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## Description: Debugging console log in `Tippy.hover` https://github.com/quarto-dev/quarto-cli/blob/5df9451723c7fe81462700c19709c0b06846de95/src/resources/formats/html/templates/quarto-html.ejs#L443 ## Steps to Reproduce: - Render a Quarto Doc to HTML - Open HTML file and search for `console.log` - Preview HTML document in browser and look at Debugging console ### Expected Result: - No developer `console.log`s ### Actual Result: - `console.log(htmlDoc.body.innerHTML);` log noise

## Description: Unable to include a reference to a video ## Steps to Reproduce: ### Expected Result: ### Actual Result: ----- ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5846 <div type='discussions-op-text'> ^{Originally posted by **johnmuchow** June 7, 2023} ### Description I am using the format {{< video local-video.mp4 >}} to include a video that is in the same folder as the .qmd file. I get the error message "The media could not be loaded, either because the server or network failed or because the format is not supported." The file is an mp4. Is there any additional debug information available to help narrow down the issue? </div>

### Bug description For quartopub, using the Safari browser, account creation and login using Google authentification isn't working. You click create an account or login, and it goes through the Google authentification, but brings you back to the login windown, and never gets you logged in to quartpub. ### Steps to reproduce Here's what happens when trying to log in using the Safari browser https://github.com/quarto-dev/quarto-cli/assets/889238/36a24818-1f6d-4786-b59a-bc38918b4e89 ### Expected behavior Login should work as it does in other browsers ### Actual behavior Unable to login, keeps bringing you back to the login window. ### Your environment Safari Version 16.2 (18614.3.7.1.5) ### Quarto check output _No response_

I get a `Permission denied` error on my Linux machine when I work on one of my network shares. I believe that Quarto tries to access `_quarto.yml` outside of my share (actually, two folders up), which I don't have permission to read and/or write. Specifically, my project is located in `/run/user/1000/gvfs/smb-share:server=pers.ad.uni-graz.at,share=fs/home/home_b/brunnerc/quarto-issue`. The Quarto source is in another subfolder, i.e. `test/test.qmd` (but that doesn't seem relevant). From the folder I mentioned, I run ``` quarto preview test/test.qmd ``` This results in the following error: ``` ERROR: PermissionDenied: Permission denied (os error 13), stat '/run/user/1000/gvfs/smb-share:server=pers.ad.uni-graz.at,share=fs/home/home_b/_quarto.yml' PermissionDenied: Permission denied (os error 13), stat '/run/user/1000/gvfs/smb-share:server=pers.ad.uni-graz.at,share=fs/home/home_b/_quarto.yml' at Object.lstatSync (deno:runtime/js/30_fs.js:305:9) at existsSync (file:///opt/quarto/bin/quarto.js:492:14) at Array.find (<anonymous>) at projectConfigFile (file:///opt/quarto/bin/quarto.js:58280:37) at file:///opt/quarto/bin/quarto.js:82866:28 at projectContext (file:///opt/quarto/bin/quarto.js:82724:32) at async Command.fn (file:///opt/quarto/bin/quarto.js:103696:25) at async Command.execute (file:///opt/quarto/bin/quarto.js:8437:13) at async quarto (file:///opt/quarto/bin/quarto.js:127540:5) at async file:///opt/quarto/bin/quarto.js:127558:9 ``` The contents of `test.qmd` does not seem to matter, since the error occurs before even reading it. This is on Arch Linux. _Originally posted by @cbrnr in https://github.com/quarto-dev/quarto-cli/issues/4594#issuecomment-1580591702_

### Bug description When I execute `r wday(Sys.Date())`, I get the expected response. However, when I try to include the character label, using `r wday(Sys.Date(), label=T)`, I get an error: > Error in wday(Sys.Date(), label = T) : unused argument (label = T) Calls: .main ... inline_exec -> hook_eval -> withVisible -> eval -> eval Execution halted I also get a pop-up with the following error:  ### Steps to reproduce ````qmd --- title: "Reproducible Error" format: html editor: visual execute: echo: false warning: false --- ## Reproducible code ````{r} library(lubrdiate) ```` Some text... `r wday(Sys.Date(), label=T)`, some more text ### Expected behavior I should see today's date in English. For example, since today is Tuesday, I should see: Some text... Tuesday, some more text ### Actual behavior Instead, I get an error and the code crashes ### Your environment IDE - 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 - Windows 10 R version 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" ### Quarto check output [>] Checking Quarto installation......OK Version: 1.2.335 Path: C:\Program Files\RStudio\resources\app\bin\quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.4 Path: C:/Users/225022/AppData/Local/Programs/Python/Python310/python.exe Jupyter: 4.10.0 Kernels: python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.2.0 Path: C:/PROGRA~1/R/R-42~1.0 LibPaths: - C:/Users/xxxx/Documents/R/win-library/4.2 - C:/Program Files/R/R-4.2.0/library rmarkdown: 2.21 [>] Checking Knitr engine render......OK

### Bug description I don't seem to be able to capture `on_selection()` or `on_click()` events for interactive plots with plotly. I've tried both native `.qmd` files and Quarto snippets inside jupyter notebooks in VSCode, by trying to display outputs with `fig.show()`. However, the events do get captured correctly inside the notebook cell output when the output is displayed with just `fig` (as the last line of the cell). But, HTML render still fails to capture the events, even in this case. ### Steps to reproduce ````qmd --- title: Quarto Unable to Capture Click Events jupyter: python3 --- ## Combining Parcats with Scatter Check out [Parallel Categories Linked Brushing section for source](https://plotly.com/python/parallel-categories-diagram/) ```{python} import plotly.graph_objects as go from ipywidgets import widgets import pandas as pd import numpy as np cars_df = pd.read_csv( "https://raw.githubusercontent.com/plotly/datasets/master/imports-85.csv" ) # Build parcats dimensions categorical_dimensions = ["body-style", "drive-wheels", "fuel-type"] dimensions = [ dict(values=cars_df[label], label=label) for label in categorical_dimensions ] # Build colorscale color = np.zeros(len(cars_df), dtype="uint8") colorscale = [[0, "gray"], [1, "firebrick"]] # Build figure as FigureWidget fig = go.FigureWidget( data=[ go.Scatter( x=cars_df.horsepower, y=cars_df["highway-mpg"], marker={"color": "gray"}, mode="markers", selected={"marker": {"color": "firebrick"}}, unselected={"marker": {"opacity": 0.3}}, ), go.Parcats( domain={"y": [0, 0.4]}, dimensions=dimensions, line={ "colorscale": colorscale, "cmin": 0, "cmax": 1, "color": color, "shape": "hspline", }, ), ] ) fig.update_layout( height=800, xaxis={"title": "Horsepower"}, yaxis={"title": "MPG", "domain": [0.6, 1]}, dragmode="lasso", hovermode="closest", ) # Update color callback def update_color(trace, points, state): # Update scatter selection fig.data[0].selectedpoints = points.point_inds # Update parcats colors new_color = np.zeros(len(cars_df), dtype="uint8") new_color[points.point_inds] = 1 fig.data[1].line.color = new_color # Register callback on scatter selection... fig.data[0].on_selection(update_color) # and parcats click fig.data[1].on_click(update_color) # Doesn't capture click events in VSCode Jupyter Notebook # fig.show(renderer="plotly_mimetype+notebook_connected") # Doesn't capture click events in .qmd fig.show() ``` ```` ### Expected behavior When you select points in the scatter plot, the corresponding rows should be highlighted in the parcats plot and when you click on the parcats plot, the corresponding points should be highlighted in the scatter plot  ### Actual behavior While you can select points in the scatter plot, the corresponding data points do not get highlighted in the parcats plot <img width="767" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/16181437/50eecce9-d2ef-4fe7-a16f-5b11d1dbdd88"> ### Your environment - IDE: VSCode - Quarto: 1.3.361 - Python: 3.9.16 - OS: Linux 8bed2c0d09ad 5.19.0-40-generic # 41~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Mar 31 16:00:14 UTC 2 x86_64 x86_64 x86_64 GNU/Linux - plotly: 5.14.1 ### Quarto check output ```bash 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: 1.3.361 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.16 Path: /home/user/venv/bin/python Jupyter: 5.3.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ```

 This is because of the `.smaller` effect on the slide applying to the callout titles. There is probably a css rule to tweak to avoid this

### Bug description `quarto render index.qmd --to md` and `quarto render index.qmd --to markdown` produce different output. ### Steps to reproduce Consider the minimal working example where `index.qmd` is ``` --- title: MWE --- ## Section This is a simple placeholder for the manuscript's main document. ``` Run `quarto render index.qmd --to md --output md_output` and `quarto render index.qmd --to markdown --output markdown_output`. Run `diff markdown_output md_output`. ### Expected behavior `markdown_output` and `md_output` will be the same. ### Actual behavior ``` 1,4c1 < --- < title: MWE < toc-title: Table of contents < --- --- > # MWE 8c5 < This is a simple placeholder for the manuscript's main document. --- > This is a simple placeholder for the manuscript’s main document. ``` ### Your environment - Ubuntu ### Quarto check output ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.126 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK ERROR: YAMLError: unexpected end of the stream within a double quoted scalar at line 3, column 1: ^ Stack trace: ^ at generateError (file:///opt/quarto/bin/quarto.js:10487:12) at throwError (file:///opt/quarto/bin/quarto.js:10490:11) at readDoubleQuotedScalar (file:///opt/quarto/bin/quarto.js:10836:12) at composeNode (file:///opt/quarto/bin/quarto.js:11309:125) at readBlockMapping (file:///opt/quarto/bin/quarto.js:11124:17) at composeNode (file:///opt/quarto/bin/quarto.js:11306:84) at readDocument (file:///opt/quarto/bin/quarto.js:11420:5) at loadDocuments (file:///opt/quarto/bin/quarto.js:11455:9) at load (file:///opt/quarto/bin/quarto.js:11460:23) at parse3 (file:///opt/quarto/bin/quarto.js:11470:12) ```

### Bug description I am having troubles by adding extensions from a GitLab repo, which I am developing. The extension seems to be downloaded but it fails when unzipping the zip-file. ### Steps to reproduce ```bash quarto add https://gitlab.cc-asp.fraunhofer.de/quarto-extensions/mdz/-/archive/main/shorty-main.zip ``` ### Expected behavior The installed extension. ### Actual behavior An error message is retrieved: ``` Quarto extensions may execute code when documents are rendered. If you do not trust the authors of the extension, we recommend that you do not install or use the extension. ? Do you trust the authors of this extension (Y/n) › Yes [✓] Downloading (|) Unzipping gzip: stdin: not in gzip format tar: Child returned status 1 tar: Error is not recoverable: exiting now [✓] Unzipping ERROR: Failed to unzip extension. gzip: stdin: not in gzip format tar: Child returned status 1 tar: Error is not recoverable: exiting now ``` ### Your environment - IDE: VScode - OS: Ubuntu ### Quarto check output ``` [✓] Checking Quarto installation......OK Version: 1.2.335 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /usr/bin/python3 Jupyter: 5.1.5 Kernels: ir, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.1.2 Path: /usr/lib/R LibPaths: - /home/miguel/R/x86_64-pc-linux-gnu-library/4.1 - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/lib/R/library rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ```

## Description: Confluence: HTML (not markdown) Anchor links not supported ## Steps to Reproduce: Create a Quarto Document with an HTML anchor link ``` --- title: "5826-confluence-html-anchor-links-images-not-supported-only-markdown" --- <img src="elephant.png"/> <a href="elephant.png">elephant-image-link</a> ``` ### Expected Result: - As with Markdown, when publishing, assets are uploaded as attachments - As with Markdown, when publishing, links are correctly replaced and supported - As with Markdown, when publishing, images are correctly replaced and supported ### Actual Result: - Assets are not uploaded as attachments - Links are not correctly replaced and supported - Images are not correctly replaced and supported #### Workaround - Use markdown links & images

### Bug description When using tinytex to create the PDF, hyphenation is not applied. When I create the PDF with the tex distrubution from Debian, the hyphenation is correct. ### Steps to reproduce Here is my test Markdown file: ```Markdown --- lang: de-DE format: pdf: latex-tinytex: false keep-tex: true --- # TEST Lange zusammengesetzte Wörter sind ein faszinierendes Phänomen der deutschen Sprache. In kaum einer anderen Sprache gibt es so viele lange und komplizierte Wörter wie im Deutschen. Diese langen Wörter können für Kinder und Grundschüler eine echte Herausforderung darstellen, aber auch Erwachsene haben oft Schwierigkeiten damit. Das liegt vor allem daran, dass die deutsche Sprache eine Reihe von Regeln hat, die es erlauben, Wörter miteinander zu verbinden. So können zum Beispiel Substantive (Nomen) mit anderen Substantiven oder Adjektiven (Eigenschaftswörtern) zu einem langen Wort verbunden werden. Das Resultat sind oft lange und komplizierte Wörter, die manchmal schwer auszusprechen sind und auch für Muttersprachler eine Herausforderung darstellen können. Einige Beispiele für lange zusammengesetzte Wörter: - Donaudampfschifffahrtselektrizitätenhauptbetriebswerkbauunterbeamtengesellschaft - Rindfleischetikettierungsüberwachungsaufgabenübertragungsgesetz - Bundesausbildungsförderungsgesetz Diese Beispiele zeigen deutlich, wie kompliziert und lang manche deutsche Wörter sein können. Dabei gibt es aber auch zahlreiche lustige lange Wörter, die jedermann zum Lachen bringen können. Wer kennt zum Beispiel nicht das berühmte Wort "Donaudampfschifffahrtskapitänsmütze"? Oder das etwas schwerer auszusprechende "Zuckerhutbefestigungsanlage"? Doch nicht alle lange zusammengesetzten Wörter sind lustig oder einfach zu merken. Es gibt auch zahlreiche komplizierte lange deutsche Wörter, die für Fremdsprachige und selbst Muttersprachler eine echte Herausforderung darstellen können. Hier sind ein paar Beispiele: - Antihumanimmundefizienzvirusserotherapie - Grundstücksverkehrsgenehmigungszuständigkeitsübertragungsverordnung - Röntgenstrahlenphotometrie Diese Wörter zeigen deutlich, dass die deutsche Sprache mitunter extrem kompliziert sein kann. Insbesondere für Ausländer, die Deutsch lernen, können diese langen und schweren Wörter eine echte Hürde darstellen. Aber auch im Schulunterricht können lange zusammengesetzte Nomen (Substantive) zur Herausforderung werden. Manchmal müssen Schülerinnen und Schüler beispielsweise in der Grundschule lange Zusammensetzungen von Nomen bilden oder schwierige Wortgebilde entziffern. Doch keine Angst: Auch wenn die deutsche Sprache manchmal etwas kompliziert erscheint, gibt es zahlreiche Tricks und Tipps, um lange Wortgebilde zu verstehen und auszusprechen. Wer zum Beispiel Schwierigkeiten damit hat, sich lange Zusammensetzungen zu merken, kann versuchen, sie in einzelne Bestandteile aufzuteilen und diese nacheinander zu lernen. Oft helfen auch Eselsbrücken oder kleine Geschichten dabei, sich schwierige Begriffe besser einzuprägen. Für Kinder und Grundschüler sind vor allem kurze und prägnante Wörter einfacher zu verstehen. Lange Wörter können dagegen schnell abschreckend wirken. Doch auch für Erwachsene kann es hilfreich sein, sich mit langen deutschen Wörtern auseinanderzusetzen. Insbesondere im Berufsleben oder im Studium können lange und komplizierte Begriffe wichtig sein. Wer sich also schon immer gefragt hat, was es mit der "Donaudampfschifffahrtselektrizitätenhauptbetriebswerkbauunterbeamtengesellschaft" auf sich hat, sollte sich die Zeit nehmen, diese faszinierende Sprache genauer zu erforschen. Fazit: Lange zusammengesetzte Wörter sind ein faszinierendes Phänomen der deutschen Sprache. Ob lustig oder kompliziert – sie bieten immer wieder neue Herausforderungen und sorgen für Verwunderung und Lachen. Und wer weiß: Vielleicht schafft es ja auch das eine oder andere lange Wort in den nächsten Duden? ``` If the option latex-tinytex is true, comes the following PDF, with the command quarto render Test.md:  The command ouput is: ```Shell ➤ quarto render Test.md pandoc to: latex output-file: Test.tex standalone: true pdf-engine: xelatex variables: graphics: true tables: true default-image-extension: pdf metadata documentclass: scrartcl classoption: - DIV=11 - numbers=noendperiod papersize: letter header-includes: - '\KOMAoption{captions}{tableheading}' block-headings: true lang: de-DE running xelatex - 1 This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode running xelatex - 2 This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode Output created: Test.pdf ``` If the option latex-tinytex is false, comes the following PDF, with the command quarto render Test.md:  It use the tex distrubution of debian The command ouput is: ```Shell ➤ quarto render Test.md pandoc to: latex output-file: Test.tex standalone: true pdf-engine: xelatex variables: graphics: true tables: true default-image-extension: pdf metadata documentclass: scrartcl classoption: - DIV=11 - numbers=noendperiod papersize: letter header-includes: - '\KOMAoption{captions}{tableheading}' block-headings: true lang: de-DE running xelatex - 1 This is XeTeX, Version 3.14159265-2.6-0.999992 (TeX Live 2020/Debian) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode running xelatex - 2 This is XeTeX, Version 3.14159265-2.6-0.999992 (TeX Live 2020/Debian) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode Output created: Test.pdf ``` I also did compare the two tex file that was produced and there where no great differrence: ```Shell ➤ diff *.tex 163c163 < \ifdefined\Shaded\renewenvironment{Shaded}{\begin{tcolorbox}[enhanced, interior hidden, borderline west={3pt}{0pt}{shadecolor}, frame hidden, boxrule=0pt, sharp corners, breakable]}{\end{tcolorbox}}\fi --- > \ifdefined\Shaded\renewenvironment{Shaded}{\begin{tcolorbox}[breakable, frame hidden, boxrule=0pt, enhanced, borderline west={3pt}{0pt}{shadecolor}, sharp corners, interior hidden]}{\end{tcolorbox}}\fi ``` ### Expected behavior I expect tinytex to do hyphenation normally as well. ### Actual behavior Currently there is no hyphenation with tinytex, so I use at the moment the debian tex. ### Your environment MX Linux (Debian 11) with Quarto installed with the deb package and tinytex installed with quarto. The debian tex was installed with the system package manager. ### Quarto check output ```bash ➤ 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: 1.3.361 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/ ```

### Bug description In a book project with repo actions defined, if a chapter has a TOC, the repo action icon will not appear in the footer if the page is displayed in mobile view. Chapters without a TOC will display the icon as expected. ### Steps to reproduce Create a book project: ``` $ quarto create-project mybook --type book $ quarto preview mybook ``` Edit _quarto.yml so it appears as follows: ``` project: type: book book: title: "mybook" author: "Norah Jones" date: "6/5/2023" repo-url: "https://github.com/quarto-dev/quarto-web/" repo-actions: [source] chapters: - index.qmd - intro.qmd - summary.qmd - references.qmd bibliography: references.bib format: html: theme: cosmo pdf: documentclass: scrreprt ``` When the project re-renders and I navigate the the Preface page, the github "View Source" icon is visible in the TOC. Switch to mobile view in the newly rendered project (ctrl-shift-m for Firefox) ### Expected behavior On the Preface page, I expect to see the github icon with "View Source" label in the footer when in mobile view. ### Actual behavior The github icon on the Preface page is missing. It appears in the footer on all the other chapter pages in mobile view, because they don't have a TOC. ### Your environment - Quarto version 1.4.122 - OS: Kubuntu 20.04 ### Quarto check output ```` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.122 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.10 Path: /usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter There is an unactivated Python environment in systemd-private-90e163f7653b4f69ae913301b284ec8a-systemd-resolved.service-YMBMlh. Did you forget to activate it? [✓] Checking R installation...........OK Version: 4.2.1 Path: /usr/lib/R LibPaths: - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/lib/R/library knitr: 1.37 rmarkdown: 2.11 [✓] Checking Knitr engine render......OK ````

### Bug description Links to file attachments not supported ### Steps to reproduce - Create a simple quarto document that creates a link to a file ``` --- title: "5815-confluence-links-to-file-attachments-not-supported" --- [quarto-hex-png](quarto-hex.png) [quarto-hex-svg](quarto-hex.svg) ``` ### Expected behavior The image is uploaded as an attachment to the document and linked. The link works and opens the attached file. Different file types are supported. ### Actual behavior No attachment is uploaded. It renders just text instead of a link. #### Workaround ``` {=confluence} <ac:link><ri:attachment ri:filename="elephant.png"/><ac:plain-text-link-body>elephant.png</ac:plain-text-link-body></ac:link> ``` ### Your environment Mac ### Quarto check output ```bash [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 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-1.7, 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 ```

## Description: Confluence: Figure Sizing is ignored ## Steps to Reproduce: - Create a simple document with an image that has its width sized ``` --- title: "Bug: Figure Sizing is ignored" --- {width=120} ``` ### Expected Result: The figure's width is 120. Note: This can be set in the CSF as so ``` ... ac:width="120" ``` ### Actual Result: The figure is of the original size.

Consider the following `quarto` document: ``` --- title: "Untitled" format: pdf --- \[x^2\] ``` Could you please make `quarto` to understand that `\[x^2\]` is equivalent to `$$x^2$$`.

