case there's something weird about Quarto's `quarto-figure` class. epubcheck is widely used, so I don't think this is a bug in the checker. You can view my project on my Github Repo [quartosample](https://github.com/richardsprague/quartosample). View the error yourself if you run epubcheck against [docs/This-is-a-book.epub](https://github.com/richardsprague/quartosample/blob/main/docs/This-is-a-book.epub) I'm on OSX 13, using Quarto 1.3.330 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

Regression occurred here: https://github.com/quarto-dev/quarto-cli/commit/6dcadb85d19dbee547f8baaec45b7b9f1dd16a99 ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5221 <div type='discussions-op-text'> ^{Originally posted by **JavOrraca** April 17, 2023} I maintain the Southern California R User Group website ([socalr.org](https://socalr.org/)) which was developed with Quarto. I attempted to upgrade to Quarto 1.3.306 but raw HTML was not rendering as expected in the site's sidebar. For reference, our GitHub repo can be found here: [github.com/socalrug/socalr.org](https://github.com/socalrug/socalr.org) Below an example code snippet from the `_quarto.yml` showing the raw HTML links in the `text` field under `contents`. Please advise if I should plan to update the project's `_quarto.yml` to work correctly with Quarto 1.3.306. Any pointers would be appreciated, thanks! 🙏 ``` sidebar: background: "#3469B6" logo: "images/logo_text_blue_background.png" pinned: true align: center tools: - icon: github href: https://github.com/socalrug text: GitHub - icon: slack href: https://socalrug.slack.com/ text: Slack - icon: linkedin href: https://www.linkedin.com/company/socalrug/ text: LinkedIn - icon: twitter href: https://twitter.com/oc_rug text: "Twitter: @oc_rug" - icon: instagram href: https://www.instagram.com/socalrug/ text: "Instagram: @socalrug" - icon: youtube href: https://www.youtube.com/@SouthernCaliforniaRUsersGroup text: YouTube - icon: envelope href: "mailto:[email protected]" style: "docked" search: true collapse-level: 1 contents: - text: '<a href="https://www.meetup.com/socal-rug/" target="_blank">Join our Meetups</a>' - href: index.qmd text: Events - text: '<a href="https://github.com/socalrug/presentations" target="_blank">Past Presentations</a>' - section: "Hackathons" contents: - text: '<a href="https://github.com/socalrug/hackathon-2022-04" target="_blank">2022-04</a>' - text: '<a href="https://github.com/socalrug/hackathon-2021-04" target="_blank">2021-04</a>' - text: '<a href="https://github.com/socalrug/hackathon-2020-04" target="_blank">2020-04</a>' - text: '<a href="https://github.com/socalrug/hackathon-2019-11" target="_blank">2019-11</a>' - text: '<a href="https://github.com/socalrug/hackathon-2019-05" target="_blank">2019-05</a>' - section: "Book Clubs" contents: - text: '<a href="https://www.meetup.com/socal-rug/events/290821300/" target="_blank">2023-01: Advanced Probabilistic ML</a>' - text: '<a href="https://www.meetup.com/socal-rug/events/284913426/" target="_blank">2022-04: Forecasting Principles and Practice</a>' - text: '<a href="https://www.meetup.com/socal-rug/events/283044538/" target="_blank">2022-01: Information Rules</a>' - text: '<a href="https://www.meetup.com/socal-rug/events/280319522/" target="_blank">2021-09: Introduction to Statistical Learning</a>' - text: '<a href="https://www.meetup.com/socal-rug/events/278765369/" target="_blank">2021-07: OpenIntro Statistics</a>' - text: '<a href="https://www.meetup.com/socal-rug/events/278831056/" target="_blank">2021-07: Communicating with Data</a>' - text: '<a href="https://www.meetup.com/socal-rug/events/276575373/" target="_blank">2021-03: Text Mining with R</a>' - text: '<a href="https://www.meetup.com/socal-rug/events/275783285/" target="_blank">2021-02: Mastering Spark with R</a>' - text: '<a href="https://www.meetup.com/socal-rug/events/275719547/" target="_blank">2021-01: R for Data Science</a>' - text: '<a href="https://www.meetup.com/socal-rug/events/272034792/" target="_blank">2020-09: Advanced R</a>' - text: '<a href="https://www.meetup.com/socal-rug/events/270076542/" target="_blank">2020-05: Applied Predictive Modeling</a>' - text: '<a href="https://www.meetup.com/socal-rug/events/268226879/" target="_blank">2020-02: Feature Engineering & Selection</a>' - text: '<a href="https://www.meetup.com/socal-rug/events/266912350/" target="_blank">2020-01: R for Data Science</a>' ```</div>

