Datasets:

hamel

/

quarto-issues

like 0

### Bug description In a website project, setting the `title-prefix` parameter has no effect, no matter where one sets it - in _quarto.yml, individual quarto documents or via a cli option. I would expect the prefix to override the website title for individual documents or directories. How to reproduce ```bash quarto create-project --type website ``` edit _quarto.yml: ```yaml project: type: website title-prefix: "noprefix" website: title: "quarto-title" navbar: left: - href: index.qmd text: Home - about.qmd format: html: theme: cosmo css: styles.css toc: true ``` edit `about.qmd` ```md --- title: "About" title-prefix: "noprefixtoo" format: html: title-prefix: "stillnoprefix" --- About this site ``` or run ```bash quarto render --metadata "title-prefix: cliprefix" ``` Quarto 1.3.324 RStudio Version 2023.05.0-daily+52 (2023.05.0-daily+52) MacOS 13.4 beta ### 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? - [ ] 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.

Creating issue to track https://github.com/quarto-dev/quarto-cli/discussions/5134#discussioncomment-5613083 In regards to "Template Partials": > In the Quarto documentation I probably didn't see it because it's under "article templates"? We have some good [docs on using Pandoc templates](https://quarto.org/docs/journals/templates.html#templates) but they are buried under "Extensions/Journal Articles". This content feels useful beyond that context and should probably exist at a higher level with appropriate linking.

### Bug description ## Setup ```bash quarto create project website test --no-open cd test quarto preview ``` I'm on linux, Pop-OS 22.04, based on Ubuntu 22.04. I noticed the issue first with Quarto `v1.3.299` (must have appeared between this and early v1.3) , but have also tested with the latest commit of quarto-cli: 024bba6387fc0abe7de1deb2640bd387fc28a692 ## Error ``` Preparing to preview [1/2] about.qmd [2/2] index.qmd ERROR: Too many open files (os error 24) Error: Too many open files (os error 24) at new FsWatcher (deno:runtime/js/40_fs_events.js:19:23) at Object.watchFs (deno:runtime/js/40_fs_events.js:64:12) at runWatcher (file:///home/jannik/projects/quarto-cli/src/project/serve/watch.ts:310:26) at Array.forEach (<anonymous>) at watchProject (file:///home/jannik/projects/quarto-cli/src/project/serve/watch.ts:351:28) at serveProject (file:///home/jannik/projects/quarto-cli/src/project/serve/serve.ts:236:25) at async Command.fn (file:///home/jannik/projects/quarto-cli/src/command/preview/cmd.ts:331:9) at async Command.execute (file:///home/jannik/projects/quarto-cli/src/vendor/deno.land/x/[email protected]/command/command.ts:1790:7) at async quarto (file:///home/jannik/projects/quarto-cli/src/quarto.ts:122:3) at async file:///home/jannik/projects/quarto-cli/src/quarto.ts:154:5 ``` This only happens for quarto projects, removing `_quarto.yml` allows previewing individual files. ## Related information Might be related to https://github.com/denoland/deno/issues/17757 ### 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 a table is inserted in a callout block, defining a label has no effect, i.e., ```` :::{.callout-note} ## Table in Callout Block @tbl-test is a table which has no reference. | Col 1 | Col 2 | | ----- | ----- | | a | b | : Caption {#tbl-test} ::: ```` produces the warning `WARNING: Unable to resolve crossref @tbl-test`. The same table works outside the callout block. I'm using quarto version 1.3.283.

### Bug description Similar to #5103 This qmd file in Docusaurus project ````qmd --- title: foo --- :::{.panel-tabset} ## Not work ```{.python filename="Python"} print("bar") ``` ## Work ```{.python} print("bar") ``` ::: ```` will be converted to this md file ````md --- title: foo --- import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; <Tabs> <TabItem value="Not work"> ```python title="Python" print("bar") ``` </TabItem> <TabItem value="Work"> ``` python print("bar") ``` </TabItem> </Tabs> ```` and rendered like this.  I tested it with the edge dev version of Quarto CLI. ```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: 99.9.9 Path: /tmp/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.2 Path: /usr/bin/python3 Jupyter: 5.3.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### 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 [Minimal Reproducible Example](https://github.com/quarto-dev/quarto-cli/files/11230763/citable-articles-page-layout-custom.zip) When using [custom page layout](https://quarto.org/docs/output-formats/page-layout.html#page-layout) in `_quarto.yml` like ``` format: html: page-layout: custom ``` the [citable article information](https://quarto.org/docs/authoring/create-citeable-articles.html) is not displayed. ## Observed Output Citable article information is **not** present.  ## Expected Output Citable article information is present as when using `page-layout: full` or `page-layout: article`.  ## Environment Output of `quarto check`: ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.324 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /usr/bin/python3 Jupyter: 5.2.0 Kernels: python3 (-) Checking Jupyter engine render....Traceback (most recent call last): File "/opt/quarto/share/jupyter/jupyter.py", line 21, in <module> from notebook import notebook_execute, RestartKernel File "/opt/quarto/share/jupyter/notebook.py", line 18, in <module> from nbclient import NotebookClient ModuleNotFoundError: No module named 'nbclient' [✓] Checking Jupyter engine render....OK ``` ### 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.

An epic on issues that require small (at most adding a paragraph) **corrections** to the docs: - [ ] https://github.com/quarto-dev/quarto-cli/issues/4462 - [ ] https://github.com/quarto-dev/quarto-cli/issues/2306 - [ ] https://github.com/quarto-dev/quarto-cli/issues/4954 - [ ] https://github.com/quarto-dev/quarto-cli/issues/4518 - [ ] https://github.com/quarto-dev/quarto-cli/issues/4519 - [ ] https://github.com/quarto-dev/quarto-cli/issues/5243

From #4936, given the name of an option, e.g. `number-sections`, it can be hard for a user to understand the context it needs to be used in, e.g. under a `format` not under `book`. It could be: * This is an educational need, i.e. some explanation somewhere that teaches people how to figure out the right context. * This is a "Reference" doc improvement, e.g. options have a more explicit link to their context. - Is the page they occur on (e.g. `number-sections` is on `formats/html.html`) sufficient? * This is a "Guide" doc improvement, e.g. when options are presented context needs to be made more explicit (or there needs to be a way for a user to easily find the context directly from the Guide page).

From #4936, it's hard to know where some of the options on the [book structure](https://quarto.org/docs/books/book-structure.html#section-numbers) page should go, e.g. section numbers: ``` number-depth: 1 ``` go under a `format` or in a document, not under `book`. Consider some combination of the following: * Could use `filename` to disambiguate: using `_quarto.yml` for `book` options, and `chapter-1.qmd` for document level yaml. * Could include more context in all YAML snippets: e.g. always explicitly include option hierarchy starting at ``` book: ``` for book options. * Be explicit in Overview that some options are `book` ones and some are relevant `format` ones, and describe conventions used in examples. * Be more explicit with the introduction of each example whether something is a `book` option or `format` option. * Reorder page to first talk about all relevant `book` options, then talk about `format` options. Be explicit about this ordering in Overview.

E.g. give example of using [pdf font options](https://quarto.org/docs/reference/formats/pdf.html#fonts) Right now, might be best after (or as part of): https://quarto.org/docs/output-formats/pdf-basics.html#output-options Suggestion from #4390 : > I think it would be very helpful to give a specific complete example (very brief) where the fonts look like the default LaTeX fonts.

### Bug description I am not sure if this is a bug or not but I thought to report it regardless. Sometimes it is helpful to set the knitr error option to `TRUE` so that a document will render no matter what. At the same time I find using the `#| eval: !expr` approach pretty useful to defensively only render certain chunks based on a condition. Unfortunately these two error handling strategies don't seem to mesh together and I wondering if that is on purpose. In the reprex below I've set the knitr option `error = TRUE` globally. That works to catch any errors in chunks. However if I try to pass a variable that has not been created because of an error in a previous chunk to `#| eval: !expr` the document will fail to render. My mental model was the knitr option should override that but the appears to not be the case. Any thoughts on whether this is a bad mental model? Thanks so much for all the continued work on quarto. ```` --- title: "Untitled" format: html: self_contained: true --- ```{r setup} knitr::opts_chunk$set(error = TRUE) ``` ```{r} stop("an error") ``` ```{r} var <- 1 + "2b" ``` ```{r} #| eval: !expr "var > 1" message("chunk worked") ``` ```` Using MacOS and VS code to render quarto. quarto check: ```md [✓] 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: 1.3.323 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.16 (Conda) Path: /Users/samalbers/mambaforge/bin/python Jupyter: 4.11.1 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.3 Path: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources LibPaths: - /Users/samalbers/Library/R/arm64/4.2/library - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library knitr: 1.41 rmarkdown: 2.18 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] 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 On [realworlddatascience.net](https://realworlddatascience.net/) homepage, I'm using custom page layout with grid listings to show selections of different types of blog content. For the "latest content" block, I show the three most recently published articles from across the site using the following YAML: ```yaml listing: - id: latest-content contents: - /case-studies - /ideas - /careers - /viewpoints - "!index.qmd" - "!flowers.qmd" sort: "date desc" type: grid categories: false sort-ui: false filter-ui: false max-items: 3 feed: false ``` I noticed yesterday than when the number of items eligible to be included in the listing passed 20, a listing pagination button appeared within the "latest content" block. When I deleted an article from the site to reduce the eligible listings to 19, the pagination button disappeared. I then tried uploading a new dummy article to bring the number of eligible items back above 20, and the pagination button reappeared. On the live version of the site, I've removed the button via a css workaround. ```css .content-container .listing-pagination { display: none; } ``` However, the bug is visible in this forked repo: https://github.com/fatso-jetson/listing-bug-demo. Screenshot of the rendered main [index.qmd](https://github.com/fatso-jetson/listing-bug-demo/blob/main/index.qmd) file is below:  Quarto version: 1.3.319 OS: Windows 10 Home, build 19044.2846 Editor: VS Code, 1.77.3, with Quarto extension, v.1.80.0 `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: 1.3.319 Path: CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.5 Path: Jupyter: 4.10.0 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/ ### 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 This qmd file will be converted to ```qmd --- title: foo --- foo[^1] [^1]: bar ``` This markdown file in a Docusaurus project. ```md --- title: foo --- foo[1] [1] bar ``` It is rendered as like this.  But Docusaurus supports footnote, so I want this Markdown output... ```md --- title: foo --- foo[^1] [^1]: bar ```  I tested the latest dev version of Quarto CLI on Debian Linux. ```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: 99.9.9 Path: /tmp/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.2 Path: /usr/bin/python3 Jupyter: 5.3.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### 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 noticed that https://github.com/quarto-dev/quarto-cli/tree/main/src/resources/formats/html/pandoc has a file named `template.html` and another file named `html.template` and their content if very similar. Do we need both files? ### 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.

Better support for Equations in Confluence, maybe by attaching them as images. https://github.com/quarto-dev/quarto-cli/issues/4948#issuecomment-1505966864

