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### Bug description Using Quarto 1.3.340 on macOS. ````markdown --- title: external format: html: link-external-icon: true --- This is a fairly lengthy sentence that has an external link to the website of the [Quarto project](https://quarto.org/). ```` When rendered, things look just fine at first: <img width="749" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/f4a0c98b-72e8-4f4c-b9d7-b2a2c4d57610"> With a slightly different screen size, the period wraps by itself: <img width="747" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/8037d3a8-3b34-4e5c-bdc8-50180937bafc"> Even narrower sees the external-link icon wrap apart from the link text: <img width="749" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/53bca89e-a194-4fd8-87e4-98d76024b2b0"> I did not expect that the link text, the external link icon, and the trailing period would be splittable. ``` [✓] 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/RStudio.app/Contents/Resources/app/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: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 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 When setting the `fig-env` or `fig-pos` in the `_quarto.yml`, there is a peculiar bug where it errors if you include single images inside of custom divs. I will show some tests which reproduce the error from the default book project in VSCode when using "New Project --> Book". I have started doing all of my figures inside of their own divs. This makes writing much longer figure captions much easier, and spellcheck actually looks at them inside of VSCode rather than when they are inside of the `[]` of a regular markdown image. The below project renders OK, including a number of subfigures. ## Renders OK ```yaml project: type: book book: title: "testing" author: "Norah Jones" date: "23/05/2023" chapters: - index.qmd - intro.qmd - summary.qmd - references.qmd bibliography: references.bib format: pdf: documentclass: scrreprt fig-pos: bp ``` ```md # Introduction This is a book created from markdown and executable code. See @knuth84 for additional discussion of literate programming. ::: {#fig-test layout-ncol="2"} {#fig-logo1} {#fig-logo2} Some logos. ::: ``` ## Doesn't Render If I leave the YAML the same but change it to just a single figure inside of the div then this fails to render: ```md # Introduction This is a book created from markdown and executable code. See @knuth84 for additional discussion of literate programming. ::: {#fig-test}  Some logos. ::: ``` ``` compilation failed- error LaTeX Error: Not in outer par mode. See the LaTeX manual or LaTeX Companion for explanation. Type H <return> for immediate help. ... l.215 \begin{figure}[bp] ``` The actual `.tex` lines that are problematic look like this, and from what I can find googling around it doesn't like setting a floating environment inside an already floating environment. ```tex \begin{figure} {\centering \begin{figure}[bp] {\centering \includegraphics{cover.png} } \end{figure} } ``` I have a solution that works if I set it up as follows: ```md ::: {#fig-test layout-ncol="1"}  Some logos. ::: ``` I found that it was mentioned in the docs about setting environments inside of divs can be unstable in latex. I propose that that the global `fig-env` or `fig-pos` might instead affect the div figure rather than what is contained within? I figure that this might also be a bit of an esoteric use, but I the ability to better write longer captions I think is crucial as opposed to the `![]()` markdown syntax, so potentially even a different way to include images in the div. # System specs: I have tested on both my windows 11 and MacOS 13.2 machines. #### Quarto Check: ```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: 1.3.353 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.11 (Conda) Path: /usr/local/Caskroom/miniconda/base/envs/mn-test/bin/python Jupyter: (None) Jupyter is not available in this Python installation. Install with conda install jupyter [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/brady/git/phd/thesis/renv/library/R-4.2/x86_64-apple-darwin17.0 - /Library/Frameworks/R.framework/Versions/4.2/Resources/library knitr: 1.39 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 Quarto fails to render accents such as tilde and hat in latex equations correctly in revealjs presentation. Below I provide a mwe. <img width="58" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/40790433/2bcd0713-7d21-4127-a913-5617a0e34ae4"> Safari 16.0, macOS 12.6, MacBook Pro M1 chip. Quarto 1.3.340. Rendered using VS code Quarto extension. ```{qmd} title: "Minimal example" format: revealjs: theme: [default] --- ## Minimal example - Tilde problem with Safari: $\tilde c$ or $\hat{c}$ ``` `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: 1.3.340 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.13 (Conda) Path: /opt/homebrew/anaconda3/bin/python Jupyter: 4.11.1 Kernels: ir, julia-1.8, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library knitr: 1.42 rmarkdown: 2.19 [✓] 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 Using Quarto 1.3.340 on macOS. Using a Quarto document containing an HTML list with an embedded div: ````markdown --- title: lists --- <ul> <li> <a href="https://posit.co/"> <div> hi </div> </a> </li> </ul> ```` When rendered, this produces a partial code fragment: <img width="346" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/5e5f6536-9401-4b03-9604-dbe780657448"> This looks to be partially related to incorrectly seeing the HTML as having inline code and partially related to some JS getting inserted into the middle of the generated HTML. Rendering to Markdown, it feels like the problem is because we are identifying only part of the document as containing an HTML chunk: ```bash quarto render index.qmd --to markdown -o index.md ``` ````markdown ```{=html} <ul> ``` ```{=html} <li> ``` `<a href="https://posit.co/">`{=html} ```{=html} <div> ``` hi </div> </a> ```{=html} </li> ``` ```{=html} </ul> ``` ```` Workaround: Avoid indenting HTML code. If all leading whitespace is removed ``` [✓] 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/RStudio.app/Contents/Resources/app/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: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 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 use a navbar instead of a sidebar in a book project, social sharing icon URLs are malformed whether I specify one or multiple services. Ref #5629 for a similar bug in sidebar. To reproduce: Create a new book project: ``` $ quarto create-project mybook --type book $ quarto preview mybook ``` Add a `sharing:` tag and a `navbar:` tag to _quarto.yml as follows: ``` project: type: book book: title: "mybook" author: "Norah Jones" date: "5/22/2023" sharing: [twitter, linkedin] navbar: title: "My Book" chapters: - index.qmd - intro.qmd - summary.qmd - references.qmd bibliography: references.bib format: html: theme: cosmo pdf: documentclass: scrreprt ``` When the site renders, choosing either sharing icon results in a redirect to an invalid URL; e.g., `https://twitter.com/intent/tweet?url=|url|` ### 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 In a book project, if I add `sharing:` metadata with one service specified, the URL assigned to the sharing icon in the rendered page is malformed. However, If I add two or more services, the URLs seem to be formatted properly. To reproduce: Create a new book project: ``` $ quarto create-project mybook --type book $ quarto preview mybook ``` Add a `sharing:` entry to _quarto.yml so it looks like: ``` project: type: book book: title: "mybook" author: "Norah Jones" date: "5/22/2023" sharing: twitter chapters: - index.qmd - intro.qmd - summary.qmd - references.qmd bibliography: references.bib format: html: theme: cosmo pdf: documentclass: scrreprt ``` After render, clicking on the "twitter" icon causes a redirect to URL: `https://twitter.com/intent/tweet?url=|url|` and of course Twitter doesn't know how to handle it. Results are similar if I use "linkedin" or "facebook" instead of "twitter". But if the `sharing:` tag looks as follows: `sharing: [twitter, linkedin]`, choosing either icon results in the expected redirect URL. OS: Kubuntu 20.04 Quarto version: 1.3.282 ### 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 Using Quarto 1.3.340 (1.3.353 also shows the same behavior) on macOS: Given the Markdown file: ````markdown --- title: callout text --- this is a paragraph this is another paragraph ::: {.panel-tabset} ## one option this is text for one option some more text for one option ## two option this is text for two option some more text for two option ::: this is some text after the tabset this is more text after the tabset ```` This is rendered with more line spacing within the panel tabset than outside. <img width="331" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/31f6b45e-55dd-428c-9470-04276248791d"> ``` [✓] 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/RStudio.app/Contents/Resources/app/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: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 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 I specify website `image:` and `open-graph: true` values, but the rendered page chooses another image for the `meta property="og:image"` content value. To reproduce: create a new weblog project: ``` $ quarto create-project myblog --type website:blog $ quarto preview myblog ``` Edit _quarto.yml so it appears as follows: ``` project: type: website website: title: "myblog" image: "/posts/post-with-code/image.jpg" open-graph: true page-footer: center: | Footer image: [](https://quarto.org/) navbar: right: - about.qmd - icon: github href: https://github.com/ - icon: twitter href: https://twitter.com format: html: theme: cosmo css: styles.css ``` The og metadata in the rendered page appears as: ``` <meta property="og:title" content="myblog"> <meta property="og:image" content="./profile.jpg"> <meta property="og:site-name" content="myblog"> ``` The image from the footer section is chosen instead of the website `image:` metadata. OS: Kubuntu 20.04 Quarto version: 1.3.282 ### 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/5613 <div type='discussions-op-text'> ^{Originally posted by **vfacta** May 19, 2023} Is it possible to change the language of the cookie consent banner to the website's main language? [#433](https://github.com/quarto-dev/quarto-cli/issues/433#issue-1172994895) already asked if it was possible to change the the text inside the pop-up, but that question seems to aim at modifying the matter of what's being said there. I don't intend to change the content per se of what is being said, but to display the translation from the default English text to the language set in the yml file. As the Cookie pop-up has, when clicked on "Change my preferences", a box for language selection close to the upper right corner, it was expected to have an automatic translation according to what was defined in the yml, as it is to other predefined texts. I don't know if this resource has already been implemented or if I'm doing something wrong. Minimal working example: - _quarto.yml ``` project: type: website lang: pt website: title: Untitled cookie-consent: true format: html: default ``` - index.qmd ``` --- title: "Lorem Cookie" --- Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. ``` </div>

Bug Template ## Description: Confluence Permission check reported in history feed ## Steps to Reproduce: - Publish Confluence pages several times - Look at the home page history feed ### Expected Result: - A very few number of permission check files are listed ### Actual Result: - Several (one per publish) permission check files are listed `quarto-permission-test-#UUID#` Related: https://github.com/quarto-dev/quarto-cli/issues/5299 We should cache the results of the first check and use that.

### Bug description Hi all, I'm using Quarto websites, with Quarto+Revealjs slides, for a course I'm teaching in the fall, and absolutely loving everything about it :) I have a very corner-case issue: I can cross-reference slides perfectly well, except for those I've given the class `.unnumbered`, which I'm using at the moment for Appendix slides (extra info, answers to questions that may come up, etc.). As far as I can tell, adding `.unnumbered` is what's breaking it, as my MWE hopefully shows. But I'm leaving in some of my front matter to show that e.g. `slide-number` is set to `true`, as is helpfully [mentioned in the docs](https://quarto.org/docs/authoring/cross-references.html#sections)! From what I know about `pandoc` and traversing nodes and etc., it seems like it's probably related to #3234, though in my case it's all within a single `.qmd` file. And, feel free to close if it's already being fixed in the newer version referenced [here](https://github.com/quarto-dev/quarto-cli/issues/2412#issuecomment-1259362430) MWE is just the following (and in a [gist](https://gist.github.com/jpowerj/32fa0c91edfb1992db4cf050b3a20b95#file-test-slides-qmd) just in case): ``` --- title: "Appendix Cross-Ref: MWE" format: revealjs: slide-number: true number-sections: true number-depth: 2 code-fold: true footnotes-hover: true scrollable: true df-print: kable --- ## First Slide See @sec-appendix-a. Then see @sec-appendix-b. ## Appendix A: Continuous RV Support {#sec-appendix-a .unnumbered} First appendix. ## Appendix B: Numbered {#sec-appendix-b} Second appendix. This one can be referenced ``` I am using the VSCode extension, so no R Studio version issues I don't think. OS is Windows 11. Here is my `quarto check` output (I'm omitting the Jupyter part just because, I have a weird Jupyter setup for research stuff, so it just produces a big error that I know how to fix but haven't fixed yet!) ``` [>] 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: 1.3.319 Path: C:\Users\jpjac\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.5 Path: C:/Python310/python.exe Jupyter: 5.3.0 Kernels: whatlies, python3 ``` Like I said, I imagine I'm in the same boat as #3234, but would love the ability to cross-reference Appendix slides/sections in future versions! Thanks so 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. - [ ] 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 ``` Quarto: 1.3.24 and 1.3.353 in VSCode Windows 10. ``` My document was running well with quarto in vscode a few days ago. However, after I added a few inline equations in a numbered list like below, the following error occurred during the compilation to PDF. 5. For one uncensored survival time, we could define $N_i(t)=I(T_i\leq t)$, and then $dN(t) = I(T_i \leq t+dt) - I(T_i \leq t) = I(t \lt T_i \leq t+dt)$ ``` compilation failed- missing packages (automatic installed disabled) Undefined control sequence. l.174 ...(T_i \leq t+dt) - I(T_i \leq t) = I(t \lt T_i \leq t+dt)\) ``` Also, there is no issues to render the equation in the Quarto assist panel. After some experimenting, I think the issue is due to the double ended inequality, such as $I(t \lt T_i \leq t+dt)$. If I placed this in the beginning of the document, no matter as inline or displayed math, the compilation would stop with the same error pointing to that. ``` quarto check A new release of Deno is available: 1.28.2 → 1.33.4 Run `deno upgrade` to install it. [>] 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: 1.3.353 Path: C:\Program Files\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.11 (Conda) Path: C:/Users/xxxxx/AppData/Local/miniforge3/envs/mytensor/python.exe Jupyter: 5.3.0 Kernels: python3, powershell, pysparkkernel, sparkkernel, sparkrkernel [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.2.3 Path: C:/PROGRA~1/R/R-42~1.3 LibPaths: - C:/Users/xxxxx/AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.3/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. - [ ] 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 A very frustrating problem, which did not exist in my previous version. I want to input the Block block in beamer as follows in QMD: :: {.block} content ::: So that it can be displayed as a block in be after compilation. This was successfully done in previous versions, but cannot be achieved in the latest(quarto-1.4.80-macos). After compilation, only content is displayed instead of the block. Has this feature been removed from new version or is it just a 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 provide the output of `quarto check` so we know which version of quarto and its dependencies you're running. - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.

### Bug description Matlab code cells in qmd files are not recognized by the Quarto Extension for VS Code:  Within such cells, there is no syntax highlighting or other language support, and the cells do not have the minitoolbar to execute them separately. Processing the qmd file works, and the code cells are executed without problem. As seen on the right side of the screenshot, syntax highlighting in Matlab script files (`.m`) works. __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: 1.3.313 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.2 Path: /usr/bin/python3 Jupyter: 4.9.1 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 17, in <module> import nbformat ModuleNotFoundError: No module named 'nbformat' [✓] Checking Jupyter engine render....OK ```` __System:__ Debian GNU/Linux 11.7, kernel 5.10.0-23-amd64 VS Code 1.78.2 Python extension 2023.8.0 Jupyter extension 2023.4.1011241018 Quarto extension 1.85.0 Jupyter matlab_kernel 0.17.1 ### 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.