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5227 <div type='discussions-op-text'> ^{Originally posted by **MinimizationOrg** April 18, 2023} Hello, Thank you for your great work! The set of features provided by Quarto is very impressive! We are converting a math heavy website from Jekyll to Quarto, and are surprised to learn that Quarto doesn't support server-side math rendering. Would it be possible to consider adding this feature? Both MathJax and KaTeX support server-side rendering for many years now, so hopefully this will not be too complicated to achieve. Another idea could be perhaps using pandoc to parse LaTeX directly. Thank you in advance for your reply!</div>

### Bug description Vanilla projects (not book or website) cannot use the publish command correctly when a separate output directory is being used. This appears to be a consequence of not being able to correctly find the path to the output file. To reproduce, clone [this template project](https://github.com/AaronGullickson/research-template) and then run: ```bash quarto publish quarto-pub analysis/analysis.qmd ``` When I do this, I get the following output: ``` ERROR: NotFound: No such file or directory (os error 2), stat '/Users/aarong/projects/research-template/analysis/_products/analysis.html' NotFound: No such file or directory (os error 2), stat '/Users/aarong/projects/research-template/analysis/_products/analysis.html' at Object.statSync (deno:runtime/js/30_fs.js:322:9) at file:///Applications/quarto/bin/quarto.js:121332:18 at Array.reduce (<anonymous>) at normalizePublishFiles (file:///Applications/quarto/bin/quarto.js:121330:45) at renderForPublish (file:///Applications/quarto/bin/quarto.js:121282:24) at async renderForPublish (file:///Applications/quarto/bin/quarto.js:109061:24) at async handlePublish (file:///Applications/quarto/bin/quarto.js:108967:26) at async publishDocument (file:///Applications/quarto/bin/quarto.js:121321:38) at async publish5 (file:///Applications/quarto/bin/quarto.js:121417:132) at async doPublish (file:///Applications/quarto/bin/quarto.js:121373:13) ``` It appears that the problem has to do with how deeply nested the qmd files are in this case. Quarto seems to be expecting it to be only nested one level deep in the project directory structure and as a result tries to find the output directory in the `analysis` subdirectory rather than in the project root directory. Changing the project type to `default` and changing the execution directory to `project` had no effect on this error. Running the command from the `analysis` subdirectory also had no effect. This is not working as of the nightly release v1.3.326 on RStudio 2022.12.0 Build 353 on Mac OSX. Output of `quarto check`: ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.326 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.2 Path: /Library/Frameworks/Python.framework/Versions/3.11/bin/python3 Jupyter: 5.2.0 Kernels: python3 (|) Checking Jupyter engine render....0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library knitr: 1.41 rmarkdown: 2.18 [✓] Checking Knitr engine render......OK ``` ### Checklist - [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

From https://github.com/quarto-ext/lightbox/issues/19, we need to improve the way we handle our pandoc 3 normalization. It's a minor improvement, but because it's an interaction with one of our extensions, I think we ought to call it a bug.