### Bug description I recently installed quarto (using the most recent official deb) from commandline on debian 11 using `dpkg -i <downloaded deb>`. I just discovered that apt on this system was stuck with the following error, rendering my system un-upgradable. ``` $ sudo apt <upgrade|install> The package quarto needs to be reinstalled, but I can't find an archive for it. ``` I was then unable to remove or upgrade quarto using standard dpkg arguments. E.g., : ``` $ sudo dpkg --purge --force-all quarto dpkg: warning: overriding problem because --force enabled: dpkg: warning: package is in a very bad inconsistent state; you should reinstall it before attempting a removal (Reading database ... 267028 files and directories currently installed.) Removing quarto (1.3.296) ... Purging configuration files for quarto (1.3.296) ... rm: cannot remove '/usr/local/bin/quarto': No such file or directory dpkg: error processing package quarto (--purge): installed quarto package post-removal script subprocess returned error exit status 1 Errors were encountered while processing: quarto ``` After manually creating `/usr/local/bin` and touching '/usr/local/bin/quarto', I was able to upgrade quarto via dpkg, and everything worked as expected. I suggest modifying the debian install scripts to check for the presence of `/usr/local/bin'. I'm running a unmodified (if old) debian system, and installing quarto caused a significant system outage on my system apparently due to lack of this directory. ## Output from quarto check ``` $quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.319 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.2 Path: /usr/bin/python3 Jupyter: 4.7.1 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 18, in <module> from nbclient import NotebookClient ModuleNotFoundError: No module named 'nbclient' [✓] Checking Jupyter engine render....OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Thanks very much to @dragonstyle for https://github.com/quarto-dev/quarto-cli/pull/5055. Listing does **not** work as expected when use provide relative file path. [Files for reproduction](https://github.com/quarto-dev/quarto-cli/files/11212420/5165.zip) When I provide a YAML file to `listing.contents` like in ``` --- title: "About" listing: id: about-listing contents: listing.yml --- About this site :::{#about-listing} ::: ``` where `listing.yml` is, **note the relative path**, ``` - path: ../post.md ``` I get a page without the listing:  The expected result, obtained when avoiding relative path, is  ## Debug Information ``` [2/3] about/index.qmd [listing] Reading listing 'about-listing' from /tmp/tmp.VQtWUWtryM/about/index.qmd [listing] Contents: listing.yml [listing] matches 1 files: [listing] Reading YAML file /tmp/tmp.VQtWUWtryM/about/listing.yml [INFO] Loaded /tmp/quarto-session94573f88/196afac0/191ef397/template.patched from /tmp/quarto-session94573f88/196afac0/191ef397/template.patched [INFO] Loaded /tmp/quarto-session94573f88/196afac0/191ef397/metadata.html from /tmp/quarto-session94573f88/196afac0/191ef397/metadata.html [INFO] Loaded /tmp/quarto-session94573f88/196afac0/191ef397/styles.html from /tmp/quarto-session94573f88/196afac0/191ef397/styles.html [INFO] Loaded /tmp/quarto-session94573f88/196afac0/191ef397/title-block.html from /tmp/quarto-session94573f88/196afac0/191ef397/title-block.html [INFO] Loaded /tmp/quarto-session94573f88/196afac0/191ef397/title-metadata.html from /tmp/quarto-session94573f88/196afac0/191ef397/title-metadata.html [INFO] Loaded /tmp/quarto-session94573f88/196afac0/191ef397/title-block.html from /tmp/quarto-session94573f88/196afac0/191ef397/title-block.html [INFO] Loaded /tmp/quarto-session94573f88/196afac0/191ef397/title-metadata.html from /tmp/quarto-session94573f88/196afac0/191ef397/title-metadata.html [INFO] Loaded /tmp/quarto-session94573f88/196afac0/191ef397/toc.html from /tmp/quarto-session94573f88/196afac0/191ef397/toc.html [trace] Parsed [Plain [Str "long"]] at line 1 [trace] Parsed [Plain [Str "en"]] at line 1 [trace] Parsed [Plain [Str "listing.yml"]] at line 1 [trace] Parsed [Plain [Str "about-listing"]] at line 1 [trace] Parsed [Plain [Str "true"]] at line 1 [trace] Parsed [Plain [Str "1.3.319"]] at line 1 [trace] Parsed [Plain [Str "cosmo"]] at line 1 [trace] Parsed [Plain [Str "About"]] at line 1 [trace] Parsed [Plain [Str "On",Space,Str "this",Space,Str "page"]] at line 1 [trace] Parsed [] at line 5 [trace] Parsed [Para [Str "About",Space,Str "this",Space,Str "site"]] at line 7 [trace] Parsed [Div ("about-listing",[],[]) []] at line 13 [trace] Parsed [Para [Span ("",["hidden"],[("render-id","quarto-int-sidebar at line 20 [trace] Parsed [Div ("quarto-navigation-envelope",["hidden"],[]) [Para [Spa at line 23 [trace] Parsed [Para [Span ("",["hidden"],[("render-id","quarto-enable-math at line 26 [trace] Parsed [] at line 29 [trace] Parsed [Para [RawInline (Format "html") "<a href=\"../post.md\">",S at line 34 [trace] Parsed [Div ("",["thumbnail"],[]) [Para [RawInline (Format "html") at line 34 [trace] Parsed [] at line 35 [trace] Parsed [Plain [RawInline (Format "html") "<a href=\"../post.md\">"] at line 36 [trace] Parsed [Div ("",["delink","listing-description"],[]) []] at line 37 [trace] Parsed [] at line 38 [trace] Parsed [Plain [RawInline (Format "html") "</a>"]] at line 38 [trace] Parsed [Div ("",["body"],[]) [Plain [RawInline (Format "html") "<a at line 38 [trace] Parsed [] at line 39 [trace] Parsed [Plain [RawInline (Format "html") "<a href=\"../post.md\">", at line 40 [trace] Parsed [Div ("",["metadata"],[]) [Plain [RawInline (Format "html") at line 40 [trace] Parsed [] at line 41 [trace] Parsed [Div ("",["quarto-post","image-right"],[("data-index","0")]) at line 41 [trace] Parsed [] at line 42 [trace] Parsed [Div ("",["list","quarto-listing-default"],[]) [Div ("",["qu at line 44 [trace] Parsed [Plain [Str "No",Space,Str "matching",Space,Str "items"]] at line 44 [trace] Parsed [Div ("",["listing-no-matching","d-none"],[]) [Plain [Str "N at line 44 [trace] Parsed [] at line 46 [trace] Parsed [Div ("",["hidden"],[("render-id","pipeline-listing-about-li at line 48 [trace] Parsed [Div ("quarto-listing-pipeline",["hidden"],[]) [Para [Span ( at line 52 [trace] Parsed [Para [Span ("",["hidden"],[("render-id","quarto-metatitle") at line 59 [trace] Parsed [Div ("quarto-meta-markdown",["hidden"],[]) [Para [Span ("", at line 63 [INFO] Running filter /opt/quarto/share/filters/main.lua [INFO] Completed filter /opt/quarto/share/filters/main.lua in 45 ms ``` ## Environment information Output of `quarto check`: ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.319 Path: /opt/quarto/bin Loaded deno-dom-native (\) Checking basic markdown render....[trace] Parsed [Plain [Str "long"]] at line 1 [trace] Parsed [Plain [Str "en"]] at line 1 [trace] Parsed [Plain [Str "true"]] at line 1 [trace] Parsed [Plain [Str "1.3.319"]] at line 1 [trace] Parsed [Plain [Str "Title"]] at line 1 [trace] Parsed [Plain [Str "Table",Space,Str "of",Space,Str "contents"]] at line 1 [trace] Parsed [] at line 5 [trace] Parsed [Header 2 ("header",[],[]) [Str "Header"]] at line 8 [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /usr/bin/python3 Jupyter: 5.2.0 Kernels: python3 (-) Checking Jupyter engine render....Traceback (most recent call last): File "/opt/quarto/share/jupyter/jupyter.py", line 21, in <module> from notebook import notebook_execute, RestartKernel File "/opt/quarto/share/jupyter/notebook.py", line 18, in <module> from nbclient import NotebookClient ModuleNotFoundError: No module named 'nbclient' [✓] Checking Jupyter engine render....OK ``` ### 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.

## Description Citation tooltip can get in a broken layout state where it "flickers". https://user-images.githubusercontent.com/674792/231461610-0d07e4bd-dac0-40e4-8011-165b41b49c3b.mov ## Steps to Reproduce: - See the attached [repo.zip](https://github.com/quarto-dev/quarto-cli/files/11211550/repo.zip) - `quarto preview` - Maximize the screen - Navigate to `Preface` - Mouse over the citation `Knuth [1984];` ### Expected Result No layout change. Citation stays in current location with tooltip to reference. ### Actual Result: Cycling reflow flickering ## Environment Mac ``` ❯ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Users/amanning/projects/github/quarto/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.2 Path: /Library/Frameworks/Python.framework/Versions/3.11/bin/python3 Jupyter: 5.2.0 Kernels: julia-1.8, julia-1.7, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library knitr: 1.42 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.

I am trying to use a filter (in this case, https://bcdavasconcelos.github.io/citetools/) which in turn relies on pandoc. My system currently has pandoc 3 in its path, and the installed quarto is 1.2 which uses pandoc 2. As a consequence, the marshalling of data is done by quarto's pandoc 2, and the demarshalling is attempted by the system's pandoc 3. I realise that this particular problem will be removed once quarto 1.3 is released, as both quarto's pandoc and my system pandoc will be v1.3. But it strikes me that there is no obvious reason for filters which are initiated within quarto to use a version of pandoc other than the one included in quarto itself — I can't think of a good outcome from that, and it could easily run into other weird incompatibilities. Could quarto be modified to ensure that Lua filters run by quarto only make the quarto pandoc installation visible to the filters?

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4722 <div type='discussions-op-text'> ^{Originally posted by **phongphuhanam** March 9, 2023} Hello, I'm using quarto to create the PDF with all the tables in LaTex format. I also need to create a docx version to share with my colleagues. As I want to cross-ref on both PDF and docx documents, I use the quarto crossref syntax (@tab-). It works fine with docx format, but for PDF I have to manually set ```param("crossref-resolve-refs", true)``` to ```param("crossref-resolve-refs", false)``` in this file [ref.lua](https://github.com/quarto-dev/quarto-cli/blob/4c629a87596818b268ff424d663fd8b0ab3c5bb2/src/resources/filters/crossref/refs.lua#L27). I want to set 'crossref-resolve-refs' to false for PDF output in quarto markdown but I couldn't find any way to do so on the Quarto website. Is there such an option exist? I tried the below setup but it did not work: ```yaml format: pdf: crossref-resolve-refs : false ``` </div>

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5139 <div type='discussions-op-text'> ^{Originally posted by **eitsupi** April 9, 2023} Quarto supports the display of line numbers in code blocks in HTLM format, etc. https://quarto.org/docs/output-formats/html-code.html The syntax is thus. ````qmd ```{.python code-line-numbers="true"} import matplotlib.pyplot as plt plt.plot([1,23,2,4]) plt.show() ``` ```` The syntax in Docusaurus seems to be as follows, ` showLineNumbers` is needed. https://docusaurus.io/docs/markdown-features/code-blocks#line-numbering ````md ```python showLineNumbers import matplotlib.pyplot as plt plt.plot([1,23,2,4]) plt.show() ``` ```` It would be great if Quarto could support this conversion.</div>

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5144 In practice, many folks are seeing this delay as a bug while Confluence is preparing the newly uploaded image attachments. I've been trying to think of ways to make this a better experience given our limitations. We could provide better messaging in the CLI log potentially that may help.

### Bug description Code is run twice (atleast for the `book` project) on `quarto render`. In the MWE below, the code appends `"Test"` to a file called `text.txt`. Starting by removing `text.txt` and running `quarto render` once leads to the file having `TestTest`, where it should just be `Test`. [test.zip](https://github.com/quarto-dev/quarto-cli/files/11197283/test.zip) Output of `quarto check` ``` ❯ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.313 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.9 (Conda) Path: /home/dhruva/.julia/conda/3/x86_64/bin/python3.10 Jupyter: 5.2.0 Kernels: julia-1.9, 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/ ``` <details> <summary> Output of quarto render </summary> <pre><code> ❯ quarto render [1/4] index.qmd [2/4] intro.qmd Starting python3 kernel...Done Executing 'intro.ipynb' Cell 1/1...Done Starting python3 kernel...Done Executing 'intro.ipynb' Cell 1/1...Done [3/4] summary.qmd [4/4] references.qmd pandoc to: latex output-file: index.tex standalone: true toc: true number-sections: true top-level-division: chapter pdf-engine: xelatex variables: graphics: true tables: true default-image-extension: pdf metadata crossref: chapters: true documentclass: scrreprt papersize: letter classoption: - DIV=11 - numbers=noendperiod header-includes: - '\KOMAoption{captions}{tableheading}' block-headings: true bibliography: - references.bib title: test author: Norah Jones date: 4/11/2023 running xelatex - 1 This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023/Arch Linux) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode running xelatex - 2 This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023/Arch Linux) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode Output created: _book/index.html </code></pre> </details> </summary> ### 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 For example: ``` kevin@MBP-P2MQ:~ $ /opt/local/bin/quarto kevin@MBP-P2MQ:~ $ /opt/local/bin/quarto --help Usage: quarto Version: 1.3.313 Description: Quarto CLI Options: -h, --help - Show this help. -V, --version - Show the version number for this program. Commands: render [input] [args...] - Render files or projects to various document types. preview [file] [args...] - Render and preview a document or website project. serve [input] - Serve a Shiny interactive document. create [type] [commands...] - Create a Quarto project or extension create-project [dir] - Create a project for rendering multiple documents convert <input> - Convert documents to alternate representations. pandoc [args...] - Run the version of Pandoc embedded within Quarto. run [script] [args...] - Run a TypeScript, R, Python, or Lua script. add <extension> - Add an extension to this folder or project install [target...] - Installs an extension or global dependency. publish [provider] [path] - Publish a document or project. Available providers include: check [target] - Verify correct functioning of Quarto installation. help [command] - Show this help or the help of a sub-command. ``` That is, invoking `quarto` (without arguments) just silently does nothing. Should it instead print help by default, or something similar? ### 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 have had a couple of instances now when copying-and-pasting text containing em-dashes in Quarto's visual mode causes RStudio to freeze. When this occurs, I cannot save changes and cannot restart the R session. The only option is to end the program using the Windows Task Manager. I can go into source mode (if I remember to do so) and move copy-and-paste without a problem. I only seems to occur when in visual mode. I may occasionally work without a problem, but eventually moving it will cause the problem. RStudio 2023.03.0+386 "Cherry Blossom" Release (3c53477afb13ab959aeb5b34df1f10c237b256c3, 2023-03-09) for Windows Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.03.0+386 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36 OS Name Microsoft Windows 11 Pro Version 10.0.22621 Build 22621 12th Gen Intel(R) Core(TM) i5-1240P, 1700 Mhz, 12 Core(s), 16 Logical Processor(s) quarto check - no idea how to find this from the description below Also interestingly, you are requesting I attach a single .qmd file for this issue, but when I tried to do this, I get a message stating that .qmd files are not supported. Hence, I have put it into a zip file and attached it that way. [em-dash bug.zip](https://github.com/quarto-dev/quarto-cli/files/11194184/em-dash.bug.zip) ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [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 trying to nest mermaid diagrams in tabsets, diagrams beyond the first one are cut off:  ````md --- title: mermaid tabsets --- ::: {.panel-tabset} ## first mermaid ```{mermaid} flowchart TD one---two ``` ## second mermaid ```{mermaid} flowchart TD three---four ``` ## third mermaid ```{mermaid} flowchart TD five---six ``` ::: ## level two ::: {.panel-tabset} ### first mermaid ```{mermaid} flowchart TD one---two ``` ### second mermaid ```{mermaid} flowchart TD three---four ``` ### third mermaid ```{mermaid} flowchart TD five---six ``` ::: ```` quarto check: ``` ❯ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.313 Path: /Users/edavidaja/.local/share/qvm/versions/v1.3.313/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.6 Path: /Users/edavidaja/.pyenv/versions/3.8.6/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.0 Path: /Library/Frameworks/R.framework/Versions/4.2/Resources LibPaths: - /Users/edavidaja/Library/R/x86_64/4.2/library - /Library/Frameworks/R.framework/Versions/4.2/Resources/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.

For books, we should use normal page geometry for pages that don't contain margin elements, like the TOC / Title page. ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5122 <div type='discussions-op-text'> ^{Originally posted by **dominicwhite** April 7, 2023} I am writing a Quarto book split over multiple chapter files. I am trying to add margin notes following this guide here: [https://quarto.org/docs/blog/posts/2022-02-17-advanced-layout/](https://quarto.org/docs/blog/posts/2022-02-17-advanced-layout/) If I add ``` reference-location: margin citation-location: margin ``` to the pdf format section my `_quarto.yml` file for the whole book then I get footnotes correctly rendered in the margins in the individual chapters. _However_, it also forces other sections, like the title page and the table of contents, to have that same margin, which I do not want. I would like to have the margin space added just in the chapters (and not on the title page or table of contents), but when I add the two settings above to the top of individual chapter files instead, either using the recommended style from the blog post: ``` --- reference-location: margin citation-location: margin --- ``` or as something like this: ``` --- format: pdf: documentclass: scrreport reference-location: margin citation-location: margin --- ``` then I get regular footnotes instead of margin notes. Is it possible to turn on margin notes only for certain chapters, and if so, what I am doing wrong with my settings?</div>

The following document can result in the code listing floating away from its annotations: ````markdown --- title: Hello World format: html --- ## Hello {{< lipsum 1-2 >}} ```{#lst-customers .r lst-cap="Customers Query"} # this is a comment that adds length to the code block # this is a comment that adds length to the code block # this is a comment that adds length to the code block library(tidyverse) # this is a comment that adds length to the code block # this is a comment that adds length to the code block # this is a comment that adds length to the code block library(palmerpenguins) penguins |> # <1> mutate( # <2> bill_ratio = bill_depth_mm / bill_length_mm, # <2> bill_area = bill_depth_mm * bill_length_mm # <2> ) # <2> ``` 1. Take `penguins`, and then, 2. add new columns for the bill ratio and bill area. {{< lipsum 3-4 >}} ```` note that we define the code listing environment as: ```latex \\@ifundefined{c@chapter}{\\newfloat{codelisting}{h}{lop}}{\\newfloat{codelisting}{h}{lop}[chapter]} ``` We should create an option for float hold, always float hold, or do something smarter here.