### Bug description # Issue When using a top or right navigation bar (non-default) and the generated PDF filename has consecutive hyphens such as `--` or `---`, those are incorrectly encoded as en and em hyphens in the PDF URL link. For example, the below Quarto Book titled `Test: A Book` will render a PDF named: ```sh $ ls _book/*.pdf _book/Test--A-Book.pdf ``` because space (` `) is encoded as a hyphen (`-`) and so is colon (`:`), which results in `--` in the PDF filename. However, the link produced in the HTML version of the book, encodes `--` as an en hyphen (–), resulting in a link to `./Test–A-Book.pdf` (= `Test%E2%80%93A-Book.pdf`); ```html $ grep "Download PDF" _book/index.html <a href="./Test–A-Book.pdf" title="Download PDF" class="quarto-navigation-tool px-1" aria-label="Download PDF"><i class="bi bi-file-pdf"></i></a> ``` # Reproducible example ```sh quarto create project book test-book cd test-book emacs _quarto.yml ## edit as below example quarto render quarto preview ``` `_quarto.yml`: ```yaml project: type: book book: title: "Test: A Book" author: "Norah Jones" date: "5/19/2023" chapters: - index.qmd - intro.qmd - summary.qmd - references.qmd downloads: [pdf] navbar: top: - icon: github bibliography: references.bib format: html: theme: cosmo pdf: documentclass: scrreprt ``` Note that the URL is indeed correct when using the default navbar, i.e. without the custom: ```sh navbar: top: - icon: github ``` # Session info This is on an up-to-date Ubuntu 22.04 Linux machine: ```sh $ 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: /home/henrik/shared/software/CBI/quarto-1.3.340/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 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: 4.3.0 Path: /home/henrik/shared/software/CBI/R-4.3.0-gcc11/lib/R LibPaths: - /home/henrik/R/x86_64-pc-linux-gnu-library/4.3-CBI-gcc11 - /home/henrik/shared/software/CBI/R-4.3.0-gcc11/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. - [ ] 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 have been using the code below in rmarkdown::knitr to MS Word docx (via `output: officedown::rdocx_document:`) successfuly to reset the numbering counter for tables and figures, inserting it where I need to reset the counter. Unfortunately it does not work in Quarto docx documents. It would be very nice to be able to use this or something similar in Quarto. ``` ```{r} #| output: false officer::run_autonum( seq_id = "fig", pre_label = "", start_at = 0, prop = fp_text( color = "white", font.size = 0) ) ## Note: Reset figure numbering NOT working in qmd ``` ``` ### 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 On Ubuntu, using Quarto 1.2.335 preview reloads when I modify local `.js` files that I require into my qmd file in ojs blocks On 1.3.353 and 1.4.78, this isn't working when I update the .js file or `echo "hi" > ` it. *It does work when I **remove** and write a new file.* `.js` file is in a resources folder, listed in `format: html: resources` yml. 1.4.78 info: ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK ``` ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.78 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 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/ ``` ### 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? - [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 attempt to put html tags in the text of the "page-footer" option, the tags are filtered out. to reproduce: create a new book project: ``` $ quarto create-project mybook --type book $ quarto preview mybook ``` Edit _quarto.yml as below: ``` project: type: book book: title: "mybook" author: "Norah Jones" date: "5/18/2023" chapters: - index.qmd - intro.qmd - summary.qmd - references.qmd page-footer: center: outside<div>inside</div> bibliography: references.bib format: html: theme: cosmo pdf: documentclass: scrreprt ``` When the project is rendered, only the word "outside" is visible in the footer. The div tags have been filtered out. Is there a way to add arbitrary content to a footer? OS: Kubuntu 20.04 Quarto version: 1.3.282 ### 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 Using Quarto 1.3.340 on macOS. Given an `index.qmd` file containing the following content, Quarto attempts to run the embedded R Markdown document. `````markdown # Simple Markdown This is a simple Markdown document containing an embedded R Markdown document. ````markdown --- title: "making a GET" --- This shows you how to perform an HTTP connection to some server. ```{r setup, echo = FALSE, include=FALSE} knitr::opts_chunk$set(echo = TRUE) ``` ```{r libraries, echo = FALSE, message = FALSE} library(httr) ``` ```{r fetch, echo = FALSE} serverURL <- "http://localhost:3939/" res <- httr::GET(serverURL, httr::write_memory()) if (httr::http_error(res)) { err <- sprintf( "%s request failed with %s", res$request$url, httr::http_status(res)$message ) message(capture.output(str(httr::content(res)))) stop(err) } ``` ```` ````` The resulting error: ```bash quarto preview index.qmd #> #> #> processing file: index.qmd #> |.................................................. | 86% [fetch] #> Quitting from lines 21-33 [fetch] (index.qmd) #> Error in `curl::curl_fetch_memory()`: #> ! Failed to connect to localhost port 3939 after 1 ms: Couldn't connect to server #> Backtrace: #> 1. httr::GET(serverURL, httr::write_memory()) #> 2. httr:::request_perform(req, hu$handle$handle) #> 4. httr:::request_fetch.write_memory(req$output, req$url, handle) #> 5. curl::curl_fetch_memory(url, handle = handle) #> #> Execution halted ``` This document was not meant to be executed. ```bash quarto inspect index.qmd | jq .engines #> [ #> "knitr" #> ] ``` ### 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 Using Quarto 1.3.340 on macOS. Given the following Markdown file named `index.md`, Quarto reports that the file must be named `*.qmd` because it contains executable code. There is no executable code in this document. `````markdown # Simple Markdown This is a simple Markdown document containing an embedded R Markdown document. ````markdown --- title: "embedded" --- This is an embedded R Markdown document contained within a simple Markdown document. ```{r setup, echo = FALSE, include=FALSE} knitr::opts_chunk$set(echo = TRUE) ``` ```` ````` The resulting error: ```bash quarto render index.md #> ERROR: You must use the .qmd extension for documents with executable code. #> #> Error: You must use the .qmd extension for documents with executable code. #> at Object.execute (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:55533:23) #> at renderExecute (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:86465:48) #> at renderFiles (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:86588:57) #> at async render (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:90675:21) #> at async Command.fn (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:90850:32) #> at async Command.execute (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:8437:13) #> at async quarto (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:127535:5) #> at async file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:127553:9 ``` Encountered when trying to adapt a mkdocs site to use Quarto without performing a bunch of file renaming. ### 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 Using Quarto 1.3.340 on macOS ```bash # Run in a brand new directory. touch index.qmd touch _quarto.yml echo '# this is a comment' > _metadata.yml quarto render #> ERROR: Directory metadata validation failed. #> #> (line 1, column 19) YAML value is missing. #> 1: # this is a comment #> ~ #> #> #> Error: Directory metadata validation failed. #> #> (line 1, column 19) YAML value is missing. #> 1: # this is a comment #> ~ #> #> at readAndValidateYamlFromFile (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:42120:15) #> at async directoryMetadataForInputFile (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:58421:26) #> at async resolveFormats (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:83119:46) #> at async renderContexts (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:82632:21) #> at async Object.renderFormats (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:82683:26) #> at async inputTargetIndex (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:83499:21) #> at async resolveInputTarget (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:83578:19) #> at async resolveItem (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:93620:26) #> at async navigationItem (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:93591:16) #> at async navbarEjsData (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:93510:28) ``` Related to https://github.com/quarto-dev/quarto-cli/issues/5600 ``` [✓] 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/RStudio.app/Contents/Resources/app/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: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 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 Using Quarto 1.3.340 on macOS ```bash # Run in a brand new directory. touch index.qmd touch _quarto.yml touch _metadata.yml quarto render #> ERROR: Internal Error: createSourceContext called with bad location. #> #> Error: Internal Error: createSourceContext called with bad location. #> at createSourceContext (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:14790:15) #> at createLocalizedError (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:14864:28) #> at file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:15006:55 #> at Array.map (<anonymous>) #> at ValidationContext.collectErrors (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:15006:32) #> at ValidationContext.validate (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:14929:21) #> at validate (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:15293:20) #> at YAMLSchema.validateParse (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:15318:34) #> at validate (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:18623:43) #> at withValidator (file:///Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto.js:15381:25) ``` This can happen with an empty `_metadata.yml` at any position in a website hierarchy. I originally encountered this while preparing a directory structure to have sub-directory configuration overrides; I first created empty `_metadata.yml` files in each directory, but started experimenting with values in only one of the YAML files. ``` [✓] 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/RStudio.app/Contents/Resources/app/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: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 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 Importing reactive values from other `.qmd` files ([docs link](https://quarto.org/docs/interactive/ojs/code-reuse.html#output)) is really useful, but those qmd files need to be rendered manually*, so it's not very smooth to develop. *Current import mechanism is to fetch the html file and process that: https://github.com/quarto-dev/quarto-ojs-runtime/blob/c2572e5688dfc7d9d584e31033e620b34b11a7d3/src/ojs-connector.js#LL301C1-L301C57 +It may be advantageous to move the import mechanism to processing the qmd contents instead of html, or to output an ojs module for importing purposes. Quarto 1.2.335 on Ubuntu.

### Bug description I would like to add more spacing between author and publication date. ```yaml --- title: Mesa Limpa description: Relatório Dinâmico sobre processos abertos do SEI - SETIC authors: - name: author1xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx - name: author2xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx date: today format: html: theme: flatly lang: pt title-block-banner: true server: shiny --- ``` ### 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.

We should recognize shortcodes that come from our parsed HTML content in `parse_md_in_html_rawblocks`.

This is a regression in 1.3 as it was fixed in 1.2 by @dragonstyle already https://github.com/quarto-dev/quarto-cli/issues/2393 * References.bib ``` @article{Cronbach_1951, doi = {10.1007/bf02310555}, year = 1951, month = {sep}, publisher = {Springer Science and Business Media {LLC}}, vol = {16}, number = {3}, pages = {297--334}, author = {Lee J. Cronbach}, title = {Coefficient alpha and the internal structure of tests}, journal = {Psychometrika} } ``` ```markdown --- title: "Citeproc" format: html bibliography: References.bib citeproc: true --- Hello [@Cronbach_1951] ```  We have a code path where `citeproc: true` should be removed : https://github.com/quarto-dev/quarto-cli/blob/e136ef277275a9ad9d4ff4599b04595c34c4f4ef/src/command/render/filters.ts#L619-L624 but it seems to still be present in the default file we generate. This is happening with current release 1.3 and pre release 1.4. So This is a regression we should probably patch for 1.3 and fix for 1.4 - this is needed to work for #5575 as we set `citeproc: false` by default, and we need user to set `citeproc: true` to change the engine.

### Bug description In a book when specifying the ``` format: html: theme: cosmo code-fold: true code-copy: true code-block-bg: true code-overflow: wrap pdf: documentclass: scrreprt code-block-bg: true ``` I cannot get `code-overflow` as an option for a pdf document.  Example comes from the template of a book within rstudio. I am running Fedora 38 and the Rstudio IDE is the 2023.05.0 Build 334 ### 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 Using de RHEL7 package v 1.3.353, I run into an GLIBC version error due to Deno # Current behavior ```bash $ /opt/quarto/"${QUARTO_VERSION}"/bin/quarto -v 1.3.353 $ /opt/quarto/"${QUARTO_VERSION}"/bin/quarto check /opt/quarto-1.2.313/1.3.353/bin/tools/deno-x86_64-unknown-linux-gnu/deno: /lib64/libc.so.6: version `GLIBC_2.18' not found (required by /opt/quarto-1.2.313/1.3.353/bin/tools/deno-x86_64-unknown-linux-gnu/deno) $ /opt/quarto/"${QUARTO_VERSION}"/bin/quarto -h /opt/quarto-1.2.313/1.3.353/bin/tools/deno-x86_64-unknown-linux-gnu/deno: /lib64/libc.so.6: version `GLIBC_2.18' not found (required by /opt/quarto-1.2.313/1.3.353/bin/tools/deno-x86_64-unknown-linux-gnu/deno) ``` # ReprEx I used the standard installation procedure on RHEL7 ```bash export QUARTO_VERSION="1.3.353" curl -o quarto.tar.gz -L "https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-amd64.tar.gz" sudo tar -zxvf quarto.tar.gz -C "/opt/quarto/${QUARTO_VERSION}" --strip-components=1 ``` ### 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 ``` $ quarto render --to pdf error: Top-level await promise never resolved await quarto(quartoArgs, (cmd)=>{ ^ at <anonymous> ``` I don't seem to be getting this error when running `quarto render --to html`. This seems to have happened all of sudden. It was working fine on my machine yesterday. I was getting an error, and I updated to the latest release and I'm still getting an error: ``` $ quarto --version 1.4.70 ``` ``` $ quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.4.70 Path: C:\Users\USER\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/USER/Miniconda3/python.exe Jupyter: 5.1.0 Kernels: python3, julia-1.9 [>] 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 - [ ] 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'm using variables for categories in the listing, they are properly parsed on the post page and the grid listing, however, they are not properly parsed in the following cases: ## My setup In the `.qmd` file of the post, the frontmatter contains the following: ````md --- title: "ABC" categories: - "{{< var kws.ds >}}" - "{{< var kws.ml >}}" - "{{< var kws.nlp >}}" - "{{< var kws.python_pkg >}}" - AI --- Here is the content of the post. ```` And these variables are defined in the `_variables.yml` file, like the following: ```yaml kws: ds: Data Science ml: Machine Learning nlp: Natural Language Processing python: Python python_pkg: Python Library ``` ## Issues - RSS feed:  - When `categories: true` in listing as can be seen below:  ## App/system versions: I'm using Quarto v1.4.37 in my VSCode v1.76.0 on macOS (13.3.1). The output of `quarto check` is: ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.1: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.37 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.0 (Conda) Path: /Users/essi/miniconda3/envs/s2s/bin/python Jupyter: 5.3.0 Kernels: s2s, openai, python3 (\) Checking Jupyter engine render....Unable to load extension: pydevd_plugins.extensions.types.pydevd_plugin_pandas_types [✓] 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 - [ ] 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 using `quarto_render('example_image.qmd', output_format = "docx")` on the sample .qmd below the resulting word document displays a discolored yellowish box around the image. **This does not appear** when rendering in using `markdown::render("example_image.rmd")`, ie not using Quarto. System is windows, using R version 4.2.3, quarto-1.3.353-win, MS Word 2016. The example_image.qmd file below. The resulting docx output: ([link](https://ibb.co/5Gxh9V3)) ```` --- title: Test including figure in docx format: docx --- ```{r} #| label: fig-elephant #| fig-cap: "This is an elephant." download.file("https://quarto.org/docs/authoring/images/crossref-figure.png", 'elephant.png', mode = 'wb') knitr::include_graphics('elephant.png') ``` ```` ``` > 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: 1.3.353 Path: C:\Program Files\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...........OK Version: 4.2.3 Path: C:/PROGRA~1/R/R-42~1.3 LibPaths: - C:/Users/user/AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.3/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 am using Quarto on a remote server I ssh into in VScode. Versions are the following: Windows 10 local - Centos 7.9 remote VScode insiders: 1.79.0 Quarto extension: 1.85.0 Quarto package on remote server: 1.3.121 I am able to run cells in my .qmd and see their output, however the Render button just produces a "Quarto Installation Not Found" error. Rendering with` quarto render test.qmd --to pdf` on the command line on the remote server in VScode works correctly. I have attached a picture showing the error and the correct conversion on the CLI. Please let me know if this features is not available yet or if I need to configure Quarto differently.  Quarto -check output: ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 2.19.2: OK Dart Sass version 1.32.8: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.121 Path: /rwthfs/rz/cluster/home/mz637064/software/quarto-1.3.121/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.15 (Conda) Path: /home/mz637064/mambaforge/bin/python Jupyter: 4.11.1 Kernels: ir, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.1 Path: /rwthfs/rz/cluster/home/mz637064/mambaforge/lib/R LibPaths: - /rwthfs/rz/cluster/home/mz637064/mambaforge/lib/R/library rmarkdown: (None) [✓] Checking R installation...........OK Version: 4.2.1 Path: /rwthfs/rz/cluster/home/mz637064/mambaforge/lib/R LibPaths: - /rwthfs/rz/cluster/home/mz637064/mambaforge/lib/R/library rmarkdown: 2.21 [✓] Checking Knitr engine render......OK quarto check 9.96s user 2.62s system 42% cpu 29.506 total ``` ### 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.