### Bug description Hello, I have a strange bug, when reading CSVs. I think that it is the fault of Quarto given the results array, which appears to end up getting interjected with html to try to set up a table? When the file extension is changed to csv, everything works as expected. Code ==== ```{ojs} result = FileAttachment("path/to/csv_saved_as_txt.txt").csv() console.dir(result) ``` Contents of file ==== ``` a, b, c 1, 2, 3 4, 5, 6 ``` Output ====  Notes ===== I am Running in VSCode on Windows 7 with Preview set to External and Render on Save [>] Checking Quarto installation......OK Version: 1.2.335 Path: C:\Users\nwilley\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] 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...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description I'm not sure how much can be done about this, but some packages use `closeAllConnections()` internally and therefore kill the connection to the quarto renderer. With this file: ````md --- title: "test" --- ```{r} closeAllConnections() ``` ```` `quarto::quarto_preview()` produces a slightly more detailed error message than `quarto::quarto_render()` with: ```md processing file: Untitled.qmd |................................... | 67% (unnamed-chunk-1)Quitting from lines 6-7 (Untitled.qmd) Error in isIncomplete(con) : invalid connection Calls: .main ... evaluate_call -> handle_output -> <Anonymous> -> isIncomplete Quitting from lines 6-7 (Untitled.qmd) Error in isOpen(con) : invalid connection Calls: .main ... <Anonymous> -> evaluate_call -> <Anonymous> -> isOpen Execution halted Error in run_serve_daemon("preview", file, NULL, args, render, port, host, : Error starting quarto ``` ## Details: This appears to be cross platform, but my device info is as follows: - OS: macOS 13.3 (22E252) (M1) - RStudio: ``` RStudio 2023.03.0+386 "Cherry Blossom" Release (3c53477afb13ab959aeb5b34df1f10c237b256c3, 2023-03-09) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.03.0+386 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36 ``` - R: ```md platform aarch64-apple-darwin20 arch aarch64 os darwin20 system aarch64, darwin20 status major 4 minor 2.2 year 2022 month 10 day 31 svn rev 83211 language R version.string R version 4.2.2 (2022-10-31) nickname Innocent and Trusting ``` - Quarto: ```md quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.326 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.1 Path: /Library/Frameworks/Python.framework/Versions/3.10/bin/python3 Jupyter: 4.10.0 Kernels: julia-1.7, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Hello, Thank you so much for this awesome piece of software! I would like to report a potential bug. When setting `collapse-below: sm` for `navbar`, the search button is dragged to the left before `sm` (and then when the width has reached `sm`, it goes back to the right). My `_quarto.yml` is as follows: ```yml project: type: website website: title: "Some Website" navbar: title: false logo: logo.svg collapse-below: sm left: - href: index.qmd text: Home - about.qmd format: html: theme: cosmo css: styles.css toc: true ``` In addition to the above issue, I would like to have a suggestion for improvement. I think the default threshold (`lg`) for collapsing is just too high. **In general, collapsing should only happen when there is not enough space left.** Therefore, it would be great if this can be implemented dynamically based on the available space, similar to Jekyll's Minimal Mistakes theme (this is a GIF image, so please click on the Play button to see animation):  ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5207 <div type='discussions-op-text'> ^{Originally posted by **rgaiacs** April 17, 2023} Similar to https://github.com/quarto-dev/quarto-cli/discussions/2841 but asking because of Bootstrap variable `enable-container-classes` introduced in https://github.com/twbs/bootstrap/pull/35005. Adding ``` /*-- scss:defaults --*/ $enable-container-classes: true; ``` to `theme` as in ``` format: html: theme: - _sass/gesis-container.scss - cosmo css: styles.css toc: true ``` still doesn't generate Bootstrap Containers classes. ## How to Reproduce 1. Download [minimal working example](https://github.com/quarto-dev/quarto-cli/files/11247525/bootstrap-containers.zip) and unzip it 2. Change directory to where the files where unzipped 3. Run `quarto preview --no-browser --render html` ## Observed Output Bootstrap Containers classes is missing.  ## Expected Output Bootstrap Containers classes is present. ## Environment Output of `quarto check` ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.324 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /usr/bin/python3 Jupyter: 5.2.0 Kernels: python3 (\) Checking Jupyter engine render....Traceback (most recent call last): File "/opt/quarto/share/jupyter/jupyter.py", line 21, in <module> from notebook import notebook_execute, RestartKernel File "/opt/quarto/share/jupyter/notebook.py", line 18, in <module> from nbclient import NotebookClient ModuleNotFoundError: No module named 'nbclient' [✓] Checking Jupyter engine render....OK ```</div>

Adding a second class onto the callouts for HTML works — One usage example is to target a callout using CSS ``` ::: {.callout-note .my-callout} Hello! ::: ``` And the CSS file: ``` .callout.callout-style-default.my-callout .callout-body { font-size: 1.0rem; } ``` _From a post by @jimjam-slam in https://github.com/quarto-dev/quarto-cli/discussions/4755#discussioncomment-5631059_ This works for HTML format as we pass attributes and classes, but not in revealjs format where it seems we don't.