## Description: TBD Problems publishing a table of Images and Links ``` <table border=0 cellpadding=20> <tr> <td> {width=120 height=139} <br /><a href="images/quarto-hex.png">quarto-hex.png</a><br /><a href="images/quarto-hex.svg">quarto-hex.svg</a> </td> <td> <img alt="Icon for quarto" src="images/quarto-icon.png" height="139"><br /><a href="images/quarto-logo.png">quarto-icon.png</a><br /><a href="images/quarto-logo.svg">quarto-icon.svg</a> </td> </tr> <tr> <td colspan=2><img alt="Logo for quarto" src="images/quarto-logo-trademark.png" height="139"><br /><a href="images/quarto-logo-trademark.png">quarto-logo-trademark.png</a><br /><a href="images/quarto-logo-trademark.svg">quarto-logo-trademark.svg</a> </tr> </table> ``` ## Steps to Reproduce: ### Expected Result: ### Actual Result:

### Bug description I have a css file which I want to incorporate into every book project of mine to establish baseline styles. I created a main copy of the file and created a symbolic link to the main copy in a project directory. But when compiling, instead of copying the link target file into the _book directory, a copy of the symbolic link file is made instead. Having a symbolic link file in the rendered static site directory is of no value. When I use e.g. `cp` to copy a symbolic link file from the command line, a new copy of the link target file is created instead of a copy of the symbolic link file. I expected the same behavior when rendering my project. I don't know if this should be considered a bug report or an enhancement request. ### Steps to reproduce _No response_ ### Expected behavior _No response_ ### Actual behavior _No response_ ### Your environment _No response_ ### Quarto check output _No response_

### Bug description The table view shows _undefined_ when a listing item does not contain date information. <img width="845" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/13888691-d84e-4f54-8ad4-bda0052bcdd4"> ### Steps to reproduce The `_quarto.yml`: ```yaml project: type: website format: html: toc: true theme: cosmos ``` The `index.qmd`: ```markdown --- title: the things listing: contents: posts type: table fields: [date, title] sort-ui: false filter-ui: false --- ``` The `posts/1.qmd` ```markdown --- title: one thing --- this is one thing ``` The `posts/2.qmd` ```markdown --- title: two thing date: Jun 3, 2023 --- this is one thing ``` ### Expected behavior A blank value should be shown when date is missing, not _undefined_. The "default" listing view is OK. <img width="797" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/6db74098-945a-48be-b52d-7e633f0d0d18"> The "grid" view is also OK. <img width="585" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/54596ba6-965e-4b6c-83aa-5ea27c976e4f"> Only the "table" view has this problem. ### Actual behavior An _undefined_ value is presented. ### Your environment _No response_ ### Quarto check output ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.353 Path: /Applications/RStudio.app/Contents/Resources/app/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ```

### Bug description The color of headings for the cerulean theme work properly in 1.3.361 but not 1.4.119. ### Steps to reproduce To reproduce render this `.qmd` document: ``` r --- title: "Untitled" format: html: theme: cerulean --- ## Quarto Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>. ## Running Code When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this: ```{r} 1 + 1 ``` You can add options to executable code like this ```{r} #| echo: false 2 * 2 ``` The `echo: false` option disables the printing of code (only output is displayed). ``` ### Expected behavior Expected behavior is what 1.3.361 produces: <img width="697" alt="quarto_1 3 361" src="https://github.com/quarto-dev/quarto-cli/assets/14161912/38e4fa00-66c2-48f2-a7ae-4212eaaaf087"> ### Actual behavior Actual behavior (1.4.119) <img width="733" alt="quarto_1 4 119" src="https://github.com/quarto-dev/quarto-cli/assets/14161912/47eb32dc-0e3d-4f59-ae08-ea397c54c508"> ### Your environment -IDE RStudio Version 2023.03.1+446 (2023.03.1+446) -OS macOS Ventura 13.3.1 (a) ### Quarto check output ``` bash joycerobbins@MacBook-Pro ~ % quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.119 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: 4.3.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ```

### Bug description Callouts, such as this note, are given a different amount of leading and trailing whitespace. <img width="808" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/21d829ff-0ef7-434b-9d5b-f50c46d4be90"> This is super nit-picky, so feel free to close as a non-issue. We noticed this because the spacing of callouts is different than what we were used to with the admonitions from mkdocs-material: https://squidfunk.github.io/mkdocs-material/reference/admonitions/#usage <img width="665" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/be71541b-ea97-438d-80d1-3dada2fc95ed"> ### Steps to reproduce The `_quarto.yml`: ```yaml project: type: website format: html: toc: true theme: cosmos ``` The `index.qmd`: ````markdown --- title: callouts --- This is text before the callout. ::: {.callout-note} We have one line. ::: This is text after the callout. ```` ### Expected behavior The leading and trailing whitespace should be consistent, which let a single-line or single-paragraph be vertically centered within the callout. ### Actual behavior _No response_ ### Your environment _No response_ ### Quarto check output ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.353 Path: /Applications/RStudio.app/Contents/Resources/app/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ```

### Bug description I followed the example at https://quarto.org/docs/publishing/confluence.html to publish the default Quarto file confluence-demo.qmd, with title specified in the yaml as "Confluence Demo". The preview resulting from `quarto preview confluence-demo.qmd` looks correct. The page that makes it to Confluence using `quarto publish confluence confluence-demo.qmd` ends up with a random hash added to the title, for example "Confluence Demo 58b33578". This hash changes to a different random value when republished. ### Steps to reproduce ````qmd --- title: "Confluence Demo" format: confluence-html --- ## Quarto Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>. ## Running Code When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this: ```{r} 1 + 1 ``` You can add options to executable code like this ```{r} #| echo: false 2 * 2 ``` ```` ### Expected behavior <img width="654" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/11002770/5607661f-8a44-4712-b351-08d62f9f3337"> ### Actual behavior <img width="734" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/11002770/5fbf5e0b-2882-4f81-9007-c1027f201540"> ### Your environment - IDE: RStudio 2023.03.1+446 - OS: macOS Monterey 12.3 - R: 4.1.2 ### 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: 1.3.326 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.9 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: 4.1.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/Nick/Code/bulkRNAseq/renv/library/R-4.1/x86_64-apple-darwin17.0 - /Library/Frameworks/R.framework/Versions/4.1/Resources/library knitr: 1.37 rmarkdown: 2.11 [✓] Checking Knitr engine render......OK

### Bug description Following up on the bug fix from #3414, the patched version of the code seems to not discover/use extension scss at all. Given just a `_variables.scss` file that includes a single line, ```scss @import "definitely/not/a/file" ``` Quarto will render the document without issue, even though this file clearly should throw an error. Possibly related - In the process of testing this out, I also couldn't seem to clear quarto's cache entirely. A previous iteration of this test used `$primary: #F00;` as the contents of the `_variables.scss` file and this is still affecting the webpage's style, even in a private browser or separate browser entirely. I've tried deleting every quarto-generated file I can find and running with `--no-cache`, but can't seem to get rid of this cached stylesheet. Perhaps this is related to the current file not throwing errors. Is there a better way to get quarto to render a project from scratch? ### Steps to reproduce 1. Clone this repo: https://github.com/dgkf/quarto-revealjs-theme-reprex (@quarto-cli-issue-5794) 2. Run `quarto preview` 3. Quarto should successfully build the webpage 4. Open `_extensions/custom/scss/_variables.scss` and observe that it should throw a SCSS file-not-found error ### Expected behavior `_variables.scss` from the extension is picked up by quarto, resulting in an error ### Actual behavior Site builds, and does not appear to use the theme scss ### Your environment - MacOS - `quarto-cli` [b5c6ddc37cb2c34e7d6da01cff13b640e97c22cc](https://github.com/quarto-dev/quarto-cli/commit/b5c6ddc37cb2c34e7d6da01cff13b640e97c22cc) (June 2, 2023) ### Quarto check output ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Users/kelkhofd/Projects/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.3 Path: /opt/homebrew/opt/[email protected]/bin/python3.11 Jupyter: 5.3.0 Kernels: julia-1.8 NOTE: No Jupyter k ``` Note, I omitted errors finding R because I run R in a docker container and quarto doesn't like that it can't find it's system temp session directory. I'm pretty sure it's unrelated to this bug.

### Bug description There is no option for .qmd files in "file > new file" in my Rstudio. ### Steps to reproduce _No response_ ### Expected behavior _No response_ ### Actual behavior _No response_ ### Your environment - RStudio 2023.03.1+446 "Cherry Blossom" Release (6e31ffc3ef2a1f81d377eeccab71ddc11cfbd29e, 2023-05-12) - Fedora release 38 (Thirty Eight) - Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.15.12 Chrome/87.0.4280.144 Safari/537.36 ### Quarto check output _No response_

We need to add documentation about #5755 to the website.

### Bug description Write a very long line of text for a code block in a list using indentation or with backtick fences but without a language tag. The grey background does not span the whole text; it is only present for the initially visible section. Here is the rendering of the example document with each code block scrolled a bit. <img width="1043" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/3c469585-3b1b-431e-850a-0e20d8e40768"> Code blocks introduced with backtick fences and language tags do not have this problem. Code blocks outside lists do not have this problem. ### Steps to reproduce The `_quarto.yml`: ```yaml project: type: website format: html: toc: true theme: cosmos ``` The `index.qmd`: ````markdown --- title: home --- ## Code blocks via indentation We like code. This code block has no language tag, so it is left with a white background. some code blocks are really long and do not know when to quit because they are presenting some information that was produced by some external tool and wrapping that text might change how it is interpreted by the reader. ## Listed code blocks via indentation * *This is also important* This code block is introduced with indentation. It has no language tag, but it is presented with a grey background. That background only spans the initially visible text and is not present when scrolling. some code blocks are really long and do not know when to quit because they are presenting some information that was produced by some external tool and wrapping that text might change how it is interpreted by the reader. ## Listed code blocks via fencing; no language * *This is important* This code block is introduced with backtick fences. It has no language tag, but it is presented with a grey background. That background only spans the initially visible text and is not present when scrolling. ``` some code blocks are really long and do not know when to quit because they are presenting some information that was produced by some external tool and wrapping that text might change how it is interpreted by the reader. ``` ## Listed code blocks via fencing; language * *This is important* This code block is introduced with backtick fences and has a language tag. It is presented with a grey background that spans the whole text. It is subject to <https://github.com/quarto-dev/quarto-cli/issues/5538> ```default some code blocks are really long and do not know when to quit because they are presenting some information that was produced by some external tool and wrapping that text might change how it is interpreted by the reader. ``` ```` ### Expected behavior Uniform treatment of code blocks without a language identifier. ### Actual behavior Partial grey backgrounds. ### Your environment - OS: macOS 12.6.6 ### Quarto check output ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.353 Path: /Applications/RStudio.app/Contents/Resources/app/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ```

### Bug description I think there may be an error with how the spacing is done in the listing of tables and figures. For example, when I get to chapter 10 figure 10 the text reads as 10.10Mosaic Confusion Matrix of Base Model . . . . . . . . . . . . . 430 here is a screen shot of the rendered pdf  after creating the repo example I decided to go further to look at the behavior at 100 figures and here the figure numbers completely overwrite the text:  ### Steps to reproduce I made a repo that has an example: [https://github.com/jkylearmstrong/quarto_figure_space_issue](https://github.com/jkylearmstrong/quarto_figure_space_issue) ### Expected behavior hopefully add an additional space in between the figure number and the figure name. ### Actual behavior   ### Your environment ```{r} paste("RStudio version", RStudio.Version()$long_version) paste("quarto version", paste(quarto::quarto_version(), sep='.')) ``` ```{r} [1] "RStudio version 2023.03.0+386" [1] "quarto version 1.4.11" ``` ```{r} tibble::enframe(Sys.info()) %>% filter(name %in% c('sysname','release','version','machine')) %>% head(10) ``` ```{r} # A tibble: 4 × 2 name value <chr> <chr> 1 sysname Windows 2 release 10 x64 3 version build 22621 4 machine x86-64 ``` ```{r} tibble::as_tibble(R.Version()) %>% tidyr::pivot_longer(everything()) %>% head(20) ``` ```{r} # A tibble: 15 × 2 name value <chr> <chr> 1 platform "x86_64-w64-mingw32" 2 arch "x86_64" 3 os "mingw32" 4 crt "ucrt" 5 system "x86_64, mingw32" 6 status "" 7 major "4" 8 minor "3.0" 9 year "2023" 10 month "04" 11 day "21" 12 svn rev "84292" 13 language "R" 14 version.string "R version 4.3.0 (2023-04-21 ucrt)" 15 nickname "Already Tomorrow" ``` ### Quarto check output ```{bash} quarto check ``` ```{bash} A new release of Deno is available: 1.28.2 → 1.33.4 Run `deno upgrade` to install it. [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.4.11 Path: C:\Program Files\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.9 (Conda) Path: C:/ProgramData/anaconda3/python.exe Jupyter: 5.2.0 Kernels: python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.3.0 Path: C:/PROGRA~1/R/R-43~1.0 LibPaths: - C:/Users/jkyle/AppData/Local/R/win-library/4.3 - C:/Program Files/R/R-4.3.0/library knitr: 1.43 rmarkdown: 2.22 [>] Checking Knitr engine render......OK ``` I don't know if `deno` is the issue, I have tried to update it however, when I run ```{bash} deno upgrade ``` from RStudio terminal I get ```{bash} 'deno' is not recognized as an internal or external command, operable program or batch file. ```

### Bug description Including a subpage of a website that renders to `revealjs` causes `quarto` to fail to discover some scss variables resulting in a scss compilation error. ### Steps to reproduce 1. Clone reproducible example in [this repo](https://github.com/dgkf/quarto-revealjs-theme-reprex) - This repo contains an extension that provides a custom `html` and `revealjs` format - The project intends to build a website with a navbar item that links to a presentation (using the `revealjs` format) - Both leverage a `_variables.scss` file `@include`ed in a theme to define a `$primary` variable 3. `quarto preview` 4. Observe build failure ### Expected behavior The website renders and the presentation navbar item takes you to a page where you can view the presentation in the browser. ### Actual behavior `quarto` fails to render the website ### Your environment - `quarto-cli` - 553fec5f3c421a8c0e9a533ef47d76c6f002e437 (from June 1) - 1.3.361 installed via homebrew - on MacOS ### 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: 1.3.361 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.3 Path: /opt/homebrew/opt/[email protected]/bin/python3.11 Jupyter: 5.3.0 Kernels: julia-1.8 NOTE: No Jupyter kernel for Python found [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ```