(The bug here is that `![]...` needs to be on a line by itself for our crossref system to pick it up.) ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5568 <div type='discussions-op-text'> ^{Originally posted by **MichelDSchmid** May 16, 2023} Hi all I have a, hopefully, small problem with cross references in a book project. ``` {#fig-bau-formen width=9.5cm} NTCs gibt es in verschiedensten Bauformen wie in @fig-bau-formen ersichtlich ist. Diese Bauformen stellen lediglich eine Auswahl der zur Verfügung stehenden Bauformen dar. ``` I'm always getting the error message: WARNING: Unable to resolve crossref @fig-bau-formen and of course I can't see a cross reference in the document, indepentend if it's in html or pdf.. I coudn't found something in the docs and I'm using quarto version 1.3.353 Thanks in advanced Mike</div>

Quarto 1.3 brought the ability to disable Quarto processing of tables, this was highlighted in a "prerelease" stand-alone page, see <https://quarto.org/docs/prerelease/1.3/tables.html>. The issue is that this page is not easy to find and this `data-quarto-disable-processing="true"` feature/trick can't be found easily without knowing what you are looking for. I believe, parts of or the whole content of the "prerelease" page could be added in a new subsection of <https://quarto.org/docs/authoring/tables.html>. Happy to make a PR later, if appropriate.

### Bug description A fontawesome shortcode no longer works in a subtitle in pre-release v1.4.63 (works in the current release): ``` --- title: "test" subtitle: "With this icon {{< fa regular heart >}}" --- This is a Quarto website. {{< fa regular heart >}} To learn more about Quarto websites visit <https://quarto.org/docs/websites>. ```{r} 1 + 1 ``` ``` <img width="755" alt="Screenshot 2023-05-16 at 12 42 40" src="https://github.com/quarto-dev/quarto-cli/assets/32419319/0e98d93c-e21f-4942-9802-a3785b7f50de"> [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK NOTE: Deno version 1.33.2 is too old. Please upgrade to 1.33.1 or later. [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.63 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: 4.3.0 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 RStudio Version 2023.03.1+446 (2023.03.1+446) MacOS Ventura 13.3.1 ### 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.

Let's take this reference in `References.bib` ```` @article{Cronbach_1951, doi = {10.1007/bf02310555}, year = 1951, month = {sep}, publisher = {Springer Science and Business Media {LLC}}, vol = {16}, number = {3}, pages = {297--334}, author = {Lee J. Cronbach}, title = {Coefficient alpha and the internal structure of tests}, journal = {Psychometrika} } ```` If we do with no reference ````markdown --- title: "Untitled" format: typst bibliography: References.bib bibliographystyle: "chicago-author-date" keep-typ: true --- Hello ```` There will be at the bottom of the file ```` #set bibliography(style: "chicago-author-date") #bibliography("References.bib") ```` It will cause typst to create a Bibliography section anyway. When a citation is added, it seems Pandoc will add some bibliography content ````markdown --- title: "Untitled" format: typst bibliography: References.bib bibliographystyle: "chicago-author-date" --- Hello [@Cronbach_1951] ```` ```` #label("refs") #label("ref-Cronbach_1951") Cronbach, Lee J. 1951. “Coefficient Alpha and the Internal Structure of Tests.” #emph[Psychometrika], no. 3 (September): 297–334. #link("https://doi.org/10.1007/bf02310555"). #set bibliography(style: "chicago-author-date") #bibliography("References.bib") ```` It seems from https://github.com/jgm/pandoc/issues/8763#issuecomment-1500387547 that it requires some tweak when citation processing is done by Pandoc. (which happens when citeproc is used) Adding `citeproc: false` to YAML header ````markdown --- title: "Untitled" format: typst bibliography: References.bib bibliographystyle: "chicago-author-date" citeproc: false --- Hello [@Cronbach_1951] ```` Will correctly output only the native typst citation processing. So it seems : * We should default to ``citeproc: false` with typst * Or we need to pass `typst-citations` as a format _Originally posted by @cderv in https://github.com/quarto-dev/quarto-cli/discussions/5502#discussioncomment-5915093_

### Bug description The following code does not render the numbers 10 and 11 for the numbered list, but if I remove "scrollable: true" from the YAML, then it renders correctly. Using MacBook Pro with Mac OS 13.3.1, RStudio IDE Version 2023.05.0-daily+358 (2023.05.0-daily+358), and quarto v. 1.4.63. ``` --- title: "test" format: revealjs: scrollable: true height: 1080 width: 1920 editor: visual --- ## Bullets 10 and 11 do not show as such 1. bullet 1 2. bullet 2 3. bullet 3 4. bullet 4 5. bullet 5 6. bullet 6 7. bullet 7 8. bullet 8 9. bullet 9 10. bullet 10 11. bullet 11 ``` <img width="1423" alt="Screenshot 2023-05-15 at 9 51 07 PM" src="https://github.com/quarto-dev/quarto-cli/assets/57681898/cb24699e-102b-43ed-8139-b59ca4a6f173"> ### 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 Hello! I am loving quarto so far and am starting to write up my dissertation using it! I'd like to add margin notes, especially because they look so wonderful in the HTML output. However, when I add a div with `.column-margin` to the document I get the error below. I apologize if I've missed anything, or if this isn't a supported use! Reproducible example: ``` --- format: pdf --- This paragraph works fine, but the marginpar below throws an error. Both work as expected in HTML output. ::: {.column-margin} Hello world ::: ``` Quarto reports an error from the LaTeX log file. I've included a few lines above the (bottom) four that Quarto gives since they look relevant: ``` Package marginnote Info: right page because not two side mode on input line 168 . Runaway argument? {\if@mn@verbose \PackageInfo {marginnote}{xpos seems to be \@mn@currxpos \ETC. ! Paragraph ended before \rlap was complete. <to be read again> \par l.168 ``` Information: | Parameter | Value | | ----------- | ------ | | Quarto Version | 1.3.340 | | IDE | VS Code 1.78.2 (but error persists when quarto is run from command line) | | OS | Windows 10 Enterprise Version 22H2 build 19045.2965 | 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: C:\Users\Rich\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.2 Path: C:/Users/Rich/AppData/Local/Programs/Python/Python310/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with py -m pip install jupyter [>] Checking R installation...........OK Version: 4.2.3 Path: C:/PROGRA~1/R/R-42~1.3 LibPaths: - C:/Users/Rich/AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.3/library knitr: 1.42 rmarkdown: 2.20 [>] Checking Knitr engine render......OK ``` ### 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. - [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 29a775f14a17d45f7e8ca9dd2bb431a3237ea021 introduced an error with `quarto preview` on Fedora 38. Running `quarto preview` in any project or on any file returns: ``` error: File exists (os error 17), symlink '/home/wojtek/bin/quarto-cli/src/webui/quarto-preview/node_modules/.deno/[email protected]/node_modules/fsevents' -> '/home/wojtek/bin/quarto-cli/src/webui/quarto-preview/node_modules/.deno/[email protected]/node_modules/fsevents' ``` The specific file referenced in the error changes, seemingly at random: ``` error: File exists (os error 17), symlink '/home/wojtek/bin/quarto-cli/src/webui/quarto-preview/node_modules/.deno/[email protected]/node_modules/esbuild-linux-arm64' -> '/home/wojtek/bin/quarto-cli/src/webui/quarto-preview/node_modules/.deno/[email protected]/node_modules/esbuild-linux-arm64' ``` For html files, the error above is all that appears. For pdf, you get the pandoc info, `running xelatex...`, `Output created: test.pdf` and only then the error. This is on Fedora 38, `quarto check` below. Works on the commits before 29a775f14a17d45f7e8ca9dd2bb431a3237ea021, and doesn't work on all commits after. <details> <summary>Quarto Check</summary> [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.1: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /home/wojtek/bin/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.3 Path: /usr/bin/python3 Jupyter: 5.3.0 Kernels: python3, octave, julia-1.9 (\) 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: 4.3.0 Path: /opt/R/4.3.0/lib64/R LibPaths: - /home/wojtek/R/x86_64-pc-linux-gnu-library/4.3 - /opt/R/4.3.0/lib64/R/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK </details> ### 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 following [the instructions for publishing a Quarto document ](https://quarto.org/docs/publishing/confluence.html)on my company's Atlassian Confluence cloud I was given the following response after providing the 'Space or Parent Page URL': `The authorization saved for Confluence is no longer valid. Please be sure you are logged into the correct Confluence account in your default web browser, then press Enter to re-authorize.` I have ensured that I am logged in to the proper Confluence account on my default browser, but the error persists. Since I am able to get to the 'Space or Parent Page' prompt, I assume that my Confluence account email and API tokens are being accepted in this process. I am running RStudio 2023.03.0 Build 386 on Windows 10 Pro. Below is the output 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: 1.3.319 Path: C:\Users\jhunter\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.7 (Conda) Path: C:/Users/jhunter/Anaconda3/python.exe Jupyter: 4.8.1 Kernels: python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.2.1 Path: C:/Users/jhunter/AppData/Local/Programs/R/R-4.2.1 LibPaths: - C:/Users/jhunter/AppData/Local/Programs/R/R-4.2.1/library knitr: 1.41 rmarkdown: 2.17 [>] Checking Knitr engine render......OK ```

### Bug description (Apologies for the initially empty bug report -- I pressed "return" on the template after typing the title and it submitted the bug). On a slide of a RevealJS presentation, an image that has a hyperlink will render without the hyperlink if it's by itself. ```markdown --- format: revealjs: center: true --- ## Slide (link won't work) [](https://google.com) ## Slide (link will work) Blah [](https://google.com) ``` I suspect that this is caused by the logic of how standalone images are rendered (and the link is ignored/stripped). Quarto 1.3.185 on Windows 10. ```terminal $ quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 2.19.2: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.185 Path: C:\Users\Cris\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.4 Path: C:/Users/Cris/AppData/Local/Programs/Python/Python310/python.exe Jupyter: 5.3.0 Kernels: python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.1.2 Path: C:/PROGRA~1/R/R-41~1.2 LibPaths: - C:/Program Files/R/R-4.1.2/library 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 I want to use the local tinytex install to produce latex/pdf output. If I install tinytex with `quarto install tinytex`, the installation completely wipes my conda/mamba python folder and replaces it with the tinytex install. I have a local xelatex install, but I wanted tinytex to deal with latex package installation etc. Here's the command I used. ``` $ quarto install tinytex ? tinytex is already installed. Do you want to update to v2023.05? (Y/n) › Yes Updating TinyTeX from undefined to v2023.05 [✓] Downloading TinyTex v2023.05 Removing undefined [✓] Removing directory Installing v2023.05 [✓] Unzipping TinyTeX-v2023.05.tar.gz [✓] Moving files Finishing update [✓] Verifying tlgpg support [✓] Default Repository: https://ctan.math.illinois.edu/systems/texlive/tlnet/ Update successful ``` Basically, this command copies the tinytex install to `/home/luser mambaforge` folder, which is my Python work environment. ### System and version information Installed quarto from conda package These diagnostics are before trying to install tinytex as detailed above. ``` $ quarto list tools [✓] Inspecting tools Tool Status Installed Latest chromium Not installed --- 869685 tinytex External Installation --- v2023.05 $ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.58.3: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /home/luser/mambaforge/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.10 (Conda) Path: /home/luser/mambaforge/bin/python 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/ ``` (I don't use R, so not bothered about the last message). My local environment: ``` $ env| grep -i quarto QUARTO_CONDA_PREFIX=/home/luser/mambaforge QUARTO_SHARE_PATH=/home/luser/mambaforge/share/quarto QUARTO_DENO=/home/luser/mambaforge/bin/deno QUARTO_DART_SASS=/home/luser/mambaforge/bin/sass QUARTO_PANDOC=/home/luser/mambaforge/bin/pandoc QUARTO_DENO_DOM=/home/luser/mambaforge/lib/deno_dom.so QUARTO_ESBUILD=/home/luser/mambaforge/bin/esbuild ```