```$ quarto render slides-01-01.qmd YAMLError: can not read a block mapping entry; a multiline key may not be an implicit key at line 7, column 1: ^ at generateError (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/vendor/deno.land/[email protected]/encoding/_yaml/loader/loader.ts:161:10) at throwError (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/vendor/deno.land/[email protected]/encoding/_yaml/loader/loader.ts:174:9) at readBlockMapping (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/vendor/deno.land/[email protected]/encoding/_yaml/loader/loader.ts:1181:16) at composeNode (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/vendor/deno.land/[email protected]/encoding/_yaml/loader/loader.ts:1502:13) at readDocument (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/vendor/deno.land/[email protected]/encoding/_yaml/loader/loader.ts:1688:3) at loadDocuments (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/vendor/deno.land/[email protected]/encoding/_yaml/loader/loader.ts:1750:5) at load (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/vendor/deno.land/[email protected]/encoding/_yaml/loader/loader.ts:1780:21) at parse (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/vendor/deno.land/[email protected]/encoding/_yaml/parse.ts:18:10) at parseWithNiceErrors (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/core/yaml.ts:291:12) at readYamlFromMarkdown (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/core/yaml.ts:104:9) at Object.target (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/execute/rmd.ts:73:18) at fileExecutionEngineAndTarget (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/execute/engine.ts:201:31) at renderContexts (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/command/render/render-contexts.ts:214:36) at Object.renderFormats (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/command/render/render-contexts.ts:315:28) at inputTargetIndex (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/project/project-index.ts:79:33) at resolveInputTarget (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/project/project-index.ts:205:23) at resolveItem (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/project/types/website/website-navigation.ts:1393:28) at resolveSidebarItem (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/project/types/website/website-navigation.ts:964:18) at resolveSidebarItems (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/project/types/website/website-navigation.ts:945:29) at async sidebarEjsData (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/project/types/website/website-navigation.ts:908:3) at async sidebarsEjsData (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/project/types/website/website-navigation.ts:878:22) at async initWebsiteNavigation (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/project/types/website/website-navigation.ts:166:27) at async Object.preRender (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/project/types/website/website.ts:105:5) at async renderProject (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/command/render/project.ts:208:5) at async Command.fn (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/command/render/cmd.ts:211:26) at async Command.execute (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/vendor/deno.land/x/[email protected]/command/command.ts:1790:7) at async quarto (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/quarto.ts:122:3) at async file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/quarto.ts:154:5 ```

```qmd quarto create-project --type website:blog demo-toc-left echo "toc-location: left" >> demo-toc-left/_quarto.yml quarto render demo-toc-left ```` From the dev version, `toc-location: left` produces an empty left sidebar and "glass" side abr at the top[^1]. <img width="1512" alt="Screenshot 2023-04-16 at 20 34 23" src="https://user-images.githubusercontent.com/8896044/232334406-57857bb9-b23a-4553-819e-bba677c90548.png"> From the latest 1.2, only the empty sidebar <img width="1508" alt="Screenshot 2023-04-16 at 20 37 53" src="https://user-images.githubusercontent.com/8896044/232334493-4a19f7e5-3886-4617-9d16-7a1a372a30f2.png"> Note that, I did not noticed unexpected behaviour with `toc-location: right` and `toc-location: body`. [^1]: Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5203