### Bug description Embedding an ipynb notebook with a markdown h1 header in its first cell, causes that header to override the title of the page. ### Steps to reproduce **some_doc.qmd** ``` --- title: real title --- # a title {{< embed notebook.ipynb >}} ``` **notebook.ipynb** A notebook with a single cell that is essentially this markdown ``` # A notebook title ``` **result** The notebook title is put at the top of the page, the rest of the notebook content where you expect it to be embedded. <img width="1186" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/2574498/ff2b2998-2776-4fd6-a5ec-80e75d28e461"> ### Expected behavior The title configured in the .qmd will be the title. Or if no title configured in the config, then the header that would normally become the title should not be overriden. ### Actual behavior Notebook title becomes header. ### Your environment MacOS ### Quarto check output (Edit: I've also checked with quarto v1.3.361 and see the same behavior) [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.2 Path: /Users/machow/.virtualenvs/plotnine-docs-demo/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.1.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library knitr: 1.39 rmarkdown: 2.14 [✓] Checking Knitr engine render......OK

````markdown --- format: revealjs --- ## test ```{{python}} 1 + 1 ``` ```` This will give  while for HTML  I believe we should have the same output for this feature to work https://quarto.org/docs/computations/execution-options.html#unexecuted-blocks Edit: See later post for more details: https://github.com/quarto-dev/quarto-cli/issues/5783#issuecomment-1573978213

### Bug description Using Quarto 1.3.340 on macOS. Similar to https://github.com/quarto-dev/quarto-cli/issues/2548 axe DevTools reports inline code and navigation elements as having less than the recommended color contrast. Currently rendered result: <img width="1026" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/b3ac6640-ea5e-458d-9019-bc9173f22707"> ### Steps to reproduce ````markdown --- title: style format: html: theme: "cosmo" toc: true toc-expand: true --- Some examples reported as having color contrast below 4.5. The `inline code` is given color of `#9753b8` and background of `#f7f7f7`. The [`inline code link`](https://quarto.org) is given a color of `#2780e3` background of `#f7f7f7`. Reported contrast of 3.71. ## h2 having `inline code` In the right-hand nav when the active item, it is given a color of `#2780e3` and background of `#ffffff`. Reported contrast of 3.97. The h2 inline code is given a color of `#9753b8` and background of `#f7f7f7`. Perhaps due to the font size, it is not reported as having contrast problems. ### h3 having `inline code` The h3 inline code is given a color of `#a164bf` and background of `#f8f8f8`. Reported contrast of 3.88. #### h4 having `inline code` The h4 inline code is given a color of `#a164bf` and background of `#f8f8f8`. Reported contrast of 3.88. ```` ### Quarto check output ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /Applications/RStudio.app/Contents/Resources/app/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ```

### Bug description Tried to see if plotly plots are correctly rendered on confluence using following snippets ### Steps to reproduce 1. Create a jupyter notebook ```python import plotly.express as px from sklearn import datasets import pandas as pd iris = datasets.load_iris() iris = pd.DataFrame(iris.data, columns=iris.feature_names) iris.columns = ["sepal_length", "sepal_width", "petal_length", "petal_width"] px.histogram(iris, x="sepal_width") ``` 2. Push it to confluence ### Expected behavior plotly plots are correctly created and rendered on cofluence like below: <img width="745" alt="CleanShot 2023-06-01 at 22 15 12@2x" src="https://github.com/quarto-dev/quarto-cli/assets/3666080/554af776-631b-4ac7-a3b7-4b206ac0b3f8"> `quarto render <path to jupyter>` correctly creates a plot in html <img width="536" alt="CleanShot 2023-06-01 at 22 18 05@2x" src="https://github.com/quarto-dev/quarto-cli/assets/3666080/8966e729-7092-40ee-87d8-222814c38f05"> ### Actual behavior <img width="725" alt="CleanShot 2023-06-01 at 22 19 05@2x" src="https://github.com/quarto-dev/quarto-cli/assets/3666080/e8f281cd-4ad4-4f23-a39c-6493ea5886e3"> ### Your environment - OS: MacOS ### Quarto check output ```bash └─> quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.353 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.12 (Conda) Path: /Users/allee/miniconda3/bin/python Jupyter: 5.3.0 Kernels: python3 (-) Checking Jupyter engine render....Traceback (most recent call last): File "/Applications/quarto/share/jupyter/jupyter.py", line 21, in <module> from notebook import notebook_execute, RestartKernel File "/Applications/quarto/share/jupyter/notebook.py", line 18, in <module> from nbclient import NotebookClient ModuleNotFoundError: No module named 'nbclient' [✓] Checking Jupyter engine render....OK ```

This is not a huge problem, but when installing `quarto` on an Ubuntu-based distro, I get the following error: ``` ln: failed to create symbolic link '/usr/local/man/quarto.1': No such file or directory ``` caused by this line: https://github.com/quarto-dev/quarto-cli/blob/9402ca9ad15b8c693fcc2c7691df3becb3d3631e/package/scripts/linux/deb/postinst#L9 which I commented out to solve the issue. I don't know if it's different for Debian, but for Ubuntu the `ln` should rather link to `/usr/share/man/man1`, I think. `quarto` still works despite the error, but getting it might be disconcerting for some.

### Bug description Using `../` when creating a listing on a website doesn't seem to work with 1.4.114 on Windows. It works with 1.3.361 on Windows however. ### Steps to reproduce The following example was the simplest I could come up with to demonstrate the issue. A file structure as follows: _quarto.yml dir1/index.qmd dir2/test.qmd The content of _quarto.yml: project: type: website website: title: "Test" sidebar: contents: - href: dir1/index.qmd text: Index format: html The content of dir1/index.qmd: --- title: "Title" listing: - id: test contents: - ../dir2/test.qmd type: table fields: [title] field-display-names: title: "Title" --- ## Section The content of dir2/test.qmd: --- title: "Slides" format: revealjs --- # Welcome! ### Expected behavior The listing/table should be populated. ### Actual behavior The listing/table ends up empty. ### Your environment IDE: Notepad++ OS: Windows 10. ### Quarto check output ``` [>] Checking Quarto installation......OK Version: 1.4.114 Path: C:\Users\au234616\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK D:\quartotest\coursesite>quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.4.114 Path: C:\Users\au234616\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.11.1 Path: C:/Users/au234616/AppData/Local/Programs/Python/Python311/python.exe Jupyter: 5.2.0 Kernels: python3 (-) Checking Jupyter engine render....0.06s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.2.3 Path: C:/PROGRA~1/R/R-42~1.3 LibPaths: - C:/Users/au234616/AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.3/library knitr: 1.40 rmarkdown: 2.20 [>] Checking Knitr engine render......OK ```

### Bug description When trying to run the Graphviz/dot template from the Quatro diagram's page in a chunk with Ctrl/Cmd+Enter, I get an error. When I select `Render on Save` the correct diagram is produced. Perhaps this is intended behaviour, but `nomnoml` has an option for a RMarkdown chunk where only that chunk is rendered. ### Steps to reproduce ````{quatro} ```{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; } ``` ```` ### Expected behavior A diagram is produced at the bottom of the chunk ### Actual behavior ``` running: dot dot12e8d768ebc4.dot -T -o dot12e8d768ebc4.dot Warning in system2(cmd, shQuote(a), stdout = TRUE, stderr = f2, env = options$engine.env) : running command ''dot' 'dot12e8d768ebc4.dot' '-T' '-o' 'dot12e8d768ebc4.dot' 2> 'dot12e8d794e94a8'' had status 1 Error in doTryCatch(return(expr), name, parentenv, handler) : Missing argument for -T flag Usage: dot [-Vv?] [-(GNE)name=val] [-(KTlso)<val>] <dot files> (additional options for neato) [-x] [-n<v>] (additional options for fdp) [-L(gO)] [-L(nUCT)<val>] (additional options for memtest) [-m<v>] (additional options for config) [-cv] -V - Print version and exit -v - Enable verbose mode -Gname=val - Set graph attribute 'name' to 'val' -Nname=val - Set node attribute 'name' to 'val' -Ename=val - Set edge attribute 'name' to 'val' -Tv - Set output format to 'v' -Kv - Set layout engine to 'v' (overrides default based on command name) -lv - Use external library 'v' -ofile - Write output to 'file' -O - Automatically generate an output filename based on the input filename with a .'format' appended. (Causes all -ofile options to be ignored.) -P - Internally generate a graph of the current plugins. -q[l] - Set level of message suppression (=1) -s[v] ``` ### Your environment - IDE: RStudio 2023.03.1+446 - OS: MacOS Ventura 13.4 ### 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: 1.3.361 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.3 Path: /opt/homebrew/opt/[email protected]/bin/python3.11 Jupyter: 5.3.0 Kernels: 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: 4.3.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library knitr: 1.43 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK

Consider this .qmd: ```` --- title: mermaid captions --- ```{mermaid} %%| fig-cap: package.json was a mistake flowchart TD subgraph wintercg deno cloudflare end bun ``` ```` Our metadata block search is brittle; we should either fix this or warn the user about the extra line break.

### Bug description When using Plotly with Quarto on GH pages, the plot does not render. ### Steps to reproduce I made a small repo to demonstrate the problem: - Repo: https://github.com/juliasilge/plotly-quarto-ghpages - Site: https://juliasilge.github.io/plotly-quarto-ghpages/ ### Expected behavior When I publish with GH pages, I expect the image to be rendered on this page: https://juliasilge.github.io/plotly-quarto-ghpages/ ### Actual behavior There is a blank space where the image should be. I _can_ write the HTML to a file and then include that, but that is not as expected. ### Your environment This happens when publishing on GH pages, like so: https://github.com/juliasilge/plotly-quarto-ghpages/blob/main/.github/workflows/quarto-publish.yaml The page looks fine if I render locally. ### Quarto check output You can look at the GH action workflow to see which versions of Quarto and such are being used.

I recently also ran into this problem and tried to create a minimal project to reproduce the error: [project.zip](https://github.com/quarto-dev/quarto-cli/files/11614422/project.zip) When rendering the document using `quarto render report/report.qmd -o alternate_name.html` I observed the following: - If `self-contained: false` the libs are not recognized by the final document - If `self-contained: true` the above *could not fetch resource* warning comes up - It only happens if the `qmd` file is in a subdirectory of the project, top-level documents seem fine ``` $ quarto --version 1.3.353 ``` _Originally posted by @p-gw in https://github.com/quarto-dev/quarto-cli/discussions/4041#discussioncomment-6049811_

### Bug description Quarto search should offer a keyboard shortcut for search. Prior art: mkdocs-material: "f", "s", "/" (https://squidfunk.github.io/mkdocs-material/setup/setting-up-navigation/) GitHub: "s" or "/"(https://docs.github.com/en/get-started/using-github/keyboard-shortcuts) As of Quarto 1.3.340, shortcuts are not available.

### Bug description Rendering document which includes `#| tbl-cap` and `datatable` still results in error, even after #5704 . Tested with most recent dev versions of quarto-cli and knitr. ### Steps to reproduce ````qmd --- title: "Untitled" subtitle: "PA2" date: 2023-05-31 author: Me toc: true toc-location: left toc-depth: 6 number-sections: true number-depth: 6 format: html: page-layout: article margin-top: 2cm margin-bottom: 2cm html-math-method: katex code-tools: false self-contained: true smooth-scroll: true editor: visual execute: echo: false warning: false error: false fig-height: 6 fig-width: 8 fig-align: center fig-pos: "h" --- ## Quarto Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>. ## Running Code When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this: ```{r global_options, include=FALSE} knitr::opts_chunk$set(fig.pos = 'h', echo=FALSE, warning=FALSE, message=FALSE, error=FALSE, fig.width=8, fig.height=6, fig.align='center') options(xtable.comment = FALSE) # options(knitr.table.format = "html") options(kableExtra.latex.load_packages = FALSE) ``` ```{r} library(DT) ``` You can add options to executable code like this ```{r table} #| column: screen-inset-right #| tbl-cap: "Table caption" mtcars %>% datatable(extensions = 'Buttons', filter = 'top', rownames= FALSE, options = list(dom = 'Blfrtip', buttons = c('copy', 'csv', 'excel', 'pdf'), lengthMenu = list(c(10,25,50,-1), c(10,25,50,"All")))) ``` The `echo: false` option disables the printing of code (only output is displayed). ```` ### Expected behavior Successful rendering ### Actual behavior ``` Quitting from lines 53-64 [table] (ReprEx.qmd) Error in `add_html_caption()`: ! unused argument (xfun::grep_sub("^[^<]*<[^>]+aria-labelledby[ ]*=[ ]*\"([^\"]+)\".*$", "\\1", x)) Backtrace: 1. global .main() 2. execute(...) 3. rmarkdown::render(...) 4. knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 5. knitr:::process_file(text, output) ... 14. sew(res, options) 15. knitr:::sew.list(x, options, ...) 16. base::lapply(x, sew, options, ...) 17. FUN(X[[i]], ...) 18. knitr:::sew.knit_asis(x, options, ...) Execution halted ``` ### Your environment _No response_ ### Quarto check output ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Users/emamusi/Documents/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.15 (Conda) Path: /Users/emamusi/miniforge3/bin/python Jupyter: 5.1.3 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.3.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library knitr: 1.43.1 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ```

### Bug description Each time I run **quarto render** in RStudio, I always get this error that quarto is unable to find installed version of R. I have attached a screenshot below.  **Here is my session info:** ```` R version 4.3.0 (2023-04-21 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) Matrix products: default locale: [1] LC_COLLATE=English_United States.utf8 [2] LC_CTYPE=English_United States.utf8 [3] LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.utf8 time zone: Africa/Lagos tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets [6] methods base other attached packages: [1] quarto_1.2 loaded via a namespace (and not attached): [1] digest_0.6.31 later_1.3.1 fastmap_1.1.1 [4] xfun_0.39 knitr_1.43 htmltools_0.5.5 [7] rmarkdown_2.21 ps_1.7.5 cli_3.6.1 [10] processx_3.8.1 compiler_4.3.0 rstudioapi_0.14 [13] tools_4.3.0 evaluate_0.21 yaml_2.3.7 [16] Rcpp_1.0.10 rlang_1.1.1 jsonlite_1.8.4 ```` **Here is the output from quarto check:** ```` $ quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK ERROR: Theme file compilation failed: Stack trace: at dartCommand (file:///C:/Users/USER/AppData/Local/Programs/Quarto/bin/quarto.js:38385:15) at eventLoopTick (ext:core/01_core.js:181:11) at async checkVersions (file:///C:/Users/USER/AppData/Local/Programs/Quarto/bin/quarto.js:85221:26) at async check (file:///C:/Users/USER/AppData/Local/Programs/Quarto/bin/quarto.js:85178:13) at async Command.fn (file:///C:/Users/USER/AppData/Local/Programs/Quarto/bin/quarto.js:85406:5) at async Command.execute (file:///C:/Users/USER/AppData/Local/Programs/Quarto/bin/quarto.js:8105:13) at async quarto (file:///C:/Users/USER/AppData/Local/Programs/Quarto/bin/quarto.js:102325:5) at async file:///C:/Users/USER/AppData/Local/Programs/Quarto/bin/quarto.js:102343:9 ```` **Please I will like to know how I can fix this?**, but I can see that quarto check shows a potential problem that theme file compilation failed but I have struggled for days now and I am unable to fix this. Thank you very much all. ### Steps to reproduce ```` --- title: "Debugging" author: "Oluwafemi Oyedele" format: html editor: visual --- # Quarto Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see https://quarto.org/. # Running Code When you click the Render button a document will be generated that includes both content and the output of embedded code. You can embed code like this: ```{r} 1 + 1 ``` You can add options to executable code like this ```{r} #| echo: false 2 * 2 ``` The echo: false option disables the printing of code (only output is displayed). ```` ### Expected behavior I expect this document to give me an html output when I run Quato render in RStudio ### Actual behavior When I render the document in RStudio it will give me an error that quarto is unable to find installed version of R  ### Your environment ```` R version 4.3.0 (2023-04-21 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) Matrix products: default locale: [1] LC_COLLATE=English_United States.utf8 [2] LC_CTYPE=English_United States.utf8 [3] LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.utf8 time zone: Africa/Lagos tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets [6] methods base other attached packages: [1] quarto_1.2 loaded via a namespace (and not attached): [1] digest_0.6.31 later_1.3.1 fastmap_1.1.1 [4] xfun_0.39 knitr_1.43 htmltools_0.5.5 [7] rmarkdown_2.21 ps_1.7.5 cli_3.6.1 [10] processx_3.8.1 compiler_4.3.0 rstudioapi_0.14 [13] tools_4.3.0 evaluate_0.21 yaml_2.3.7 [16] Rcpp_1.0.10 rlang_1.1.1 jsonlite_1.8.4 ```` ### Quarto check output ```` $ quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK ERROR: Theme file compilation failed: Stack trace: at dartCommand (file:///C:/Users/USER/AppData/Local/Programs/Quarto/bin/quarto.js:38385:15) at eventLoopTick (ext:core/01_core.js:181:11) at async checkVersions (file:///C:/Users/USER/AppData/Local/Programs/Quarto/bin/quarto.js:85221:26) at async check (file:///C:/Users/USER/AppData/Local/Programs/Quarto/bin/quarto.js:85178:13) at async Command.fn (file:///C:/Users/USER/AppData/Local/Programs/Quarto/bin/quarto.js:85406:5) at async Command.execute (file:///C:/Users/USER/AppData/Local/Programs/Quarto/bin/quarto.js:8105:13) at async quarto (file:///C:/Users/USER/AppData/Local/Programs/Quarto/bin/quarto.js:102325:5) at async file:///C:/Users/USER/AppData/Local/Programs/Quarto/bin/quarto.js:102343:9 ```` **But I dont know how to fix the theme file compilation failed**

## Description: Deno Warnings: "files" configuration is deprecated. Please use "include" and "exclude" instead ## Steps to Reproduce: - Execute Deno via CLI ### Expected Result: - No warnings ### Actual Result: - ` "files" configuration is deprecated. Please use "include" and "exclude" instead.`

cf https://github.com/quarto-dev/quarto-cli/discussions/3207#discussioncomment-6042430 I can repro this in 1.4 and 1.3 both.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5714 <div type='discussions-op-text'> ^{Originally posted by **bryanwhiting** May 27, 2023} ### Description This isn't helpful: ``` Cell 1/20...Done Cell 2/20...Done Cell 3/20...Done Cell 4/20...Done Cell 5/20...Done Cell 6/20...Done ``` What would be helpful is for it to print the name of the code chunk, like Rmarkdown does.</div>

### Bug description When inside a project such as a website, if the last document to be rendered includes `embed-resources: true`, the shared "libs" is embedded, thus is missing for the project. Behaviour initially discovered in #5738. `embed-resources` should raise a warning and be ignored inside a Quarto project. ### Steps to reproduce ````sh cat << EOF > _quarto.yml project: type: website website: title: "Quarto-project-embed-resources" navbar: left: - href: index.qmd text: Home - zzz.qmd EOF cat << EOF > index.qmd --- title: "Quarto-project-embed-resources" --- This is a Quarto website. To learn more about Quarto websites visit <https://quarto.org/docs/websites>. EOF cat << EOF > zzz.qmd --- title: 'Reveal.js Presentation' format: revealjs embed-resources: true --- ## Slide EOF ```` ```sh quarto render ``` ### Expected behavior ``` tree _site -L 2 _site ├── index.html ├── search.json ├── site_libs │ ├── bootstrap │ ├── clipboard │ ├── quarto-html │ ├── quarto-nav │ ├── quarto-search │ └── revealjs └── zzz.html 8 directories, 3 files ``` ### Actual behavior ``` tree _site -L 2 _site ├── index.html ├── search.json └── zzz.html 1 directory, 3 files ``` ### Your environment - VSCode Insiders - macOS Ventura 13.4 ### Quarto check output <img width="1111" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/8896044/3fed9b29-585b-4db5-9c00-5260af2b8afb">

### Bug description Colors or R warnings (see 1 in the figure) in Quarto are marked with symbols (see 2, 3). These symbols must not be present. ### Steps to reproduce ````qmd ```{r} with(airquality, table(OzHi = Ozone > 80, Month)) |> DescTools::Desc(plotit = FALSE) ``` ```` ### Expected behavior No extra symbols of color codes. e.g. ``` /.../ Mantel-Haenszel Chi-squared: X-squared = 1.1306, df = 1, p-value = 0.2876 Warning message: Exp. counts < 5: Chi-squared approx. may be incorrect!! Contingency Coeff. 0.287 Cramer's V 0.300 Kendall Tau-b 0.065 /.../ ``` If possible, the colored output would be appreciated too. But at least no extra symbols would be nice too. ### Actual behavior ``` /.../ Mantel-Haenszel Chi-squared: X-squared = 1.1306, df = 1, p-value = 0.2876  Warning message: Exp. counts < 5: Chi-squared approx. may be incorrect!!  Contingency Coeff. 0.287 Cramer's V 0.300 Kendall Tau-b 0.065 /.../ ```  ### Your environment RStudio Edition : Desktop [Open Source] RStudio Version : 2023.6.0.401 OS Version : Windows 10 x64 (build 19045) R Version : R version 4.3.0 (2023-04-21 ucrt) Quarto: : 1.4.111 ### Quarto check output ```bash $ quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.4.111 Path: C:\Users\user\AppData\Local\Programs\Quarto\bin CodePage: 1257 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.15 (Conda) Path: C:/Users/user/anaconda3/python.exe Jupyter: 5.2.0 Kernels: ir, julia-1.9, proj-ml-1, python3 (\) Checking Jupyter engine render....2023-05-30 19:08:32,583 - traitlets - ERROR - Failed to run command: ['C:\\Users\\user\\anaconda3\\envs\\proj-ml-1\\python.exe', '-m', 'ipykernel_launcher', '-f', 'C:\\Users\\user\\AppData\\Local\\Temp\\tmp5bcejmxp.json'] PATH='C;C:\\Program Files\\Git\\Users\\user\\anaconda3;C;C:\\Program Files\\Git\\Users\\user\\anaconda3\\Scripts;C:\\Users\\user\\anaconda3;C:\\Users\\user\\anaconda3\\Library\\mingw-w64\\bin;C:\\Users\\user\\anaconda3\\Library\\usr\\bin;C:\\Users\\user\\anaconda3\\Library\\bin;C:\\Users\\user\\anaconda3\\Scripts;C:\\Users\\user\\anaconda3\\bin;C:\\Users\\user\\anaconda3\\condabin;C:\\Program Files\\RStudio\\resources\\app\\resources\\terminal\\bash\\bin;C:\\Program Files\\Git\\mingw64\\bin;C:\\Program Files\\Git\\usr\\local\\bin;C:\\Program Files\\Git\\usr\\bin;C:\\Program Files\\Git\\usr\\bin;C:\\Program Files\\Git\\mingw64\\bin;C:\\Program Files\\Git\\usr\\bin;C:\\Program Files\\RStudio\\resources\\app\\resources\\terminal\\bash\\bin;C:\\Users\\user\\anaconda3\\Scripts;C:\\Users\\user\\anaconda3;C:\\RBuildTools\\4.3\\x86_64-w64-mingw32.static.posix\\bin;C:\\RBuildTools\\4.3\\usr\\bin;C:\\Program Files\\R\\R-4.3.0\\bin\\x64;C:\\Program Files\\Microsoft MPI\\Bin;C:\\Python39\\Scripts;C:\\Python39;C:\\Rtools\\bin;C:\\ProgramData\\Boxstarter;C:\\Program Files\\ImageMagick-7.0.8-Q16;C:\\Rtools\\bin;C:\\Program Files (x86)\\Common Files\\Oracle\\Java\\javapath;C:\\Rtools\\mingw_32\\bin;C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v8.0\\bin;C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v8.0\\libnvvp;C:\\Program Files\\ImageMagick-6.9.3-Q16;C:\\ProgramData\\Oracle\\Java\\javapath;C:\\Program Files (x86)\\Intel\\iCLS Client;C:\\Program Files\\Intel\\iCLS Client;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0;C:\\Program Files\\Intel\\Intel(R) Management Engine Components\\DAL;C:\\Program Files (x86)\\Intel\\Intel(R) Management Engine Components\\DAL;C:\\Program Files\\Intel\\Intel(R) Management Engine Components\\IPT;C:\\Program Files (x86)\\Intel\\Intel(R) Management Engine Components\\IPT;C:\\Program Files\\Intel\\WiFi\\bin;C:\\Program Files\\Common Files\\Intel\\WirelessCommon;C:\\Program Files (x86)\\NVIDIA Corporation\\PhysX\\Common;C:\\Program Files (x86)\\Aspell\\bin;C:\\Windows\\system32;C:\\Windows;C:\\Windows\\System32\\Wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0;C:\\Program Files (x86)\\QuickTime\\QTSystem;C:\\Program Files\\MiKTeX 2.9\\miktex\\bin\\x64;C:\\Program Files\\R\\R-3.4.0\\library\\tcltk\\libs\\x64;C:\\WINDOWS\\System32\\OpenSSH;C:\\Users\\user\\AppData\\Local\\Programs\\orca;C:\\Program Files\\Microsoft VS Code\\bin;C:\\Program Files\\R\\R-3.5.1\\bin;C:\\ProgramData\\chocolatey\\bin;C:\\Program Files\\NVIDIA Corporation\\NVIDIA NvDLISR;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0;C:\\WINDOWS\\System32\\OpenSSH;C:\\Program Files\\SourceGear\\Common\\DiffMerge;C:\\Program Files\\Git LFS;C:\\Program Files\\TortoiseSVN\\bin;C:\\Program Files\\dotnet;C:\\Program Files (x86)\\Common Files\\Acronis\\VirtualFile;C:\\Program Files (x86)\\Common Files\\Acronis\\VirtualFile64;C:\\Program Files (x86)\\Common Files\\Acronis\\SnapAPI;C:\\Program Files\\Crucial\\Crucial Storage Executive;C:\\Program Files (x86)\\Microsoft SQL Server\\150\\Tools\\Binn;C:\\Program Files\\Microsoft SQL Server\\150\\Tools\\Binn;C:\\Program Files (x86)\\Microsoft SQL Server\\150\\DTS\\Binn;C:\\Program Files\\Microsoft SQL Server\\150\\DTS\\Binn;C:\\Program Files\\Microsoft SQL Server\\Client SDK\\ODBC\\170\\Tools\\Binn;C:\\Program Files\\Azure Data Studio\\bin;C:\\Program Files\\PuTTY;C:\\Program Files\\gs\\gs9.56.1\\bin;C:\\Program Files\\Docker\\Docker\\resources\\bin;C:\\ProgramData\\DockerDesktop\\version-bin;C:\\Program Files\\gnuplot\\bin;C:\\Program Files (x86)\\Meld;C:\\Program Files\\nodejs;C:\\Program Files\\Git\\cmd;C:\\Program Files\\PowerShell\\7;C:\\Users\\user\\AppData\\Local\\P[>] Checking Jupyter engine render....OK ```

Idea is to convert options that we know about as we already have a list for in chunk YAML.