### Bug description Suppose you've got the following in `test.qmd`: ```` --- title: Test jupyter: jupytext: formats: 'ipynb,md' kernelspec: display_name: Python 3 (ipykernel) language: python name: python3 --- ```{python} while True: pass ``` ```` and then you, ill-advisedly, run ``` quarto preview test.qmd ``` After the machine spins for a bit you realize your error and hit `^C`. This kills quarto but *not* (apparently, on my machine; `Debian 6.1.7-1 (2023-01-18) x86_64 GNU/Linux`) the python kernel (which is still visible in `top`, for instance). Changing the cell to ```` ```{python} while True: break ``` ```` instead and re-running `quarto preview test.qmd` does not get python out of its infinite loop; neither does doing the same change without having killed quarto. I haven't found a way to kill the python kernel besides finding the PID from top and killing it manually. Is there a better way to deal with this (besides `daemon: false` in the config)? ps. I can deal with this with only minor annoyance; but this seems major - I'd not want to assign my stats class to use quarto knowing they could well hit this, for instance. ``` $ 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: 3.11.2 Path: /usr/bin/python3 Jupyter: 4.12.0 Kernels: ir, python3 (\) Checking Jupyter engine render....0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.2 Path: /usr/lib/R LibPaths: - /home/peter/R - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/lib/R/library knitr: 1.36 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 Good day, RStudio Version 2023.03.0+386 (2023.03.0+386) R version 4.2.2 MacOS Ventura 13.3.1 on a Apple M1 Max The output of `quarto check` is included at the end. I have set up a clean Quarto website with default settings for `_quarto.yml` etc. The problem I am experiencing concerns producing a `kableExtra` formatted table in an HTML rendered page. Providing the table's name as `#| tbl-cap: "The table's caption"` at the start of the code chunk does not result in the intended outcome. A normal kable is produced. However, providing the table's name as `#| fig-cap: "The table's caption"` at the start of the code chunk DOES result in the intended outcome. Herewith a minimal reproducible example: ``` --- title: "The sparrow data" tbl-cap-location: top --- ```{r} #| message: false library(tidyverse) library(kableExtra) ``` Jerrold H. Zar's sparrow data: ```{r} sparrows <- tibble(age = c(3, 4, 5, 6, 8, 9, 10, 11, 12, 14, 15, 16, 17), wing = c(1.4, 1.5, 2.2, 2.4, 3.1, 3.2, 3.2, 3.9, 4.1, 4.7, 4.5, 5.2, 5.0)) ``` Providing the table's name as `#| tbl-cap: "The table's caption specified in the code chunk"` at the start of the code chunk does not result in the intended outcome. ```{r} #| tbl-cap: "The table's caption specified in the code chunk" kbl(sparrows, caption = "The table's caption given to code kableExtra::kbl", col.names = c("Age (days)", "Wing length (mm)")) |> kable_classic(bootstrap_options = "striped", full_width = FALSE) ``` Providing the table's name as `#| fig-cap: "The table's caption specified in the code chunk"` at the start of the code chunk DOES result in the intended outcome. ```{r} #| fig-cap: "The table's caption specified in the code chunk" kbl(sparrows, caption = "The table's caption given to kableExtra::kbl", col.names = c("Age (days)", "Wing length (mm)")) |> kable_classic(bootstrap_options = "striped", full_width = FALSE) ``` ``` Another issue is that the R installation is not found by `quarto check` when it is there (see below). I must still report this as a reparate issue. **[✓] 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: 1.3.302 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.13 (Conda) Path: /Users/ajsmit/opt/anaconda3/bin/python 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/** Thank you kindly, AJ Smit ### 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 MWE adapted from the block-layout section of the docs: ````md --- title: "bug" format: beamer --- ## test Taken from <https://quarto.org/docs/authoring/figures.html#block-layout> ::: {layout-ncol=2} ### List One - Item A - Item B - Item C ### List Two - Item X - Item Y - Item Z ::: ```` When I compile the above minimal example, I get an error from tex: ``` updating tlmgr updating existing packages compilation failed- error LaTeX Error: \begin{beamercolorbox} on input line 223 ended by \end{minipage} . See the LaTeX manual or LaTeX Companion for explanation. Type H <return> for immediate help. ... l.223 \end{frame} ``` but when I change it to "format: pdf" everything compiles okay. Earlier layout examples on that documentation (for aligning images) work fine in beamer. What's up? I see elsewhere in the quarto docs an alternative way for making multiple columns, <https://quarto.org/docs/presentations/beamer.html#multiple-columns> but there is a certain attraction to the shorter form in this MWE. Environment: ``` quarto 1.2.475 running on Mac 13.2.1 ``` quarto check: ``` [✓] Checking Quarto installation......OK Version: 1.2.475 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.1 Path: /Users/stephen/.pyenv/versions/3.11.1/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.3 Path: /opt/homebrew/Cellar/r/4.2.3/lib/R LibPaths: - /Users/stephen/NOBACKUP/RLIB - /opt/homebrew/Cellar/r/4.2.3/lib/R/library 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 Hi, I'm trying out quarto 1.3.313, and noted an error when trying to render a qmd file with a graphviz diagram to PDF. Here's an example: ````md --- title: "PDF Test" format: pdf --- ```{dot} graph G { layout=neato run -- intr; intr -- runbl; runbl -- run; run -- kernel; kernel -- zombie; kernel -- sleep; kernel -- runmem; sleep -- swap; swap -- runswap; runswap -- new; runswap -- runmem; new -- runmem; sleep -- runmem; } ``` ```` The error I got with xelatex is: ``` compilation failed- error Unable to load picture or PDF file 'undefined.pdf'. <to be read again> } l.160 ...[width=5.5in,height=3.5in]{undefined.pdf} ``` In the output .tex file, the relevant lines are ``` \begin{figure}[H] {\centering \includegraphics[width=5.5in,height=3.5in]{undefined.pdf} } \end{figure} ``` The file is rendered with no problem in quarto 1.2.475. Do you have any idea why this happens? I'm using Pandoc 3.1.2, with Ubuntu 22.04. Here is my RStudio version: RStudio 2023.03.0+386 "Cherry Blossom" Release (3c53477afb13ab959aeb5b34df1f10c237b256c3, 2023-03-09) for Ubuntu Jammy Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) rstudio/2023.03.0+386 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36 And `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: 1.3.313 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.7.6 (Conda) Path: /home/markl/.julia/conda/3/bin/python3 Jupyter: 4.6.1 Kernels: python3, julia-1.7 (-) Checking Jupyter engine render....Traceback (most recent call last): File "/opt/quarto/share/jupyter/jupyter.py", line 21, in <module> from notebook import notebook_execute, RestartKernel File "/opt/quarto/share/jupyter/notebook.py", line 18, in <module> from nbclient import NotebookClient ModuleNotFoundError: No module named 'nbclient' [✓] Checking Jupyter engine render....OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description When I render a book project to PDF with a flextable printed, I get the following error: ``` compilation failed- error Undefined control sequence. <argument> \Oldarrayrulewidth l.260 ...ngth{\Oldarrayrulewidth}{\arrayrulewidth} ``` It produces this error on this minimal example in a newly created Quarto book project (showing just index.qmd): ```` # Preface {.unnumbered} This is a Quarto book. To learn more about Quarto books visit <https://quarto.org/docs/books>. ```{r} library(flextable) ``` df <- data.frame(c(1:3),c(4:6)) flextable(df) ```` (and the _quarto.yml:) ``` project: type: book book: title: "flextable_book_test" author: "Norah Jones" date: "4/7/2023" chapters: - index.qmd - intro.qmd - summary.qmd - references.qmd bibliography: references.bib format: html: theme: cosmo pdf: documentclass: scrreprt editor: visual ``` If I render a PDF outside of a book project (even with an scrreprt document class), it works perfectly fine. Any ideas what could be causing it to only throw this error in the book project? I'm running RStudio 2023.03.0, Build 386, with Quarto version 1.3.310: ``` C:\Users\jonathan.peake\OneDrive - Florida Fish and Wildlife Conservation\Documents\FIM Data Projects\flextable_book_test>quarto check A new release of Deno is available: 1.28.2 → 1.32.3 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: 1.3.310 Path: C:\Users\jonathan.peake\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.7 Path: C:/Users/jonathan.peake/AppData/Local/Programs/Python/Python310/python.exe Jupyter: 4.11.1 Kernels: python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.2.1 Path: C:/PROGRA~1/R/R-42~1.1 LibPaths: - C:/Users/jonathan.peake/Documents/R - C:/Program Files/R/R-4.2.1/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 When adding a table with inline code in an appendix, the inline code is shown instead of the values. ### Minimal Example In **RStudio 2023.03.0 Build 386** I have created a Quarto Book named "Minimal Example", and added the following table at the end of the `intro.qmd` file: ``` ## Table | $n$ | $k$ | $\pi =$ 0.05 | 0.10 | 0.15 | 0.20 | 0.25 | 0.30 | 0.35 | 0.40 | 0.45 | 0.50 | |--:|--:|-------------:|-----:|-----:|-----:|-----:|-----:|-----:|-----:|-----:|-----:| | 1 | 0 | 0.9500 | 0.9000 | 0.8500 | 0.8000 | 0.7500 | 0.7000 | 0.6500 | 0.6000 | 0.5500 | 0.5000 | | 1 | 1 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | | | | | | | | | | | | | | | 2 | 0 | `r round(pbinom(q = 0, size = 2, prob = 0.05), digits = 4)` | 0.8100 | `r round(pbinom(q = 0, size = 2, prob = 0.15), digits = 4)` | 0.6400 | `r round(pbinom(q = 0, size = 2, prob = 0.25), digits = 4)` | 0.4900 | `r round(pbinom(q = 0, size = 2, prob = 0.35), digits = 4)` | 0.3600 | `r round(pbinom(q = 0, size = 2, prob = 0.45), digits = 4)` | 0.2500 | | 2 | 1 | `r round(pbinom(q = 1, size = 2, prob = 0.05), digits = 4)` | 0.9900 | `r round(pbinom(q = 1, size = 2, prob = 0.15), digits = 4)` | 0.9600 | `r round(pbinom(q = 1, size = 2, prob = 0.25), digits = 4)` | 0.9100 | `r round(pbinom(q = 1, size = 2, prob = 0.35), digits = 4)` | 0.8400 | `r round(pbinom(q = 1, size = 2, prob = 0.45), digits = 4)` | 0.7500 | | 2 | 2 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | | | | | | | | | | | | | | ``` I have also created a file named `appendix-table.qmd` with the following content: ``` # The Binomial Distribution $P(y \leq k)$ for $y \sim \mbox{Bin}(n, \pi)$. Please note that these tables provide cumulative probabilities. | $n$ | $k$ | $\pi =$ 0.05 | 0.10 | 0.15 | 0.20 | 0.25 | 0.30 | 0.35 | 0.40 | 0.45 | 0.50 | |--:|--:|-------------:|-----:|-----:|-----:|-----:|-----:|-----:|-----:|-----:|-----:| | 1 | 0 | 0.9500 | 0.9000 | 0.8500 | 0.8000 | 0.7500 | 0.7000 | 0.6500 | 0.6000 | 0.5500 | 0.5000 | | 1 | 1 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | | | | | | | | | | | | | | | 2 | 0 | `r round(pbinom(q = 0, size = 2, prob = 0.05), digits = 4)` | 0.8100 | `r round(pbinom(q = 0, size = 2, prob = 0.15), digits = 4)` | 0.6400 | `r round(pbinom(q = 0, size = 2, prob = 0.25), digits = 4)` | 0.4900 | `r round(pbinom(q = 0, size = 2, prob = 0.35), digits = 4)` | 0.3600 | `r round(pbinom(q = 0, size = 2, prob = 0.45), digits = 4)` | 0.2500 | | 2 | 1 | `r round(pbinom(q = 1, size = 2, prob = 0.05), digits = 4)` | 0.9900 | `r round(pbinom(q = 1, size = 2, prob = 0.15), digits = 4)` | 0.9600 | `r round(pbinom(q = 1, size = 2, prob = 0.25), digits = 4)` | 0.9100 | `r round(pbinom(q = 1, size = 2, prob = 0.35), digits = 4)` | 0.8400 | `r round(pbinom(q = 1, size = 2, prob = 0.45), digits = 4)` | 0.7500 | | 2 | 2 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | | | | | | | | | | | | | | ``` When rendering the `_quarto.yml` file: ``` project: type: book book: title: "Minimal example" author: "Norah Jones" date: "4/7/2023" chapters: - index.qmd - intro.qmd - summary.qmd - references.qmd appendices: - appendix-table.qmd bibliography: references.bib ``` with the command `quarto render --to pdf` in the console, the first table in the intro is created as expected. However, the same table in the appendix displays the inline code instead of the values. **I expected to see the same table as in the intro.** I updated on April 7, 2023 to quarto version 1.3.310 and the appendix table was working in my previous version (quarto version 1.2.475). In the end I went back to quarto version 1.2.475, to be able to create my book with the intended table in the appendix. In my humble opinion it is a bit premature to put the candidate release as default download on https://quarto.org/docs/get-started/ and suggest to leave the default on the current release. ### Output from `cat /etc/os-release` ``` username@machinename:~$ cat /etc/os-release NAME="Linux Mint" VERSION="20.3 (Una)" ID=linuxmint ID_LIKE=ubuntu PRETTY_NAME="Linux Mint 20.3" VERSION_ID="20.3" HOME_URL="https://www.linuxmint.com/" SUPPORT_URL="https://forums.linuxmint.com/" BUG_REPORT_URL="http://linuxmint-troubleshooting-guide.readthedocs.io/en/latest/" PRIVACY_POLICY_URL="https://www.linuxmint.com/" VERSION_CODENAME=una UBUNTU_CODENAME=focal ``` ### quarto check output ``` username@machinename:~$ 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: 1.3.310 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.10 Path: /usr/bin/python3 Jupyter: 4.10.0 Kernels: julia-1.8, python3, ir [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.3 Path: /usr/lib/R LibPaths: - /home/username/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: 2.21 [✓] 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.