### Bug description I am trying to setup and run Quarto on Windows 10 using Miniconda virtual environment for running Jupyter. I installed Quarto using the CLI 1.3.353 from https://quarto.org/docs/get-started/ into the recommended folder, for all users. I set up a fresh Miniconda virtual environment and downloaded the hello.ipynb and have that saved on the C: drive On trying to run quarto preview hello.ipynb or quarto render hello.ipynb --to html in the Minconda terminal I get "The system cannot find the path specified" Looked through the issues and found some past issues that suggest Linux /Windows path differences, that were resolved, but might the case with this. quarto check returns the same message in the terminal ### 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 I posted the [issue](https://discourse.pymc.io/t/slow-pymc-sampling-using-the-introductory-example/12122) at PyMC thinking it may have been related to PyMC's installation, it turned out to be an issue with running the code in a qmd document. Basically, running PyMC sampling in qmd does not stop even if the number of draws is 1. ``` import pymc as pm import numpy as np import arviz as az RANDOM_SEED = 8927 rng = np.random.default_rng(RANDOM_SEED) alpha, sigma = 1, 1 beta = [1, 2.5] size = 100 X1 = np.random.randn(size) X2 = np.random.randn(size) * 0.2 Y = alpha + beta[0] * X1 + beta[1] * X2 + rng.normal(size=size) * sigma` basic_model = pm.Model() with basic_model: alpha = pm.Normal('alpha', mu=0, sigma=10) beta = pm.Normal('beta', mu=0, sigma=10, shape=2) sigma = pm.HalfNormal('sigma', sigma=1) mu = alpha + beta[0] * X1 + beta[1] * X2 Y_obs = pm.Normal('Y_obs', mu=mu, sigma=sigma, observed=Y) with basic_model: idata = pm.sample(draws=1) ``` Here you can see with sampling with 1 draw has been running for 48 minutes and more. And there is no progress bar after the sampling initialization message.  Running the same code in VS Code jupyter notebook took only 25.6 seconds (and with 4000 draws no less)  I don't know how to troubleshoot the issue with quarto since I can only tell that python interpreter is busy but there are no warnings or error messages during the sampling. My Quarto version is 1.3.283 and my OS is 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. - [ ] 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 you can see below the copy code button scrolls with the code. I think it should remain fixed on the right. Am I wrong? I'm using quarto 1.4.43.  The site is live here https://pnrr.datibenecomune.it/fonti/regis/mappa.html#costruire-filtri-di-visualizzazione-a-mano ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.1: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.43 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.2 Path: /usr/bin/python3 Jupyter: 5.1.2 Kernels: bash, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.0.4 Path: /usr/lib/R LibPaths: - /home/aborruso/R/x86_64-pc-linux-gnu-library/4.0 - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/lib/R/library knitr: 1.41 rmarkdown: 2.19 [✓] 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 The [Quarto 1.3 release notes say](https://quarto.org/docs/prerelease/1.3/pdf.html#remote-images) remote images will be fetched in PDF but this snippet ``` --- title: "Quarto Playground" format: pdf ---  ``` gives me the error ``` pandoc to: latex output-file: remote-images.tex standalone: true pdf-engine: xelatex variables: graphics: true tables: true default-image-extension: pdf metadata documentclass: scrartcl classoption: - DIV=11 - numbers=noendperiod papersize: letter header-includes: - '\KOMAoption{captions}{tableheading}' block-headings: true title: Quarto Playground 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 updating tlmgr updating existing packages compilation failed- error Unable to load picture or PDF file 'https://nso1.b-cdn.net/wp-content/uploads/2016/04/Full-Image-medium-scaled.jpg'. <to be read again> } l.160 ...ads/2016/04/Full-Image-medium-scaled.jpg} see /home/wball/work/quarto-mwe/remote-images.log for more information. ``` when I run `quarto render`. I tried with [the Wikipedia logo](https://en.wikipedia.org/static/images/icons/wikipedia.png) or [an image from today's featured article](https://upload.wikimedia.org/wikipedia/commons/3/37/Rockwell-Norman-LOC.jpg), both of which worked as expected. I also tried downloading the ill-behaved image and checking that it is, in fact, a JPEG: ``` $ file Full-Image-medium-scaled.jpg Full-Image-medium-scaled.jpg: JPEG image data, JFIF standard 1.01, aspect ratio, density 1x1, segment length 16, baseline, precision 8, 2560x2560, components 3 ``` I also tried escaping the dashes (`-` → `\-`), placing the URL in quotes and using `pdflatex` instead of `xelatex`, none of which worked. I'm not sure if this is a pandoc issue but a quick search online and in their issues didn't turn up anything obvious and I'm not familiar enough with it to create a relevant test. This is Fedora 37 with the following output 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: 1.3.340 Path: /home/wball/Downloads/quarto-1.3.340/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.3 Path: /usr/bin/python3 Jupyter: 5.2.0 Kernels: python3 (-) Checking Jupyter engine render....[IPKernelApp] WARNING | debugpy_stream undefined, debugging will not be enabled [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.3 Path: /usr/lib64/R LibPaths: - /home/wball/R/x86_64-redhat-linux-gnu-library/4.2 - /usr/lib64/R/library - /usr/share/R/library knitr: 1.42 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 Adding the `filename` chunk option to a beamer document creates an error. Reprex: ````md --- format: beamer: keep-tex: true --- ```{r} #| filename: "file" #| echo: true 5 + 5 ``` ```` You get: ``` compilation failed- error LaTeX Error: Not in outer par mode. ``` Diffing with and without the `filename` chunk you get: ```diff \begin{frame}[fragile] +\begin{codelisting} +\caption{\texttt{file}} \begin{Shaded} \begin{Highlighting}[] \DecValTok{5} \SpecialCharTok{+} \DecValTok{5} \end{Highlighting} \end{Shaded} +\end{codelisting} \begin{verbatim} [1] 10 \end{verbatim} \end{frame} ``` The error is to do with the `codelisting` environment, specifically inside beamer (the exact same code works on `format: pdf`). I don't know enough LaTeX to say what the solution would be. This is on Fedora 38, latest nightly release. <details> <summary>Quarto Check</summary> [✓] 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: /home/wojtek/bin/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.3 Path: /usr/bin/python3 Jupyter: 5.3.0 Kernels: python3, octave, julia-1.9 (\) 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: 4.3.0 Path: /opt/R/4.3.0/lib64/R LibPaths: - /home/wojtek/R/x86_64-pc-linux-gnu-library/4.3 - /opt/R/4.3.0/lib64/R/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK </details> ### 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.

```qmd --- title: "Quarto Playground" format: html --- This is a playground for Quarto. {{< meta title>}} ``` In 1.3, the above code would compile without complaining about the malformed shortcode and does nothing. In 1.4, it produces an error[^1] that is a bit mysterious and could be improved. ```txt Error running Lua: ...arto-cli/src/resources//pandoc/datadir/lpegshortcode.lua:111: attempt to concatenate a nil value stack traceback: [C]: in function 'lpeg.match' ...s/quarto/quarto-cli/src/resources/filters/qmd-reader.lua:116: in function 'parse_shortcodes' ...s/quarto/quarto-cli/src/resources/filters/qmd-reader.lua:133: in function 'Reader' ERROR: Error at renderFiles (file:///Users/mcanouil/Projects/quarto/quarto-cli/src/command/render/render-files.ts:539:23) at eventLoopTick (ext:core/01_core.js:181:11) at async render (file:///Users/mcanouil/Projects/quarto/quarto-cli/src/command/render/render-shared.ts:97:18) at async renderForPreview (file:///Users/mcanouil/Projects/quarto/quarto-cli/src/command/preview/preview.ts:430:24) at async render (file:///Users/mcanouil/Projects/quarto/quarto-cli/src/command/preview/preview.ts:189:22) at async preview (file:///Users/mcanouil/Projects/quarto/quarto-cli/src/command/preview/preview.ts:206:18) at async Command.fn (file:///Users/mcanouil/Projects/quarto/quarto-cli/src/command/preview/cmd.ts:356:7) at async Command.execute (file:///Users/mcanouil/Projects/quarto/quarto-cli/src/vendor/deno.land/x/[email protected]/command/command.ts:1790:7) at async quarto (file:///Users/mcanouil/Projects/quarto/quarto-cli/src/quarto.ts:122:3) at async file:///Users/mcanouil/Projects/quarto/quarto-cli/src/quarto.ts:154:5 ``` [^1]: Better than previous behaviour in my opinion.

The following works as expected in 1.3 while in 1.4, the shortcode is not evaluated but printed instead. ```qmd --- format: html title: "{{< meta subtitle >}}" subtitle: "Twitter" --- ```

### Bug description I just tried to embed my first video using a "shortcode" as described in [the docs](https://quarto.org/docs/authoring/videos.html) with something like this: ``` # Just a video {{< "video" "https://nso1.b-cdn.net/wp-content/uploads/2016/04/DKIST-First-Light-MZ-fullFOV-loop_FHD-H264.mp4" >}} ``` When I try to render to HTML, I get: ``` ERROR: invalid shortcode: "video" "https://nso1.b-cdn.net/wp-content/uploads/2016/04/DKIST-First-Light-MZ-fullFOV-loop_FHD-H264.mp4" Error: invalid shortcode: "video" "https://nso1.b-cdn.net/wp-content/uploads/2016/04/DKIST-First-Light-MZ-fullFOV-loop_FHD-H264.mp4" at parseShortcode (file:///home/wball/Downloads/quarto-1.3.340/bin/quarto.js:55007:15) at isBlockShortcode (file:///home/wball/Downloads/quarto-1.3.340/bin/quarto.js:54945:16) at breakQuartoMd (file:///home/wball/Downloads/quarto-1.3.340/bin/quarto.js:55108:32) at validateDocumentFromSource (file:///home/wball/Downloads/quarto-1.3.340/bin/quarto.js:84332:22) at renderFiles (file:///home/wball/Downloads/quarto-1.3.340/bin/quarto.js:86518:48) at async renderProject (file:///home/wball/Downloads/quarto-1.3.340/bin/quarto.js:86794:25) at async Command.fn (file:///home/wball/Downloads/quarto-1.3.340/bin/quarto.js:90850:32) at async Command.execute (file:///home/wball/Downloads/quarto-1.3.340/bin/quarto.js:8437:13) at async quarto (file:///home/wball/Downloads/quarto-1.3.340/bin/quarto.js:127535:5) at async file:///home/wball/Downloads/quarto-1.3.340/bin/quarto.js:127553:9 ``` but if I remove the quotation marks around `"video"`, i.e. have a document with ``` # Just a video {{< video "https://nso1.b-cdn.net/wp-content/uploads/2016/04/DKIST-First-Light-MZ-fullFOV-loop_FHD-H264.mp4" >}} ``` the compilation works as expected. So I suspect this is just a mistake in the document (or it's fallen out of sync with how the shortcode works) but I hesitate to open a PR because I'm surprised this hasn't been reported before... This is Fedora 37 with the following `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: 1.3.340 Path: /home/wball/Downloads/quarto-1.3.340/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.3 Path: /usr/bin/python3 Jupyter: 5.2.0 Kernels: python3 (\) Checking Jupyter engine render....[IPKernelApp] WARNING | debugpy_stream undefined, debugging will not be enabled [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.3 Path: /usr/lib64/R LibPaths: - /home/wball/R/x86_64-redhat-linux-gnu-library/4.2 - /usr/lib64/R/library - /usr/share/R/library knitr: 1.42 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 There is an issue with the documentation for slides, visible on at least these pages: - https://quarto.org/docs/presentations/ - https://quarto.org/docs/presentations/revealjs/ - https://quarto.org/docs/presentations/powerpoint.html - https://quarto.org/docs/presentations/beamer.html The examples listed there look like this: ``` --- format: revealjs--- ``` instead of this: ``` --- format: revealjs --- ``` If one copy&pastes the "bad" versions, quarto rejects this input with an error: ``` ERROR: Expected front matter to end with '---' ``` ### 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.

References to lines of code using `# <n>` are only displayed correctly in the first tabset: ```` --- title: "test" format: html editor: visual --- ::: {.panel-tabset} ## tab1 ```{r} 2 * 2 # <1> ``` 1. test1 ## tab2 ```{r} 2 * 2 # <1> ``` 1. test2 ::: ::: {.panel-tabset} ## tab1 ```{r} 2 * 2 # <1> ``` 1. test1 ## tab2 ```{r} 2 * 2 # <1> ``` 1. test2 ::: ````

### Bug description I've been trying to emulate some Tufte-like elements from the [example HTML in the Quarto gallery](https://quarto-dev.github.io/quarto-gallery/page-layout/tufte.html) but I'm finding that the margin figures aren't being properly scaled. Here's a short Quarto markdown example: ```` # MWE ```{python} #| fig-cap: "ReLU function" #| column: margin #| echo: false import matplotlib.pyplot as pl pl.plot([-1, 0, 1], [0, 0, 1]) pl.show() ``` Some text. Here's a margin figure. Here's some more text and a main figure. ```{python} #| fig-cap: "ReLU function" #| echo: false import matplotlib.pyplot as pl pl.plot([-1, 0, 1], [0, 0, 1]) pl.show() ``` ```` which I build with this `_quarto.yml`: ``` format: html: default ``` and `quarto render mwe.qmd` with Quarto 1.3.340 on Fedora 37 (more system info at the end). I've pinned a relevant change down to the package `matplotlib-inline`. With version 0.1.5, I get too large a figure in the margin. With 0.1.3, the margin figure is scaled correctly. (0.1.4 has been yanked from PyPI.) I noticed that the [changes between 0.1.3 and 0.1.5](https://github.com/ipython/matplotlib-inline/compare/0.1.3...0.1.5) include some matplotlib rcParams but adding those to a local `matplotlibrc` file didn't fix the scaling. At a glance, I'm not sure the main-column figure is being expanded to fill the column any more either. I'm using Python 3.11 on Fedora 37 (though I encountered this with 3.9 on a Ubuntu 22.04 container too). `quarto check` gives: ``` [✓] 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: /home/wball/Downloads/quarto-1.3.340/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.3 Path: /usr/bin/python3 Jupyter: 5.2.0 Kernels: python3 (|) Checking Jupyter engine render....[IPKernelApp] WARNING | debugpy_stream undefined, debugging will not be enabled [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.3 Path: /usr/lib64/R LibPaths: - /home/wball/R/x86_64-redhat-linux-gnu-library/4.2 - /usr/lib64/R/library - /usr/share/R/library knitr: 1.42 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ``` Here are some verison numbers for potentially relevant Python packages (selected from `pip freeze`): ``` bokeh==3.0.3 colorama==0.4.6 colour==0.1.5 ipykernel==6.15.2 ipython==8.5.0 ipython-genutils==0.2.0 ipywidgets==8.0.4 jupyter==1.0.0 jupyter-console==6.6.2 jupyter-events==0.6.3 jupyter_client==7.4.9 jupyter_core==5.2.0 jupyter_server==2.3.0 jupyter_server_terminals==0.4.4 jupyterlab-pygments==0.2.2 jupyterlab-widgets==3.0.5 kaleido==0.2.1 Markdown==3.3.7 MarkupSafe==2.1.1 matplotlib==3.6.3 matplotlib-inline==0.1.5 nbclassic==1.0.0 nbclient==0.7.2 nbconvert==7.2.9 nbformat==5.7.3 notebook==6.5.2 notebook_shim==0.2.3 pandocfilters==1.5.0 pycairo==1.21.0 Pygments==2.14.0 PyQt5==5.15.9 PyQt5-sip==12.11.0 qtconsole==5.4.0 QtPy==2.1.0 widgetsnbextension==4.0.5 ``` ### 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 am attempting to install a quarto extension for section bibliographies into a Quarto Book project using PowerShell. https://github.com/pandoc-ext/section-bibliographies#quarto When I attempt to do so, I receive this error  My project has my company's `http_proxy` and `https_proxy` defined in the `.Rprofile` It is not clear from `quarto help` how the user would verify quarto can see these proxy settings. ### 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.