### Bug description When using automatically extracted listing descriptions, descriptions are kept empty when the rendered content does not contain a paragraph. Content can have quite a bit of text (within lists, for example), and depending on the presentation of those lists, the description can be empty. ### Steps to reproduce Given a Quarto website project using the `_quarto.yml`: ````yaml project: type: website website: title: Some Product Documentation site-url: https://docs.example.com/product/news/ navbar: left: - text: "home" file: index.qmd ```` The `index.qmd` page: ````markdown --- title: Some Product Release Notes listing: contents: releases type: default feed: true sort: "version desc" format: html: toc-depth: 2 --- ## Introduction The notes for each release follow. ```` The three `releases/2023.05.0.md`, `releases/2023.03.0.md`, and `releases/2023.01.0d` files: ````markdown --- title: Some Product 2023.05.0 version: 2023.05.0 date: May 10, 2023 --- ## New * This is a thing that is new. * This is another thing that is new. ## Fixed * This is a fixed thing. ```` ````markdown --- title: Some Product 2022.03.0 version: 2023.03.0 date: March 24, 2022 --- ## New * This is a thing that is new. ```` ````markdown --- title: Some Product 2023.01.0 version: 2023.01.0 date: Jan 15, 2023 --- ## New * This is a compact list that declares new things. * There are lots of words here, but the list is kept compact. ## Fixed * This is a fixed thing. ```` Render or preview this site. ### Expected behavior The listing view should should include text from each item and retain the list-like nature of the content. ### Actual behavior When rendered, not all items have content and those that do have lost their list presentation. <img width="528" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/4488077c-f20a-417f-b071-1dc6e5d9ba8d"> In this example, the 2023.05.0 item has list items separated by blank lines, meaning it is styled as lists with paragraph items. This is enough for the listing code to extract the item text the item description. The 2023.03.0 item has a one-element list. Because there is only one list item, it is not given paragraphs for its items. The 2023.01.1 item has multiple lists, but they do not have blank lines separating the items, which causes them to be styled as lists without paragraphs. The lack of paragraphs means that the listing item description is empty. ### Your environment - OS: macOS Monterey 12.6.5 ### Quarto check output ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /Applications/RStudio.app/Contents/Resources/app/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ```

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5409 <div type='discussions-op-text'> ^{Originally posted by **mccarthy-m-g** May 3, 2023} The sidebar appearance on small screens changed somewhere in v1.3. In previous versions it just took the page's title and added an arrow to the right of it; you could click the title or arrow to bring down the sidebar. Whereas now there's a page icon followed by a breadcrumb for the current page; you can only click the small icon to bring down the sidebar. I can't find the relevant issue or PR where this change occurred, but I was wondering if it's currently possible to revert to the old style small screen sidebar? The old appearance and UX worked better for me and my website, but I don't want to be stuck on an older version of Quarto just to keep this how it was.</div>

My problem is related to the run time, but not exactly the same as https://github.com/quarto-dev/quarto-cli/issues/1152 My error looks like this: I am publishing 77 html quarto files to Netlify with each page having at least one image in the `![]()` format. To get a sense of the amount of content and whether this is the problem, my website I was able to publish is [here](https://nd-upgrade.netlify.app). There does not seem to be a solution for non-code related run times. I cannot tell which file is in `bin/quarto.js:109513:17` to address it. <img width="633" alt="Screenshot 2023-05-28 at 9 33 24 AM" src="https://github.com/quarto-dev/quarto-cli/assets/81820608/4f997347-86e6-4276-bf56-db0b8777c157"> _Originally posted by @sophiestrazie in https://github.com/quarto-dev/quarto-cli/issues/1152#issuecomment-1566143267_

### Bug description We are using the GitHub action to publish the website in this repository: https://github.com/gesiscss/quarto-workshop to https://gesiscss.github.io/quarto-workshop/ but the action does not produce the `site_libs` folder with the required libraries. rendering it locally does produce the `site_libs` folder (quarto 1.3.151). The GA was setup according to the documentation on quarto.org. This is the `publish.yml` file ```yaml on: workflow_dispatch: push: branches: main name: Quarto Publish jobs: build-deploy: runs-on: ubuntu-latest permissions: contents: write steps: - name: Check out repository uses: actions/checkout@v3 - name: Set up Quarto uses: quarto-dev/quarto-actions/setup@v2 - name: Render and Publish uses: quarto-dev/quarto-actions/publish@v2 with: target: gh-pages env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} ``` Edit: using `lib-dir: "libs"` to change the default "site_libs" folder also did not fix the issue ### Steps to reproduce deploy https://github.com/gesiscss/quarto-workshop in a different github account ### Expected behavior _No response_ ### Actual behavior _No response_ ### Your environment _No response_ ### Quarto check output _No response_

### Bug description I updated a few things at once and kableExtra output in Quarto HTML doesn't seem to act as expected. I use ` kableExtra::kable_styling( bootstrap_options = c("basic", "hover"), full_width=FALSE)` which displays correctly inline for RStudio (screenshot 1), but once rendered it's striped and full width (screenshot 2).   ### Steps to reproduce ```` --- title: "Untitled" format: html --- ```{r setup} library(tidyverse) library(kableExtra) ``` ```{r} iris %>% kable() %>% kableExtra::kable_styling( bootstrap_options = c("basic", "hover"), full_width=FALSE) ``` ```` i played around with the following chunk options but neither produce my expected output ``` #| output: asis #| layout: [-10, 80, -10] ``` ### Expected behavior Quarto HTML should look like the inline version (screenshot 1) ### Actual behavior Quarto HTML ignores striped and full width (screenshot 2) ### Your environment RStudio 2023.03.1+446 "Cherry Blossom" Release (6e31ffc3ef2a1f81d377eeccab71ddc11cfbd29e, 2023-05-09) for windows Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.03.1+446 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36 R version 4.3.0 (2023-04-21 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044) loaded via a namespace (and not attached): [1] httr_1.4.6 svglite_2.1.1 cli_3.6.1 knitr_1.43 [5] rlang_1.1.1 xfun_0.39 stringi_1.7.12 glue_1.6.2 [9] colorspace_2.1-0 htmltools_0.5.5 scales_1.2.1 rmarkdown_2.21 [13] evaluate_0.21 munsell_0.5.0 kableExtra_1.3.4 fastmap_1.1.1 [17] lifecycle_1.0.3 stringr_1.5.0 compiler_4.3.0 rvest_1.0.3 [21] rstudioapi_0.14 systemfonts_1.0.4 digest_0.6.31 viridisLite_0.4.2 [25] R6_2.5.1 magrittr_2.0.3 webshot_0.5.4 tools_4.3.0 [29] xml2_1.3.4 ### Quarto check output ``` C:\Users\negat>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: 1.3.361 Path: C:\Users\negat\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.6 Path: C:/Users/negat/AppData/Local/Programs/Python/Python39/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with py -m pip install jupyter There is an unactivated Python environment in miniconda3. Did you forget to activate it? [>] Checking R installation...........OK Version: 4.3.0 Path: C:/PROGRA~1/R/R-43~1.0 LibPaths: - C:/Users/negat/AppData/Local/R/win-library/4.3 - C:/Program Files/R/R-4.3.0/library knitr: 1.43 rmarkdown: 2.21 [>] Checking Knitr engine render......OK ```

### Bug description In the recently released **knitr** version 1.43 a bug was fixed relating to cropping of pdf images on Windows. Previously an external Ghostscript executable was unnecessarily being checked for. This is unnecessary on Windows because (only on Windows) TeXLive/TinyTeX and MikTeX all bundle their own version of Ghostscript within their installations. Quarto copied the incorrect **knitr** logic, so I recommend updating as per **knitr**. Please see <https://github.com/yihui/knitr/issues/2246> for more information and <https://github.com/yihui/knitr/commit/4953bec489479bcef6eeb2f52cb9be40daabe47b> for the updated logic in **knitr**. I think the fix will need to come around here <https://github.com/quarto-dev/quarto-cli/blob/d62f23fcee4cfad08fd004a540aba099ff5c7303/src/resources/rmd/execute.R#L277> ### Steps to reproduce _No response_ ### Expected behavior _No response_ ### Actual behavior _No response_ ### Your environment _No response_ ### Quarto check output _No response_

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5691 <div type='discussions-op-text'> ^{Originally posted by **DOSull** May 26, 2023} This is a very general question about possible future directions, not something likely to get fixed overnight. In short, I find the decision to overload markdown heading levels 1 and 2 by causing them to introduce section and slide breaks in revealjs decks a very strange one! In a standard reveal html page you can do this ``` <section data-markdown> # This will be H1 ## and this will be H2 </section> ``` The slideshow structure is based on HTML `<section> ` tag (nested to create vertical sections). Overloading markdown `#` and `##` as has been done in quarto forces the use of raw HTML `<h1>` and `<h2>` tags to get those formats in slides. It seems an odd decision to me. Is there any chance of it being changed or of a setting being made available that would allow access to heading levels 1 and 2 formats without recourse to raw HTML? I've been using reveal for several years and this is an obstacle to me transitioning to generating my slides using quarto! </div>

### Bug description Chromium does not install ### Steps to reproduce In any project, running `quarto install tool chromium` fails. ### Expected behavior Should install successfully ### Actual behavior ``` ERROR: TypeError: Relative import path "puppeteer/mod.ts" not prefixed with / or ./ or ../ Stack trace: at async getPuppeteer (file:///opt/quarto/bin/quarto.js:35241:24) at async fetcher (file:///opt/quarto/bin/quarto.js:35370:22) at async Object.installed (file:///opt/quarto/bin/quarto.js:35300:24) at async toolSummary (file:///opt/quarto/bin/quarto.js:82880:27) at async updateOrInstallTool (file:///opt/quarto/bin/quarto.js:83039:21) at async Command.fn (file:///opt/quarto/bin/quarto.js:86622:17) at async Command.execute (file:///opt/quarto/bin/quarto.js:8104:13) at async quarto (file:///opt/quarto/bin/quarto.js:102201:5) at async file:///opt/quarto/bin/quarto.js:102219:9 ``` ### Your environment OS: Arch Linux ### Quarto check output <details> <summary> <pre>quarto check</pre> </summary> <pre> [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.78 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.9 (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/ </pre> </details>

### Bug description As with the current development version of Quarto, the shortcodes are no longer read in "HTML tables with embedded markdown" (1.3 feature). ### Steps to reproduce Render the following document using Quarto 1.3.361 and development version: ````qmd --- format: html --- ```{=html} <table> <caption><span data-qmd="As described in @Lovelace1864, computers are great."></span></caption> <thead> <tr> <th><span data-qmd="_Header 1_"></span></th> <th><span data-qmd="_Header 2_"></span></th> </tr> </thead> <tbody> <tr> <td><span data-qmd="{{< video https://www.youtube.com/embed/wo9vZccmqwc >}}"></span></td> <td>Regular output</td> </tr> </tbody> </table> ``` ```` ### Expected behavior <img width="733" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/8896044/b4201521-1628-4831-bc78-fc34bbd623c4"> ### Actual behavior <img width="732" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/8896044/78fd225f-0447-4dd0-879d-e32e29fbb7ad"> ### Your environment - IDE: VSCode Insiders - OS: macOS Ventura 13.4 ### Quarto check output <img width="1202" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/8896044/c2a717f3-02c5-4b23-99f1-aab424d5ad19">

### Bug description 👋🏻 Hi, I was trying to publish my website via the GitHub actions process described [here](https://quarto.org/docs/publishing/github-pages.html) ### Steps to reproduce Hopefully you are able to directly see the error from this [link](https://github.com/robcrystalornelas/robcrystalornelas.github.io/actions/runs/5106055750/jobs/9178022980). The first time I saw the error was when uploading an image in this [commit](https://github.com/robcrystalornelas/robcrystalornelas.github.io/commit/4b0d52727c3fa3a98d9d84d0a10ff1b45871e89a). Then the actions job automatically ran, and threw the error linked above. The error message in the action is pasted below and is at the step `publish to github pages and render` ```python Rendering for publish: [1/6] portfolio.qmd ERROR: Error resolving header-includes- unable to open file includes.html ERROR: Error at renderFiles (file:///opt/quarto/bin/quarto.js:86657:30) at async renderProject (file:///opt/quarto/bin/quarto.js:86798:25) at async renderForPublish (file:///opt/quarto/bin/quarto.js:121188:33) at async renderForPublish (file:///opt/quarto/bin/quarto.js:109087:24) at async Object.publish4 [as publish] (file:///opt/quarto/bin/quarto.js:120457:26) at async publishSite (file:///opt/quarto/bin/quarto.js:121225:[38](https://github.com/robcrystalornelas/robcrystalornelas.github.io/actions/runs/5106055750/jobs/9178022980#step:5:40)) at async publish5 (file:///opt/quarto/bin/quarto.js:121443:61) at async doPublish (file:///opt/quarto/bin/quarto.js:121[39](https://github.com/robcrystalornelas/robcrystalornelas.github.io/actions/runs/5106055750/jobs/9178022980#step:5:41)9:13) at async publishAction (file:///opt/quarto/bin/quarto.js:121[41](https://github.com/robcrystalornelas/robcrystalornelas.github.io/actions/runs/5106055750/jobs/9178022980#step:5:43)0:9) at async Command.fn (file:///opt/quarto/bin/quarto.js:121387:9) ``` ### Expected behavior I was expecting the action to successfully run and then my webpage would be automatically updated. ### Actual behavior The action step `publish to github pages and render` failed and threw the error mentioned above. ### Your environment OS: ventura 13.3.1 Working just in the GitHub UI editing the qmd files directly ### Quarto check output ```bash [✓] Checking Quarto installation......OK Version: 1.1.189 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 in stallation....OK Version: 3.7.6 (Conda) Path: /Users/robcrystalornelas/opt/anaconda3/bin/python Jupyter: 4.6.1 Kernels: python3, ir [✓] Checking Jupyter engine render....OK (\) Checking R installation...Unable to locate an installed version of R. ```

### Bug description I am publishing 77 html quarto files to Netlify with each page having at least one image in the `![]()` format. To get a sense of the amount of content and whether this is the problem, my website I was able to publish is [here](https://nd-upgrade.netlify.app). There does not seem to be a solution for non-code related run times. I cannot tell which file is in `bin/quarto.js:109513:17` to address it. <img width="633" alt="Screenshot 2023-05-28 at 9 33 24 AM" src="https://github.com/quarto-dev/quarto-cli/assets/81820608/4f997347-86e6-4276-bf56-db0b8777c157"> ### Steps to reproduce In R terminal: `quarto publish netlify` ### Expected behavior (base) mycomputer:Neurodivergent Upgrade myname $ quarto publish netlify ? Publish update to: › https://nd-upgrade.netlify.app (Netlify - [email protected]) Rendering for publish: [ 1/77] personal-ideals.qmd [ 2/77] stats-ocd.qmd [ 3/77] uni-professionalism.qmd [ 4/77] university-respect.qmd [ 5/77] explainer-cohesive-solidarity.qmd [ 6/77] stats-happy.qmd [ 7/77] explainer-neurodiversity.qmd [ 8/77] explainer-ableism.qmd [ 9/77] about-mission.qmd [10/77] personal-friends.qmd [11/77] personal-communication.qmd [12/77] work-ideals.qmd [13/77] personal-self-concept.qmd [14/77] uni-study-strategies.qmd [15/77] personal-parenthood.qmd [16/77] stats-trigger.qmd [17/77] personal-family.qmd [18/77] stats-autism.qmd [19/77] explainer-accessible-boundaries.qmd [WARNING] This document format requires a nonempty <title> element. Defaulting to 'quarto-input7c135172' as the title. To specify a title, use 'title' in metadata or --metadata title="...". [20/77] about-support-business.qmd [21/77] personal-burnout.qmd [22/77] uni-coding.qmd [23/77] work.qmd [24/77] work-advocate.qmd [25/77] work-networking.qmd [26/77] work-respect.qmd [27/77] explainer-adhd.qmd [28/77] stats-memory.qmd [29/77] personal-sensory.qmd [30/77] work-hiring-accommodations.qmd [31/77] work-interviews.qmd [32/77] uni-class-projects.qmd [33/77] work-conflicts.qmd [34/77] general-values.qmd [35/77] explainer-sensory.qmd [36/77] personal-safety.qmd [37/77] index.qmd [38/77] general-portfolio.qmd [39/77] general.qmd [40/77] explainer-autism.qmd [41/77] about.qmd [42/77] uni-testing.qmd [43/77] domestic.qmd [44/77] uni-essays.qmd [45/77] uni-research.qmd [46/77] personal-dopamine.qmd [47/77] uni-grad-school.qmd [48/77] personal-ef.qmd [49/77] work-unemployment.qmd [50/77] personal.qmd [51/77] explainer-accommodation.qmd [52/77] stats-sad.qmd [53/77] uni-models.qmd [54/77] uni-summer.qmd [55/77] personal-overcome-trauma.qmd [56/77] uni-self-advocating.qmd [57/77] work-established-career.qmd [58/77] explainer-strat-ig.qmd [59/77] personal-emotions.qmd [60/77] personal-introspection.qmd [61/77] uni-accommodations.qmd [62/77] explainer-meltdown.qmd [63/77] stats.qmd [64/77] uni-semester.qmd [65/77] personal-meditate.qmd [66/77] work-early-career-decisions.qmd [67/77] uni-pick-class.qmd [68/77] uni-labs.qmd [69/77] explainer.qmd [70/77] explainer-masking.qmd [71/77] resources.qmd [72/77] personal-sleep.qmd [73/77] uni-roommates.qmd [74/77] work-resume-tips.qmd [75/77] personal-romantic.qmd [76/77] university.qmd [77/77] personal-severe-depression.qmd **[✓] Preparing to publish site** **[✓] Uploading files (complete)** **[✓] Deploying published site** **[✓] Published site: https://sophie-strassmann.netlify.app** (base)mycomputer:Neurodivergent Upgrade myname$ ### Actual behavior (base) mycomputer:Neurodivergent Upgrade myname $ `quarto publish netlify` ? Publish update to: › https://nd-upgrade.netlify.app (Netlify - [email protected]) Rendering for publish: [ 1/77] personal-ideals.qmd [ 2/77] stats-ocd.qmd [ 3/77] uni-professionalism.qmd [ 4/77] university-respect.qmd [ 5/77] explainer-cohesive-solidarity.qmd [ 6/77] stats-happy.qmd [ 7/77] explainer-neurodiversity.qmd [ 8/77] explainer-ableism.qmd [ 9/77] about-mission.qmd [10/77] personal-friends.qmd [11/77] personal-communication.qmd [12/77] work-ideals.qmd [13/77] personal-self-concept.qmd [14/77] uni-study-strategies.qmd [15/77] personal-parenthood.qmd [16/77] stats-trigger.qmd [17/77] personal-family.qmd [18/77] stats-autism.qmd [19/77] explainer-accessible-boundaries.qmd [WARNING] This document format requires a nonempty <title> element. Defaulting to 'quarto-input7c135172' as the title. To specify a title, use 'title' in metadata or --metadata title="...". [20/77] about-support-business.qmd [21/77] personal-burnout.qmd [22/77] uni-coding.qmd [23/77] work.qmd [24/77] work-advocate.qmd [25/77] work-networking.qmd [26/77] work-respect.qmd [27/77] explainer-adhd.qmd [28/77] stats-memory.qmd [29/77] personal-sensory.qmd [30/77] work-hiring-accommodations.qmd [31/77] work-interviews.qmd [32/77] uni-class-projects.qmd [33/77] work-conflicts.qmd [34/77] general-values.qmd [35/77] explainer-sensory.qmd [36/77] personal-safety.qmd [37/77] index.qmd [38/77] general-portfolio.qmd [39/77] general.qmd [40/77] explainer-autism.qmd [41/77] about.qmd [42/77] uni-testing.qmd [43/77] domestic.qmd [44/77] uni-essays.qmd [45/77] uni-research.qmd [46/77] personal-dopamine.qmd [47/77] uni-grad-school.qmd [48/77] personal-ef.qmd [49/77] work-unemployment.qmd [50/77] personal.qmd [51/77] explainer-accommodation.qmd [52/77] stats-sad.qmd [53/77] uni-models.qmd [54/77] uni-summer.qmd [55/77] personal-overcome-trauma.qmd [56/77] uni-self-advocating.qmd [57/77] work-established-career.qmd [58/77] explainer-strat-ig.qmd [59/77] personal-emotions.qmd [60/77] personal-introspection.qmd [61/77] uni-accommodations.qmd [62/77] explainer-meltdown.qmd [63/77] stats.qmd [64/77] uni-semester.qmd [65/77] personal-meditate.qmd [66/77] work-early-career-decisions.qmd [67/77] uni-pick-class.qmd [68/77] uni-labs.qmd [69/77] explainer.qmd [70/77] explainer-masking.qmd [71/77] resources.qmd [72/77] personal-sleep.qmd [73/77] uni-roommates.qmd [74/77] work-resume-tips.qmd [75/77] personal-romantic.qmd [76/77] university.qmd [77/77] personal-severe-depression.qmd [✓] Preparing to publish site **ERROR: ApiError: Generic Error** **ApiError: Generic Error** ** at catchErrorCodes (file:///Applications/quarto/bin/quarto.js:109492:15)** **at file:///Applications/quarto/bin/quarto.js:109513:17*** (base)mycomputer:Neurodivergent Upgrade myname$ ### Your environment - IDE: 2023.03.1+446 - OS: MacOS Ventura 13.3 - R: 4.2.2 ### 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: 1.3.326 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.13 (Conda) Path: /Applications/anaconda3/bin/python Jupyter: 5.3.0 Kernels: python3, ir [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK

### Bug description fig-xxx for an included_url (such as an interactive graph or a leaflet map) is not accepted as a figure by quarto (bookdown seems to work that way [https://bookdown.org/yihui/rmarkdown-cookbook/include-url.html](https://bookdown.org/yihui/rmarkdown-cookbook/include-url.html)). More generally it would be nice to allow user to include any content (if aware) as a figure or a table (a table can sometime be rendered as an image ?). here is a reprex: ````qmd --- title: "fig" format: html editor: visual --- ## Quarto Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>. here is a map [@fig-map], working as expected, but html saved is not a figure [@fig-maphtml] ```{r} #| label: fig-map #| fig-cap: a leaflet interactive map leaflet::leaflet() |> leaflet::addTiles() ``` ```{r} #| label: fig-maphtml #| fig-cap: a leaflet interactive map leaflet::leaflet() |> leaflet::addTiles() |> htmlwidgets::saveWidget("map.html") knitr::include_url("map.html") ``` the end. ```` ### Steps to reproduce _No response_ ### Expected behavior _No response_ ### Actual behavior _No response_ ### Your environment _No response_ ### Quarto check output _No response_

### Bug description `Quarto` version 1.4.90 unlike recent previous versions is not working with `sparkline`. ### Steps to reproduce ````qmd --- title: "Test sparklines" format: html --- ```{r} sparkline::sparkline(0) # load sparkline javascript dependencies ``` ```` ### Expected behavior Should load `jQuery` dependencies to set up for sparklines, with no visible output. ### Actual behavior ```` Quitting from lines 7-8 [unnamed-chunk-1] (spark.qmd) Error in `add_html_caption()`: ! unused argument (xfun::grep_sub("^[^<]*<[^>]+aria-labelledby[ ]*=[ ]*\"([^\"]+)\".*$", "\\1", x)) Backtrace: 1. global .main() 2. execute(...) 3. rmarkdown::render(...) 4. knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 5. knitr:::process_file(text, output) ... 14. sew(res, options) 15. knitr:::sew.list(x, options, ...) 16. base::lapply(x, sew, options, ...) 17. FUN(X[[i]], ...) 18. knitr:::sew.knit_asis(x, options, ...) Execution halted ```` ### Your environment - OS: Ubuntu 22.04 popOS - knitr 1.43 - R 4.3.0 ### Quarto check output ```bash [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.90 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.3.0 Path: /usr/lib/R LibPaths: - /home/harrelfe/R/x86_64-pc-linux-gnu-library/4.3 - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/lib/R/library knitr: 1.43 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ```

### Bug description The latest release, `quarto-1.3.361` is missing the Windows ZIP file: `quarto-1.3.361-win.zip`. ### Steps to reproduce _No response_ ### Expected behavior _No response_ ### Actual behavior _No response_ ### Your environment _No response_ ### Quarto check output _No response_

### Bug description If you want to use a font from a file you need to use a lot of `../` to get to the right area. If both your `styles.scss` file and the font files are in the same directory as `index.qmd` you need to prefix the file names with `../../../../../` since the compiled scss ends up in `index_files/libs/revealjs/dist/theme/quarto.css` but the fonts stay where they are. ### Steps to reproduce Repo: https://github.com/EmilHvitfeldt/quarto-custom-font-revealjs-reprex Page: https://emilhvitfeldt.github.io/quarto-custom-font-revealjs-reprex/ ### Expected behavior It would be lovely if the `@font-face` could be specified with the following code ```scss @font-face { font-family: 'FiraCode'; src: url('FiraCode-Regular.woff2') format('woff2'), url('FiraCode-Regular.woff') format('woff'); } ``` ### Actual behavior Where as now, you have to specify to a variant of ```scss @font-face { font-family: 'FiraCode'; src: url('../../../../../FiraCode-Regular.woff2') format('woff2'), url('../../../../../FiraCode-Regular.woff') format('woff'); } ``` ### Your environment - IDE: Version 2023.05.0-daily+206 (2023.05.0-daily+206) - OS: macOS Monterey version 12.6 ### Quarto check output ```bash [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.92 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.7 (Conda) Path: /Users/emilhvitfeldt/miniforge3/bin/python Jupyter: (None) Jupyter is not available in this Python installation. Install with conda install jupyter [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources LibPaths: - /Users/emilhvitfeldt/Library/R/arm64/4.2/library - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library knitr: 1.43 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ```

### Bug description Quarto 1.3.340 on macOS The `_quarto.yml` ````yaml project: type: website website: navbar: left: - text: "home" file: index.qmd ```` The `index.qmd` ````markdown # alpha Alpha is first. Consider nothing else. ## First {#First} The first section contains the first set of properties which must appear after `[First]` in the configuration file. ### `First` Settings {#First.Settings} #### `SomeFirstSettingEnabled` {#First.SomeFirstSettingEnabled} Enable the jump start examples for onboarding. #### `AnotherFirstSettingName` {#First.AnotherFirstSettingName} Indicates how Posit Connect attempts to match the R version associated with uploaded content with the R versions available on the system. ## Second {#Second} The second section contains the second set of properties which must appear after `[Second]` in the configuration file. ### `Second` Settings {#Second.Settings} #### `SomeSecondSettingEnabled` {#Second.SomeSecondSettingEnabled} Enable the jump start examples for onboarding. #### `AnotherSecondSettingName` {#Second.AnotherSecondSettingName} Indicates how Posit Connect attempts to match the R version associated with uploaded content with the R versions available on the system. ## Third {#Third} The third section contains the third set of properties which must appear after `[Third]` in the configuration file. ### `Third` Settings {#Third.Settings} #### `SomeThirdSettingEnabled` {#Third.SomeThirdSettingEnabled} Enable the jump start examples for onboarding. #### `AnotherThirdSettingName` {#Third.AnotherThirdSettingName} Indicates how Posit Connect attempts to match the R version associated with uploaded content with the R versions available on the system. ## Fourth {#Fourth} The fourth section contains the fourth set of properties which must appear after `[Fourth]` in the configuration file. ### `Fourth` Settings {#Fourth.Settings} #### `SomeFourthSettingEnabled` {#Fourth.SomeFourthSettingEnabled} Enable the jump start examples for onboarding. #### `AnotherFourthSettingName` {#Fourth.AnotherFourthSettingName} Indicates how Posit Connect attempts to match the R version associated with uploaded content with the R versions available on the system. ```` The "AnotherFirstSettingName" term is not found. <img width="531" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/4c7b8f8a-f7ff-4780-846e-c10946f57177"> The "jump start" query repeats results. <img width="870" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/5708dd8c-6d89-40f7-8966-20911207bcce"> ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /Applications/RStudio.app/Contents/Resources/app/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ``` ### Steps to reproduce _No response_ ### Expected behavior _No response_ ### Actual behavior _No response_ ### Your environment _No response_ ### Quarto check output _No response_

### Bug description Adding `?q=&` to just about any URL will crash the page. This happens on my site built with Quarto, but also yours (and others I tried in your website gallery). For example: https://quarto.org/docs/get-started/?q=& ### Steps to reproduce Go to https://quarto.org/docs/get-started/?q=& ### Expected behavior Page loads ### Actual behavior Page starts loading and keeps going, eventually crashing:  In Safari, it takes much longer to stop trying:  ### Your environment macOS 13.3.1, Chrome 112.0.5615.137 and Safari 16.4 (18615.1.26.110.1) ### Quarto check output _No response_

### Bug description Using Quarto 1.3.340 on macOS. Given a website with the following layout: ``` _quarto.yml alpha.qmd beta.qmd index.qmd include/ _common.qmd _default_details.qmd _other_details.qmd ``` The `quarto.yml`: ```yaml project: type: website website: navbar: left: - text: "Home" file: index.qmd - text: "alpha" file: alpha.qmd - text: "beta" file: beta.qmd ``` The contents of `index.qmd` are not interesting. Here is `alpha.qmd` ````markdown --- title: alpha --- Alpha is first. Consider nothing else. ```{r, include = FALSE} PROFILE <- "default" ``` ```{r, child = "include/_common.qmd"} ``` There is nothing else to say about alpha. ```` Here is `beta.qmd` ````markdown --- title: beta --- Beta is a hammer bot. ```{r, include = FALSE} PROFILE <- "beta" ``` ```{r, child = "include/_common.qmd"} ``` The common stuff is out of the way. Give thanks to beta. ```` The `include/_common.qmd` needs to use two conditional knitr chunks: ````markdown This is the common include file. We are the `r#PROFILE` profile. - Be prepared. Some very interesting text is about to appear. ```{r, child=if(PROFILE=="default") "include/_default_details.qmd"} ``` ```{r, child=if(PROFILE!="default") "include/_other_details.qmd"} ``` After we gave you all of that, is there anything more? ```` The two nested include files are fairly simple. The `include/_default_details.qmd`: ````markdown - The details you get by default are amazing. ```` The `include/_other_details.qmd`: ````markdown - When you are not the default, you can often feel left behind. ```` This is quite a lot of complexity, especially when `include/_common.qmd` contains many conditional blocks. It would be good to avoid the need for R and knitr to accomplish: 1. Per-document variables that can be used by included files for text replacement with variable short-codes. 2. Per-document variables that can be used by included files to make decisions about what text to include in the render. This example was the result of porting an include file from mkdocs that looked like: ````markdown This is the common include file. We are the {{ PROFILE }} profile. - Be prepared. Some very interesting text is about to appear. {% if PROFILE == "default" %} - The details you get by default are amazing. {% else %} - When you are not the default, you can often feel left behind. {% endif %} After we gave you all of that, is there anything more? ```` ### Steps to reproduce _No response_ ### Expected behavior _No response_ ### Actual behavior _No response_ ### Your environment _No response_ ### Quarto check output _No response_

### Bug description The following produces a collapsed box in html but not in revealjs: ``` ::: {.callout-caution collapse="true"} ## Caution caution!! ::: ``` Manjaro Linux quarto version 1.3.353 installed from AUR ``` $ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.353 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.10 Path: /usr/bin/python3 Jupyter: 4.9.2 Kernels: julia-1.8, julia-1.7, ir, julia-1.9, python3 (\) Checking Jupyter engine render....Exception ignored in: <function BaseEventLoop.__del__ at 0x7fa214c0e8c0> Traceback (most recent call last): File "/usr/lib/python3.10/asyncio/base_events.py", line 690, in __del__ self.close() File "/usr/lib/python3.10/asyncio/unix_events.py", line 68, in close super().close() File "/usr/lib/python3.10/asyncio/selector_events.py", line 87, in close self._close_self_pipe() File "/usr/lib/python3.10/asyncio/selector_events.py", line 94, in _close_self_pipe self._remove_reader(self._ssock.fileno()) File "/usr/lib/python3.10/asyncio/selector_events.py", line 272, in _remove_reader key = self._selector.get_key(fd) File "/usr/lib/python3.10/selectors.py", line 191, in get_key return mapping[fileobj] File "/usr/lib/python3.10/selectors.py", line 72, in __getitem__ fd = self._selector._fileobj_lookup(fileobj) File "/usr/lib/python3.10/selectors.py", line 226, in _fileobj_lookup return _fileobj_to_fd(fileobj) File "/usr/lib/python3.10/selectors.py", line 42, in _fileobj_to_fd raise ValueError("Invalid file descriptor: {}".format(fd)) ValueError: Invalid file descriptor: -1 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.3.0 Path: /home/gkraemer/progs/R/R-4.3.0 LibPaths: - /home/gkraemer/progs/R/R-4.3.0/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [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, # Current situation {knitr} has a recent update to v1.43 that makes rendering of R code chunks with htmlwidgets fails with ```bash $ quarto render Reprex.Rmd processing file: Reprex.Rmd 1/5 2/5 [setup] 3/5 4/5 [DT htmlwidget] Quitting from lines 15-16 [DT htmlwidget] (Reprex.Rmd) Error in `add_html_caption()`: ! unused argument (xfun::grep_sub("^[^<]*<[^>]+aria-labelledby[ ]*=[ ]*\"([^\"]+)\".*$", "\\1", x)) Backtrace: 1. global .main() 2. execute(...) 3. rmarkdown::render(...) 4. knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 5. knitr:::process_file(text, output) ... 14. sew(res, options) 15. knitr:::sew.list(x, options, ...) 16. base::lapply(x, sew, options, ...) 17. FUN(X[[i]], ...) 18. knitr:::sew.knit_asis(x, options, ...) Execution halted ``` This is not specific to {DT}, but also occurs with other htmlwidgets related packages : {collapsibleTree}, ... # ReprEx Reprex.qmd is the following (code chunk separator manually edited for correct rendering here): ```qmd --- title: "ReprEx htmlwidget" format: html --- ``{r setup} library(DT) xfun::session_info('knitr') `` ``{r DT htmlwidget} datatable(iris) `` ``` # Workaround Downgrading {knitr} to 1.42 workaround the problem : ## same rendering result with knitr 1.42 ```bash $ quarto render Reprex.qmd processing file: Reprex.qmd output file: Reprex.knit.md pandoc to: html output-file: Reprex.html standalone: true section-divs: true html-math-method: mathjax wrap: none default-image-extension: png metadata document-css: false link-citations: true date-format: long lang: en title: ReprEx htmlwidget Output created: Reprex.html $ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.353 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.16 (Conda) Path: /usr/local/Caskroom/miniconda/base/envs/r-reticulate/bin/python Jupyter: (None) Jupyter is not available in this Python installation. Install with conda install jupyter [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ``` # Session Info ## quarto version ```bash $ quarto -V 1.3.353 ``` ## Rstudio version Rstudio version ( as it also occurs in Rstudio ) : RStudio 2023.03.1+446 "Cherry Blossom" Release (6e31ffc3ef2a1f81d377eeccab71ddc11cfbd29e, 2023-05-09) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.03.1+446 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36 ## quarto check ```bash $ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.353 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.16 (Conda) Path: /usr/local/Caskroom/miniconda/base/envs/r-reticulate/bin/python Jupyter: (None) Jupyter is not available in this Python installation. Install with conda install jupyter [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library knitr: 1.43 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 hovering on a code annotation and the corresponding code is highlighted, there is a slider appearing at the bottom like this. Perhaps the highlighting is a tad too wide?   This is using Quarto v. 1.4.90 on Windows. Minimal example: --- format: html: code-annotations: hover --- ```{r} test <- mtcars # <1> ``` 1. Annotations ### 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.

We can use a confluence-specific shortcode to render the Page Tree Macro using a Confluence Raw Block. "Is the currently a way to create page-level Table of Contents? Perhaps specified at the Project level?" https://github.com/quarto-dev/quarto-cli/discussions/2003#discussioncomment-6001293

## Description: When publishing Confluence sites, only published changed documents. ## Steps to Reproduce: - Create a Confluence site - Publish to Confluence - Notice all pages are published - Make one edit on a single document - Publish to Confluence ### Desired Result: - Only one page is published. ### Actual Result: - The entire site is re-published ---- As posted here: https://github.com/quarto-dev/quarto-web/discussions/673#discussioncomment-6006768 "One question/feature request: Can I publish the minimal changes possible? For example, if I have 200 documents already published in Confluence using Quarto and I need to add one more, can I just publish that one document without having to re-render and publish all of them again? For example, I have Confluence integration with Slack, and every time I publish, I get notifications for all documents..."

Something like `pdf-engine: tinytex` should fail validation and we should limit valid values to pdf engines that we know and support. See #5677 List of engines: https://github.com/quarto-dev/quarto-cli/blob/912a8ac65dea297cc01082419d66e3535fbc84e5/src/config/pdf.ts#L73C1-L76

### Bug description When I create a quarto website with a single sidebar, it gets shown across all pages. However, if I add an additional sidebar entry, e.g. with `- id: dummy-sidebar`, it shows the original sidebar on only the relevant pages. (I'm running quarto version 1.3.340) Here an example setup where the sidebar displays on the home page. **_quarto.yml** ```yaml project: type: website website: sidebar: - contents: - reference/index.qmd id: reference # note that uncommenting below fixes the issue #- id: dummy-sidebar ``` **index.qmd** ``` --- title: homepage --- I am a test page ``` **reference/index.qmd** ``` --- title: reference --- I am the reference page ``` ### 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.

here: https://quarto.org/docs/websites/website-navigation.html target sets the target attribute of the link, allowing for things like new windows when clicking navbar or sidebar links.

### Bug description Thanks for the amazing work on quarto, it's been a fantastic resource for which we keep discovering new applications! First, apologies if this is not actually the best repository to report issues with quarto documentation, but this is where the link "Report an Issue with this page" points on your documentation, https://quarto.org/docs/publishing/github-pages.html, so I figured I'd start here. Maybe those docs can point to a different issue tracker if that's preferred? On that page, under [publish action](https://quarto.org/docs/publishing/github-pages.html#publish-action) the docs read: > before configuring the publishing action, it’s important that you run quarto publish gh-pages locally, once. This will create the `_publish.yml` configuration required by the subsequent invocations of the GitHub Action. To do this, run the following from within your project: I think this should be `publish.yml` without an underscore. The rest of the docs refer to it with no underscore. More importantly, I and colleagues frequently see a quarto error ``` ERROR: No _publish.yml file available (_publish.yml specifying a destination required for non-interactive publish) ``` when trying to publish with a GitHub Action. This is a confusing error, because the only mention of a `_publish.yml` file (with underscore) is the one above, which I am pretty sure is not what the error `ERROR: No _publish.yml ` is referring to. It sounds like this is a top-level config file, similar to `_quarto.yml`, but I'm not sure because I cannot find documentation describing it. It is a bit of a weird error, because it is very explicit in saying that such a file is required for non-interactive publication and yet github repositories configured to do non-interactive publishing don't have such a file, so I am worried that the error message is both spurious and asserting a requirement that is (no longer?) a requirement? I believe this is related to https://github.com/quarto-dev/quarto-actions/issues/50. Thanks for considering! ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

As discovered in #5567, some `id` attributes are using translation/content which makes it hard to track using CSS, especially in a multi-language context. It seems, Anchor.js is doing this because there is no `id` set. ~~Adding the `id` in <https://github.com/quarto-dev/quarto-cli/blob/main/src/format/html/format-html-appendix.ts#L337-L354> could solve this (not sure, if it's the right place).~~ It seems, the TypeScript `prependHeading()` probably needs an id argument for when it is used in `insertReferencesTitle()` (https://github.com/quarto-dev/quarto-cli/blob/main/src/format/html/format-html-appendix.ts#L143-L150). Generally, when "anchored" class is added, an `id` should also be set. I did not see this issue elsewhere (_i.e._, anywhere else but appendix citation) when quickly looking at the codebase. For example, the h2 title for appendix section is given the content as the `id` attribute. ````qmd --- title: "Quarto Playground" author: "Quarto" format: html citation: true lang: es --- This is a playground for Quarto. ```` <table> <tr> <th>Raw</th> <th>Processed</th> </tr> <tr> <td> ````html <div id="quarto-appendix" class="default"> <section class="quarto-appendix-contents"> <h2 class="anchored quarto-appendix-heading">Cómo citar</h2> <div> <div class="quarto-appendix-secondary-label">BibTeX</div> <pre class="sourceCode code-with-copy quarto-appendix-bibtex"> <code class="sourceCode bibtex"> @online{untitled, author = {, Quarto}, title = {Quarto Playground}, langid = {es} } </code> <button title="Copiar al portapapeles" class="code-copy-button"><i class="bi"></i></button> </pre> <div class="quarto-appendix-secondary-label">Por favor, cita este trabajo como:</div> <div id="ref-untitled" class="csl-entry quarto-appendix-citeas" role="listitem"> Quarto. n.d. <span>“Quarto Playground.”</span> </div> </div> </section> </div> ```` </td> <td> ````html <div id="quarto-appendix" class="default"> <section class="quarto-appendix-contents"> <h2 class="anchored quarto-appendix-heading" id="cómo-citar">Cómo citar<a class="anchorjs-link " aria-label="Anchor" data-anchorjs-icon="" href="#cómo-citar" style="font: 1em / 1 anchorjs-icons; margin-left: 0.1875em; padding-right: 0.1875em; padding-left: 0.1875em;"></a> </h2> <div> <div class="quarto-appendix-secondary-label">BibTeX</div> <pre class="sourceCode code-with-copy quarto-appendix-bibtex"> <code class="sourceCode bibtex"> @online{untitled, author = {, Quarto}, title = {Quarto Playground}, langid = {es} } </code> <button title="Copiar al portapapeles" class="code-copy-button"><i class="bi"></i></button> </pre> <div class="quarto-appendix-secondary-label">Por favor, cita este trabajo como:</div> <div id="ref-untitled" class="csl-entry quarto-appendix-citeas" role="listitem"> Quarto. n.d. <span>“Quarto Playground.”</span> </div> </div> </section> </div> ```` </td> </tr> </table>