Adding Pandoc version used in our tool as API endpoint info Possible solutions: - Add information RStudio IDE JSON https://www.rstudio.com/wp-content/downloads.json - Add information in our JSON https://quarto.org/docs/download/_download.json - https://github.blog/2023-03-28-introducing-self-service-sboms/

## Description I have a Pandas data frame `hours`, which I want to display (in a Quarto document rendered to HTML) such that values above 180 are red. ```python hs = hours.style hs.applymap(lambda value: 'color: red' if value > 180 else '') ``` This works, but in the process the nice default styling of data frames is lost: numbers have lots of unnecessary 0 decimals, columns are extremely narrow, the background is uniform white instead of alternating with gray. I looked at the HTML code, and saw that in standard display of dataframes, the `table` element has the property `class="dataframe"`. So I added it: ```python hs = hours.style hs.set_table_attributes('class="dataframe"') hs.applymap(lambda value: 'color: red' if value > 180 else '') ``` This is partially successful, the display looks decent, though not identical to the standard style. However, the red coloring is gone. I also tried ```python hs = hours.style hs.applymap(lambda value: 'color: red' if value > 180 else '') hs.set_table_attributes('class="dataframe"') ``` but with the same outcome. Finally, I followed the advice in a comment on https://stackoverflow.com/questions/71911644/pandas-styler-using-set-table-styles-along-with-applymap, to use `'color: red !important'`, again without effect. Looking at the HTML code, it appears that `applymap` is implemented by inserting a `style` element directly before the table: ```html <style type="text/css"> #T_1ad9f_row6_col2, #T_1ad9f_row9_col1, #T_1ad9f_row9_col2, #T_1ad9f_row45_col0, #T_1ad9f_row45_col2 { color: red !important; } </style> <table id="T_1ad9f"> ``` This element is omitted as soon as I use `set_table_attributes`. ## Minimal, fully reproducible example ``````markdown --- jupyter: python3 --- create dataframe ```{python} import pandas as pd df = pd.DataFrame({'a': [1, 2, 3], 'b': [4, 5, 6]}) ``` nicely styled display ```{python} df ``` highlighting numbers red removes the styling ```{python} def mapfunction(value): if value > 4: return 'color: red' else: return '' df.style.applymap(mapfunction) ``` trying to restore the styling removes the highlighting ```{python} df.style.applymap(mapfunction).set_table_attributes('class="dataframe"') ``` regardless of the order ```{python} df.style.set_table_attributes('class="dataframe"').applymap(mapfunction) ``` `````` ## `quarto check` `````` [✓] Checking Quarto installation......OK Version: 1.2.335 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.5 (Conda) Path: /home/ca/.conda/envs/std/bin/python3 Jupyter: 4.10.0 Kernels: python3, matlab, matlab_connect [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.0.4 Path: /usr/lib/R LibPaths: - /home/ca/.local/lib/R - /usr/lib/R/site-library - /usr/lib/R/library rmarkdown: 2.11 [✓] Checking Knitr engine render......OK `````` ## Operating system Debian GNU/Linux 11.6, kernel 5.10.0-21-amd64 ## Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description I created the default book project via the CLI, using `quarto create-project mybook --type book`, then changed the `_quarto.yml` date entry from the default hard-wired date to ` date: "`r Sys.Date()`"` and when rendered/previewed, the date is reported as "Invalid Date". This works fine for a website, so I'm wondering if this is a bug or intentional (due to an underlying belief about how a book should "work"). Setting `engine: knitr` does not change anything. On macOS 12.6.4; `quarto check` gives: ``` ^C~/Desktop/mybook> quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Users/bryanhanson/Documents/Professional/Research/R_Pkgs/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.2 Path: /usr/local/opt/[email protected]/bin/python3.11 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ``` ### Checklist - [ ] 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 1.3.310, with this URL: https://substackcdn.com/image/fetch/w_1456,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%253A%252F%252Fsubstack-post-media.s3.amazonaws.com%252Fpublic%252Fimages%252Fced5d5ad-a0d6-44aa-b6f5-73c0a937d016_3553x5273.jpeg ``` 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 LaTeX Error: Cannot determine size of graphic in index_files/mediabag/ced5d5ad-a0d6-44aa-b.webp (no BoundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H <return> for immediate help. ... l.1296 ...iles/mediabag/ced5d5ad-a0d6-44aa-b.webp} ``` My _quarto.yml: ```yaml pdf: papersize: "Letter" mainfont: "Georgia" documentclass: scrbook standalone: true ``` ```sh quarto list tools [✓] Inspecting tools Tool Status Installed Latest chromium Not installed --- 869685 tinytex Up to date v2023.04 v2023.04 ``` ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

````markdown --- title: foo format: commonmark keep-md: true --- ```{.python filename="matplotlib.py"} import matplotlib.pyplot as plt plt.plot([1,23,2,4]) plt.show() ``` ```` This outputs with latest 1.3 ````markdown # foo ``` python import matplotlib.pyplot as plt plt.plot([1,23,2,4]) plt.show() ``` ```` but it outputs with latest 1.2 release ````markdown foo ================ <div class="code-with-filename"> **matplotlib.py** ``` python import matplotlib.pyplot as plt plt.plot([1,23,2,4]) plt.show() ``` </div> ```` It was lost in https://github.com/quarto-dev/quarto-cli/pull/4118/files#diff-3c9439f2bc27c905f44644b44dee252c2d2729b5da73484cbfc22e814137f98d while introducing `DecoratedCodeBlock` I believe. @cscheid is it a regression on purpose ? Or could we port back the old behavior ? Previously we did ````lua return pandoc.Div( { pandoc.Plain{pandoc.Strong{pandoc.Str(filename)}}, el:clone() }, pandoc.Attr("", {"code-with-filename"}) ) ```` for non HTML format and now we just return the content of the code block https://github.com/quarto-dev/quarto-cli/blob/37ce04581238dc036985fcdab20534aaf78732de/src/resources/filters/customnodes/decoratedcodeblock.lua#L106-L109 (from a discussion in https://github.com/quarto-dev/quarto-cli/issues/5101)

### Bug description Using [Quarto variables](https://quarto.org/docs/authoring/variables.html) makes a lot of sense when dealing with customisations. Variables can include markdown, but in our experience it's limited to hyperlinks and some basic formatting. Titles are not taken into account, code blocks are rendered as lines of verbatim code, bullet points are rendered as a long list of options. I generated a sample project with different types of markdown content to be included in the following repo: <https://github.com/tverbeiren/markdown_variables>. Further info is available in the `index.qmd` and the `README.md` that is generated from it. A number of attempts have been made already with different YAML multiline options, escaping of characters, adding extra newlines. Without success. This has been tested with Quarto v1.3.310 on Mac Ventura. ### 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 operating system you're running. If on Linux, please provide the specific distribution.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5098 <div type='discussions-op-text'> ^{Originally posted by **ypislon** April 5, 2023} Dear quarto team, as a new user of Quarto I would appreciate a more consistent documentation in the "reference" sections on the website by noting what the default values are for all options. In most cases, the default values are explicitly mentioned, but in some, they are not. This would help when diving deeper into the configuration and setup of Quarto projects.</div>

### Bug description When linking from a slide deck to a plain HTML-format page using a link like `[link](/index.qmd)` displays as plaintext QMD in the browser. I expected this to display as properly-rendered HTML. Changing the link to `[link](/index.html)` resolves the issue, but break's Quarto's ability to detect broken internal links (e.g. no warnings are thrown if I link to a non-existent file `[link](/foo.html)`) #### Reproducing from repo _Reproduction repository: https://github.com/MattF-NSIDC/sscce-quarto-slides-link-to-html-issue_ Clone the repo, run `quarto preview` (or render), and click the link in the slide deck. Your browser URL bar should show `.../index.qmd` instead of `.../index.html` and the content displayed should be plaintext. Expected this to be properly rendered HTML. #### Reproducing from scratch 1. Create the project ``` quarto create-project --type=website ``` 2. Create a slides directory with `_metadata.yml` which overrides the format of the directory's contents to `revealjs`. 3. Create a `slides/test.qmd` which has a link to `index.qmd`. 4. Render or preview the site ``` quarto preview ``` 5. Navigate to the slide deck in the browser, and click the "Go home" link 6. Observe the browser shows plaintext instead of expected HTML, and the URL bar says `/slides/test.qmd` instead of the expected `slides/test.html`. 7. The issue can be resolved by editing `slides/test.qmd` to link to `/index.html` instead of `/index.qmd`. **NOTE**: This breaks the ability of Quarto to detect broken links (e.g. it will be happy with linking `/foo.html` even though that doesn't exist). ### Versions * RStudio: None * OS: Ubuntu 20.04 * Quarto: 1.2.335, 1.3.262, 1.3.309 #### Quarto check ``` $ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.262 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.10 Path: /usr/bin/python3 Jupyter: 4.6.3 Kernels: python3 (/) Checking Jupyter engine render..../usr/lib/python3/dist-packages/requests/__init__.py:89: RequestsDependencyWarning: urllib3 (1.26.14) or chardet (3.0.4) doesn't match a supported version! warnings.warn("urllib3 ({}) or chardet ({}) doesn't match a supported " Traceback (most recent call last): File "/opt/quarto/share/jupyter/jupyter.py", line 21, in <module> from notebook import notebook_execute, RestartKernel File "/opt/quarto/share/jupyter/notebook.py", line 18, in <module> from nbclient import NotebookClient ModuleNotFoundError: No module named 'nbclient' [✓] Checking Jupyter engine render....OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Hello, I receive the following error during quarto preview of a website build: `ERROR: PermissionDenied: Access is denied. (os error 5), stat 'NETWORK\PATH\quarto_site_error\_site'` To trigger the error, all of the following have had to be true. * Previewing a website. * Directory is on a network drive (which I am not the administrator of) * The qmd file has any script rendering a leaflet or mapview map (likely caused by htmlwidgets) Happens in either RStudio or VScode. Rendering works fine; only affects the preview. Using Windows. Full reproduction here: https://github.com/arthurgailes/repro_quarto_preview_error quarto.yml: ``` project: type: website ``` Quarto check: Version: 1.2.269 Path: C:\Program Files\Quarto\bin CodePage: 1252 Thank you for your help. ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] 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 the following qmd file is rendered in the Docusaurus project, the first callout block is not rendered correctly. ````qmd --- title: foo --- ## test ::::{.panel-tabset} ### Not work :::{.callout-important} This is important ::: foo ### Work bar :::{.callout-important} This is important ::: :::: ```` It seems that a blank line is required between `<TabItem value="Not work">` and `:::important`. ````md --- title: foo --- import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; ## test {#test} <Tabs> <TabItem value="Not work"> :::important This is important ::: foo </TabItem> <TabItem value="Work"> bar :::important This is important ::: </TabItem> </Tabs> ````  I tested it with 1.2 and the edge unreleased version on Debian Linux. ```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: 99.9.9 Path: /tmp/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.2 Path: /usr/bin/python3 Jupyter: 5.3.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### 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 ~~This qmd file includes "include" short code~~ -> include should be `{{< include _part.qmd >}}` ```qmd --- title: foo --- {{ <include _part.qmd> }} ``` is converted to this md file in docusaurus project. ```md --- title: foo --- {{ \<include \_part.qmd\> }} ```  Using the edge version unreleased Quarto CLI on Debian Linux. ```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: 99.9.9 Path: /tmp/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.2 Path: /usr/bin/python3 Jupyter: 5.3.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### 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 This qmd file includes filename attribute ````qmd --- title: foo --- ```{python filename="Python"} print("Hello, world.") ``` ```{.python filename="Python"} print("Hello, world.") ``` ```` is convert to this md file in Docusaurus project. ````md --- title: foo --- ``` python print("Hello, world.") ``` ``` text Hello, world. ``` ```python title="Python" print("Hello, world.") ``` ```` Displayed as like this.  Using the edge version unreleased Quarto CLI on Debian Linux. ```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: 99.9.9 Path: /tmp/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.2 Path: /usr/bin/python3 Jupyter: 5.3.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

I suggest adding the commenting mechanisms to the official tutorial. The commenting mechanism is essential for review in document collaboration through git repo. The commenting mechanism helps two or more persons collaborate based on Quarto document. _Originally posted by @wangzk in https://github.com/quarto-dev/quarto-cli/issues/696#issuecomment-1496778552_

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5092 <div type='discussions-op-text'> ^{Originally posted by **israelarevalo** April 4, 2023} I just updated to the newest release of Quarto and my html tables created through sjPlot are not displaying correctly on my html documents. All libraries are updated on both my windows and Mac machines and they are both yielding the same issue. The html file displays the text the table is supposed to contain, but no formatting as usually contained within an sjPlot. Any ideas from the community?</div>

We should be nicer in attempting to parsing tables while third-party libraries adapt to our new behavior. ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5092 <div type='discussions-op-text'> ^{Originally posted by **israelarevalo** April 4, 2023} I just updated to the newest release of Quarto and my html tables created through sjPlot are not displaying correctly on my html documents. All libraries are updated on both my windows and Mac machines and they are both yielding the same issue. The html file displays the text the table is supposed to contain, but no formatting as usually contained within an sjPlot. Any ideas from the community?</div>

### Bug description Hello, I noticed that in a list of tables there are duplicates when the document is knitted to pdf and the table is spread across multiple pages. Is there a setting or workaround to fix this? Take care F ### 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'm trying to render this page as PDF. ```qmd --- title: Non-standard URL ---  ``` Breaks with this error: ``` running xelatex - 1 This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode updating tlmgr updating existing packages compilation failed- error Unable to load picture or PDF file 'badurl_files/mediabag/https://bucket.jpeg'. <to be read again> } l.159 ...adurl_files/mediabag/https://bucket.jpeg} ``` Quarto version 1.3.306 OSX 13.3 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description When I implement "loud" citations, e.g., "... Berry (2021) ...", **only the year is hyperlinked, not the name(s)**. Is this intentional? Seems odd. PDF format. I have "link-citations: true" in my yaml header. Default citation method. Have tried changing document class etc. RStudio version 2023.03.0+386. macOS Ventura 13.3 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: 1.3.302 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.2 Path: /opt/homebrew/opt/[email protected]/bin/python3.11 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library knitr: 1.42 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK Thanks ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [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.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5080 <div type='discussions-op-text'> ^{Originally posted by **sje30** April 4, 2023} I'm trying to use --resource-path to point to a different folder for where I store images. With the following simple example: ```` --- title: "test 1" resource-path: ["/tmp"] format: html: embed-resources: true --- # Generate a plot ```{r} png(file="/tmp/temp.png") plot(1:10) dev.off() ``` # show the plot v1  # show the plot v2  ```` when I render in quarto, v1 of the plot appears, but not v2. quarto render temp.qmd However, if I run pandoc from the command line, it works (as in the plot appears twice): pandoc --resource-path='/tmp' --self-contained -s -o temp.html temp.qmd what am I missing? Thanks, Stephen ``` pandoc v 3.1.1 quarto v 1.2.475 running on Mac ```</div>

Multiple background images work with Quarto + revealjs, but they do not embed into the combined HTML file with `embed-resources`. MWE: ```{r} --- title: "Untitled" format: revealjs embed-resources: true --- ## Test {background-image="image1.jpg, image2.jpg, image3.jpg, image4.jpg" background-size="50% 50%,50% 50%,50% 50%,50% 50%" background-position="top right,top left,bottom left,bottom right"} ## Local image embeds fine  ## URL image also embeds  ```