_Edited: based on @cderv comment and with additional examples_ ## Considering the below example for Quarto `fig-alt` attribute: ```md ## Section {fig-alt="Quarto Logo"} ``` |`quarto pandoc index.qmd --from markdown --to docx -o index.docx` | `quarto render index.qmd --to docx`| |:-:|:-:| | <img width="1624" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/8896044/5fea046c-6e6f-43b7-9033-faf69d0bbca0"> | <img width="1624" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/8896044/b78b2635-e82b-4b0e-a887-0a95272233cc"> | ## Using Pandoc markup, caption + alt text ends up in Word alt text (so no real issues): ```md ## Section  ``` |`quarto pandoc index.qmd --from markdown --to docx -o index.docx` | `quarto render index.qmd --to docx`| |:-:|:-:| | <img width="1624" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/8896044/c6869aa3-a8d0-4c9d-ab45-b790434323e9"> | <img width="1624" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/8896044/fbffb4be-c25d-43d0-b08a-0834da27cc03"> | ## Using computations: ````md ## Section ```{r} #| label: fig-plot #| fig-cap: "A caption for a plot" #| fig-alt: "An alt text for a plot" plot(1) ``` ```` |`quarto pandoc index.qmd --from markdown --to docx -o index.docx` | `quarto render index.qmd --to docx`| |:-:|:-:| | Obviously not working | <img width="1624" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/8896044/4f50db00-abbc-4dfc-8aa4-d09b4344cda6"> | Note that computation with figures will generate the following markdown (for both `knitr`/`Jupyter`): ```md {#fig-plot fig-alt='An alt text for a plot'} ``` --- The initial question also mentioned `pdf`, but I don't even know how to show alternative text in PDF. --- ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5511 <div type='discussions-op-text'> ^{Originally posted by **IZE85** May 12, 2023} In MS Word, one is able to "add alternative text to a shape, picture, chart, SmartArt graphic, or other object to help people with visual disabilities." When I add alternative text to a figure via "fig-alt" it gets exported via HTML. Unfortunately, when knitting to formats like Word or PDF, my fig-alt text is saved/deposited somewhere, if I'm correct. At least, for MS Word, I cannot see the alternative text in the "alternative text" field, MS Word provides for figures. My question: Is it possible for the fig-alt text to find its way into the MS Word Alternative text field and have something similar for PDFs? Thank you in advance! Ad alternative text: "Alt text helps people with visual disabilities understand pictures and other graphical content. When someone using a screen reader comes across a picture in a document, they will hear the alt text describing the picture; without alt text, they will only know they've reached a picture without knowing what the picture shows." Source: https://support.microsoft.com/en-us/office/add-alternative-text-to-a-shape-picture-chart-smartart-graphic-or-other-object-44989b2a-903c-4d9a-b742-6a75b451c669</div>

### Bug description Hello, To briefly explain the situation, I am an R user, but since all of the project participants are python users, I was conducting statistical analysis using both python and R. However, when using R chunk and python chunk at the same time, it seems that the order of subcaptions is not rendered as I intended. Should the simultaneous use of multiple quarto engines be discouraged? In other words, if I choose to use Python, should I stick with Python? ```` --- title-block-banner: true title: "Something1" subtitle: "Something2" date: 2023-04-03 author: "Someone" institute: "Something3" format: html: #pdf: #documentclass: scrartcl #papersize: a4 toc: true number-sections: true lot: true lof: true code-fold: true #df-print: paged fig-width: 15 fig-height: 15 #fontfamily: libertinus #colorlinks: true execute: warning: false message: false echo: false --- # Analysis With R ## Load Packages ```{r} #| eval: false # install.packages('tidyverse') # install.packages('reticulate') # install.packages('arrow') library(tidyverse) library(reticulate) library(knitr) library(kableExtra) #library(arrow) #library(readr) options(dplyr.summarise.inform = FALSE) ``` # Anlaysis with Python ## Load Packages ```{python load_packages} import pandas as pd import numpy as np import matplotlib.pyplot as plt import seaborn as sns import sklearn import itertools import os from IPython.display import display, Markdown # for dynamic documentation from tabulate import tabulate # for dynamic documentation from pandas.api.types import CategoricalDtype # for factoring categorical variables from sklearn.metrics import confusion_matrix #, accuracy_score, precision_score, recall_score, f1_score pd.set_option('display.max_rows', 100) # pd.set_option('display.max_columns', 10) # pd.set_option('display.width', 1000) pd.options.mode.chained_assignment = None ``` ## Data Load ```{python} # Long form data generation data1 = {'dataid': np.repeat(range(0,100), 6), 'cycle': np.tile(range(6), 100), 'rfu': np.random.randn(600), 'scenario': np.repeat('scenario00',600), 'template': np.repeat([chr(i) for i in range(65, 71)],100)} # Convert to pandas DataFrame unnested_dsp_error_data = pd.DataFrame(data1) ``` ## Function List ```{python, funtions} def plot_error_signals(dataid_list,title=None,x_limits=None,y_limits=None): temp2=unnested_dsp_error_data[unnested_dsp_error_data.dataid.isin(dataid_list)] plt.title(title) for i in dataid_list: temp=unnested_dsp_error_data[(unnested_dsp_error_data.dataid==i)] plt.plot(temp.cycle,temp.rfu) if x_limits or y_limits: plt.ylim(x_limits,y_limits) else: plt.ylim(temp2.rfu.min()*0.9,temp2.rfu.max()*1.1) ``` ## Qualititative Analysis ```{python, DSP_grand_confusion_errors} #| label: dsp_grand_confusion_errors #| fig-cap: "DSP Grand Missclassifed Signals" #| echo: fenced error_dataid=unnested_dsp_error_data.dataid.unique().tolist() plot_error_signals(error_dataid) plt.show() ``` ```{python, DSP_error_signals_templates} #| label: DSP_error_signals_templates #| fig-cap: "DSP Error Signals Grouped By Templates" #| fig-subcap: #| - "A" #| - "B" #| - "C" #| - "D" #| - "E" #| - "F" #| layout-ncol: 2 #| echo: fenced template_list=[chr(i) for i in range(65, 71)] for template in template_list: temp_dataid=unnested_dsp_error_data[unnested_dsp_error_data.template==template].dataid.unique() plot_error_signals(temp_dataid,title=template) plt.show() ``` ```` the rendered output is like the following:  ### 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 Currently illustrated at: https://quarto.org/docs/authoring/variables.html The [source](https://github.com/quarto-dev/quarto-web/blob/bc76beb02e76ce2b615068423128482c7f107070/docs/authoring/variables.qmd#L11-L13 ) doesn't have any quotes: ```` ``` {.markdown shortcodes="false"} {{< meta title >}} ``` ```` But when rendered they have been added: ``` {{< "meta" "title" >}} ``` Rendering with dev quarto. (No issue on 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. - [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 Quarto fails when `x` in `knitr::asis_output(x)` has `length(x) != 1`. See PR #5505 for a solution. #### Minimal reproducible example Example qmd: ````md --- title: Fix asis_output format: html engine: knitr --- `asis_output` with one string: ```{r} knitr::asis_output("* one\n* two") ``` `asis_output` with two strings: ```{r} knitr::asis_output(c("* one\n", "* two\n")) ``` `asis_output` with zero strings: ```{r} knitr::asis_output(character(0)) ``` ```` The second codeblock generates a warning: In grepl("^<\\w+[ >]", x) && grepl("<\\/\\w+>\\s*$", x) : 'length(x) = 2 > 1' in coercion to 'logical(1)' While the third codeblock produces an error: Error in if (grepl("^<\\w+[ >]", x) && grepl("<\\/\\w+>\\s*$", x) && !grepl("^<div class=\"kable-table\">", : missing value where TRUE/FALSE needed Calls: .main ... sew -> <Anonymous> -> lapply -> FUN -> wrap_asis_output <details><summary>Command output</summary> $ quarto render demo_qmd.qmd processing file: demo_qmd.qmd |....................................................| 100% (unnamed-chunk-3)Quitting from lines 21-22 (demo_qmd.qmd) Error in if (grepl("^<\\w+[ >]", x) && grepl("<\\/\\w+>\\s*$", x) && !grepl("^<div class=\"kable-table\">", : missing value where TRUE/FALSE needed Calls: .main ... sew -> <Anonymous> -> lapply -> FUN -> wrap_asis_output In addition: Warning message: In grepl("^<\\w+[ >]", x) && grepl("<\\/\\w+>\\s*$", x) : 'length(x) = 2 > 1' in coercion to 'logical(1)' Execution halted </details> #### Expected output I expect the intermediary markdown to look like this (but then in html and not in markdown): <details><summary>demo_qmd.md</summary> ````md # Fix asis_output `asis_output` with one string: ```{r} knitr::asis_output("* one\n* two") ``` * one * two `asis_output` with two strings: ```{r} knitr::asis_output(c("* one\n", "* two\n")) ``` * one * two `asis_output` with zero strings: ```{r} knitr::asis_output(character(0)) ``` ```` </details> #### Comparison to Rmarkdown With RMarkdown, this code works just fine: <details><summary>demo_rmd.Rmd</summary> ````md --- title: Fix asis_output output: html_document --- `asis_output` with one string: ```{r} knitr::asis_output("* one\n* two") ``` `asis_output` with two strings: ```{r} knitr::asis_output(c("* one\n", "* two\n")) ``` `asis_output` with zero strings: ```{r} knitr::asis_output(character(0)) ``` ```` </details> <details><summary>Command output</summary> $ Rscript -e 'rmarkdown::render("demo_rmd.Rmd")' processing file: demo_rmd.Rmd output file: demo_rmd.knit.md /usr/bin/pandoc +RTS -K512m -RTS demo_rmd.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output demo_rmd.html --lua-filter /home/rcannood/R/x86_64-redhat-linux-gnu-library/4.2/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/rcannood/R/x86_64-redhat-linux-gnu-library/4.2/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /home/rcannood/R/x86_64-redhat-linux-gnu-library/4.2/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpxfSAAT/rmarkdown-str9883135bff75b.html Output created: demo_rmd.html </details> ### 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. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description While building a website using Quarto, a link that contains `--` (e.g., <https://docs.gitlab.com/ee/topics/git/git_rebase.html#--force-with-lease-flag>) is broken **because `--` is converted to an en dash `–`.** However, this only seems to happen for links in the `_quarto.yml` config file. Steps to reproduce: 1. Create a new web project in Quarto 2. Add a link containing `--` to `_quarto.yml`, for example: ```yml project: type: website website: title: "quarto-bug" navbar: left: - href: index.qmd text: Home - about.qmd - href: https://docs.gitlab.com/ee/topics/git/git_rebase.html#--force-with-lease-flag text: "Broken link with dash-dash" format: html: theme: cosmo css: styles.css toc: true ``` 3. Render the page 4. The link now contains an en dash instead of `--` ``` # Expected https://docs.gitlab.com/ee/topics/git/git_rebase.html#--force-with-lease-flag # Actual https://docs.gitlab.com/ee/topics/git/git_rebase.html#%E2%80%93force-with-lease-flag ``` Note that in this particular case, the user is still directed to the correct page, but not to the correct reference. *** I am on Windows 10, below is the output of `quarto check`. The issue is also present on the latest nightly release. ``` [>] 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: C:\Users\<MyUserName>\AppData\Local\Programs\Quarto\bin CodePage: 1250 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....(None) Unable to locate an installed version of Python 3. Install Python 3 from https://www.python.org/downloads/ [>] Checking R installation...........OK Version: 4.3.0 Path: C:/PROGRA~1/R/R-43~1.0 LibPaths: - C:/Users/<MyUserName>/AppData/Local/R/win-library/4.3 - C:/Program Files/R/R-4.3.0/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. - [ ] 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 Using Quarto 1.3.340 on macOS 12.6.5, as included in the recent RStudio IDE daily 2023.05.0-daily+325, but this problem can be seen using that Quarto installation by itself, outside the IDE. ````markdown --- title: revealjs lists format: revealjs --- ## Slide This is some text. 1. first 2. second This is more text. * bullet * bill ```` When rendered and viewed in Safari, the ordered list elements are not aligned with the other content. <img width="268" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/abd298b5-ea91-43ef-a040-acc961139d61"> ``` [✓] 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/RStudio.app/Contents/Resources/app/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: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 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 _No response_ ### 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 I tried to render a reveal.js presentation into pptx instead and found an error. I created a repo to demo the error here: <https://github.com/anielsen001/quarot-pptx-bug-000>. The problem is that I have a background-image on a slide like this: ``` ## Quarto {background-image="/img/quarto.png" background-size="contain" background-opacity=0.1} Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>. ``` The reveal.js render works fine, but when rendering to pptx, it cannot find the image, and i get this error message: ```06:56 $ quarto render pandoc to: revealjs output-file: pptx-bug-1.html standalone: true wrap: none default-image-extension: png html-math-method: method: mathjax url: >- https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS_HTML-full slide-level: 2 metadata link-citations: true width: 1050 height: 700 margin: 0.1 center: false navigationMode: linear controlsLayout: edges controlsTutorial: false hash: true history: true hashOneBasedIndex: false fragmentInURL: false transition: none backgroundTransition: none pdfSeparateFragments: false lang: en auto-stretch: true title: pptx-bug-1 pandoc to: pptx output-file: pptx-bug-1.pptx default-image-extension: png metadata title: pptx-bug-1 pandoc: /img/quarto.png: withBinaryFile: does not exist (No such file or directory) ``` I believe it has to do with how I specify the path to the background image, but it works for reveal.js. I'm not sure how to specify it for pptx rendering. I think that the syntax for one should work for both. I'd like to be able to simply add a new type of output and have my existing content just work. I'm using quarto version 1.3.340 on the command line, on Ubuntu 20.04. here's the output of `quarto check`: ``` 07:00 $ 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: 3.8.3 Path: /home/apn/sw/bin/python3 Jupyter: 4.10.0 Kernels: julia-1.8, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.3 Path: /usr/lib/R LibPaths: - /home/apn/R/x86_64-pc-linux-gnu-library/4.2 - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/lib/R/library knitr: 1.42 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? - [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 ```` --- title-block-banner: true title: "Something1" subtitle: "Something2" date: 2023-04-03 author: "Someone" institute: "Something3" format: html: toc: true number-sections: true lot: true lof: true code-fold: true fig-width: 15 fig-height: 15 execute: warning: false message: false echo: false --- ```` ```` ```{python, error_signals} #| label: error_signals #| fig-cap: "Error Signals Grouped By Targets" #| fig-subcap: #| - "a" #| - "b" #| - "c" #| - "d" #| - "e" #| - "f" #| layout-ncol: 2 # for target in targets: # temp_dataid=unnested_error_data[unnested_error_data.target==target].dataid.unique() # plot_error_signals(temp_dataid,title=target) # plt.show() plt.plot([1,23,2,4]) plt.show() plt.plot([8,65,23,90]) plt.show() plt.plot([1,3,2,4]) plt.show() plt.plot([1,1,1,1]) plt.show() plt.plot([1,2,3,4]) plt.show() plt.plot([4,3,2,1]) plt.show() ``` ```` the rendered output:  ### 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.