### Bug description On https://quarto.org/docs/download/ not possible to download v1.4 anymore: 

### Bug description ref discussion https://github.com/quarto-dev/quarto-cli/discussions/5664 As of ver 1.4.80, Quarto does not allow the capability to 'get into' the kernel in a repl session. Quarto could implement something like a `--debug` that would allow the user to debug errors by intercepting stack traces. Or, in the case of jupyter, it could use or give kernel connection information.

### Bug description ``` # quarto use template quarto-journals/elsevier ``` Then edit paper.qmd and remove `R` code from examples in the last 2 sections, since I don't have R ``` # quarto render paper.qmd running xelatex - 1 command xelatex not found, attempting install finding package for xelatex > 1 package to install > installing xelatex (1 of 1) ERROR: tlmgr returned a non zero status code 'C:\Users\Vladimir' is not recognized as an internal or external command, operable program or batch file. ``` My home folder is "c:\Users\Vladimir Alexiev", and I guess `tlmgr` gets confused by the space in the folder name. (More precisely, I have this in the environment:) ``` # set HOME HOME=d:\ HOMEDRIVE=C: HOMEPATH=\Users\Vladimir Alexiev ``` I don't particularly want to use `xelatex`, I want to use `tinytex` as recommended at https://quarto.org/docs/output-formats/pdf-engine.html . But that leads to https://github.com/quarto-dev/quarto-cli/issues/5677 Versions: ``` # cygcheck -V cygcheck (cygwin) 3.3.4 System Checker for Cygwin # cygcheck -s ## This is a very small part, let me know if you want a full dump Cygwin Configuration Diagnostics Current System Time: Thu May 25 12:06:28 2023 Windows 10 Professional Ver 10.0 Build 19045 Cygwin DLL version info: DLL version: 3.3.4 # uname CYGWIN_NT-10.0 # quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.353 Path: C:\Program Files\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.4 Path: C:/Python310/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with py -m pip install jupyter [>] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` The full `paper.qmd` file is below: ``` --- title: Short Paper subtitle: A Short Subtitle author: - name: Alice Anonymous email: [email protected] affiliations: - id: some-tech name: Some Institute of Technology department: Department Name address: Street Address city: City state: State postal-code: Postal Code attributes: corresponding: true note: This is the first author footnote. - name: Bob Security email: [email protected] affiliations: - id: another-u name: Another University department: Department Name address: Street Address city: City state: State postal-code: Postal Code note: | Another author footnote, this is a very long footnote and it should be a really long footnote. But this footnote is not yet sufficiently long enough to make two lines of footnote text. - name: Cat Memes email: [email protected] affiliations: - ref: another-u note: Yet another author footnote. - name: Derek Zoolander email: [email protected] affilations: - ref: some-tech abstract: | This is the abstract. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vestibulum augue turpis, dictum non malesuada a, volutpat eget velit. Nam placerat turpis purus, eu tristique ex tincidunt et. Mauris sed augue eget turpis ultrices tincidunt. Sed et mi in leo porta egestas. Aliquam non laoreet velit. Nunc quis ex vitae eros aliquet auctor nec ac libero. Duis laoreet sapien eu mi luctus, in bibendum leo molestie. Sed hendrerit diam diam, ac dapibus nisl volutpat vitae. Aliquam bibendum varius libero, eu efficitur justo rutrum at. Sed at tempus elit. keywords: - keyword1 - keyword2 date: last-modified bibliography: bibliography.bib format: elsevier-pdf: keep-tex: true journal: name: Automation in Construction formatting: preprint model: 3p cite-style: super --- Please make sure that your manuscript follows the guidelines in the Guide for Authors of the relevant journal. It is not necessary to typeset your manuscript in exactly the same way as an article, unless you are submitting to a camera-ready copy (CRC) journal. For detailed instructions regarding the elsevier article class, see <https://www.elsevier.com/authors/policies-and-guidelines/latex-instructions> # Bibliography styles Here are two sample references: @Feynman1963118 @Dirac1953888. By default, natbib will be used with the `authoryear` style, set in `classoption` variable in YAML. You can sets extra options with `natbiboptions` variable in YAML header. Example ``` natbiboptions: longnamesfirst,angle,semicolon ``` There are various more specific bibliography styles available at <https://support.stmdocs.in/wiki/index.php?title=Model-wise_bibliographic_style_files>. To use one of these, add it in the header using, for example, `biblio-style: model1-num-names`. ## Using CSL If `cite-method` is set to `citeproc` in `elsevier_article()`, then pandoc is used for citations instead of `natbib`. In this case, the `csl` option is used to format the references. By default, this template will provide an appropriate style, but alternative `csl` files are available from <https://www.zotero.org/styles?q=elsevier>. These can be downloaded and stored locally, or the url can be used as in the example header. # Equations Here is an equation: $$ f_{X}(x) = \left(\frac{\alpha}{\beta}\right) \left(\frac{x}{\beta}\right)^{\alpha-1} e^{-\left(\frac{x}{\beta}\right)^{\alpha}}; \alpha,\beta,x > 0 . $$ Inline equations work as well: $\sum_{i = 2}^\infty\{\alpha_i^\beta\}$ # Figures and tables @fig-meaningless is generated # Tables Tables can also be generated, as shown in @tbl-simple example. # References {-} ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description ``` # quarto use template quarto-journals/elsevier # quarto install tool tinytex ``` Edit `paper.qmd` preamble and put that `pdf-engine`. So now it looks like: ```yaml format: elsevier-pdf: pdf-engine: tinytex keep-tex: true journal: name: Automation in Construction formatting: preprint model: 3p cite-style: super ``` Then: ``` # quarto render paper.qmd --log-level info --log log.txt --debug ## quarto render paper.qmd --log-level info --log log.txt --debug --to elsevier-pdf : same result ERROR: The format pdf does not support providing any template partials. Error: The format pdf does not support providing any template partials. at runPandoc (file:///C:/Program%20Files/Quarto/bin/quarto.js:80075:23) at async renderPandoc (file:///C:/Program%20Files/Quarto/bin/quarto.js:81042:26) at async Object.onRender (file:///C:/Program%20Files/Quarto/bin/quarto.js:86671:36) at async renderFiles (file:///C:/Program%20Files/Quarto/bin/quarto.js:86634:25) at async render (file:///C:/Program%20Files/Quarto/bin/quarto.js:90678:21) at async Command.fn (file:///C:/Program%20Files/Quarto/bin/quarto.js:90853:32) at async Command.execute (file:///C:/Program%20Files/Quarto/bin/quarto.js:8437:13) at async quarto (file:///C:/Program%20Files/Quarto/bin/quarto.js:127539:5) at async file:///C:/Program%20Files/Quarto/bin/quarto.js:127557:9 ``` A similar problem is discussed in https://github.com/quarto-dev/quarto-cli/discussions/1555 and was diagnosed by @dragonstyle to " incorrectly configuring our PDF rendering when the engine was `latexmk`". I'm trying to use `tinytex` as recommended at https://quarto.org/docs/output-formats/pdf-engine.html , and I don't have any `template-partials` in the preamble (but I guess that `quarto-journals/elsevier` uses them extensively) Versions: ``` # uname CYGWIN_NT-10.0 # quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.353 Path: C:\Program Files\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.4 Path: C:/Python310/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with py -m pip install jupyter [>] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` The complete `paper.qmd` is below: ````markdown --- title: Short Paper subtitle: A Short Subtitle author: - name: Alice Anonymous email: [email protected] affiliations: - id: some-tech name: Some Institute of Technology department: Department Name address: Street Address city: City state: State postal-code: Postal Code attributes: corresponding: true note: This is the first author footnote. - name: Bob Security email: [email protected] affiliations: - id: another-u name: Another University department: Department Name address: Street Address city: City state: State postal-code: Postal Code note: | Another author footnote, this is a very long footnote and it should be a really long footnote. But this footnote is not yet sufficiently long enough to make two lines of footnote text. - name: Cat Memes email: [email protected] affiliations: - ref: another-u note: Yet another author footnote. - name: Derek Zoolander email: [email protected] affilations: - ref: some-tech abstract: | This is the abstract. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vestibulum augue turpis, dictum non malesuada a, volutpat eget velit. Nam placerat turpis purus, eu tristique ex tincidunt et. Mauris sed augue eget turpis ultrices tincidunt. Sed et mi in leo porta egestas. Aliquam non laoreet velit. Nunc quis ex vitae eros aliquet auctor nec ac libero. Duis laoreet sapien eu mi luctus, in bibendum leo molestie. Sed hendrerit diam diam, ac dapibus nisl volutpat vitae. Aliquam bibendum varius libero, eu efficitur justo rutrum at. Sed at tempus elit. keywords: - keyword1 - keyword2 date: last-modified bibliography: bibliography.bib format: elsevier-pdf: pdf-engine: tinytex keep-tex: true journal: name: Automation in Construction formatting: preprint model: 3p cite-style: super --- Please make sure that your manuscript follows the guidelines in the Guide for Authors of the relevant journal. It is not necessary to typeset your manuscript in exactly the same way as an article, unless you are submitting to a camera-ready copy (CRC) journal. For detailed instructions regarding the elsevier article class, see <https://www.elsevier.com/authors/policies-and-guidelines/latex-instructions> # Bibliography styles Here are two sample references: @Feynman1963118 @Dirac1953888. By default, natbib will be used with the `authoryear` style, set in `classoption` variable in YAML. You can sets extra options with `natbiboptions` variable in YAML header. Example ``` natbiboptions: longnamesfirst,angle,semicolon ``` There are various more specific bibliography styles available at <https://support.stmdocs.in/wiki/index.php?title=Model-wise_bibliographic_style_files>. To use one of these, add it in the header using, for example, `biblio-style: model1-num-names`. ## Using CSL If `cite-method` is set to `citeproc` in `elsevier_article()`, then pandoc is used for citations instead of `natbib`. In this case, the `csl` option is used to format the references. By default, this template will provide an appropriate style, but alternative `csl` files are available from <https://www.zotero.org/styles?q=elsevier>. These can be downloaded and stored locally, or the url can be used as in the example header. # Equations Here is an equation: $$ f_{X}(x) = \left(\frac{\alpha}{\beta}\right) \left(\frac{x}{\beta}\right)^{\alpha-1} e^{-\left(\frac{x}{\beta}\right)^{\alpha}}; \alpha,\beta,x > 0 . $$ Inline equations work as well: $\sum_{i = 2}^\infty\{\alpha_i^\beta\}$ # Figures and tables @fig-meaningless is generated # Tables Tables can also be generated, as shown in @tbl-simple example. # References {-} ```` ### 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.

Pull documents from Confluence, converting the documents to local qmd files in a Quarto Confluence project. I could imagine a collaboration workflow in which someone edits in Confluence and I run a command to pull in their changes, make my own edits on top of theirs and then run quarto publish confluence https://github.com/quarto-dev/quarto-cli/discussions/2003#discussioncomment-5996371

### Bug description ``` # quarto help Usage: quarto Version: 1.3.124 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. ``` The above doesn't mention the `list` command described here: https://quarto.org/docs/output-formats/pdf-engine.html#managing-tex . The command itself works fine: ``` # quarto list -h Usage: quarto list <type> Version: 1.3.124 Description: Lists an extension or global dependency. Options: -h, --help - Show this help. --log <level> - Path to log file --log-level <level> - Log level (info, warning, error, critical) --log-format <format> - Log format (plain, json-stream) --quiet - Suppress console output. --profile - Active project profile(s) Commands: help [command] - Show this help or the help of a sub-command. Examples: List installed extensions: quarto list extensions List global tools: quarto list tools # quarto list tools [>] Inspecting tools Tool Status Installed Latest tinytex Up to date v2023.05 v2023.05 ``` Versions: ``` # uname CYGWIN_NT-10.0 # quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 2.19.2: OK Dart Sass version 1.32.8: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.124 Path: C:\Program Files\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.4 Path: C:/Python310/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with py -m pip install jupyter [>] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### 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 dynamically created tabs that contain figures with `purrr::walk`. In the past, I think `fig.asp` worked. But now including `fig.asp` in the chunk options doesn't display the tabs. Here is the reproducible code: ```` --- title: "fig.asp breaks panel-tabset" format: html --- ```{r setup, include=FALSE} library(tidyverse) df=iris fig_fxn = function(x){ df %>% filter(Species==x) %>% ggplot(aes(Sepal.Length)) + geom_histogram() } ``` ## first tab with no fig.asp ::: {.panel-tabset} ```{r } #| output: asis levels(df$Species) %>% walk( function(x){ cat(paste("###", x, "\n")) fig_fxn(x) %>% print() } ) ``` ::: ## second tab with fig.asp ::: {.panel-tabset} ```{r fig.asp=.25} #| output: asis levels(df$Species) %>% walk( function(x){ cat(paste("###", x, "\n")) fig_fxn(x) %>% print() } ) ``` ::: ```` **RStudio IDE Version** RStudio 2023.03.1+446 "Cherry Blossom" Release (6e31ffc3ef2a1f81d377eeccab71ddc11cfbd29e, 2023-05-09) for windows Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.03.1+446 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36 **Operation System** Edition Windows 10 Pro Version 21H2 Installed on ‎9/‎12/‎2020 OS build 19044.2965 Experience Windows Feature Experience Pack 1000.19041.1000.0 **quarto check output** [>] Checking Quarto installation......OK Version: 1.0.37 Path: C:\Users\negat\AppData\Local\Programs\Quarto\bin\ CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.6 Path: C:/Users/negat/AppData/Local/Programs/Python/Python39/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with py -m pip install jupyter There is an unactivated Python environment in miniconda3. Did you forget to activate it? [>] Checking R installation...........OK Version: 4.3.0 Path: C:/PROGRA~1/R/R-43~1.0 LibPaths: - C:/Users/negat/AppData/Local/R/win-library/4.3 - C:/Program Files/R/R-4.3.0/library 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 If we have the following code inside of a Lua filter that is included as a `quarto` extension: ```lua -- Sample initialization local example_text = [[ <script> // the hello world program document.write('Hello, World!'); </script> ]] -- Insert the web initialization -- https://quarto.org/docs/extensions/lua-api.html#includes quarto.doc.include_text("in-header", example_text) ``` The `quarto.doc.include_text()` fails to include the text inside of the `header` under the `revealjs` format. However, it works under the `html` format option. Per the Lua documentation at: <https://quarto.org/docs/extensions/lua-api.html#includes> I feel like this should be a bug as the `revealjs` format is a version of an `html` document. You can experiment and see more details on the `quarto.doc.include_text()` use with the filter here: https://github.com/coatless/quarto-ext-revealjs-bug ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

Using callouts in the margin causes some inconsistent indentation behaviour with headers. If I place the callout like so: ````md --- title: "doc" format: html: self-contained: true page-layout: full --- # weird indentation when page-layout: full ::::{.column-margin} :::{.callout-note} ## SIDE CALLOUT Some text ::: :::: # Correct indentation Some more text ```` I get the following: <img width="1203" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/18472598/aa073af1-24f4-48ff-a588-08e5e17bddd4"> If I comment out `page-layout: full` I get this: <img width="1099" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/18472598/58bfdf63-72ba-40c9-8c00-e41d73257909"> Similarly if I remove the callout but keep the page-layout as full I get a normal output. I am using vscode ``` quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.353 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.16 (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. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description In Quarto 1.4, when creating callouts in a shortcode, the necessary "code" doesn't make it to the latex. The callout gets printed but without the box around it. In html I have the impression that the callout doesn't show at all. I have created a small extension that showcases this : [https://github.com/Nenuial/callout-test](https://github.com/Nenuial/callout-test) It can be installed using `quarto add nenuial/callout-test` The shortcode is `{{< callout-test >}}` Quarto check information on MacOS: ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.84 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.3 Path: /usr/local/opt/[email protected]/bin/python3.11 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.1 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 Using Quarto 1.3.340 on macOS Given the Quarto document: ````markdown --- title: raw --- ```{=html} <p id="raw" <!-- this is an important comment --> class="raw" > apples are red. </p> ``` ```` This content is rendered to look like: <img width="281" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/206ecf21-ffe8-44b1-8758-1d3458c20e4a"> Asking Quarto to process the file: ```bash quarto pandoc raw.qmd -f markdown -t html ``` is fine: ```html <p id="raw" <!-- this is an important comment --> class="raw" > apples are red. </p> ``` The generated HTML by Quarto (extracted from the full doc): ```html <p id="raw" <!--="" this="" is="" an="" important="" comment="" --=""> class="raw" &gt; apples are red. </p> ``` The presence of the HTML comment is causing trouble. Without that comment, Quarto can handle this content without 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: 1.3.340 Path: /Applications/RStudio.app/Contents/Resources/app/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description The hover feature for cross-references of sections, equations, etc. doesn't work for me when compiling books. No errors are given, just nothing happens when hovering the links. If I compile a standalone document such as: --- format: html --- # Introduction This is a book created from markdown and executable code. See @knuth84 for additional discussion of literate programming. In @sec-test something will happen. ## Test {#sec-test} Here's an equation $$ x^2=1 $$ {#eq-test} In @eq-test there's an equation. then it works fine. If I instead `quarto create project book` and include the following as a chapter # Introduction This is a book created from markdown and executable code. See @knuth84 for additional discussion of literate programming. In @sec-test something will happen. ## Test {#sec-test} Here's an equation $$ x^2=1 $$ {#eq-test} In @eq-test there's an equation. then hovering doesn't work for the section and equation reference. This is using Quarto 1.4.84 on 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. - [ ] 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 With the newest Quarto version (1.4.84) on Windows, I now get an error when trying to label a table created with `gt()`. A minimal example: --- format: html --- # Title ```{r} #| echo: false #| tbl-cap: "Caption." #| label: tbl-test library(gt) gt(mtcars) ``` which results in this error: Error running filter C:/Users/au234616/AppData/Local/Programs/Quarto/share/filters/main.lua: ...616/AppData/Local/Programs/Quarto/share/filters/main.lua:9301: attempt to call a string value (field 'html_table_caption') stack traceback: ...616/AppData/Local/Programs/Quarto/share/filters/main.lua:9139: in local 'fn' ...616/AppData/Local/Programs/Quarto/share/filters/main.lua:2120: in function <...616/AppData/Local/Programs/Quarto/share/filters/main.lua:2114> (...tail calls...) [C]: in ? [C]: in method 'walk' ...616/AppData/Local/Programs/Quarto/share/filters/main.lua:178: in function 'run_emulated_filter' ...616/AppData/Local/Programs/Quarto/share/filters/main.lua:566: in local 'callback' ...616/AppData/Local/Programs/Quarto/share/filters/main.lua:577: in upvalue 'run_emulated_filter_chain' ...616/AppData/Local/Programs/Quarto/share/filters/main.lua:610: in function <...616/AppData/Local/Programs/Quarto/share/filters/main.lua:607> stack traceback: ...616/AppData/Local/Programs/Quarto/share/filters/main.lua:178: in function 'run_emulated_filter' ...616/AppData/Local/Programs/Quarto/share/filters/main.lua:566: in local 'callback' ...616/AppData/Local/Programs/Quarto/share/filters/main.lua:577: in upvalue 'run_emulated_filter_chain' ...616/AppData/Local/Programs/Quarto/share/filters/main.lua:610: in function <...616/AppData/Local/Programs/Quarto/share/filters/main.lua:607> ### 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.