### Bug description Hello, Thanks for making quarto, it's super cool 😄 If I embed a Jupyter cell as described here: https://quarto.org/docs/authoring/notebook-embed.html in a small document `test.qmd`: ``` --- title: Exploration of penguin characteristics author: Norah Jones toc: true format: html: code-fold: true --- # Embedded report {{< embed penguins.ipynb >}} ``` and render the document with: ``` $ quarto render test.qmd --to html --execute --no-cache -o test.html ``` The code in the embedded Jupyter notebook isn't evaluated. This isn't what I expect with the `--execute` flag. Instead, to update the Jupyter cell content dynamically I have to run: ``` $ jupyter nbconvert --to notebook --inplace --execute penguins.ipynb $ quarto render test.qmd --to html --execute --no-cache -o test.html ``` I'm not sure if this is expected behaviour, but it took me a little while to figure out. Thanks! ### 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? N/A - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. maxOS 13.3 - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running. ``` [✓] 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: 1.3.296 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.5 Path: /Library/Frameworks/Python.framework/Versions/3.10/bin/python3 Jupyter: 5.3.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library knitr: 1.39 rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ```

### Bug description I tried the Docusaurus format with Quarto 1.3 and noticed that quite a few features are no longer working. - `code-fold: true` does not work - YAML front matter is not output to .md files - If a call out block is included, rendering will fail I tested with quarto cli 1.3.306 and [email protected] on Linux (Debian or Ubuntu) ```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: 1.3.306 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.2 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/ ``` I get an error when I add the following qmd file to the Docusaurus sample project and run `quarto preview`. ````qmd --- title: foo --- :::{.callout-note} This is callout ::: ```` ```sh $ quarto preview Preparing to preview [1/1] docs/test.qmd Error running filter /opt/quarto/share/filters/main.lua: Inline, list of Inlines, or string expected, got nil while retrieving function argument content while retrieving arguments for function Header stack traceback: ...share/extensions/quarto/docusaurus/docusaurus_writer.lua:73: in function <...share/extensions/quarto/docusaurus/docusaurus_writer.lua:70> (...tail calls...) /opt/quarto/share/filters/main.lua:71: in function </opt/quarto/share/filters/main.lua:70> (...tail calls...) [C]: in ? [C]: in method 'walk' /opt/quarto/share/filters/main.lua:171: in function 'run_emulated_filter' ...share/extensions/quarto/docusaurus/docusaurus_writer.lua:49: in field 'handle' /opt/quarto/share/filters/main.lua:742: in function </opt/quarto/share/filters/main.lua:739> [C]: in ? [C]: in method 'walk' /opt/quarto/share/filters/main.lua:4116: in function </opt/quarto/share/filters/main.lua:4114> [C]: in ? [C]: in method 'walk' /opt/quarto/share/filters/main.lua:171: in function 'run_emulated_filter' /opt/quarto/share/filters/main.lua:449: in local 'callback' /opt/quarto/share/filters/main.lua:454: in upvalue 'run_emulated_filter_chain' /opt/quarto/share/filters/main.lua:495: in function </opt/quarto/share/filters/main.lua:476> stack traceback: /opt/quarto/share/filters/main.lua:171: in function 'run_emulated_filter' ...share/extensions/quarto/docusaurus/docusaurus_writer.lua:49: in field 'handle' /opt/quarto/share/filters/main.lua:742: in function </opt/quarto/share/filters/main.lua:739> [C]: in ? [C]: in method 'walk' /opt/quarto/share/filters/main.lua:4116: in function </opt/quarto/share/filters/main.lua:4114> [C]: in ? [C]: in method 'walk' /opt/quarto/share/filters/main.lua:171: in function 'run_emulated_filter' /opt/quarto/share/filters/main.lua:449: in local 'callback' /opt/quarto/share/filters/main.lua:454: in upvalue 'run_emulated_filter_chain' /opt/quarto/share/filters/main.lua:495: in function </opt/quarto/share/filters/main.lua:476> stack traceback: /opt/quarto/share/filters/main.lua:4116: in function </opt/quarto/share/filters/main.lua:4114> [C]: in ? [C]: in method 'walk' /opt/quarto/share/filters/main.lua:171: in function 'run_emulated_filter' /opt/quarto/share/filters/main.lua:449: in local 'callback' /opt/quarto/share/filters/main.lua:454: in upvalue 'run_emulated_filter_chain' /opt/quarto/share/filters/main.lua:495: in function </opt/quarto/share/filters/main.lua:476> stack traceback: /opt/quarto/share/filters/main.lua:171: in function 'run_emulated_filter' /opt/quarto/share/filters/main.lua:449: in local 'callback' /opt/quarto/share/filters/main.lua:454: in upvalue 'run_emulated_filter_chain' /opt/quarto/share/filters/main.lua:495: in function </opt/quarto/share/filters/main.lua:476> ``` The following qmd files are converted to an empty md file. ```qmd --- title: foo --- ``` I think this is a serious regression and I recommend adding Docusaurus format tests to this repository. (Docusaurus integration is really great!) ### 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.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4888 <div type='discussions-op-text'> ^{Originally posted by **kernie** March 19, 2023} Hi! I have defined a section ``` format-resources: - resources/fonts/Eurostile.ttf - resources/formats/pdf/eforms.sty ``` in the `pdf`area and with `latex-auto-mk: true` these get copied into the execution dir. However, I want to establish an own compilation chain and use external latexmk... When I set this to `latex-auto-mk: false` it starts rendering but complains: ``` Error producing PDF. ! LaTeX Error: File `eforms.sty' not found. ``` Can somebody enlighten me, what I'm doing wrong? How can I get more debug output? Thank you!</div>

In `src/project/types/website/listing/website-listing-read.ts`, `listItemFromMeta` is currently outputting `any`, but is used as `ListingItem` downstream, so it should be validated as such. It's not a regression from 1.2 but it'll definitely break if the types are wrong coming in from the yaml.

### Bug description Good day, My system specifications are: * MacOS Ventura 13.3 * M1 Mac * Quarto v1.3.302, to which I upgraded from the previous version, v1.2.475 * RStudio Version 2023.03.0+386 After the upgrade I encounter the folowing error when I render a Quarto document (with R code included) to html from within RStudio and I have been unable to find a solution or even a mention of this problem elsewhere on the internet: ``` ERROR: Error resolving include-after- unable to open file js.html ``` The website being rendered is https://tangledbank.netlify.app/, which was made with Quarto v1.2.475 within RStudio. I have not tried to render the website Quarto v1.3.302 outside of RStudio. The output of `quarto check` is here: ``` [✓] 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: 1.3.302 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.13 (Conda) Path: /Users/ajsmit/opt/anaconda3/bin/python 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/ ``` Don't believe the output that says that a version of R cannot be found on my system--it is there and it works. Herewith a reproducible example: ``` --- date: "2021-01-01" title: "4. A problem file" subtitle: "Getting familiar with data handling in R" bibliography: ../../references.bib csl: ../../marine-biology.csl format: html: toc-location: right --- # My heaidng My text. This problem occurs whether or not I include code chunks. ``` Has this been encountered before? And if so, are you aware or any solutions? I am unsure whether this an issue on my end, or something the developers should know about. PS: The Checklist asks for a .qmd file that reproduces the problem, but the system does not actually allow .qmd files to be uploaded. Thank you, AJ Smit ### 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.

We made this decision early on in the development to only focus on Confluence Cloud as Atlassian is EoLing Confluence Server in favor of Cloud. More information on this can be found here: https://www.atlassian.com/migration/assess/journey-to-cloud. Although Server is being EoLed, it does seem that there will be some long-standing installations of Confluence Data Center which will continue on without a Cloud migration. We should consider this epic as adding support for Data Center. As we build up a potential case for this, we will link in issues as they are posted. ---- ## Resources - [Data Center 2023 Roadmap](https://community.atlassian.com/t5/Jira-articles/Data-Center-s-Roadmap-23/ba-p/2330068) - [Generate Trial License](https://my.atlassian.com/license/evaluation) - [Personal Access Tokens](https://confluence.atlassian.com/enterprise/using-personal-access-tokens-1026032365.html) - [Atlassian Community](https://community.atlassian.com/) - [Download Archives](https://www.atlassian.com/software/confluence/download-archives) - [Confluence Docker Container](https://hub.docker.com/r/atlassian/confluence-server)

### Bug description Markdown citation placed in notes div is rendered on slide. Reproducible example follows: ``` --- title: "Another test of Reveal.js" format: revealjs: default docx: default --- ## Here is a slide It's got some text on it. :::{.notes} Speaker notes go here.[^1] [^1]: Citation goes here; should be in notes but appears on slide. ::: ``` Using macOS; happens using emacs with terminal or RStudio 2023.03.0+386 (2023.03.0+386) quarto check output follows ``` ✓] 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: 1.3.302 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.2 Path: /opt/homebrew/opt/[email protected]/bin/python3.11 Jupyter: 5.3.0 Kernels: python3 (\) Checking Jupyter engine render....0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library knitr: 1.42 rmarkdown: 2.20 [✓] 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'm using Quarto for my GitHub page. Command lines for rendering & publishing (`quarto render` and `quarto publish gh-pages`) My Quarto version is 1.3.302 on MacOS Ventura 13.2.1 On the rendered and published website, when first clicking on a section on the table of contents (TOC), the page seems to scroll a little bit but does not scroll to the chosen section. It only scrolls to the correct place after the second click (on the same section). I tested this on Chrome, Edge, and Safari and have this problem on all of them. On Chrome and Edge, if at first I go to the website link with tail specifying a section, for example `#code-cell` (section Code Cell), then I will be landed at the right section of the page. However, if after that I change the website link to navigate to another section, say to `#equation` (section Equation), then the page does not move anywhere at all. This remains even after I refresh the website multiple times. However, I do not encounter this issue with Safari. Below is the HTML output for the TOC. ```HTML <!-- content --> <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar"> <!-- sidebar --> <!-- margin-sidebar --> <div id="quarto-margin-sidebar" class="sidebar margin-sidebar"> <nav id="TOC" role="doc-toc" class="toc-active"> <h2 id="toc-title">On this page</h2> <ul> <li><a href="#markdown" id="toc-markdown" class="nav-link active" data-scroll-target="#markdown">Markdown</a></li> <li><a href="#code-cell" id="toc-code-cell" class="nav-link" data-scroll-target="#code-cell">Code Cell</a></li> <li><a href="#equation" id="toc-equation" class="nav-link" data-scroll-target="#equation">Equation</a></li> </ul> </nav> </div> ``` Output of `quarto check` > [✓] Checking versions of quarto binary dependencies... > Pandoc version 3.1.1: OK > Dart Sass version 1.55.0: OK > [✓] Checking versions of quarto dependencies......OK > [✓] Checking Quarto installation......OK > Version: 1.3.302 > Path: /Users/nguyenmts/Applications/quarto/bin > > [✓] Checking basic markdown render....OK > > [✓] Checking Python 3 installation....OK > Version: 3.10.9 (Conda) > Path: /Users/nguyenmts/anaconda3/bin/python > Jupyter: 5.2.0 > 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/ ### 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.

- Is the h3 font size too close to h2, dampening the visual hierarchy? - Is vertical spacing around headers too tight, making the text harder on the eyes and more difficult to scan? Particularly h2 and h3 - May be a bug: there is no vertical space between h1 and the description when it's shown. I'd try 8-16 px - Is the header description font size too small? Reference designs (Nature, New York Times, Distill, and Tailwind) consistently used a slightly larger size than the base font size. I'd try 19px - With the base font size reduced from 20px to 17px, is the content width too wide? On a large display, reference designs are 600-750px, and Quarto is ~850px. ### Suggestion Here is a side-by-side comparison after making some of these changes. Left is original. On the right, I have: - Decreased h3 font-size from 23px to 20px - Increased h2 top and bottom margins from 34 17 to 49 24 - Increased h3 top and bottom margins from 25.5 8.5 to 40 20. <img width="1916" alt="image" src="https://user-images.githubusercontent.com/559360/229340301-6cbc6901-4278-4ecc-87f7-1134e3daac00.png"> cc @allenmanning @dragonstyle

### Bug description Hello, I've noticed, that the code annotation for languages such as C/C++ & VHDL doesn't work correctly. It seems to handle R & Python code neatly, but with the previously mentioned languages, it does detect the annotation, but doesn't replace it with the circle numbering. ## Snippet Following snippet... ````qmd ``` vhdl type state is (S0, S1, S2); signal c_st, n_st : state; p_seq: process (rst, clk) -- <1> begin if rst = ’1’ then c_st <= S0; elsif rising_edge(clk) then c_st <= n_st; end if; end process; p_com: process (i, c_st) -- <2> begin -- <2> -- default assignments -- <2> n_st <= c_st; -- remain in current state -- <2> o <= ’1’; -- most frequent value -- <2> -- specific assignments -- <2> case c_st is -- <2> when S0 => -- <2> if i = "00" then -- <2> n_st <= S1; -- <2> end if; -- <2> end case; end process; ``` 1. [*Memorizing*]{.underline} (sequentielle Logik) 2. [*Memoryless*]{.underline} (kombinatorische Logik) ```cpp int main(void) { uint8_t test; // <1> } // <1> void testing(int a) { // <2> a += a; // <2> } // <2> ``` 1. Hello World 2. This is just a test ```r library(tidyverse) library(palmerpenguins) penguins |> # <1> mutate( # <2> bill_ratio = bill_depth_mm / bill_length_mm, # <2> bill_area = bill_depth_mm * bill_length_mm # <2> ) # <2> ``` 1. Take `penguins`, and then, 2. add new columns for the bill ratio and bill area. ```python thislist = ["apple", "banana", "cherry"] thislist.remove("banana") # <1> print(thislist) # <2> ``` 1. Remove `banana` from the list 2. Print list ```` ...produces:  notice the comment blocks right next to the code.  ## `quarto check` ```cmd [>] 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: 1.3.302 Path: C:\Users\joelv\AppData\Local\Apps\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.4 Path: C:/Users/joelv/AppData/Local/Programs/Python/Python310/python.exe Jupyter: 4.9.2 Kernels: python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.2.2 Path: C:/PROGRA~1/R/R-4.2.2 LibPaths: - C:/Users/joelv/AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.2/library knitr: 1.41 rmarkdown: 2.20 [>] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description If I use biblatex with APA citation style and use a language for which biblatex-apa doesn't have a special definition, I get some errors about undefined control sequences. Check the following MWE (`.bib `file content does not matter as soon as it contains the "citation", entry): ````md --- format: pdf: lang: cs-CZ cite-method: biblatex biblio-style: apa bibliography: refs.bib --- [@citation] ```` results in ``` compilation failed- Error compiling latex Undefined control sequence. <argument> \datecircaprint \mkbibdateapalongextra {labelyear}{labelyeardivis... l.167 \autocite{citation} ``` Note that this is all because `biblatex-apa` doesn't have any `czech-apa` format. It's easy to solve using ```latex \DeclareLanguageMapping{czech}{american-apa} ``` Now I get to the point of my issue – **there is no way how to include the line above at the correct place in the `.tex` document without replacing the whole `template.tex`.** It has to be placed after `babel` and `biblatex`, so I cannot use `include-in-header`, it has to be in the preamble, so `before-body` isn't an option either. I think the solution may be to create a new template partial wrapping around this bibliography setup that would be easier to replace, benefiting from the template's other components getting updated along with quarto. <details><summary>Versions</summary> RStudio 2023.05.0-daily+165 macOS Ventura 13.3 quarto check: [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.299 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.9 (Conda) Path: /Users/netik/.julia/conda/3/bin/python3 Jupyter: 5.3.0 Kernels: julia-1.8, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.3 Path: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources LibPaths: - /Users/netik/Documents/git/diplomka/renv/library/R-4.2/aarch64-apple-darwin20 - /Users/netik/Library/Caches/org.R-project.R/R/renv/sandbox/R-4.2/aarch64-apple-darwin20/fd29d0b8 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.

This would prevent issue like #5052 as we could find them sooner than a user report As we own **knitr** repo, we could do some clever automation. it could be triggered by each commit on **knitr**, and at least once before making a new release. Anyhow, this is to be done at some point.

TBD Chatting with @samperman it would be useful to some teams to have slack channels Automated channels - Pre-release (spam with everything) "log-level verbose" - Release (Just releases including back-patches) "log-level info"