### Bug description I am preparing a quarto presentation for Tuesday the 18th. Everything was going well, and then I had some problems not being able to render the .qmd. Now today I get a parsing error. I am only including the YAML rather than the entire .qmd and the rendering stops at line 5. ```` YAML parse exception at line 5, column 0, while scanning a simple key: could not find expected ':' ```` Here is my YAML: ```` --- title: "My Presentation" author: "Me" date: 04/18/2023 date-format: long format: revealjs: chalkboard: true incremental: true bibliography: references.bib --- ```` I am able to render and have no problem with your YAML. ```` --- title: "Quarto Presentations" subtitle: "Create beautiful interactive slide decks with Reveal.js" format: revealjs: slide-number: true chalkboard: buttons: false preview-links: auto logo: images/quarto.png css: styles.css footer: <https://quarto.org> resources: - demo.pdf --- ```` ``` I have the pleasure of using R-Studio Version 2023.03.0+386 (2023.03.0+386) I am using MacOS Ventura 13.3.1 [✓] Checking Quarto installation......OK Version: 1.2.475 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ```` Would love to concentrate on my presentation rather than moving everything over to a Xarangan presentation - which is also very wonderful. Thanks for your help. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Hi there, I was using code annotation + code highlight (code-line-numbers) simultaneously on a `revealjs` presentation and got the following output: <img width="1198" alt="Screenshot 2023-04-15 at 5 45 42 PM" src="https://user-images.githubusercontent.com/25586362/232256241-14b798fd-52ca-4479-be59-3a77c29e5f5c.png"> Here is the exact code I used: ````{md} ```{r} #| label: across #| echo: true #| eval: true #| fig-align: center #| code-line-numbers: "3|4,5|6,7|8|9|10,11" penguins |> summarise( .by = species, # <1> across( .cols = where(is.numeric), # <2> .fns = list(mean = mean, median = median, variance = var), # <3> .names = "{.fn}_{.col}", # <4> na.rm = TRUE ) ) ``` ```` 1. This argument replaces the `group_by` verb avoiding one pipe step 2. Here we will iterate through all the columns that are numeric. 3. This is a named list of all the functions we want to execute over the defined columns 4. This is called string interpolation, and here will create the names of the newly created variables by appending the name of the function `{.fn}` that appeared on the `.fns` list of functions to each name of the columns `{.col}` separated by the underscore `_`. *** I am using: macOS 13.2.1 22D68 x86_64 (macOS Big Sur) R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Quarto: v1.3.326 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description The `<img />` tags are not rendered properly in v1.3.326 ```` ```{mermaid} flowchart TD X --> Q[<img src='https://quarto.org/quarto.png' width='154' height='36' /><br/>Some image] ``` ```` With v1.2.475  With v1.3.326  ### Linux distribution Ubuntu 20.04.6 LTS (Focal Fossa) ### Quarto check #### `1.2.475` ``` [✓] Checking Quarto installation......OK Version: 1.2.475 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.11 Path: /venv/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` #### `1.3.326` ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.326 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.11 Path: /venv/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description When I run `quarto render` - in a website project - with a project-wide `lang: cs` setting in `quarto.yml`, I see: ``` [WARNING] Could not load translations for cs translations/cs.yaml: YAML parse exception at line 3, column 13: mapping values are not allowed in this context [WARNING] The term Abstract has no translation defined. ``` And the language-relevant elements in the rendered documents are not translated. _quarto_yml: ```yaml project: type: website website: title: "quarto-title" navbar: left: - href: index.qmd text: Home - about.qmd format: html: theme: cosmo lang: cs css: styles.css toc: true ``` Quarto 1.3.324 MacOS 13.4 beta Quarto check (I do have R installed, not sure why that check fails.) ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.324 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.2 Path: /opt/homebrew/opt/[email protected]/bin/python3.11 Jupyter: 5.1.3 Kernels: python3, ir (|) Checking Jupyter engine render....0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.