## Description: Local videos with video shortcode in website projects fail to load. May be related to https://github.com/quarto-dev/quarto-cli/issues/3892. ## Steps to Reproduce: - Create a simple website project `quarto create-project mysite --type website` - `cd mysite` - Add `local-video.mp4` so it is in the root of the site. - Update `index.qmd` ``` --- title: '' --- {{< video local-video.mp4 >}} ``` - `quarto preview mysite` ### Expected Result: The video loads. ### Actual Result: The video does not load. Console error: `/local-video.mp4 (404: Not Found)` #### Workaround - Manually copy `local-video.mp4` to `_site` directory. It now works.

## Description: [run-smokes Deno deprecation warnings](https://github.com/quarto-dev/quarto-cli/issues/5495) ## Steps to Reproduce: - Create a pull request and check the logs or ``` ./run-tests.sh unit/schema-validation/schema-schema.test.ts ``` ### Expected Result: No warnings in Deno logs ### Actual Result:  ``` Annotations 8 warnings run-smokes (ubuntu-latest) "files" configuration is deprecated. Please use "include" and "exclude" instead. run-smokes (ubuntu-latest) propertyNames and case convention detection are mutually exclusive. run-smokes (ubuntu-latest) propertyNames and case convention detection are mutually exclusive. run-smokes (ubuntu-latest) propertyNames and case convention detection are mutually exclusive. run-smokes (windows-latest) "files" configuration is deprecated. Please use "include" and "exclude" instead. run-smokes (windows-latest) propertyNames and case convention detection are mutually exclusive. run-smokes (windows-latest) propertyNames and case convention detection are mutually exclusive. run-smokes (windows-latest) propertyNames and case convention detection are mutually exclusive. ```

### Bug description The following code seems as if it should work, but it crashes the compile by creating this in the class option for the tex source: `xcolor=\{dvipsnames\}`: ``` --- title: test format: beamer: classoption: - "xcolor={dvipsnames}" --- # Here is a slide Here is \textcolor{ForestGreen}{forestgreen} ``` This is the fix from [tex.stackexchange](https://tex.stackexchange.com/questions/685310/how-to-color-specific-text-using-beamer-format-in-quarto): ``` --- title: test format: beamer: classoption: - '`xcolor={dvipsnames}`{=latex}' --- # Here is a slide Here is \textcolor{ForestGreen}{forestgreen} ``` The first example works if you remove braces, but as pointed out by the person who provided the solution, sometimes you need braces, though not here. The syntax for the fix is unnatural and will (IMO) cause much wailing and gnashing of teeth. Tested with quarto 1.4.37 on Ubuntu 22.04. [quartoissue.zip](https://github.com/quarto-dev/quarto-cli/files/11447344/quartoissue.zip) [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.1: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.37 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /usr/bin/python3 Jupyter: 4.9.1 Kernels: ir, python2, python3 (|) Checking Jupyter engine render....[IPKernelApp] WARNING | debugpy_stream undefined, debugging will not be enabled [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.3.0 Path: /usr/lib/R LibPaths: - /data/rmcd/R/x86_64-pc-linux-gnu-library/4.3 - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/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.

### Bug description quarto-cli: latest pre-release (1.4.51 at the time I'm writing this bug description) O/S: Arch Linux (I'm maintainer of `rstudio-desktop` and `quarto-cli` AUR packages) Build script src/webui/quarto-preview/build.ts assumes we're inside the git repo. If it runs against the source code from release archive, `git ls-files` returns `fatal: not a git repository (or any of the parent directories): .git` , however the error message gets suppressed. Effectively there is no notification if the mentioned module is not built. Quick'n'dirty solution to me was to force rebuild quarto-preview: [quarto-cli-pre-release/force_build_quarto_preview_js.diff](https://github.com/trap000d/aur/blob/master/quarto-cli-pre-release/force_build_quarto_preview_js.diff) P.S. I've spotted it only because noticed the warning message in RStudio (2023.03.0.386) console: "Can't find quarto-preview.js" Output of `quarto check`: ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.0.1: OK Dart Sass version 1.62.0: OK NOTE: Deno version 1.33.0 is too old. Please upgrade to 1.33.1 or later. [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.51 Path: /usr/lib/quarto-cli/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.3 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: 4.3.0 Path: /usr/lib64/R LibPaths: - /home/trap000d/R/x86_64-pc-linux-gnu-library/4.3 - /usr/lib/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. - [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 a smaller example based on the documentation website: ````qmd --- format: html provider: gh-pages --- ```yaml {{< meta provider >}} workflow_dispatch: ``` ```` | 1.3.340 | dev | |:-------:|:---:| | <img width="217" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/8896044/e97f2cee-bdde-42b9-be75-ddcf7d3cf79e"> | <img width="311" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/8896044/127a1769-9917-48cc-b273-657c9c35cd52"> | Issue initially observed in https://github.com/quarto-dev/quarto-web/edit/main/docs/publishing/github-pages.qmd (https://quarto.org/docs/publishing/github-pages.html#publish-action) --- Using VSCode on MacOS Apple Silicon chip <img width="1436" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/8896044/85667819-566d-458e-8226-c1b4b788fe06"> ### 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 _No response_ ### 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/5484 <div type='discussions-op-text'> ^{Originally posted by **cudawarped** May 10, 2023} I can use [code annotation](https://quarto.org/docs/authoring/code-annotation.html#annotation-syntax) inside a single [callouts](https://quarto.org/docs/authoring/callouts.html#markdown-syntax) block without any issues, however if I try to use it in a second call outblock it fails. e.g. the "more addition" annotation is not shown in ```` ::: {.callout-tip} Python annotation 1 ```{.python} 1 + 1 # <1> ``` 1. addition ::: ::: {.callout-tip} Python annotation 2 ```{.python} 1 + 1 # <1> ``` 1. more addition ::: ```` </div>

This is related to discussion #3209 and suggested as an enhancement. For all outputs it would be great if the (supplemental) table and figure numbers could be prefixed with a letter, e.g., naming supplementary figures and tables as 'Figure S1' and 'Table S1'. It's currently possible to use `fig-title: Figure S` to achieve 'Figure S 1', but it's not really ideal.

Having more than one inline OJS element `` ${x} `` combined with inline styling `` [foo]{style="color:red;"} `` fails to render properly, although it works having more than one of one or the other, and having one element combining both. ```` ```{r} ojs_define(x = "inline OJS") ``` Multiple inline OJS elements in a single paragraph work: ${x} and ${x}. Multiple [inline]{style="color: red;"} styles [work]{style="color: red;"}. One [${x}]{style="color: red;"} element with inline style works in the same paragraph as another [inline style]{style="color: red;"}. One [${x}]{style="color: red;"} element with inline style works in the same paragraph as another non-styled ${x} element. One [${x}]{style="color: red;"} element with inline style **does not work** in the same paragraph as another styled [${x}]{style="color: red;"} element. ```` This is with `` sessionInfo() ``: ``` R version 4.3.0 (2023-04-21) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.0 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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: Europe/Vienna tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] htmlwidgets_1.6.2 compiler_4.3.0 fastmap_1.1.1 cli_3.6.1 [5] tools_4.3.0 htmltools_0.5.5 rstudioapi_0.14 yaml_2.3.7 [9] rmarkdown_2.21 knitr_1.42 xfun_0.39 digest_0.6.31 [13] jsonlite_1.8.4 rlang_1.1.1 evaluate_0.21 ```

### Bug description I recently reinstalled quarto and now the render function is no longer working. When I use the CLI or the render button I get `YAMLError: bad indentation of a mapping entry at line 5, column 10: jupyter: python3` I've rendered these same files before, using the current indents (or lack thereof), and even when I try various combinations of single, double indent or spaces, the same error appears. I'm not sure what's gone wrong. Trying to attach a .qmd says that the file is not supported [index.txt](https://github.com/quarto-dev/quarto-cli/files/11436666/index.txt) I'm using Windows 10, VS Code ``` 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: 1.3.319 Path: C:\Users\Welp Windows 10\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.11.1 Path: C:/Users/Welp Windows 10/AppData/Local/Programs/Python/Python311/python.exe Jupyter: 5.1.3 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) ``` ### 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 To reproduce: ``` git clone https://github.com/matthew-brett/test-quarto-3 cd test-quarto-3 quarto render ``` This gives warning: ``` WARNING: Shortcode 'var first' not found ``` for current `main` (commit c6e7de939) but no warning and correct output for v1.4.37. The page generating the warning consists of: ~~~ A {{< var first >}} code. Another {{< var second >}} code. ~~~ The warning requires the var markupe to run over more than one line. This is on macOS 13.3.1 on M2. ``` $ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.1: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Users/mb312/dev_trees/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.11 Path: /Users/mb312/.virtualenvs/resampling-with/bin/python3 Jupyter: 5.3.0 Kernels: python3, ir [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.3.0 Path: /opt/homebrew/Cellar/r/4.3.0_1/lib/R LibPaths: - /Users/mb312/Library/R/arm64/4.3/library - /opt/homebrew/lib/R/4.3/site-library - /opt/homebrew/Cellar/r/4.3.0_1/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.

### Bug description Hi, #5411 I reported some redundant `preview` reload requests. This was using Firefox. Chromium isn't making the same requests **and is noticeably more responsive** (important because I could be being misled by browser tools). I found the mechanism to reload is `window.location.reload(true)` in both cases. [From MDN](https://developer.mozilla.org/en-US/docs/Web/API/Location/reload) `true` used here is a Netscape-era non-standard way to tell the browser to force a reload from the server "which apparently eventually got picked up in Firefox" (+is kinda widely used). I don't think we need `true` because although I've mostly been using Firefox I'm sure this works in other browsers, and because local resources appear to have the following header: `no-store, max-age=0` So I expect removing `true` should improve reload performance on Firefox with no impact on other browsers. Happy to do PR and some of my own testing, but change appears to be kinda trivial if I amn't missing something. Declan ### 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 When adding "embed-resources: true" to a working Quarto site with RSS enabled, no RSS xml file was generated, and at render a warning message appeared that the xml file could not be fetched. To reproduce: Create a new website project: ``` $ quarto create-project mysite --type website ``` Edit _quarto.yml so its contents are as below: ``` project: type: website website: title: "mysite" site-url: https://www.myblogexample.io description: "A great sample blog" navbar: left: - href: index.qmd text: Home - about.qmd right: - icon: rss href: about.xml format: html: theme: cosmo css: styles.css toc: true embed-resources: false ``` Edit about.qmd as below: ``` --- title: "Listing Example" listing: contents: "*" type: default categories: true feed: true --- ``` At this point, `quarto render mysite` works as expected, and about.xml is created Now in _quarto.yml, change `embed-resources: false` to `embed-resources: true`. Execute `quarto render mysite` again. The following output appears: ``` $ quarto render mysite [1/2] index.qmd [2/2] about.qmd [WARNING] Could not fetch resource about.xml Output created: _site/index.html ``` Clicking on the RSS icon of the newly-rendered navbar returns a 404 error, and there is no RSS xml file in the _site subdirectory. Strangely, "quarto preview" appears to render the site correctly. OS: Kubuntu 20.04 Quarto version: 1.3.282 ``` $ 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: 1.3.282 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 The new version breaks the zotero.lua, which is a popular lua filter that allows to link citation to zotero in Word output. Yaml: ``` --- title: '****' author: 'NA' format: docx: reference-doc: manuscript_style.docx bibliography: /Users/A.Y/OneDrive - Harvard University/My Library.bib csl: /Users/A.Y/Zotero/styles/nature.csl filters: - zotero.lua --- ``` ``` Error running filter /Applications/quarto/share/filters/main.lua: zotero.lua:70: attempt to index a nil value (global '_G') stack traceback: [C]: in upvalue 'orig_require' [string "..."]:1353: in function 'require' zotero.lua:1716: in local 'chunk' /Applications/quarto/share/filters/main.lua:4073: in local 'callback' [string "..."]:1789: in function <[string "..."]:1787> (...tail calls...) /Applications/quarto/share/filters/main.lua:368: in function 'make_wrapped_user_filters' /Applications/quarto/share/filters/main.lua:15395: in main chunk ``` See also this issue https://github.com/retorquere/zotero-better-bibtex/issues/2497 And here https://github.com/quarto-dev/quarto-cli/issues/1206 Any idea how could I make it work again? On MacOS, Quarto 1.3340 ### 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.

- [ ] Review Test Deps Doc: https://github.com/quarto-dev/quarto-cli/compare/0ebedb6cedf1...e09272956ab0 - [ ] Refactor Confluence unit tests to use BDD style.