````markdown --- title: "Test" format: html keep-md: true --- Test to add caption under a plotly graph ```{r} #| label: fig-plotly #| fig-cap: "My figure caption here" #| echo: false #| message: false library(plotly) fig <- plot_ly(midwest, x = ~percollege, color = ~state, type = "box") fig ``` ```` It seems we are missing some fenced div where the figure caption should have been applied ```` --- title: "Test" format: html keep-md: true --- Test to add caption under a plotly graph ::: {.cell} ```{=html} <! --plotly html in here --> ``` ::: ```` I believe this is supposed to work. I get the same results with `v1.2.475` oddly. So not a 1.3 regression, unless one of the patch version introduced this. Probably something in the knitr hooks. I'll have a look but if anyone has clues, please share

Hi, I think there might be a small bug with rendering qmd files to ipynb. When I render a theorem, the markdown in the Python notebook contains an extra space, which means that the heading of the theorem doesn't appear in bold as intended. Minimum working example below. ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5032 <div type='discussions-op-text'> ^{Originally posted by **aletroux** March 30, 2023} Hi, I've just discovered Quarto and am experimenting it with the aim of using it for teaching - it's a Python module so I'd be generating a mixture of notes (html/pdf) and ipynb notebooks. I have the following input file (I called it test.qmd) ``` ::: {#thm-line} # Line The equation of any straight line, called a linear equation, can be written as: $$ y = mx + b $$ ::: ::: proof Here is the proof. ::: ``` When I render this file using "quarto test.qmd --to ipynb" I get a Python notebook with the following text: ``` <span class="theorem-title">**Theorem 1 (Line) **</span>The equation of any straight line, called a linear equation, can be written as: $$ y = mx + b $$ <span class="proof-title">*Proof*. </span>Here is the proof. ``` I have two questions. 1) There is an extra space after "Theorem 1 (Line)" and before the "**" which means that the text isn't rendered in bold as intended. I wonder whether this is due to a problem with my markdown, or is it perhaps a bug? (Rendering either the qmd or the ipynb file to html or pdf doesn't have this problem...) 2) Is there a way to disable the html tags? I appreciate ipynb is an intermediate format for producing html, but it would be nice to be able to provide students with ipynb files without the extra markdown needed by Quarto, and without the html tags.</div>

- Could the show/hide animation be made smoother?[^animation] - Is the hover effect on nav items too subtle - could it benefit from a brighter color or an underline? - Should we consider an svg logo instead of png? - Is the nav item font size too large?[^font-size] Perhaps try ~14px? - Is the horizontal spacing between nav items too small?[^spacing] Perhaps try ~26px? [^animation]: Quarto's navbar animates when it hides as the user scrolls down, and when it shows as the user scrolls back up. The animation causes the navbar to clip the main content, and the left navigation sidebar and right ToC to jump down, which can be distracting. [Material](https://squidfunk.github.io/mkdocs-material/getting-started/) has an interesting approach which results in a smoother animation. [^font-size]: Referenced designs have a ratio of nav item to body font size of >= 0.8. I've compiled these in [a spreadsheet](https://docs.google.com/spreadsheets/d/1NtJuzwDFfr4MPjvqtEGK_XCccPyPtyB6uo7dMQaF1_A/edit?usp=sharing). [^spacing]: Referenced designs have an average spacing ~26px, which is around what I'd try for Quarto. See [spreadsheet](https://docs.google.com/spreadsheets/d/1NtJuzwDFfr4MPjvqtEGK_XCccPyPtyB6uo7dMQaF1_A/edit?usp=sharing).

### Bug description Follow up to https://github.com/quarto-dev/quarto-cli/issues/4903 [Files for reproduction](https://github.com/quarto-dev/quarto-cli/files/11119409/5048.zip) When I provide a YAML file to `listing.contents` like in ``` --- title: "About" listing: id: about-listing contents: listing.yml --- About this site :::{#about-listing} ::: ``` where `listing.yml` is ``` - path: ../foo/post.md ``` I get  Note that some metadata was improperly read or processed. This is the same output that I get if I use ``` --- title: "About" listing: id: about-listing contents: - path: post.md --- About this site :::{#about-listing} ::: ``` The expected result is  that is already obtained by removing the keyword `path` like in ``` --- title: "About" listing: id: about-listing contents: - post.md --- About this site :::{#about-listing} ::: ``` Remove the the keyword `path` in the YAML file raises an error reported at https://github.com/quarto-dev/quarto-cli/issues/4903. # Environment information Output of `quarto check`: ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.296 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /usr/bin/python3 Jupyter: 5.2.0 Kernels: python3 (-) Checking Jupyter engine render....Traceback (most recent call last): File "/opt/quarto/share/jupyter/jupyter.py", line 21, in <module> from notebook import notebook_execute, RestartKernel File "/opt/quarto/share/jupyter/notebook.py", line 18, in <module> from nbclient import NotebookClient ModuleNotFoundError: No module named 'nbclient' [✓] Checking Jupyter engine render....OK ``` ### 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.

With an upcoming release, it would be nice to be able to point people to some documentation on what it means to upgrade Quarto. For instance, RStudio users who rely on the bundled Quarto, may have never installed Quarto themselves. Should they install 1.3, or should they wait for a version of RStudio that bundles it? Do they need to do anything if they install 1.3 now, but later install RStudio with a more recent version of Quarto? We might include: * How to get basic info on your current install * Recommendations for when and how to upgrade * Common "gotchas" when you have more than one Quarto version installed * What to do if you need to downgrade your Quarto version

### Bug description Hi there, I just noticed the mobile breadcrumb doesn't show the 2nd tier correctly... This should probably be Formats > Presentations > PowerPoint Looks like it shows the first link in that second menu instead? I see it happening on quarto.org as well as my project. Thank you!  --- OS: MacOS 3.2.1 (22D68) 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: 1.3.296 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: 5.2.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.1.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library knitr: 1.38 rmarkdown: 2.13 [✓] 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.

See https://github.com/machow/quartodoc/issues/82. This specific crash happens because `Meta` can't store `Attr` objects. (I'm sure there are other objects in that category as well.)

### Bug description Hi, im having an bug, that subscripts in julia code does not get printed out. I'm attaching example to reproduce the bug. I suppose theres missing step in conversion from julia to markdown. ```` --- title: "Subscript example" date: "5/22/2021" format: pdf: default jupyter: julia-1.8 --- ## Minimal example Working subcript here x~3~. ```{julia} x₃ = 3 ``` ```` OS MacOS 13.3 MacTeX 2023 ``` [✓] Checking Quarto installation......OK Version: 1.2.335 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.8 Path: /Library/Frameworks/Python.framework/Versions/3.10/bin/python3 Jupyter: 5.2.0 Kernels: julia-1.8, 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 was not able to attach *.qmd file, so i changed it to *.txt, hope it does not confuse anyone. [subscript_example.txt](https://github.com/quarto-dev/quarto-cli/files/11112979/subscript_example.txt) ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [x] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

From discussion in https://github.com/quarto-dev/quarto-cli/discussions/4755 * `html` format support some variables for callout (https://quarto.org/docs/output-formats/html-themes.html#callouts) * This is because it is part of bootstrap SCSS file that we compile ( * For revealjs, this is just a `<style>` node that [we insert in header](https://github.com/quarto-dev/quarto-cli/blob/242276f1af2bce3a93560c55d7087cf98fafec6c/src/format/reveal/format-reveal.ts#L282-L284) of document (https://github.com/quarto-dev/quarto-cli/blob/main/src/resources/formats/html/styles-callout.html) We should make that part of the default theme for revealjs, so that it is compile as a SASS theme, and variables can also be used (see https://github.com/quarto-dev/quarto-cli/discussions/4755#discussioncomment-5476737 by @EllaKaye)

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5033 <div type='discussions-op-text'> ^{Originally posted by **gdietl** March 30, 2023} In the proof environment of bookdown, the end has been marked by a square, commonly used as the QED symbol. However, using quarto, the end of the proof is not specified. Is there an easy way to add this symbol to the proof environment?</div>

## Steps to recreate the bug 1. Creating a new project `quarto create-project mybook --type book` 2. Edit `intro.qmd` with following: ```markdown # Introduction ## My first section ## My second section ``` :point_up: Works as expected :point_down:  3. Edit `intro.qmd` again and create sections using code blocks: ~~~qmd # Introduction ```{python} #| echo: false from IPython.display import display, Markdown display(Markdown("## My first section")) display(Markdown("## My second section")) ``` ~~~ This produces the sections as expected, but notice the **missing toc on the right**.  ## Environment ```bash # Ubuntu 22.04 >>> quarto --version 1.2.335 ```

### Bug description Big quarto fan here - congrats on building such a fabulous system. I'm running into a small Mastodon issue. The following ``` navbar: right: - icon: mastodon href: https://mastodon.social/@marcelsalathe aria-label: Mastodon ``` Renders as ``` <a class="nav-link" href="https://mastodon.social/(marcelsalathe?)" rel="" target=""><i class="bi bi-mastodon" role="img" aria-label="Mastodon"> ``` Everything nice, except the broken URL. I could add `ref: https://mastodon.social/%40marcelsalathe` (this is what I currently do at [https://www.digitalepibook.com/](https://www.digitalepibook.com/) but I'd prefer the original URL to render correctly in the HTML source code. My relevant 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: 1.3.272 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK ``` I'm on MacOS 12.5.1 ### 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 I am working on a quarto book and included some julia chunk like ``` \```{julia} #| out-width: 80% JULIA CODE \``` ``` If the document contains no R code, i.e., Jupyter is used to generate the figures, the size of the figure is 100% instead of 80%. However, if I insert some R code such that knitr is used to compile the Julia code, the size is correctly set to 80%

Try this filter called `custom.lua` ```` function Meta(meta) meta["new"] = "new meta" return meta end ```` Then ````markdown --- title: "Untitled" format: gfm filters: ["custom.lua"] --- What is defined in the lua filter: "{{< meta new >}}" ```` If I run this with quarto 1.2 , I get the meta ```` Untitled ================ What is defined in the lua filter: “new meta” ```` If I run this with latest 1.3, I get an issue ````markdown # Untitled What is defined in the lua filter: “**?meta:new**” ```` Warning is being thrown ```` WARNING: Unknown meta key new specified in a metadata Shortcode. ```` Possibly a regression to look into. Unless we think this was not desired behavior. Though it seems expected to me to be able to expose custom meta defined in a filter through the meta shortcode. I know one extension who does not work anymore https://github.com/mcanouil/quarto-lua-env

When rendering a website, markdown that appears in the sidebar item content is not properly rendered in breadcrumbs. For example: ```yml project: type: website website: title: "Foo" sidebar: contents: - href: index.qmd text: " Home" - href: about.qmd text: " About" format: html: theme: cosmo css: styles.css toc: true ``` Results in raw markdown images appearing in breadcrumbs.

`render-on-save` does not seem to be included in the autocompletion list under `editor:` in yaml.

Related to #4966, having some SASS variables to control the tippy box (`.tippy-box`) could be useful I guess. ```scss $code-annotation-tippy-bg $code-annotation-tippy-color ``` _Originally posted by @mcanouil in https://github.com/quarto-dev/quarto-cli/issues/4966#issuecomment-1488839766_

Because we have full control over AST processing now, we can make custom AST nodes respond to "aspects". Let me explain. We already have the ability to visit "any" custom node by adding a `Custom` entry to the filter. But this trick is probably more generally useful. Imagine if a node could register with quarto that it will respond to `CanHold` (so that in latex formats, it knows to render itself in a way robust to `outer par` issues). Then, nodes that need their contents to hold can just write a filter that sets all `CanHold` callers correctly.

### Bug description It is really exciting to see `quarto` addressing the challenge of publishing content to Confluence! I gave it a try but unfortunately I have not been able to connect to my on-prem Confluence. This seems to be because on-prem versions of confluence do not have API tokens. Instead they have personal access tokens ([PAT](https://confluence.atlassian.com/enterprise/using-personal-access-tokens-1026032365.html)). Do you think you could support PAT, in addition to API tokens? Note that I have tried passing a PAT instead of the expected API token but that did not work (the error was `"x-seraph-loginreason": "AUTHENTICATED_FAILED"`, and I was using `quarto-1.3.290`) ### 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 From a new website project created using ``` $ quarto create-project . --type website ``` Add `page-footer` as [illustrated in the documentation](https://quarto.org/docs/websites/website-navigation.html#page-footer) such as ``` page-footer: left: "Copyright 2021, Norah Jones" ``` make the render process fail with ``` ERROR: TypeError: Cannot read properties of undefined (reading 'style') TypeError: Cannot read properties of undefined (reading 'style') at quartoBootstrapDefaults (file:///opt/quarto/bin/quarto.js:123006:80) at layerQuartoScss (file:///opt/quarto/bin/quarto.js:122686:9) at resolveBootstrapScss (file:///opt/quarto/bin/quarto.js:122735:22) at boostrapExtras (file:///opt/quarto/bin/quarto.js:124241:25) at themeFormatExtras (file:///opt/quarto/bin/quarto.js:125763:16) at Object.formatExtras (file:///opt/quarto/bin/quarto.js:125237:102) at async runPandoc (file:///opt/quarto/bin/quarto.js:79912:60) at async renderPandoc (file:///opt/quarto/bin/quarto.js:80945:26) at async Object.onRender (file:///opt/quarto/bin/quarto.js:86565:36) at async renderFiles (file:///opt/quarto/bin/quarto.js:86528:25) ``` ## Additional Information Single line page footer works as expected, for example ``` page-footer: "Copyright 2021, Norah Jones" ``` ## Environment Output of `quarto check` ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.294 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....(None) Unable to locate an installed version of Python 3. Install Python 3 from https://www.python.org/downloads/ [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

This is a follow-up issue for the discussion here: > Should we do a more general review of our patterns to see if we have more instances of `[]` doing unexpected things? _Originally posted by @cscheid in https://github.com/quarto-dev/quarto-cli/pull/4993#pullrequestreview-1361351276_