Attempt to setup a local dev environment for Confluence Data Center. ## Testing Notes - [Confluence Docker Container](https://hub.docker.com/r/atlassian/confluence-server) with [PostgreSQL 15](https://postgresapp.com/documentation/) - Version: `[Atlassian Confluence](https://www.atlassian.com/software/confluence) 8.3.0-tinymce6-m01`. This appears to be the [latest version](https://confluence.atlassian.com/doc/confluence-8-3-release-notes-1236928237.html). ## Differences - Diverging CSF between Cloud and Data Center (not formally documented, see below) - Diverging REST API calls between [Cloud](https://developer.atlassian.com/cloud/confluence/rest/v1/intro/#auth) and [Data Center](https://developer.atlassian.com/server/confluence/confluence-server-rest-api/) [Limited DC API Reference](https://docs.atlassian.com/ConfluenceServer/rest/8.3.1/#api/content-createContent) - Diverging Authentication Schemes [Cloud](https://developer.atlassian.com/cloud/confluence/basic-auth-for-rest-apis/) and [Data Center](https://confluence.atlassian.com/enterprise/using-personal-access-tokens-1026032365.html) ## Performance - ~6 minutes startup time - Very slow page loading and navigation ## Resources - https://docs.atlassian.com/ (note I don't see 8.3 listed for docs) - https://developer.atlassian.com/server/confluence/confluence-server-rest-api/ - https://confluence.atlassian.com/enterprise/using-personal-access-tokens-1026032365.html ## Diverging CSF between Cloud and Data Center ### Visual Editor  Cloud  Data Center ### 3x3 Table CSF Differences #### Cloud ```` <p>Hello World - Cloud</p> <table data-layout="default" ac:local-id="6dd03c13-cc0e-43d6-ab64-7d0c0f25b56b"> <tbody> <tr> <th> <p /></th> <th> <p /></th> <th> <p /></th></tr> <tr> <td> <p /></td> <td> <p /></td> <td> <p /></td></tr> <tr> <td> <p /></td> <td> <p /></td> <td> <p /></td></tr></tbody></table> <p /> ```` Data Center ```` <p>Hello World - Data Center</p> <p><br /></p> <table><colgroup><col /><col /><col /></colgroup> <tbody> <tr> <th scope="col"><br /></th> <th scope="col"><br /></th> <th scope="col"><br /></th></tr> <tr> <td><br /></td> <td><br /></td> <td><br /></td></tr> <tr> <td><br /></td> <td><br /></td> <td><br /></td></tr></tbody></table> ```` ### Cloud Quarto-Generated Table CSF Test [From this test doc in cloud.](https://allenmanning.atlassian.net/wiki/spaces/QUARTOCONF/pages/32964644/Tables+-+Doc) ```` <h2>Overview</h2> <p>Quarto includes a number of features aimed at making it easy to to author and customize markdown table output, including:</p> <ul> <li> <p>Specifying column alignment and widths.</p></li> <li> <p>Providing captions, subcaptions, and cross-references.</p></li> <li> <p>Generating tables dynamically from executable code cells.</p></li></ul> <p>This article covers using these features in-depth.</p> <h2>Markdown Tables</h2> <p>The most commonly used markdown table is known as a pipe table. Pipe tables support specifying per column alignment as well as captions. For example:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="b3bd32d6-6297-4d36-ad2a-c65a5bade675"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[| Default | Left | Right | Center | |---------|:-----|------:|:------:| | 12 | 12 | 12 | 12 | | 123 | 123 | 123 | 123 | | 1 | 1 | 1 | 1 | : Demonstration of pipe table syntax]]></ac:plain-text-body></ac:structured-macro> <p>Here is the table rendered to HTML:</p> <table data-layout="default" ac:local-id="089c4898-9a1a-40fc-9911-f71a8141a658"><colgroup><col style="width: 170.0px;" /><col style="width: 170.0px;" /><col style="width: 170.0px;" /><col style="width: 170.0px;" /></colgroup> <tbody> <tr> <th> <p>Default</p></th> <th> <p>Left</p></th> <th> <p style="text-align: right;">Right</p></th> <th> <p style="text-align: center;">Center</p></th></tr> <tr> <td> <p>12</p></td> <td> <p>12</p></td> <td> <p style="text-align: right;">12</p></td> <td> <p style="text-align: center;">12</p></td></tr> <tr> <td> <p>123</p></td> <td> <p>123</p></td> <td> <p style="text-align: right;">123</p></td> <td> <p style="text-align: center;">123</p></td></tr> <tr> <td> <p>1</p></td> <td> <p>1</p></td> <td> <p style="text-align: right;">1</p></td> <td> <p style="text-align: center;">1</p></td></tr></tbody></table> <p> Demonstration of pipe table syntax </p> <p>The beginning and ending pipe characters are optional, but pipes are required between all columns. The colons indicate column alignment as shown. The header cannot be omitted, however you can simulate a headerless table by including a header with blank cells.</p> <p>Since the pipes indicate column boundaries, columns need not be vertically aligned, as they are in the above example. So, this is a perfectly legal (though ugly) pipe table:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="65d5cb5d-19a7-4020-83b7-e48e0c6b90e1"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[fruit| price -----|-----: apple|2.05 pear|1.37 orange|3.09]]></ac:plain-text-body></ac:structured-macro> <table data-layout="default" ac:local-id="a07f78f0-0858-4726-8860-d4a82476ddbb"><colgroup><col style="width: 340.0px;" /><col style="width: 340.0px;" /></colgroup> <tbody> <tr> <th> <p>fruit</p></th> <th> <p style="text-align: right;">price</p></th></tr> <tr> <td> <p>apple</p></td> <td> <p style="text-align: right;">2.05</p></td></tr> <tr> <td> <p>pear</p></td> <td> <p style="text-align: right;">1.37</p></td></tr> <tr> <td> <p>orange</p></td> <td> <p style="text-align: right;">3.09</p></td></tr></tbody></table> <p>The cells of pipe tables cannot contain block elements like paragraphs and lists, and cannot span multiple lines. If a pipe table contains a row whose markdown content is wider than the column width (see <code>columns</code> option), then the table will take up the full text width and the cell contents will wrap, with the relative cell widths determined by the number of dashes in the line separating the table header from the table body.</p> <p>For example <code>---|-</code> would make the first column 3/4 and the second column 1/4 of the full text width. On the other hand, if no lines are wider than column width, then cell contents will not be wrapped, and the cells will be sized to their contents.</p> <h3>Authoring</h3> <p>For simple tables with only a few cells it&rsquo;s straightforward to create them directly in markdown. As tables get larger, it makes sense to use an authoring tool. Some table authoring tools to consider include:</p> <table data-layout="default" ac:local-id="7617e19d-8685-4ead-b02e-0048a7745799"><colgroup><col style="width: 340.0px;" /><col style="width: 340.0px;" /></colgroup> <tbody> <tr> <td> <p><a href="https://tablesgenerator.com/markdown_tables">TablesGenerator</a></p></td> <td> <p>Online tool for generating markdown tables</p></td></tr> <tr> <td> <p><a href="https://www.emacswiki.org/emacs/TableMode">Emacs TableMode</a></p></td> <td> <p>Text based table creation and editing capabilities for Emacs.</p></td></tr> <tr> <td> <p><a href="/docs/visual-editor/content.qmd#editing-tables">Quarto Visual Editor</a></p></td> <td> <p>Visual editor for <code>.qmd</code> files with table editing support.</p></td></tr></tbody></table> <h2>Column Widths</h2> <p><span style="color: rgb(255,165,0);">Not Yet Supported - Confluence parses-out %-based styling when saving to CFT</span> <a href="https://github.com/allenmanning/confluence/issues/24">24</a></p> <p>Above we describe a means of specifying column widths using the relative number of dashes in each column header (e.g.&nbsp;<code>---|-</code> to get a 75% / 25% split for a two-column table).</p> <p>You can also explicitly specify columns widths using the <code>tbl-colwidths</code> attribute or document-level option. For an individual markdown table, add the attribute after the caption. For example:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="25862faa-5d7a-43ac-b7be-a23235e0af7f"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[| fruit | price | |--------|--------| | apple | 2.05 | | pear | 1.37 | | orange | 3.09 | : Fruit prices {tbl-colwidths="[75,25]"}]]></ac:plain-text-body></ac:structured-macro> <table data-layout="default" ac:local-id="9c44d28d-5b6c-40bd-84bb-9b570699479d"><colgroup><col style="width: 340.0px;" /><col style="width: 340.0px;" /></colgroup> <tbody> <tr> <th> <p>fruit</p></th> <th> <p>price</p></th></tr> <tr> <td> <p>apple</p></td> <td> <p>2.05</p></td></tr> <tr> <td> <p>pear</p></td> <td> <p>1.37</p></td></tr> <tr> <td> <p>orange</p></td> <td> <p>3.09</p></td></tr></tbody></table> <p> Fruit prices </p> <p>If your table doesn&rsquo;t have a caption, then you can still specify only <code>tbl-colwidths</code>:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="4474222d-7c4e-4318-ab7b-6ca2321bd7c1"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[: {tbl-colwidths="[75,25]"}]]></ac:plain-text-body></ac:structured-macro> <h2>Cross References</h2> <p><span style="color: rgb(255,165,0);">Not Yet Supported - Table Cross References</span> <a href="https://github.com/allenmanning/confluence/issues/25">25</a></p> <p>For tables produced by executable code cells, include a label with a <code>tbl-</code> prefix to make them cross-referenceable. For example:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="ae22fc61-a0b5-4ad5-aa5a-669b8029906b"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[```{python} #| label: tbl-planets #| tbl-cap: Planets from IPython.display import Markdown from tabulate import tabulate table = [["Sun",696000,1989100000], ["Earth",6371,5973.6], ["Moon",1737,73.5], ["Mars",3390,641.85]] Markdown(tabulate( table, headers=["Planet","R (km)", "mass (x 10^29 kg)"] )) ``` ]]></ac:plain-text-body></ac:structured-macro> <table data-layout="default" ac:local-id="da588703-3b80-4546-9a67-6839343bf362"><colgroup><col style="width: 226.67px;" /><col style="width: 226.67px;" /><col style="width: 226.67px;" /></colgroup> <tbody> <tr> <th> <p>Planet</p></th> <th> <p style="text-align: right;">R (km)</p></th> <th> <p style="text-align: right;">mass (x 10^29 kg)</p></th></tr> <tr> <td> <p>Sun</p></td> <td> <p style="text-align: right;">696000</p></td> <td> <p style="text-align: right;">1.9891e+09</p></td></tr> <tr> <td> <p>Earth</p></td> <td> <p style="text-align: right;">6371</p></td> <td> <p style="text-align: right;">5973.6</p></td></tr> <tr> <td> <p>Moon</p></td> <td> <p style="text-align: right;">1737</p></td> <td> <p style="text-align: right;">73.5</p></td></tr> <tr> <td> <p>Mars</p></td> <td> <p style="text-align: right;">3390</p></td> <td> <p style="text-align: right;">641.85</p></td></tr></tbody></table> <p> Table&nbsp;1: Planets </p> <p>For markdown tables, add a caption below the table, then include a <code>#tbl-</code> label in braces at the end of the caption. For example:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="bb6269c4-8dea-49c8-8292-b3ecaafdd8fd"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[| Col1 | Col2 | Col3 | |------|------|------| | A | B | C | | E | F | G | | A | G | G | : My Caption {#tbl-letters} See @tbl-letters.]]></ac:plain-text-body></ac:structured-macro> <p>Which looks like this when rendered to HTML:</p> <table data-layout="default" ac:local-id="b6d5ad50-57be-4e66-b609-cc19b15adb84"><colgroup><col style="width: 226.67px;" /><col style="width: 226.67px;" /><col style="width: 226.67px;" /></colgroup> <tbody> <tr> <th> <p>Col1</p></th> <th> <p>Col2</p></th> <th> <p>Col3</p></th></tr> <tr> <td> <p>A</p></td> <td> <p>B</p></td> <td> <p>C</p></td></tr> <tr> <td> <p>E</p></td> <td> <p>F</p></td> <td> <p>G</p></td></tr> <tr> <td> <p>A</p></td> <td> <p>G</p></td> <td> <p>G</p></td></tr></tbody></table> <p> Table&nbsp;2: My Caption </p> <p>See <a href="/wiki/download/attachments/32964644/Table%C2%A02?api=v2">#tbl-letters</a>.</p> <h3>Subtables</h3> <p>You may want to create a composition of several sub-tables. To do this, create a div with a main identifier, then apply sub-identifiers (and optional caption text) to the contained tables. For example:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="8c910d2d-9941-47fa-b66d-9386044b7168"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[::: {#tbl-panel layout-ncol=2} | Col1 | Col2 | Col3 | |------|------|------| | A | B | C | | E | F | G | | A | G | G | : First Table {#tbl-first} | Col1 | Col2 | Col3 | |------|------|------| | A | B | C | | E | F | G | | A | G | G | : Second Table {#tbl-second} Main Caption ::: See @tbl-panel for details, especially @tbl-second.]]></ac:plain-text-body></ac:structured-macro> <p>Which looks like this when rendered to HTML:</p> <table data-layout="default" ac:local-id="640b2608-cfd9-4784-b178-dd703e42d185"><colgroup><col style="width: 340.0px;" /><col style="width: 340.0px;" /></colgroup> <tbody> <tr> <td> <table style="width: 98.0%;"> <colgroup> <col style="width: 32.0%;" /> <col style="width: 32.0%;" /> <col style="width: 32.0%;" /> </colgroup> <thead> <tr class="header"> <th>Col1</th> <th>Col2</th> <th>Col3</th> </tr> </thead> <tbody> <tr class="odd"> <td>A</td> <td>B</td> <td>C</td> </tr> <tr class="even"> <td>E</td> <td>F</td> <td>G</td> </tr> <tr class="odd"> <td>A</td> <td>G</td> <td>G</td> </tr> </tbody> </table> <p style="text-align: center;"> (a) First Table </p></td> <td> <table style="width: 98.0%;"> <colgroup> <col style="width: 32.0%;" /> <col style="width: 32.0%;" /> <col style="width: 32.0%;" /> </colgroup> <thead> <tr class="header"> <th>Col1</th> <th>Col2</th> <th>Col3</th> </tr> </thead> <tbody> <tr class="odd"> <td>A</td> <td>B</td> <td>C</td> </tr> <tr class="even"> <td>E</td> <td>F</td> <td>G</td> </tr> <tr class="odd"> <td>A</td> <td>G</td> <td>G</td> </tr> </tbody> </table> <p style="text-align: center;"> (b) Second Table </p></td></tr></tbody></table> <p>Table&nbsp;3: Main Caption</p> <p>See <a href="/wiki/download/attachments/32964644/Table%C2%A03?api=v2">#tbl-panel</a> for details, especially <a>#tbl-second</a>.</p> <p>Note that the &ldquo;Main Caption&rdquo; for the table is provided as the last block within the containing div.</p> <h2>Caption Location</h2> <p><span style="color: rgb(255,165,0);">Not Yet Supported - Caption Location</span> <a href="https://github.com/allenmanning/confluence/issues/26">26</a></p> <p>By default, table captions are positioned above tables. You can modify this behavior using the <code>tbl-cap-location</code> option. For example:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="c742d22e-bb21-4008-a6b2-55db138ce7ff"><ac:parameter ac:name="language">yaml</ac:parameter><ac:plain-text-body><![CDATA[--- tbl-cap-location: top ---]]></ac:plain-text-body></ac:structured-macro> <p>Note that this option is specified at the top level so that it can be shared by both PDF and HTML formats. If you are only targeting a single format you can place it alongside other <code>format</code> specific options.</p> <p>Valid values for the caption location include:</p> <table data-layout="default" ac:local-id="612768bf-83eb-4a7c-bbb6-afe6fe9f9130"><colgroup><col style="width: 340.0px;" /><col style="width: 340.0px;" /></colgroup> <tbody> <tr> <th> <p>Value</p></th> <th> <p>Description</p></th></tr> <tr> <td> <p><code>top</code></p></td> <td> <p>Position the caption above the table.</p></td></tr> <tr> <td> <p><code>bottom</code></p></td> <td> <p>Position the caption below the table.</p></td></tr> <tr> <td> <p><code>margin</code></p></td> <td> <p>Position the caption in the margin.</p></td></tr></tbody></table> <p>See the article on <a href="article-layout.qmd#margin-captions">Article Layout</a> for additional details on placing captions in the margin.</p> <h2>Computations</h2> <p>All of the options described above work for tables produced by executable code cells. For example, here we use the Python <a href="https://pypi.org/project/tabulate/">tabulate</a> package along with the <code>Markdown()</code> function from the IPython <a href="https://ipython.readthedocs.io/en/stable/api/generated/IPython.display.html#">display</a> module to print a markdown table:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="5eaa6853-402f-49d0-bbc2-0606e4a2bb4b"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[```{python} #| label: tbl-planet-measures #| tbl-cap: Planets from IPython.display import Markdown from tabulate import tabulate table = [["Sun",696000,1989100000], ["Earth",6371,5973.6], ["Moon",1737,73.5], ["Mars",3390,641.85]] Markdown(tabulate( table, headers=["Planet","R (km)", "mass (x 10^29 kg)"] )) ``` ]]></ac:plain-text-body></ac:structured-macro> <table data-layout="default" ac:local-id="daa933db-11ad-46b2-880f-451525c6bed8"><colgroup><col style="width: 107.0px;" /><col style="width: 399.0px;" /><col style="width: 253.0px;" /></colgroup> <tbody> <tr> <th> <p>Planet</p></th> <th> <p style="text-align: right;">R (km)</p></th> <th> <p style="text-align: right;">mass (x 10^29 kg)</p></th></tr> <tr> <td> <p>Sun</p></td> <td> <p style="text-align: right;">696000</p></td> <td> <p style="text-align: right;">1.9891e+09</p></td></tr> <tr> <td> <p>Earth</p></td> <td> <p style="text-align: right;">6371</p></td> <td> <p style="text-align: right;">5973.6</p></td></tr> <tr> <td> <p>Moon</p></td> <td> <p style="text-align: right;">1737</p></td> <td> <p style="text-align: right;">73.5</p></td></tr> <tr> <td> <p>Mars</p></td> <td> <p style="text-align: right;">3390</p></td> <td> <p style="text-align: right;">641.85</p></td></tr></tbody></table> <p> Table&nbsp;4: Planets </p> <p>Here we apply the <code>tbl-cap</code> and <code>tbl-colwidths</code> options to a code cell that uses the knitr <code>kable()</code> function to write a markdown table:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="420e61e1-ba15-4faf-9a8f-57c0f0a921f0"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[```{r} #| label: tbl-cars #| tbl-cap: "Cars" #| tbl-colwidths: [60,40] library(knitr) kable(head(cars)) ```]]></ac:plain-text-body></ac:structured-macro> <p>If your code cell produces multiple tables, you can also specify subcaptions and layout using cell options:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="e93c7f19-c10b-4bf2-a9a4-00b4e90927f1"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[```{r} #| label: tbl-example #| tbl-cap: "Example" #| tbl-subcap: #| - "Cars" #| - "Pressure" #| layout-ncol: 2 #| echo: fenced library(knitr) kable(head(cars)) kable(head(pressure)) ```]]></ac:plain-text-body></ac:structured-macro> <h2>Grid Tables</h2> <p>Grid tables are a more advanced type of markdown tables that allow arbitrary block elements (multiple paragraphs, code blocks, lists, etc.). For example:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="6eddf26a-9810-477f-a9b3-de2e3d67618d"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[+---------------+---------------+--------------------+ | Fruit | Price | Advantages | +===============+===============+====================+ | Bananas | $1.34 | - built-in wrapper | | | | - bright color | +---------------+---------------+--------------------+ | Oranges | $2.10 | - cures scurvy | | | | - tasty | +---------------+---------------+--------------------+ : Sample grid table.]]></ac:plain-text-body></ac:structured-macro> <p>The row of <code>=</code>s separates the header from the table body, and can be omitted for a headerless table. Cells that span multiple columns or rows are not supported.</p> <p>This is what the table looks like when rendered to markdown:</p> <table data-layout="full-width" ac:local-id="39a920dc-f4fd-43ab-9238-7b8406a4903c"><colgroup><col style="width: 214.02px;" /><col style="width: 214.02px;" /><col style="width: 301.57px;" /></colgroup> <tbody> <tr> <th> <p>Fruit</p></th> <th> <p>Price</p></th> <th> <p>Advantages</p></th></tr> <tr> <td> <p>Bananas</p></td> <td> <p>$1.34</p></td> <td> <ul> <li> <p>built-in wrapper</p></li> <li> <p>bright color</p></li></ul></td></tr> <tr> <td> <p>Oranges</p></td> <td> <p>$2.10</p></td> <td> <ul> <li> <p>cures scurvy</p></li> <li> <p>tasty</p></li></ul></td></tr></tbody></table> <p> Sample grid table. </p> <p>Alignments can be specified as with pipe tables, by putting colons at the boundaries of the separator line after the header:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="fb2f6f88-095f-4086-b0af-494cdc8a8400"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[+---------------+---------------+--------------------+ | Right | Left | Centered | +==============:+:==============+:==================:+ | Bananas | $1.34 | built-in wrapper | +---------------+---------------+--------------------+]]></ac:plain-text-body></ac:structured-macro> <table data-layout="wide" ac:local-id="bf1ce2b6-76c3-480e-a45f-218502f24f18"><colgroup><col style="width: 208.38px;" /><col style="width: 208.38px;" /><col style="width: 274.69px;" /></colgroup> <tbody> <tr> <th> <p style="text-align: right;">Right</p></th> <th> <p>Left</p></th> <th> <p style="text-align: center;">Centered</p></th></tr> <tr> <td> <p style="text-align: right;">Bananas</p></td> <td> <p>$1.34</p></td> <td> <p style="text-align: center;">built-in wrapper</p></td></tr></tbody></table> <p>For headerless tables, the colons go on the top line instead:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="30d85944-ceff-41a8-830d-766e3b65a529"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[+--------------:+:--------------+:------------------:+ | Right | Left | Centered | +---------------+---------------+--------------------+]]></ac:plain-text-body></ac:structured-macro> <table data-layout="wide" ac:local-id="391f234b-aa13-4261-bcbd-1daeda0e0457"><colgroup><col style="width: 208.38px;" /><col style="width: 208.38px;" /><col style="width: 274.69px;" /></colgroup> <tbody> <tr> <td> <p style="text-align: right;">Right</p></td> <td> <p>Left</p></td> <td> <p style="text-align: center;">Centered</p></td></tr></tbody></table> <p>Note that grid tables are quite awkward to write with a plain text editor (because unlike pipe tables, the column indicators must align). Here are some tools that can assist with creating grid tables:</p> <ul> <li> <p>Emacs&rsquo; <a href="https://www.gnu.org/software/emacs/manual/html_node/emacs/Text-Based-Tables.html">table-mode</a> (<code>M-x table-insert</code>)</p></li> <li> <p>Quarto <a href="https://quarto.org/docs/visual-editor/content.html#editing-tables">Visual Editor</a></p></li></ul> ```` In Data Center using a Source Editor plugin, attempt to paste in the same CSF. Result:  - Visual editor seems to render it. - Failure on save: ```` Generic error: {"readyState":4,"responseText":"{\"statusCode\":400,\"data\":{\"authorized\":true,\"valid\":false,\"allowedInReadOnlyMode\":true,\"errors\":[{\"message\":{\"key\":\"xhtml.editor.parse.failed\",\"args\":[\"7\",\"214\",\"Undeclared namespace prefix &quot;ac&quot; (for attribute &quot;local-id&quot;)\\n at [row,col {unknown-source}]: [7,214]\"]}}],\"successful\":false},\"message\":\"Validation failure when converting format\",\"reason\":\"Bad Request\"}","responseJSON":{"statusCode":400,"data":{"authorized":true,"valid":false,"allowedInReadOnlyMode":true,"errors":[{"message":{"key":"xhtml.editor.parse.failed","args":["7","214","Undeclared namespace prefix &quot;ac&quot; (for attribute &quot;local-id&quot;)\n at [row,col {unknown-source}]: [7,214]"]}}],"successful":false},"message":"Validation failure when converting format","reason":"Bad Request"},"status":400,"statusText":"error"} ```` Seems to be an unsupported CSF entity, which suggests an older CSF and editor version. After the error, cancelling and re-editing allowed it to be saved with some issues...  