Consider providing a warning or error when a listing points at a path that doesn't resolve to any files or inputs (e.g. it is producing an empty listing or pointing at a path that doesn't exist at all).

### Bug description To reproduce: ``` git clone https://github.com/matthew-brett/test-quarto-2 cd test-quarto-2 quarto render ``` This gives error: ``` Error running filter /Users/mb312/dev_trees/quarto-cli/src/resources/filters/main.lua: ...ees/quarto-cli/src/resources/filters/./common/tables.lua:107: attempt to call a nil value (method 'clone') ... ``` The page generating the error consists only of: ~~~ ```{r} kableExtra::kable(cars, caption = 'Caption {#tbl-veh-numbers}') ``` ~~~ The error requires the caption to run over more than one line, and to contain the table label. New issue opened as requested from: https://github.com/quarto-dev/quarto-cli/issues/5392 This is on macOS 13.3.1 on M2. ``` $ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.1: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Users/mb312/dev_trees/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.11 Path: /Users/mb312/.virtualenvs/resampling-with/bin/python3 Jupyter: 5.3.0 Kernels: python3, ir [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.3.0 Path: /opt/homebrew/Cellar/r/4.3.0_1/lib/R LibPaths: - /Users/mb312/Library/R/arm64/4.3/library - /opt/homebrew/lib/R/4.3/site-library - /opt/homebrew/Cellar/r/4.3.0_1/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.

### Bug description Not sure if this is an Rstudio or Quarto issue. Setup: This issue persists in * Quarto 1.4.37 * Rstudio 2023.03.0 Build 386 * R 4.3.0 * Windows 11 (all updated) * Windows 11 has been set to accept long paths (confirmed by checking registry key HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\FileSystem\LongPathsEnabled equals 1 * I suspect {fs} involved somehow, which has version 1.6.2 Problem: Rendering a chunk (pressing green triangle button) or running "manually" with Ctrl+Enter fails for reading in a file (e.g. `readRDS()`) if filepath is longer than 260 (cf. MAX_PATH). Error message does not direct the user towards this cause, but _moving files to a lower working directory solves the problem_. ``` Error in gzfile(file, "rb") : cannot open the connection Warning: cannot open compressed file 'Behov omkring kvalitetsutvikling/uni_cat_prop_plot/I_hvilken_grad_opplever_dere_at_følgende_prøver__undersøkelser__verktøy_og_datakilder_er_nyttige_i_d.rds', probable reason 'No such file or directory'Error in gzfile(file, "rb") : cannot open the connection ``` Interestingly, pressing Render or using quarto::quarto_render _does_ work nevertheless. Though it can be cumbersome without the "inline preview" feature (which is otherwise awesome). Moreover, the problem is an even greater issue when using ``` execute: cache: true ``` since it adds the long hash to the filename. ``` r long_path <- paste0(tempdir(), "/sdfsdfsdfwfhwebfwhjebfewhjbwhjbfehbfjewh/smnfbkjebfwhjefbwefbewhj/smbfehbfsehmsbemfhbsemhs/skfbjhebfwhjebfwhjebfewhe/mhesbmehfbmhsbmhebf/sjefbshembfmshfb/msbfeshef/bhsfbsemhfbsmhfesb/mshfbshmesbfsm/sbefhbsmhebfmhesb/mshbfsmhebfesm/hbsmfsmehfbs") dir.create(long_path, recursive = TRUE) saveRDS(letters, paste0(long_path, "test_obj.rds")) cat(paste0('---\nformat: html\n---\n\n```{r}\nx <- readRDS("test_obj.rds")\nx\n```'), file=paste0(long_path, "/test.qmd")) rstudioapi::documentOpen(paste0(long_path, "/test.qmd")) #> Error: RStudio not running # Run chunk manually ``` ^{Created on 2023-05-08 with [reprex v2.0.2](https://reprex.tidyverse.org)} ^{Created on 2023-05-08 with [reprex v2.0.2](https://reprex.tidyverse.org)} quarto check: Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.1: OK Version: 1.4.37 Path: C:\Users\py128\AppData\Local\Programs\Quarto 1.4.37\bin CodePage: 1252 Checking Python 3 installation....(None) Unable to locate an installed version of Python 3. Install Python 3 from https://www.python.org/downloads/ Version: 4.3.0 Path: C:/PROGRA~1/R/R-43~1.0 LibPaths: - C:/Users/py128/AppData/Local/R/win-library - C:/Program Files/R/R-4.3.0/library knitr: 1.42 rmarkdown: 2.21 (everything else says 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 Adding the `attr-output` option in an R chunk has no effect on the rendered html (i.e., the attribute does not get added). Reprex: ```` ```{r} #| error: true #| warning: true #| message: true #| attr-output: "style='color: blue;'" #| attr-error: "style='color: yellow;'" #| attr-warning: "style='color: orange;'" #| attr-message: "style='color: green;'" #| results: asis cat("something") stop("something") warning("something") message("something") ``` ````  ### 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: 3.9.6 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: 4.3.0 Path: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources LibPaths: - /Users/andyteucher/Library/R/arm64/4.3/library - /Library/Frameworks/R.framework/Versions/4.3-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. - [ ] 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.

### Bug description Sorry for my reckless response in #5395. I should first create a minimal example to reproduce the problem. I'm not sure if this is a bug😵‍💫, but thanks for your response. ## Quarto Version ``` [>] 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:\R\Quarto\bin CodePage: 936 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.8.10 Path: D:/Program Files/Python38/python.exe Jupyter: 5.2.0 Kernels: python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.2.1 Path: D:/R/R-4.2.1 LibPaths: - D:/R/R-4.2.1/library knitr: 1.42 rmarkdown: 2.21 [>] Checking Knitr engine render......OK ``` ## Operating System and IDE ``` Windows 11 RStudio 2023.03.0 Build 386 ``` ## Steps to reproduce 1. Open RStudio and create a new Quarto Book project. 2. Open `_quarto.yml` and add `asciidoc: default` to the `format:`. 3. Render Book. The stack trace is: ``` ERROR: NotFound: 系统找不到指定的文件。 (os error 2) NotFound: 系统找不到指定的文件。 (os error 2) at Object.readTextFileSync (deno:runtime/js/40_read_file.js:42:16) at ServeRenderManager.fileRenderHash (file:///D:/R/Quarto/bin/quarto.js:103114:33) at file:///D:/R/Quarto/bin/quarto.js:103092:46 at Array.forEach (<anonymous>) at ServeRenderManager.onRenderResult (file:///D:/R/Quarto/bin/quarto.js:103089:23) at serveProject (file:///D:/R/Quarto/bin/quarto.js:103200:19) at async Command.fn (file:///D:/R/Quarto/bin/quarto.js:103742:13) at async Command.execute (file:///D:/R/Quarto/bin/quarto.js:8437:13) at async quarto (file:///D:/R/Quarto/bin/quarto.js:127535:5) at async file:///D:/R/Quarto/bin/quarto.js:127553:9 ``` And my `_quarto.yml` file is like: ```yaml project: type: book book: title: "example" author: "Norah Jones" date: "2023/5/8" chapters: - index.qmd - intro.qmd - summary.qmd - references.qmd bibliography: references.bib format: html: theme: cosmo asciidoc: default editor: visual ``` ### 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 Using `lang: pl` causes Quarto to show this error: ``` [WARNING] Could not load translations for pl translations/pl.yaml: YAML parse exception at line 3, column 9: mapping values are not allowed in this context [WARNING] The term Abstract has no translation defined. ``` Other languages work. `_language_pl.yml` seems fine. ```md --- title: "Polish translation" format: html lang: pl --- Zażółć gęsią jaźń. ``` `quarto check` output: ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.1: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.36 Path: /opt/quarto/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...........OK Version: 4.3.0 Path: /usr/lib64/R LibPaths: - /home/jakub/R/x86_64-pc-linux-gnu-library/4.3 - /usr/lib/R/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ``` Operating System: Manjaro Linux KDE Plasma Version: 5.27.4 KDE Frameworks Version: 5.105.0 Qt Version: 5.15.9 Kernel Version: 6.1.25-1-MANJARO (64-bit) Graphics Platform: X11 Processors: 8 × 11th Gen Intel® Core™ i5-11300H @ 3.10GHz Memory: 31.1 GiB of RAM Graphics Processor: Mesa Intel® Xe Graphics Manufacturer: HP Product Name: HP Pavilion Gaming Laptop 17-cd2xxx System Version: Type1ProductConfigId ### 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 In https://github.com/quarto-dev/quarto-cli/commit/9cf8ffa5eb5cfd5922eb7949ca17fd4325db797f#diff-714357551c8de50d816a92a684e8370e04f8b18c7441f311e4a81a1c2eb28132, the dist dir was basically replaced with a new notion of a package working dir. This was disruptive to the conda recipe, since setting the QUARTO_DIST_DIR was how we told `quarto-bld` to put stuff into the conda package. Unfortunately, we can't readily adjust the conda recipe to the new pattern, because the QUARTO_PACKAGE_PATH that sets the pkgWorkingBase is used for both internal scripts and for what conda wants to be an external path. Now conda/quarto can address this maybe 2 ways: 1. conda can patch https://github.com/quarto-dev/quarto-cli/commit/9cf8ffa5eb5cfd5922eb7949ca17fd4325db797f#diff-714357551c8de50d816a92a684e8370e04f8b18c7441f311e4a81a1c2eb28132R65 such that we can set an env var instead of just extending QUARTO_PACKAGE_PATH 2. Perhaps a better long-term solution is to make a new installer script, similar to https://github.com/quarto-dev/quarto-cli/blob/main/package/src/macos/installer.ts, that doesn't create a tarball, but instead just copies files into OUT_DIR (minus vendored stuff that conda provides in other packages). Conda recipe would then need to call this new command from bld.ts, like https://github.com/quarto-dev/quarto-cli/blob/main/package/src/bld.ts#L93 Either way, we'll be happy to prototype this in the conda recipe at https://github.com/conda-forge/quarto-feedstock/pull/7 ### 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 Commit c5b6176 seems to have broken our Panflute filters. As of that commit, when we do `quarto render`, we get the following traceback: ``` Traceback (most recent call last): File "/Users/mb312/dev_trees/test-quarto/a_filter", line 19, in <module> main() File "/Users/mb312/dev_trees/test-quarto/a_filter", line 13, in main return run_filter(action, File "/Users/mb312/dev_trees/panflute/panflute/io.py", line 230, in run_filter return run_filters([action], *args, **kwargs) File "/Users/mb312/dev_trees/panflute/panflute/io.py", line 203, in run_filters doc = load(input_stream=input_stream) File "/Users/mb312/dev_trees/panflute/panflute/io.py", line 61, in load doc = json.loads(in_text, object_hook=from_json) File "/opt/homebrew/Cellar/[email protected]/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/json/__init__.py", line 359, in loads return cls(**kw).decode(s) File "/opt/homebrew/Cellar/[email protected]/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/opt/homebrew/Cellar/[email protected]/3.10.11/Frameworks/Python.framework/Versions/3.10/lib/python3.10/json/decoder.py", line 353, in raw_decode obj, end = self.scan_once(s, idx) File "/Users/mb312/dev_trees/panflute/panflute/elements.py", line 1424, in from_json assert (len(data) == 1) or (len(data) == 2 and 'c' in data) AssertionError Error running filter /Users/mb312/dev_trees/quarto-cli/src/resources/filters/main.lua: Error running filter /Users/mb312/dev_trees/test-quarto/a_filter: Filter returned error status 1 ``` The reproducer below shows that this is - at least - when there is markup of form `{{< var a_var >}}` or `{{< meta title >}}`. This turns out to be because the JSON passed down into Panflute breaks on a Panflute assumption. Reproducer : clone <https://github.com/matthew-brett/test-quarto> and `quarto render`. Investigation of JSON - to get JSON passed to filter, use development version of `panflute`. Patch `panflute` with: ```diff diff --git a/panflute/io.py b/panflute/io.py index d95d81e..5160767 100644 --- a/panflute/io.py +++ b/panflute/io.py @@ -55,7 +55,10 @@ def load(input_stream=None): input_stream = io.TextIOWrapper(sys.stdin.buffer, encoding='utf-8') # Load JSON and validate it - doc = json.load(input_stream, object_hook=from_json) + in_text = input_stream.read() + with open('here.json', 'wt') as fobj: + fobj.write(in_text) + doc = json.loads(in_text, object_hook=from_json) # Notes: # - The hook gets called for dicts (not lists), and the deepest dicts ``` Add any Panflute filter to list of filters in `_quarto.yml`. The `test-quarto` project above has one such, called `a_filter`. Run `quarto render` to get error (and write `here.json`, the input JSON to the filter). Now run: ```python import json from panflute import elements contents = open('source/here.json', 'rt').read() json.loads(contents, elements.from_json) ``` reproduces the error. Running on macOS 13.3.1. ``` $ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.1: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Users/mb312/dev_trees/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.11 Path: /Users/mb312/.virtualenvs/resampling-with/bin/python3 Jupyter: 5.3.0 Kernels: ir NOTE: No Jupyter kernel for Python found [✓] Checking R installation...........OK Version: 4.3.0 Path: /opt/homebrew/Cellar/r/4.3.0_1/lib/R LibPaths: - /Users/mb312/Library/R/arm64/4.3/library - /opt/homebrew/lib/R/4.3/site-library - /opt/homebrew/Cellar/r/4.3.0_1/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.

### Bug description Hovering over the circled numbers to the right of code is ignored. I'm running under Ubuntu 22.04. ### 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 a footnote is reused, it is duplicated. This is the case at least for `html`, `pdf`, and `revealjs`. ```qmd --- format: html: default pdf: default revealjs: default --- Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed non risus. Suspendisse lectus tortor, dignissim sit amet, adipiscing nec, ultricies sed, dolor. Cras elementum ultrices diam. Maecenas ligula massa, varius a, semper congue, euismod non, mi.[^1] Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed non risus. Suspendisse lectus tortor, dignissim sit amet, adipiscing nec, ultricies sed, dolor. Cras elementum ultrices diam. Maecenas ligula massa, varius a, semper congue, euismod non, mi.[^1] [^1]: This is the first footnote. ``` | `html` | `pdf` | |:------:|:-----:| | <img width="703" alt="image" src="https://user-images.githubusercontent.com/8896044/236572912-0cc8aafa-abd1-4c4b-a5e1-98decf32e23c.png"> | <img width="405" alt="image" src="https://user-images.githubusercontent.com/8896044/236573618-78ccb500-7e0a-4b4a-b690-c39bbe08f468.png"> | --- For instance the expected results would be the one that can be seen on GitHub. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed non risus. Suspendisse lectus tortor, dignissim sit amet, adipiscing nec, ultricies sed, dolor. Cras elementum ultrices diam. Maecenas ligula massa, varius a, semper congue, euismod non, mi.[^1] Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed non risus. Suspendisse lectus tortor, dignissim sit amet, adipiscing nec, ultricies sed, dolor. Cras elementum ultrices diam. Maecenas ligula massa, varius a, semper congue, euismod non, mi.[^1] [^1]: This is the first footnote. --- Quarto: latest development version OS: MacOS Apple Silicon IDE: VSCode <img width="1433" alt="image" src="https://user-images.githubusercontent.com/8896044/236573856-494a95d4-f2bc-43c1-b3b1-6caca08a6f54.png"> ### 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.

Posit Cloud is adding support for publishing static content. `quarto publish` should support publishing through Cloud.