### Bug description On macOS 11.7.3 and running Quarto current release 1.2.475. When rendering the following .qmd file with Quarto... ````md --- title: Quarto Computations jupyter: python3 format: docusaurus-md --- ## Plotly ```{python} import plotly.express as px import plotly.io as pio gapminder = px.data.gapminder() gapminder2007 = gapminder.query("year == 2007") fig = px.scatter(gapminder2007, x="gdpPercap", y="lifeExp", color="continent", size="pop", size_max=60, hover_name="country") fig.show() ``` ```` And then previewing the .md output with Docusaurus, I receive the following error: ``` Module build failed (from ./node_modules/@docusaurus/mdx-loader/lib/index.js): SyntaxError: /Users/scott/Projects/docusaurus/docs/notebooks/computations.md: Unterminated template. (19:3) 17 | </script> 18 | > 19 | `,` | ^ 20 | <div> <div id="7cac0eab-2184-4bbd-88fe-9e4b92a8b847" class="plotly-graph-div" style="height:525px; width:100%;"></div> <script type="text/javascript"> require(["plotly"], function(Plotly) { window.PLOTLYENV=window.PLOTLYENV || {}; if (document.getElementById("7cac0eab-2184-4bbd-88fe-9e4b92a8b847")) { Plotly.newPlot( "7cac0eab-2184-4bbd-88fe-9e4b92a8b847", [{"hovertemplate":"<b>%{hovertext}</b><br><br>continent=Asia<br>gdpPercap=%{x}<br>lifeExp=%{y}<br>pop=%{marker.size}<extra></extra>","hovertext":["Afghanistan","Bahrain","Bangladesh","Cambodia","China","Hong Kong, China","India","Indonesia","Iran","Iraq","Israel","Japan","Jordan","Korea, Dem. Rep.","Korea, Rep.","Kuwait","Lebanon","Malaysia","Mongolia","Myanmar","Nepal","Oman","Pakistan","Philippines","Saudi Arabia","Singapore","Sri Lanka","Syria","Taiwan","Thailand","Vietnam","West Bank and Gaza","Yemen, Rep."],"legendgroup":"Asia","marker":{"color":"#636efa","size":[31889923,708573,150448339,14131858,1318683096,6980412,1110396331,223547000,69453570,27499638,6426679,127467972,6053193,23301725,49044790,2505559,3921278,24821286,2874127,47761980,28901790,3204897,169270617,91077287,27601038,4553009,20378239,19314747,23174294,65068149,85262356,4018332,22211743],"sizemode":"area","sizeref":366300.86,"symbol":"circle"},"mode":"markers","name":"Asia","orientation":"v","showlegend":true,"x":[974.5803384,29796.04834,1391.253792,1713.778686,4959.114854,39724.97867,2452.210407,3540.651564,11605.71449,4471.061906,25523.2771,31656.06806,4519.461171,1593.06548,23348.139730000006,47306.98978,10461.05868,12451.6558,3095.7722710000007,944.0,1091.359778,22316.19287,2605.94758,3190.481016,21654.83194,47143.17964,3970.095407,4184.548089,28718.27684,7458.396326999998,2441.576404,3025.349798,2280.769906],"xaxis":"x","y":[43.828,75.635,64.062,59.723,72.961,82.208,64.69800000000001,70.65,70.964,59.545,80.745,82.603,72.535,67.297,78.623,77.58800000000002,71.993,74.241,66.803,62.069,63.785,75.64,65.483,71.688,72.777,79.972,72.396,74.143,78.4,70.616,74.249,73.422,62.698],"yaxis":"y","type":"scatter"},{"hovertemplate":"<b>%{hovertext}</b><br><br>continent=Europe<br>gdpPercap=%{x}<br>lifeExp=%{y}<br>pop=%{marker.size}<extra></extra>","hovertext":["Albania","Austria","Belgium","Bosnia and Herzegovina","Bulgaria","Croatia","Czech Republic","Denmark","Finland","France","Germany","Greece","Hungary","Iceland","Ireland","Italy","Montenegro","Netherlands","Norway","Poland","Portugal","Romania","Serbia","Slovak Republic","Slovenia","Spain","Sweden","Switzerland","Turkey","United Kingdom"],"legendgroup":"Europe","marker":{"color":"#EF553B","size":[3600523,8199783,10392226,4552198,7322858,4493312,10228744,5468120,5238460,61083916,82400996,10706290,9956108,301931,4109086,58147733,684736,16570613,4627926,38518241,10642836,22276056,10150265,5447502,2009245,40448191,9031088,7554661,71158647,60776238],"sizemode":"area","sizeref":366300.86,"symbol":"circle"},"mode":"markers","name":"Europe","orientation":"v","showlegend":true,"x":[5937.029525999998,36126.4927,33692.60508,7446.298803,10680.79282,14619.222719999998,22833.30851,35278.41874,33207.0844,30470.0167,32170.37442,27538.41188,18008.94444,36180.78919,40675.99635,28569.7197,9253.896111,36797.93332,49357.19017,15389.924680000002,20509.64777,10808.47561,9786.534714,18678.31435,25768.25759,28821.0637,33859.74835,37506.41907,8458.276384,33203.26128],"xaxis":"x","y":[76.423,79.829,79.441,74.852,73.005,75.748,76.486,78.332,79.313,80.657,79.406,79.483,73.33800000000002,81.757,78.885,80.546,74.543,79.762,80.196,75.563,78.098,72.476,74.002,74.663,77.926,80.941,80.884,81.70100000000002,71.777,79.425],"yaxis":"y","type":"scatter"},{"hovertemplate":"<b>%{hovertext}</b><br><br>continent=Africa<br>gdpPercap=%{x}<br>lifeExp=%{y}<br>pop=%{marker.size}<extra></extra>","hovertext":["Algeria","Angola","Benin","Botswana","Burkina Faso","Burundi","Cameroon","Central African Republic","Chad","Comoros","Congo, Dem. Rep.","Congo, Rep.","Cote d'Ivoire","Djibouti","Egypt","Equatorial Guinea","Eritrea","Ethiopia","Gabon","Gambia","Ghana","Guinea","Guinea-Bissau","Kenya","Lesotho","Liberia","Libya","Madagascar","Malawi","Mali","Mauritania","Mauritius","Morocco","Mozambique","Namibia","Niger","Nigeria","Reunion","Rwanda","Sao Tome and Principe","Senegal","Sierra Leone","Somalia","South Africa","Sudan","Swaziland","Tanzania","Togo","Tunisia","Uganda","Zambia","Zimbabwe"],"legendgroup":"Africa","marker":{"color":"#00cc96","size":[33333216,12420476,8078314,1639131,14326203,8390505,17696293,4369038,10238807,710960,64606759,3800610,18013409,496374,80264543,551201,4906585,76511887,1454867,1688359,22873338,9947814,1472041,35610177,2012649,3193942,6036914,19167654,13327079,12031795,3270065,1250882,33757175,19951656,2055080,12894865,135031164,798094,8860588,199579,12267493,6144562,9118773,43997828,42292929,1133066,38139640,5701579,10276158,29170398,11746035,12311143],"sizemode":"area","sizeref":366300.86,"symbol":"circle"},"mode":"markers","name":"Africa","orientation":"v","showlegend":true,"x":[6223.367465,4797.231267,1441.284873,12569.85177,1217.032994,430.0706916,2042.09524,706.016537,1704.063724,986.1478792,277.5518587,3632.557798,1544.750112,2082.4815670000007,5581.180998,12154.08975,641.3695236000002,690.8055759,13206.48452,752.7497265,1327.60891,942.6542111,579.2317429999998,1463.249282,1569.331442,414.5073415,12057.49928,1044.770126,759.3499101,1042.581557,1803.151496,10956.99112,3820.17523,823.6856205,4811.060429,619.6768923999998,2013.977305,7670.122558,863.0884639000002,1598.435089,1712.472136,862.5407561000002,926.1410683,9269.657808,2602.394995,4513.480643,1107.482182,882.9699437999999,7092.923025,1056.380121,1271.211593,469.70929810000007],"xaxis":"x","y":[72.301,42.731,56.728,50.728,52.295,49.58,50.43,44.74100000000001,50.651,65.152,46.462,55.322,48.328,54.791,71.33800000000002,51.57899999999999,58.04,52.947,56.735,59.448,60.022,56.007,46.38800000000001,54.11,42.592,45.678,73.952,59.44300000000001,48.303,54.467,64.164,72.801,71.164,42.082,52.90600000000001,56.867,46.859,76.442,46.242,65.528,63.062,42.56800000000001,48.159,49.339,58.556,39.613,52.517,58.42,73.923,51.542,42.38399999999999,43.487],"yaxis":"y","type":"scatter"},{"hovertemplate":"<b>%{hovertext}</b><br><br>continent=Americas<br>gdpPercap=%{x}<br>lifeExp=%{y}<br>pop=%{marker.size}<extra></extra>","hovertext":["Argentina","Bolivia","Brazil","Canada","Chile","Colombia","Costa Rica","Cuba","Dominican Republic","Ecuador","El Salvador","Guatemala","Haiti","Honduras","Jamaica","Mexico","Nicaragua","Panama","Paraguay","Peru","Puerto Rico","Trinidad and Tobago","United States","Uruguay","Venezuela"],"legendgroup":"Americas","marker":{"color":"#ab63fa","size":[40301927,9119152,190010647,33390141,16284741,44227550,4133884,11416987,9319622,13755680,6939688,12572928,8502814,7483763,2780132,108700891,5675356,3242173,6667147,28674757,3942491,1056608,301139947,3447496,26084662],"sizemode":"area","sizeref":366300.86,"symbol":"circle"},"mode":"markers","name":"Americas","orientation":"v","showlegend":true,"x":[12779.37964,3822.137084,9065.800825,36319.23501,13171.63885,7006.580419,9645.06142,8948.102923,6025.3747520000015,6873.262326000001,5728.353514,5186.050003,1201.637154,3548.3308460000007,7320.8802620000015,11977.57496,2749.320965,9809.185636,4172.838464,7408.905561,19328.70901,18008.50924,42951.65309,10611.46299,11415.80569],"xaxis":"x","y":[75.32,65.554,72.39,80.653,78.553,72.889,78.782,78.273,72.235,74.994,71.878,70.259,60.916,70.19800000000001,72.567,76.195,72.899,75.53699999999998,71.752,71.421,78.74600000000002,69.819,78.242,76.384,73.747],"yaxis":"y","type":"scatter"},{"hovertemplate":"<b>%{hovertext}</b><br><br>continent=Oceania<br>gdpPercap=%{x}<br>lifeExp=%{y}<br>pop=%{marker.size}<extra></extra>","hovertext":["Australia","New Zealand"],"legendgroup":"Oceania","marker":{"color":"#FFA15A","size":[20434176,4115771],"sizemode":"area","sizeref":366300.86,"symbol":"circle"},"mode":"markers","name":"Oceania","orientation":"v","showlegend":true,"x":[34435.367439999995,25185.00911],"xaxis":"x","y":[81.235,80.204],"yaxis":"y","type":"scatter"}], {"template":{"data":{"histogram2dcontour":[{"type":"histogram2dcontour","colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0.0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1.0,"#f0f921"]]}],"choropleth":[{"type":"choropleth","colorbar":{"outlinewidth":0,"ticks":""}}],"histogram2d":[{"type":"histogram2d","colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0.0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1.0,"#f0f921"]]}],"heatmap":[{"type":"heatmap","colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0.0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1.0,"#f0f921"]]}],"heatmapgl":[{"type":"heatmapgl","colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0.0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1.0,"#f0f921"]]}],"contourcarpet":[{"type":"contourcarpet","colorbar":{"outlinewidth":0,"ticks":""}}],"contour":[{"type":"contour","colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0.0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1.0,"#f0f921"]]}],"surface":[{"type":"surface","colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0.0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1.0,"#f0f921"]]}],"mesh3d":[{"type":"mesh3d","colorbar":{"outlinewidth":0,"ticks":""}}],"scatter":[{"fillpattern":{"fillmode":"overlay","size":10,"solidity":0.2},"type":"scatter"}],"parcoords":[{"type":"parcoords","line":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"scatterpolargl":[{"type":"scatterpolargl","marker":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"bar":[{"error_x":{"color":"#2a3f5f"},"error_y":{"color":"#2a3f5f"},"marker":{"line":{"color":"#E5ECF6","width":0.5},"pattern":{"fillmode":"overlay","size":10,"solidity":0.2}},"type":"bar"}],"scattergeo":[{"type":"scattergeo","marker":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"scatterpolar":[{"type":"scatterpolar","marker":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"histogram":[{"marker":{"pattern":{"fillmode":"overlay","size":10,"solidity":0.2}},"type":"histogram"}],"scattergl":[{"type":"scattergl","marker":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"scatter3d":[{"type":"scatter3d","line":{"colorbar":{"outlinewidth":0,"ticks":""}},"marker":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"scattermapbox":[{"type":"scattermapbox","marker":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"scatterternary":[{"type":"scatterternary","marker":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"scattercarpet":[{"type":"scattercarpet","marker":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"carpet":[{"aaxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"baxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"type":"carpet"}],"table":[{"cells":{"fill":{"color":"#EBF0F8"},"line":{"color":"white"}},"header":{"fill":{"color":"#C8D4E3"},"line":{"color":"white"}},"type":"table"}],"barpolar":[{"marker":{"line":{"color":"#E5ECF6","width":0.5},"pattern":{"fillmode":"overlay","size":10,"solidity":0.2}},"type":"barpolar"}],"pie":[{"automargin":true,"type":"pie"}]},"layout":{"autotypenumbers":"strict","colorway":["#636efa","#EF553B","#00cc96","#ab63fa","#FFA15A","#19d3f3","#FF6692","#B6E880","#FF97FF","#FECB52"],"font":{"color":"#2a3f5f"},"hovermode":"closest","hoverlabel":{"align":"left"},"paper_bgcolor":"white","plot_bgcolor":"#E5ECF6","polar":{"bgcolor":"#E5ECF6","angularaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"radialaxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"ternary":{"bgcolor":"#E5ECF6","aaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"baxis":{"gridcolor":"white","linecolor":"white","ticks":""},"caxis":{"gridcolor":"white","linecolor":"white","ticks":""}},"coloraxis":{"colorbar":{"outlinewidth":0,"ticks":""}},"colorscale":{"sequential":[[0.0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1.0,"#f0f921"]],"sequentialminus":[[0.0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1.0,"#f0f921"]],"diverging":[[0,"#8e0152"],[0.1,"#c51b7d"],[0.2,"#de77ae"],[0.3,"#f1b6da"],[0.4,"#fde0ef"],[0.5,"#f7f7f7"],[0.6,"#e6f5d0"],[0.7,"#b8e186"],[0.8,"#7fbc41"],[0.9,"#4d9221"],[1,"#276419"]]},"xaxis":{"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","automargin":true,"zerolinewidth":2},"yaxis":{"gridcolor":"white","linecolor":"white","ticks":"","title":{"standoff":15},"zerolinecolor":"white","automargin":true,"zerolinewidth":2},"scene":{"xaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white","gridwidth":2},"yaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white","gridwidth":2},"zaxis":{"backgroundcolor":"#E5ECF6","gridcolor":"white","linecolor":"white","showbackground":true,"ticks":"","zerolinecolor":"white","gridwidth":2}},"shapedefaults":{"line":{"color":"#2a3f5f"}},"annotationdefaults":{"arrowcolor":"#2a3f5f","arrowhead":0,"arrowwidth":1},"geo":{"bgcolor":"white","landcolor":"#E5ECF6","subunitcolor":"white","showland":true,"showlakes":true,"lakecolor":"white"},"title":{"x":0.05},"mapbox":{"style":"light"}}},"xaxis":{"anchor":"y","domain":[0.0,1.0],"title":{"text":"gdpPercap"}},"yaxis":{"anchor":"x","domain":[0.0,1.0],"title":{"text":"lifeExp"}},"legend":{"title":{"text":"continent"},"tracegroupgap":0,"itemsizing":"constant"},"margin":{"t":60}}, {"responsive": true} ).then(function(){ 21 | 22 | var gd = document.getElementById('7cac0eab-2184-4bbd-88fe-9e4b92a8b847'); at instantiate (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:653:32) at constructor (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:947:12) at JSXParserMixin.raise (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:3261:19) at Object.unterminated (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:2281:20) at readStringContents (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:1970:14) at JSXParserMixin.readTemplateToken (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:3168:9) at JSXParserMixin.getTokenFromCode (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:2843:14) at JSXParserMixin.getTokenFromCode (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:7031:11) at JSXParserMixin.nextToken (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:2384:10) at JSXParserMixin.next (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:2305:10) at JSXParserMixin.eat (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:2309:12) at JSXParserMixin.expect (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:3633:10) at JSXParserMixin.parseExprList (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:11970:14) at JSXParserMixin.parseArrayLike (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:11879:26) at JSXParserMixin.parseExprAtom (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:11148:23) at JSXParserMixin.parseExprAtom (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:6998:20) at JSXParserMixin.parseExprSubscripts (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:10870:23) at JSXParserMixin.parseUpdate (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:10853:21) at JSXParserMixin.parseMaybeUnary (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:10829:23) at JSXParserMixin.parseMaybeUnaryOrPrivate (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:10667:61) at JSXParserMixin.parseExprOps (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:10672:23) at JSXParserMixin.parseMaybeConditional (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:10649:23) at JSXParserMixin.parseMaybeAssign (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:10610:21) at /Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:10580:39 at JSXParserMixin.allowInAnd (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:12250:16) at JSXParserMixin.parseMaybeAssignAllowIn (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:10580:17) at JSXParserMixin.parseVar (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:13188:91) at JSXParserMixin.parseVarStatement (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:13027:10) at JSXParserMixin.parseStatementContent (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:12624:23) at JSXParserMixin.parseStatementLike (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:12544:17) at JSXParserMixin.parseStatementListItem (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:12524:17) at JSXParserMixin.parseExportDeclaration (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:13767:17) at JSXParserMixin.maybeParseExportDeclaration (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:13722:31) at JSXParserMixin.parseExport (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:13646:29) at JSXParserMixin.parseStatementContent (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:12656:27) at JSXParserMixin.parseStatementLike (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:12544:17) at JSXParserMixin.parseModuleItem (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:12521:17) at JSXParserMixin.parseBlockOrModuleBlockBody (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:13116:36) at JSXParserMixin.parseBlockBody (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:13109:10) at JSXParserMixin.parseProgram (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:12435:10) at JSXParserMixin.parseTopLevel (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:12425:25) at JSXParserMixin.parse (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:14245:10) at parse (/Users/scott/Projects/docusaurus/node_modules/@babel/parser/lib/index.js:14286:38) at parser (/Users/scott/Projects/docusaurus/node_modules/remark-mdx/node_modules/@babel/core/lib/parser/index.js:54:34) at parser.next (<anonymous>) at normalizeFile (/Users/scott/Projects/docusaurus/node_modules/remark-mdx/node_modules/@babel/core/lib/transformation/normalize-file.js:99:38) at normalizeFile.next (<anonymous>) at run (/Users/scott/Projects/docusaurus/node_modules/remark-mdx/node_modules/@babel/core/lib/transformation/index.js:31:50) at run.next (<anonymous>) at transform (/Users/scott/Projects/docusaurus/node_modules/remark-mdx/node_modules/@babel/core/lib/transform.js:27:41) ``` Specifically, I ran `quarto preview` from the root of my Docusaurus project. I also tried with the Quarto 1.3.290 release candidate and there's no error but the code cell instead just prints out: ```Unable to display output for mime type(s): text/html``` However, this RC build has other major issues with Docuaurus-compatible output. For example, `panel-tabset` and `callout-note` elements do not render into the Docusaurus-compatible markup at all. More version info: ``` $ quarto check [✓] Checking Quarto installation......OK Version: 1.2.475 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /usr/local/opt/[email protected]/bin/python3.9 Jupyter: 5.2.0 Kernels: mu_venv-38-20210430-234249, python3 [✓] 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. - [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.