### Bug description [The authoring guide on tables](https://quarto.org/docs/authoring/tables.html#computations) provided an example producing multiple tables in R in a single code cell. However, when using Python to do so, only the last table shows in the output, with its subcaption wrongly assigned to be the first one stated in `tbl-subcap`. Here's a minimal example, modified from the code provided in the guide mentioned above. `````md --- title: "Test" --- ```{python} #| label: tbl-planet-measures #| tbl-cap: Planets #| tbl-subcap: #| - "Planets" #| - "Satellites" #| layout-ncol: 2 #| echo: false from IPython.display import Markdown from tabulate import tabulate table1 = [["Earth",6371,5973.6], ["Mars",3390,641.85]] table2 = [["Moon",1737,73.5]] Markdown(tabulate( table1, headers=["Planet","R (km)", "mass (x 10^29 kg)"] )) Markdown(tabulate( table2, headers=["Planet","R (km)", "mass (x 10^29 kg)"] )) ``` ````` In contrast, multiple figures work well in Python. Here's a comprehensive qmd file illustrating the issue. [index.md](https://github.com/quarto-dev/quarto-cli/files/11404725/index.md)  Apologize if I've missed something obvious. Thanks. --- Quarto version: 1.3.340 system: Windows 11 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: C:\Program Files\Quarto\bin CodePage: 936 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.8.13 (Conda) Path: C:/Users/sun123zxy/.conda/envs/data/python.exe Jupyter: 4.11.1 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/ ``` ### 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 adding a `title-block-banner` the `.quarto-title-meta` div is not affected by the `page-layout: full`. The issue is reproduced here: <https://github.com/KaiWaldrant/quarto-title-meta>. This has also been tested on the latest nightly build. I've also searched the issues but could not find a related one. result:  expected:  reference (without `title-block-banner: black`):  qmd file used: ```markdown --- title: "quarto-title-meta" title-block-banner-color: white title-block-banner: black page-layout: full date: "2021/09" date-format: "MMMM, YYYY" author: Kai Waldrant categories: - competition - code --- :::{layout="[[30,70]]"} ::::{.section-header} ## Summary :::: ::::{.section-content} Scaling from a dozen cells a decade ago to millions of cells today, single-cell measurement technologies are driving a revolution in the life sciences. Recent advances make it possible to measure multiple high-dimensional modalities (e.g. DNA accessibility, RNA, and proteins) simultaneously in the same cell. Such data provides, for the first time, a direct and comprehensive view into the layers of gene regulation that drive biological diversity and disease. In this competition for [NeurIPS 2021,](https://neurips.cc/Conferences/2021/CompetitionTrack) we present three tasks on multimodal single-cell data using a first-of-its-kind multi-omics benchmarking dataset. Teams will predict one modality from another and learn representations of multiple modalities measured in the same cells. Progress will reveal how a common genetic blueprint gives rise to distinct cell types and processes, as a foundation for improving human health. {{< video https://www.youtube.com/embed/y5YbM0tbvCo >}} To learn more, you can watch a [lecture](https://www.youtube.com/watch?v=ZXDILOyiy7A) presented at the Broad Institute's Models Inferences and Algorithms meeting (<a href="https://drive.google.com/file/d/1olW-WN-kHYuG15MSgAK3GUqNtMCPFBq3/view?usp=sharing" style="color: #EB5252;">slides</a>). :::: ::: ``` os: fedora 37 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: /home/kai/opt/quarto-1.3.340/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.

- [x] #5320 - [x] #5322 - [x] #5247 - [x] stdlib vendoring (up to 0.185.0) - [x] decide what needs to happen with `import 'node:...'` - [x] decide what to do with unsupported `safe: true` in dotenv.ts - [x] ~~fix our dependence on `deno bundle`~~ make sure we can `deno bundle` for now - [ ] revealjs (up to 4.5.0) - [ ] update plugins ## Other dependencies from `./configuration` https://github.com/quarto-dev/quarto-cli/pull/5419/ ``` export DENO_DOM=v0.1.35-alpha-artifacts export DARTSASS=1.55.0 export ESBUILD=0.15.6 export BOOTSTRAP=ec93879c66ddf48ceec7ecf35401bdf0a93a0a77 export BOOTSTRAP_FONT=1.10.0 export BOOTSWATCH=5.2.2 export ANCHOR_JS=4.3.1 export POPPER_JS=2.11.4 export CLIPBOARD_JS=2.0.11 export TIPPY_JS=6.3.7 export PDF_JS=2.8.335 export REVEAL_JS_MENU=2.1.0 export REVEAL_JS_CHALKBOARD=a88c134e2cf3c7780448db003e7329c3cbd8cfb4 export REVEAL_JS_PDFEXPORT=2.0.1 export LIST_JS=2.3.1 export DAY_JS=1.11.6 export ZENSCROLL_JS=4.0.2 export GITHUB_MARKDOWN_CSS=5.2.0 export AUTOCOMPLETE_JS=1.7.3 export FUSE_JS=6.6.2 export ALGOLIA_SEARCH_JS=4.5.1 export ALGOLIA_SEARCH_INSIGHTS_JS=2.0.3 ```

I'm using Quarto with Hugo and a theme that incorporates a very odd Katex syntax for math equations: it users \\( and \\) as delimiters. Rendering pages from Quarto causes the parentheses to be stripped and several lines of js/jquery to appear at the start of the .md file. To get my code to display correctly, I need to delete the js/jquery and correct the delimiters. I've tested on other pages and they don't have similar issues with the random js. I think it's a Pandoc setting that's causing the behavior with the delimiters but have no idea about the js. If there could be a toggle or if Katex could be supported that'd be appreciated.

### Bug description After I added the field "cookie-consent" under the `website` key, I got the error message: `Field "cookie-consent" has value implicit, which must instead be an object`. The same happened with the "express" qualifier. But there is no error message if I use "true" or "false". And "true" opens a window the first time: "We use cookies" and adds "Cookie Preferences" to the footer. I used the [reference documentation](https://quarto.org/docs/reference/projects/websites.html#meta-project-type-upper) for "Website" but also the [Website Tools docs under Guide](https://quarto.org/docs/websites/website-tools.html). One of the links in the TOC on the right side of the docs "Website Tools" website says, "Cookie Consent" but this link does not work. It opens a submenu with "Cookie Preferences" and "Custom Script and Cookie Consent." Again, these links do not work. Could it be that the documentation is not up-to-date? I am using: - R version 4.3.0 (2023-04-21), - RStudio Version 2023.03.0+386 (2023.03.0+386) - Quarto Version: 1.4.36 from the latest nightly release (but tested I it also with Version 1.3.340) - MacBook Pro, Ventura 13.3.1 ### 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 last section on a long page (especially if is short) will not highlight and expand in the TOC.

`create-project` removed `install` out of date description `use` missing `remove` missing `tools` missing `update` missing `uninstall` missing

### Bug description For this document: ```` --- title: "Mermaid" format: html: mermaid-format: png --- ```{mermaid} %%| echo: fenced flowchart LR A[Hard edge] --> B(Round edge) B --> C{Decision} C --> D[Result one] C --> E[Result two] ``` ```` I see this error: ```text jjallaire@jjallairesMBP2 julia-cwd % quarto preview /Users/jjallaire/quarto/bugs/julia-cwd/subdir/mermaid.qmd --no-browser --no-watch-inputs ERROR: TypeError: Relative import path "puppeteer/mod.ts" not prefixed with / or ./ or ../ TypeError: Relative import path "puppeteer/mod.ts" not prefixed with / or ./ or ../ at async getPuppeteer (file:///Applications/quarto/bin/quarto.js:35175:24) at async fetcher (file:///Applications/quarto/bin/quarto.js:35304:22) at async getBrowserExecutablePath (file:///Applications/quarto/bin/quarto.js:35308:28) at async criClient (file:///Applications/quarto/bin/quarto.js:35694:28) at async file:///Applications/quarto/bin/quarto.js:35677:22 at async Semaphore.runExclusive (file:///Applications/quarto/bin/quarto.js:35361:29) at async Object.createPngsFromHtml (file:///Applications/quarto/bin/quarto.js:35858:44) at async makePng (file:///Applications/quarto/bin/quarto.js:62939:72) at async Object.cell (file:///Applications/quarto/bin/quarto.js:63004:20) at async Promise.all (index 0) ``` In development mode it still fails but I see a different behavior. The 'Check file' for puppeteer is called and then hangs: ```text jjallaire@jjallairesMBP2 julia-cwd % quarto preview /Users/jjallaire/quarto/bugs/julia-cwd/subdir/mermaid.qmd --no-browser --no-watch-inputs Check file:///Users/jjallaire/quarto/quarto-cli/src/resources/vendor/deno-land/x/puppeteer@9-0-2/mod.ts ``` ### 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 Throughout the different releases, there have been various rendering issues with Mermaid in Quarto. I understand that there's a lot of moving parts to keep track of, so no judgement there. I just noticed a new one with Quarto 1.3, so I thought I'd do a more thorough investigation. I created [this repo](https://github.com/data-intuitive/mermaid-demos-in-quarto) which gets rendered to [this site](https://mermaid-demos-in-quarto.netlify.app/syntax/flowchart.html), which should be a mirror of the [mermaidjs](https://mermaid.js.org/syntax/flowchart.html) syntax documentation. Since Quarto 1.3 uses mermaid 9.1.1, I went back to the earliest version of mermaid js which had the syntax examples in the docs, which happened to be version 9.3.0. I used [this script](https://github.com/data-intuitive/mermaid-demos-in-quarto/blob/main/_script.R) to translate the md files in the mermaid repository to qmd files in my repository. ## Issues in Quarto v1.3 (See comment below for issues in Quarto v1.4, since some issues have already been fixed by upgrading to mermaid 10) Flow charts: - [ ] No background for text on links makes the labels less readable. [Example](https://mermaid-demos-in-quarto.netlify.app/syntax/flowchart.html#text-on-links), [Expected](https://mermaid.js.org/syntax/flowchart.html#text-on-links) - [ ] Character escaping doesn't work. [Example](https://mermaid-demos-in-quarto.netlify.app/syntax/flowchart.html#entity-codes-to-escape-characters), [Expected](https://mermaid.js.org/syntax/flowchart.html#entity-codes-to-escape-characters) - [ ] :exclamation: :exclamation: Backgrounds of subgraphs in the Flowchart makes the chart unreadable (also in dark mode). [Example](https://mermaid-demos-in-quarto.netlify.app/syntax/flowchart.html#subgraphs), [Expected](https://mermaid.js.org/syntax/flowchart.html#subgraphs)  - [ ] Interactive tooltips don't work. [Example](https://mermaid-demos-in-quarto.netlify.app/syntax/flowchart.html#interaction), [Expected](https://mermaid.js.org/syntax/flowchart.html#interaction). - [ ] Html code is not escaped - similar to previously mentioned escaping issues. [Example](https://mermaid-demos-in-quarto.netlify.app/syntax/flowchart.html#css-classes), [Expected](https://mermaid.js.org/syntax/flowchart.html#css-classes) - [ ] Fontawesome icons are not rendered. [Example](https://mermaid-demos-in-quarto.netlify.app/syntax/flowchart.html#basic-support-for-fontawesome), [Expected](https://mermaid.js.org/syntax/flowchart.html#basic-support-for-fontawesome) Sequence diagrams: - [ ] Background and labels is rendered behind vertical line, resulting in less readability. [Example](https://mermaid-demos-in-quarto.netlify.app/syntax/sequencediagram#loops), [Expected](https://mermaid.js.org/syntax/sequenceDiagram.html#loops). Class diagrams: - [ ] Generics are not rendered properly. [Example](https://mermaid-demos-in-quarto.netlify.app/syntax/classdiagram#generic-types), [Expected](https://mermaid.js.org/syntax/classDiagram.html#generic-types) - [ ] Html code in labels. [Example](https://mermaid-demos-in-quarto.netlify.app/syntax/classdiagram#labels-on-relations), [Expected](https://mermaid.js.org/syntax/classDiagram.html#labels-on-relations) - [ ] Background in concurrency diagram is coloured wrong. [Example](https://mermaid-demos-in-quarto.netlify.app/syntax/statediagram#concurrency) [Expected](https://mermaid.js.org/syntax/stateDiagram.html#concurrency) This was all rendered with quarto 1.3.340. <details><summary>Output of quarto check</summary> [✓] 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: /home/rcannood/opt/quarto-1.3.340/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.3 Path: /usr/bin/python3 Jupyter: 5.2.0 Kernels: python3, julia-1.7, 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. 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: 4.2.3 Path: /usr/lib64/R LibPaths: - /home/rcannood/R/x86_64-redhat-linux-gnu-library/4.2 - /usr/local/lib/R/library - /usr/lib64/R/library - /usr/share/R/library knitr: 1.42 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK </details> ### 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/5407 <div type='discussions-op-text'> ^{Originally posted by **astoeriko** May 3, 2023} Some of my figure captions are quite long, so I would like to split them into several lines in the source code for better readability. What is the right syntax for this? Based on the instructions for mermaid diagrams that I found [here](https://github.com/quarto-dev/quarto-cli/discussions/1816) I tried as follows: ```{python} #| fig-cap: | #| This is a caption for my figure. #| It is long, so I put it onto two lines import numpy as np import matplotlib.pyplot as plt plt.plot(np.arange(10)) ``` But when I run `quarto render`, I get an error: ``` Executing 'test.ipynb' Cell 1/1...ERROR: None of the known patterns match for It is long, so I put it onto two lines ``` It runs fine if I put all the caption onto one line, but this is impractical with caption that are several sentences long. ```{python} #| fig-cap: "This is a caption for my figure. It is long, so I put it onto two lines." import numpy as np import matplotlib.pyplot as plt plt.plot(np.arange(10)) ``` </div>

We no longer need to run pandoc 3.1.2 through Rosetta, and the native version is ~2x faster.