Error: - The error appears to be caused by placing attributed code inside a callout - Issue could be that we're incorrectly turning this into a code listing - Issue could be that we don't properly support code listings in callouts ``` LaTeX Error: Not in outer par mode. See the LaTeX manual or LaTeX Companion for explanation. Type H <return> for immediate help. ... l.221 ``` repro: ````markdown --- title: Hello format: pdf keep-tex: true --- ::: {.callout-note} If the `www-frame-origin` option is set to `same` or `any` instead of a URI, you must add the following setting with the actual URI: ```{.ini filename="/etc/rstudio/rsession.conf"} tutorial-api-client-origin=http://localhost:8080 ``` ::: ```` relevant tex diff: **Good** ```latex \begin{tcolorbox}[enhanced jigsaw, left=2mm, rightrule=.15mm, arc=.35mm, toprule=.15mm, coltitle=black, bottomtitle=1mm, titlerule=0mm, opacityback=0, breakable, opacitybacktitle=0.6, toptitle=1mm, colbacktitle=quarto-callout-note-color!10!white, colback=white, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Note}, bottomrule=.15mm, leftrule=.75mm] If the \texttt{www-frame-origin} option is set to \texttt{same} or \texttt{any} instead of a URI, you must add the following setting with the actual URI: \textbf{/etc/rstudio/rsession.conf} \begin{Shaded} \begin{Highlighting}[] \DataTypeTok{tutorial{-}api{-}client{-}origin}\OtherTok{=}\StringTok{http://localhost:8080} \end{Highlighting} \end{Shaded} \end{tcolorbox} ``` **Bad** ```latex \begin{tcolorbox}[enhanced jigsaw, leftrule=.75mm, arc=.35mm, toptitle=1mm, left=2mm, colback=white, breakable, colbacktitle=quarto-callout-note-color!10!white, bottomtitle=1mm, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Note}, bottomrule=.15mm, titlerule=0mm, opacityback=0, colframe=quarto-callout-note-color-frame, toprule=.15mm, rightrule=.15mm, opacitybacktitle=0.6, coltitle=black] If the \texttt{www-frame-origin} option is set to \texttt{same} or \texttt{any} instead of a URI, you must add the following setting with the actual URI: \begin{codelisting} \caption{\texttt{/etc/rstudio/rsession.conf}} \begin{Shaded} \begin{Highlighting}[] \DataTypeTok{tutorial{-}api{-}client{-}origin}\OtherTok{=}\StringTok{http://localhost:8080} \end{Highlighting} \end{Shaded} \end{codelisting} \end{tcolorbox} ```

### Bug description ```yaml --- format: html --- I am `r 5+25` years old. ``` output is  ```sh quarto check knitr (/) Checking R installation...........loading Sprague .Rprofile [✓] Checking R installation...........OK Version: 4.2.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library knitr: 1.41 rmarkdown: 2.19 [✓] Checking Knitr engine render......OK ``` quarto version 1.3.294 I'm on Mac OSX 13.2.1 ### 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 Note the weird non-standard URL below (contains commas and other punctuation) ``` --- title: Clabbered milk date: '2017-02-02' categories: - food --- Here is a blog post, blah blah. Note how the following images both display just fine from within this post.   But inside the grid view, the image preview is broken. ``` Find a working full example at this repo: [richardsprague/quartosample: extrapage](https://github.com/richardsprague/quartosample/tree/extrapage) Using 1.3.294 on a Mac OS 13.2 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

`src/project/project-index.ts` has a O(n^2) performance bug, and that makes large projects impossibly slow to render.

### Bug description Greetings, I just tried updating from 1.2475 to RC 1.3.290 and this RC breaks code that previously ran. I am running RStudio Version 2023.03.0+386 (2023.03.0+386) on macOS, R version 4.2.3 (2023-03-15) Here is a minimal case... the warning message is WARNING: Unable to resolve crossref @tbl-a WARNING: Unable to resolve crossref @tbl-b But this runs fine reinstalling the previous stable release (1.2.475) Thanks for your incredible efforts and contributions to the community. I scanned and didn't see this reported, if it has kindly accept my apologies. Jeff --- title: "Untitled" format: revealjs --- ## Issue ::: {.panel-tabset} ## A @tbl-a ```{r} #| label: tbl-a #| tbl-cap: a knitr::kable(table(rbinom(100,2,.5))) ``` ## B @tbl-b ```{r} #| label: tbl-b #| tbl-cap: b knitr::kable(table(rbinom(100,2,.5))) ``` ::: ## Not Issue - Below continues to work fine ### C @tbl-c ```{r} #| label: tbl-c #| tbl-cap: c knitr::kable(table(rbinom(100,2,.5))) ``` [issue.pdf](https://github.com/quarto-dev/quarto-cli/files/11094065/issue.pdf) 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: 1.3.290 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.2 Path: /Applications/Xcode.app/Contents/Developer/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: 4.2.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description My listing grid lays each item correctly for the following directory, but the preview image doesn't display. As expected (and consistent with the behavior in 1.2) a directory like this one generates a website that shows each of the rendered .md and .qmd files contained within `/grid`. The preview images also display, except for the one associated with the .md file contained in a subdirectory (`/grid/diet/`). ```sh grid ├── diet │   ├── 2017-02-02-clabbered-milk.md │   └── diet-assets │   └── clabberedMilk.jpg ├── famous_deaths.qmd ├── gridpost.qmd ├── microbiome-assets │   └── coverPersonalScience-quarto.jpg └── psm.qmd ``` Output:  I expected to see the preview image contained in the 'clabbered milk' file. Reproducible example in this repo [richardsprague/quartosample: extrapage](https://github.com/richardsprague/quartosample/tree/extrapage) (Maybe related to [#4998: Preview images are distorted](https://github.com/quarto-dev/quarto-cli/issues/4998)) Using 1.3.290 on OSX 13.2.1 ### 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. - [ ] 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 a nice listing grid that renders correctly, but the preview images are distorted. Apparently, `preview-image` is trying to make the entire image fit within the confines of `class="thumbnail-image card-img"`. On 1.2, it crops the image rather than distort it. Here's the html:  Reproducible example in this repo [richardsprague/quartosample: extrapage](https://github.com/richardsprague/quartosample/tree/extrapage) Using 1.3.290 on OSX 13.2.1 ### 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. - [ ] 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 would like to use Mermaid diagrams in Quarto file and render it to PowerPoint slides, here is a minimal example: ````markdown --- title: "Untitled" format: pptx --- ## slides 1 ```{mermaid} graph TD A1--> B1 A2 --> B1 A3 --> B1 A4--> B1 A5 --> B1 ``` ## slides 2 test ```` Then I got the error below: ``` Error: Failed to get chrome version at criClient (file:///D:/App/Quarto/bin/quarto.js:57271:15) at async file:///D:/App/Quarto/bin/quarto.js:57239:22 at async Semaphore.runExclusive (file:///D:/App/Quarto/bin/quarto.js:56923:29) at async Object.createPngsFromHtml (file:///D:/App/Quarto/bin/quarto.js:57447:44) at async makePng (file:///D:/App/Quarto/bin/quarto.js:83960:72) at async makeDefault (file:///D:/App/Quarto/bin/quarto.js:84018:24) at async Object.cell (file:///D:/App/Quarto/bin/quarto.js:84041:20) at async Promise.all (index 0) at async Object.document (file:///D:/App/Quarto/bin/quarto.js:57677:25) at async handleLanguageCells (file:///D:/App/Quarto/bin/quarto.js:57648:42) ``` I have already tried to update chrome and quarto to the latest version and tried the command "quarto install tools chromium", but still got the error. If I render the file to html, it works. And here is 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: 1.3.290 Path: D:\App\Quarto\bin CodePage: 936 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.15 (Conda) Path: D:/App/Anaconda3/python.EXE Jupyter: 5.1.1 Kernels: python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.2.2 Path: D:/App/R-4.2.2 LibPaths: - D:/App/R-4.2.2/library knitr: 1.42 rmarkdown: 2.20 [>] Checking Knitr engine render......OK Quarto version: 1.3.290 Chrome version: Version 111.0.5563.147 (Official Build) (64-bit) operating system: Win 10 ``` ### 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.

Support an option to 'dim` the un-annotated code by default (to draw attention to the annotated code). If the reader mouse's over the code block, activate all the code. For example, default mode: <img width="1224" alt="Screenshot 2023-03-27 at 7 27 05 PM" src="https://user-images.githubusercontent.com/261654/228089396-adaf1faf-407b-4e2c-8a10-369743a8995c.png">

### Bug description Code line numbers in revealjs presentations contain links which take you to the first slide when clicked. ````md --- title: "Untitled" format: revealjs --- ```{r} #| echo: true 1 + 1 ``` ```` <img width="393" alt="image" src="https://user-images.githubusercontent.com/99931354/228086119-687e8109-d36c-4420-8a1b-817ab4d55234.png"> Info: * IDE: Rstudio 2023.3.0.386 * Quarto version: 1.3.290 * OS: Windows 11 (22000.1696) ``` [>] 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: 1.3.290 Path: C:\Users\XXX\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....(None) Unable to locate an installed version of Python 3. Install Python 3 from https://www.python.org/downloads/ [>] Checking R installation...........OK Version: 4.2.3 Path: C:/PROGRA~1/R/R-42~1.3 LibPaths: - C:/Users/XXXAppData/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 ## Description If I perform an action in the speaker view, it doesn't happen in the normal presentation. For example I might click on a tabset's tab in the speaker view, but nothing happens in the presentation shown to the audience. It changes only in the speaker view. ## Example ```md --- title: Revealjs presentation format: revealjs --- ::: {.panel-tabset} ### First First. ### Second Second. ::: ``` I click on tab Second in the speaker view and nothing happens in the presentation. The active tab changes only in the speaker view. ## 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: 1.3.287 Path: C:\Users\username\AppData\Local\Programs\Quarto\bin CodePage: 1250 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.6 Path: C:/Users/username/AppData/Local/Programs/Python/Python310/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/ ``` ## System Windows 10 ### 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.