Converted Data Center Storage format after an attempted save of cloud CSF, fail save, exit, and re-edit. ```` <h2>Overview</h2> <p>Quarto includes a number of features aimed at making it easy to to author and customize markdown table output, including:</p> <ul> <li> <p>Specifying column alignment and widths.</p></li> <li> <p>Providing captions, subcaptions, and cross-references.</p></li> <li> <p>Generating tables dynamically from executable code cells.</p></li></ul> <p>This article covers using these features in-depth.</p> <h2>Markdown Tables</h2> <p>The most commonly used markdown table is known as a pipe table. Pipe tables support specifying per column alignment as well as captions. For example:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="b3bd32d6-6297-4d36-ad2a-c65a5bade675"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[| Default | Left | Right | Center | |---------|:-----|------:|:------:| | 12 | 12 | 12 | 12 | | 123 | 123 | 123 | 123 | | 1 | 1 | 1 | 1 | : Demonstration of pipe table syntax]]></ac:plain-text-body></ac:structured-macro> <p>Here is the table rendered to HTML:</p> <table class="wrapped"><colgroup><col style="width: 170.0px;" /><col style="width: 170.0px;" /><col style="width: 170.0px;" /><col style="width: 170.0px;" /></colgroup> <tbody> <tr> <th> <p>Default</p></th> <th> <p>Left</p></th> <th> <p style="text-align: right;">Right</p></th> <th> <p style="text-align: center;">Center</p></th></tr> <tr> <td> <p>12</p></td> <td> <p>12</p></td> <td> <p style="text-align: right;">12</p></td> <td> <p style="text-align: center;">12</p></td></tr> <tr> <td> <p>123</p></td> <td> <p>123</p></td> <td> <p style="text-align: right;">123</p></td> <td> <p style="text-align: center;">123</p></td></tr> <tr> <td> <p>1</p></td> <td> <p>1</p></td> <td> <p style="text-align: right;">1</p></td> <td> <p style="text-align: center;">1</p></td></tr></tbody></table> <p>Demonstration of pipe table syntax</p> <p>The beginning and ending pipe characters are optional, but pipes are required between all columns. The colons indicate column alignment as shown. The header cannot be omitted, however you can simulate a headerless table by including a header with blank cells.</p> <p>Since the pipes indicate column boundaries, columns need not be vertically aligned, as they are in the above example. So, this is a perfectly legal (though ugly) pipe table:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="65d5cb5d-19a7-4020-83b7-e48e0c6b90e1"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[fruit| price -----|-----: apple|2.05 pear|1.37 orange|3.09]]></ac:plain-text-body></ac:structured-macro> <table class="wrapped"><colgroup><col style="width: 340.0px;" /><col style="width: 340.0px;" /></colgroup> <tbody> <tr> <th> <p>fruit</p></th> <th> <p style="text-align: right;">price</p></th></tr> <tr> <td> <p>apple</p></td> <td> <p style="text-align: right;">2.05</p></td></tr> <tr> <td> <p>pear</p></td> <td> <p style="text-align: right;">1.37</p></td></tr> <tr> <td> <p>orange</p></td> <td> <p style="text-align: right;">3.09</p></td></tr></tbody></table> <p>The cells of pipe tables cannot contain block elements like paragraphs and lists, and cannot span multiple lines. If a pipe table contains a row whose markdown content is wider than the column width (see <code>columns</code> option), then the table will take up the full text width and the cell contents will wrap, with the relative cell widths determined by the number of dashes in the line separating the table header from the table body.</p> <p>For example <code>---|-</code> would make the first column 3/4 and the second column 1/4 of the full text width. On the other hand, if no lines are wider than column width, then cell contents will not be wrapped, and the cells will be sized to their contents.</p> <h3>Authoring</h3> <p>For simple tables with only a few cells it’s straightforward to create them directly in markdown. As tables get larger, it makes sense to use an authoring tool. Some table authoring tools to consider include:</p> <table class="wrapped"><colgroup><col style="width: 340.0px;" /><col style="width: 340.0px;" /></colgroup> <tbody> <tr> <td> <p><a href="https://tablesgenerator.com/markdown_tables">TablesGenerator</a></p></td> <td> <p>Online tool for generating markdown tables</p></td></tr> <tr> <td> <p><a href="https://www.emacswiki.org/emacs/TableMode">Emacs TableMode</a></p></td> <td> <p>Text based table creation and editing capabilities for Emacs.</p></td></tr> <tr> <td> <p><a href="http://localhost:8090/docs/visual-editor/content.qmd#editing-tables">Quarto Visual Editor</a></p></td> <td> <p>Visual editor for <code>.qmd</code> files with table editing support.</p></td></tr></tbody></table> <h2>Column Widths</h2> <p><span style="color: rgb(255,165,0);">Not Yet Supported - Confluence parses-out %-based styling when saving to CFT</span> <a href="https://github.com/allenmanning/confluence/issues/24">24</a></p> <p>Above we describe a means of specifying column widths using the relative number of dashes in each column header (e.g. <code>---|-</code> to get a 75% / 25% split for a two-column table).</p> <p>You can also explicitly specify columns widths using the <code>tbl-colwidths</code> attribute or document-level option. For an individual markdown table, add the attribute after the caption. For example:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="25862faa-5d7a-43ac-b7be-a23235e0af7f"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[| fruit | price | |--------|--------| | apple | 2.05 | | pear | 1.37 | | orange | 3.09 | : Fruit prices {tbl-colwidths="[75,25]"}]]></ac:plain-text-body></ac:structured-macro> <table class="wrapped"><colgroup><col style="width: 340.0px;" /><col style="width: 340.0px;" /></colgroup> <tbody> <tr> <th> <p>fruit</p></th> <th> <p>price</p></th></tr> <tr> <td> <p>apple</p></td> <td> <p>2.05</p></td></tr> <tr> <td> <p>pear</p></td> <td> <p>1.37</p></td></tr> <tr> <td> <p>orange</p></td> <td> <p>3.09</p></td></tr></tbody></table> <p>Fruit prices</p> <p>If your table doesn’t have a caption, then you can still specify only <code>tbl-colwidths</code>:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="4474222d-7c4e-4318-ab7b-6ca2321bd7c1"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[: {tbl-colwidths="[75,25]"}]]></ac:plain-text-body></ac:structured-macro> <h2>Cross References</h2> <p><span style="color: rgb(255,165,0);">Not Yet Supported - Table Cross References</span> <a href="https://github.com/allenmanning/confluence/issues/25">25</a></p> <p>For tables produced by executable code cells, include a label with a <code>tbl-</code> prefix to make them cross-referenceable. For example:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="ae22fc61-a0b5-4ad5-aa5a-669b8029906b"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[```{python} #| label: tbl-planets #| tbl-cap: Planets from IPython.display import Markdown from tabulate import tabulate table = [["Sun",696000,1989100000], ["Earth",6371,5973.6], ["Moon",1737,73.5], ["Mars",3390,641.85]] Markdown(tabulate( table, headers=["Planet","R (km)", "mass (x 10^29 kg)"] )) ``` ]]></ac:plain-text-body></ac:structured-macro> <table class="wrapped"><colgroup><col style="width: 226.67px;" /><col style="width: 226.67px;" /><col style="width: 226.67px;" /></colgroup> <tbody> <tr> <th> <p>Planet</p></th> <th> <p style="text-align: right;">R (km)</p></th> <th> <p style="text-align: right;">mass (x 10^29 kg)</p></th></tr> <tr> <td> <p>Sun</p></td> <td> <p style="text-align: right;">696000</p></td> <td> <p style="text-align: right;">1.9891e+09</p></td></tr> <tr> <td> <p>Earth</p></td> <td> <p style="text-align: right;">6371</p></td> <td> <p style="text-align: right;">5973.6</p></td></tr> <tr> <td> <p>Moon</p></td> <td> <p style="text-align: right;">1737</p></td> <td> <p style="text-align: right;">73.5</p></td></tr> <tr> <td> <p>Mars</p></td> <td> <p style="text-align: right;">3390</p></td> <td> <p style="text-align: right;">641.85</p></td></tr></tbody></table> <p>Table 1: Planets</p> <p>For markdown tables, add a caption below the table, then include a <code>#tbl-</code> label in braces at the end of the caption. For example:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="bb6269c4-8dea-49c8-8292-b3ecaafdd8fd"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[| Col1 | Col2 | Col3 | |------|------|------| | A | B | C | | E | F | G | | A | G | G | : My Caption {#tbl-letters} See @tbl-letters.]]></ac:plain-text-body></ac:structured-macro> <p>Which looks like this when rendered to HTML:</p> <table class="wrapped"><colgroup><col style="width: 226.67px;" /><col style="width: 226.67px;" /><col style="width: 226.67px;" /></colgroup> <tbody> <tr> <th> <p>Col1</p></th> <th> <p>Col2</p></th> <th> <p>Col3</p></th></tr> <tr> <td> <p>A</p></td> <td> <p>B</p></td> <td> <p>C</p></td></tr> <tr> <td> <p>E</p></td> <td> <p>F</p></td> <td> <p>G</p></td></tr> <tr> <td> <p>A</p></td> <td> <p>G</p></td> <td> <p>G</p></td></tr></tbody></table> <p>Table 2: My Caption</p> <p>See <a href="http://localhost:8090/wiki/download/attachments/32964644/Table%C2%A02?api=v2">#tbl-letters</a>.</p> <h3>Subtables</h3> <p>You may want to create a composition of several sub-tables. To do this, create a div with a main identifier, then apply sub-identifiers (and optional caption text) to the contained tables. For example:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="8c910d2d-9941-47fa-b66d-9386044b7168"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[::: {#tbl-panel layout-ncol=2} | Col1 | Col2 | Col3 | |------|------|------| | A | B | C | | E | F | G | | A | G | G | : First Table {#tbl-first} | Col1 | Col2 | Col3 | |------|------|------| | A | B | C | | E | F | G | | A | G | G | : Second Table {#tbl-second} Main Caption ::: See @tbl-panel for details, especially @tbl-second.]]></ac:plain-text-body></ac:structured-macro> <p>Which looks like this when rendered to HTML:</p> <table class="wrapped"><colgroup><col style="width: 340.0px;" /><col style="width: 340.0px;" /></colgroup> <tbody> <tr> <td> <table class="wrapped" style="width: 98.0%;" data-mce-resize="false"><colgroup> <col style="width: 32.0%;" /> <col style="width: 32.0%;" /> <col style="width: 32.0%;" /> </colgroup> <thead> <tr class="header"> <th>Col1</th> <th>Col2</th> <th>Col3</th></tr></thead> <tbody> <tr class="odd"> <td>A</td> <td>B</td> <td>C</td></tr> <tr class="even"> <td>E</td> <td>F</td> <td>G</td></tr> <tr class="odd"> <td>A</td> <td>G</td> <td>G</td></tr></tbody></table> <p style="text-align: center;">(a) First Table</p></td> <td> <table class="wrapped" style="width: 98.0%;" data-mce-resize="false"><colgroup> <col style="width: 32.0%;" /> <col style="width: 32.0%;" /> <col style="width: 32.0%;" /> </colgroup> <thead> <tr class="header"> <th>Col1</th> <th>Col2</th> <th>Col3</th></tr></thead> <tbody> <tr class="odd"> <td>A</td> <td>B</td> <td>C</td></tr> <tr class="even"> <td>E</td> <td>F</td> <td>G</td></tr> <tr class="odd"> <td>A</td> <td>G</td> <td>G</td></tr></tbody></table> <p style="text-align: center;">(b) Second Table</p></td></tr></tbody></table> <p>Table 3: Main Caption</p> <p>See <a href="http://localhost:8090/wiki/download/attachments/32964644/Table%C2%A03?api=v2">#tbl-panel</a> for details, especially <a>#tbl-second</a>.</p> <p>Note that the “Main Caption” for the table is provided as the last block within the containing div.</p> <h2>Caption Location</h2> <p><span style="color: rgb(255,165,0);">Not Yet Supported - Caption Location</span> <a href="https://github.com/allenmanning/confluence/issues/26">26</a></p> <p>By default, table captions are positioned above tables. You can modify this behavior using the <code>tbl-cap-location</code> option. For example:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="c742d22e-bb21-4008-a6b2-55db138ce7ff"><ac:parameter ac:name="language">yaml</ac:parameter><ac:plain-text-body><![CDATA[--- tbl-cap-location: top ---]]></ac:plain-text-body></ac:structured-macro> <p>Note that this option is specified at the top level so that it can be shared by both PDF and HTML formats. If you are only targeting a single format you can place it alongside other <code>format</code> specific options.</p> <p>Valid values for the caption location include:</p> <table class="wrapped"><colgroup><col style="width: 340.0px;" /><col style="width: 340.0px;" /></colgroup> <tbody> <tr> <th> <p>Value</p></th> <th> <p>Description</p></th></tr> <tr> <td> <p><code>top</code></p></td> <td> <p>Position the caption above the table.</p></td></tr> <tr> <td> <p><code>bottom</code></p></td> <td> <p>Position the caption below the table.</p></td></tr> <tr> <td> <p><code>margin</code></p></td> <td> <p>Position the caption in the margin.</p></td></tr></tbody></table> <p>See the article on <a href="http://localhost:8090/article-layout.qmd#margin-captions">Article Layout</a> for additional details on placing captions in the margin.</p> <h2>Computations</h2> <p>All of the options described above work for tables produced by executable code cells. For example, here we use the Python <a href="https://pypi.org/project/tabulate/">tabulate</a> package along with the <code>Markdown()</code> function from the IPython <a href="https://ipython.readthedocs.io/en/stable/api/generated/IPython.display.html">display</a> module to print a markdown table:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="5eaa6853-402f-49d0-bbc2-0606e4a2bb4b"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[```{python} #| label: tbl-planet-measures #| tbl-cap: Planets from IPython.display import Markdown from tabulate import tabulate table = [["Sun",696000,1989100000], ["Earth",6371,5973.6], ["Moon",1737,73.5], ["Mars",3390,641.85]] Markdown(tabulate( table, headers=["Planet","R (km)", "mass (x 10^29 kg)"] )) ``` ]]></ac:plain-text-body></ac:structured-macro> <table class="wrapped"><colgroup><col style="width: 107.0px;" /><col style="width: 399.0px;" /><col style="width: 253.0px;" /></colgroup> <tbody> <tr> <th> <p>Planet</p></th> <th> <p style="text-align: right;">R (km)</p></th> <th> <p style="text-align: right;">mass (x 10^29 kg)</p></th></tr> <tr> <td> <p>Sun</p></td> <td> <p style="text-align: right;">696000</p></td> <td> <p style="text-align: right;">1.9891e+09</p></td></tr> <tr> <td> <p>Earth</p></td> <td> <p style="text-align: right;">6371</p></td> <td> <p style="text-align: right;">5973.6</p></td></tr> <tr> <td> <p>Moon</p></td> <td> <p style="text-align: right;">1737</p></td> <td> <p style="text-align: right;">73.5</p></td></tr> <tr> <td> <p>Mars</p></td> <td> <p style="text-align: right;">3390</p></td> <td> <p style="text-align: right;">641.85</p></td></tr></tbody></table> <p>Table 4: Planets</p> <p>Here we apply the <code>tbl-cap</code> and <code>tbl-colwidths</code> options to a code cell that uses the knitr <code>kable()</code> function to write a markdown table:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="420e61e1-ba15-4faf-9a8f-57c0f0a921f0"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[```{r} #| label: tbl-cars #| tbl-cap: "Cars" #| tbl-colwidths: [60,40] library(knitr) kable(head(cars)) ```]]></ac:plain-text-body></ac:structured-macro> <p>If your code cell produces multiple tables, you can also specify subcaptions and layout using cell options:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="e93c7f19-c10b-4bf2-a9a4-00b4e90927f1"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[```{r} #| label: tbl-example #| tbl-cap: "Example" #| tbl-subcap: #| - "Cars" #| - "Pressure" #| layout-ncol: 2 #| echo: fenced library(knitr) kable(head(cars)) kable(head(pressure)) ```]]></ac:plain-text-body></ac:structured-macro> <h2>Grid Tables</h2> <p>Grid tables are a more advanced type of markdown tables that allow arbitrary block elements (multiple paragraphs, code blocks, lists, etc.). For example:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="6eddf26a-9810-477f-a9b3-de2e3d67618d"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[+---------------+---------------+--------------------+ | Fruit | Price | Advantages | +===============+===============+====================+ | Bananas | $1.34 | - built-in wrapper | | | | - bright color | +---------------+---------------+--------------------+ | Oranges | $2.10 | - cures scurvy | | | | - tasty | +---------------+---------------+--------------------+ : Sample grid table.]]></ac:plain-text-body></ac:structured-macro> <p>The row of <code>=</code>s separates the header from the table body, and can be omitted for a headerless table. Cells that span multiple columns or rows are not supported.</p> <p>This is what the table looks like when rendered to markdown:</p> <table class="wrapped"><colgroup><col style="width: 214.02px;" /><col style="width: 214.02px;" /><col style="width: 301.57px;" /></colgroup> <tbody> <tr> <th> <p>Fruit</p></th> <th> <p>Price</p></th> <th> <p>Advantages</p></th></tr> <tr> <td> <p>Bananas</p></td> <td> <p>$1.34</p></td> <td> <ul> <li> <p>built-in wrapper</p></li> <li> <p>bright color</p></li></ul></td></tr> <tr> <td> <p>Oranges</p></td> <td> <p>$2.10</p></td> <td> <ul> <li> <p>cures scurvy</p></li> <li> <p>tasty</p></li></ul></td></tr></tbody></table> <p>Sample grid table.</p> <p>Alignments can be specified as with pipe tables, by putting colons at the boundaries of the separator line after the header:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="fb2f6f88-095f-4086-b0af-494cdc8a8400"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[+---------------+---------------+--------------------+ | Right | Left | Centered | +==============:+:==============+:==================:+ | Bananas | $1.34 | built-in wrapper | +---------------+---------------+--------------------+]]></ac:plain-text-body></ac:structured-macro> <table class="wrapped"><colgroup><col style="width: 208.38px;" /><col style="width: 208.38px;" /><col style="width: 274.69px;" /></colgroup> <tbody> <tr> <th> <p style="text-align: right;">Right</p></th> <th> <p>Left</p></th> <th> <p style="text-align: center;">Centered</p></th></tr> <tr> <td> <p style="text-align: right;">Bananas</p></td> <td> <p>$1.34</p></td> <td> <p style="text-align: center;">built-in wrapper</p></td></tr></tbody></table> <p>For headerless tables, the colons go on the top line instead:</p><ac:structured-macro ac:name="code" ac:schema-version="1" ac:macro-id="30d85944-ceff-41a8-830d-766e3b65a529"><ac:parameter ac:name="language">markdown</ac:parameter><ac:plain-text-body><![CDATA[+--------------:+:--------------+:------------------:+ | Right | Left | Centered | +---------------+---------------+--------------------+]]></ac:plain-text-body></ac:structured-macro> <table class="wrapped"><colgroup><col style="width: 208.38px;" /><col style="width: 208.38px;" /><col style="width: 274.69px;" /></colgroup> <tbody> <tr> <td> <p style="text-align: right;">Right</p></td> <td> <p>Left</p></td> <td> <p style="text-align: center;">Centered</p></td></tr></tbody></table> <p>Note that grid tables are quite awkward to write with a plain text editor (because unlike pipe tables, the column indicators must align). Here are some tools that can assist with creating grid tables:</p> <ul> <li> <p>Emacs’ <a href="https://www.gnu.org/software/emacs/manual/html_node/emacs/Text-Based-Tables.html">table-mode</a> (<code>M-x table-insert</code>)</p></li> <li> <p>Quarto <a href="https://quarto.org/docs/visual-editor/content.html#editing-tables">Visual Editor</a></p></li></ul> ````

### Bug description Initially discovered when discussing in #5637, formalising as separate bug report. If the there is a multi-line `![]()` specifying a figure, it will compile successfully, but if the `fig-env` is set globally in the `_quarto.yml` then it fails to compile. If the `fig-env: bp` is remove it compiles successfully. ### `_quarto.yml` ```yaml project: type: book book: title: "testing" author: "Norah Jones" date: "23/05/2023" chapters: - index.qmd - intro.qmd - summary.qmd - references.qmd s bibliography: references.bib format: pdf: documentclass: scrreprt fig-env: bp ``` ### `intro.qmd` ```md # Introduction This is a book created from markdown and executable code. See @knuth84 for additional discussion of literate programming. { #fig-logo } ``` ### Compilation Error ```md compilation failed- error LaTeX Error: Environment bp undefined. See the LaTeX manual or LaTeX Companion for explanation. Type H <return> for immediate help. ... l.211 \begin{bp} ``` ### Offending Lines in `index.tex` ```tex \begin{bp} {\centering \includegraphics{cover.png} } \caption{\label{fig-logo}A multi-line caption. With the next line here. And and now another line.} \end{bp} ``` Testing on MacOS 13.2. ### `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: 1.3.353 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.10 (Conda) Path: /usr/local/Caskroom/miniconda/base/bin/python Jupyter: (None) Jupyter is not available in this Python installation. Install with conda install jupyter [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library knitr: 1.41 rmarkdown: 2.17 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description If I create a book project and add a navbar to it, then (as expected) the sidebar search field is removed and a search icon is added to the navbar. But If I switch to mobile view in a browser (ctrl-shift-m on Firefox), or look at the site on a mobile phone, then a search icon is added to the collapsible "sidebar" menu near the top, while the original search icon in the navbar remains. To reproduce: Create a new book project: ``` $ quarto create-project mybook --type book $ quarto preview mybook ``` Add a navbar tag to _quarto.yml as follows: ``` project: type: book book: title: "mybook" author: "Norah Jones" date: "5/23/2023" navbar: title: "My Book" chapters: - index.qmd - intro.qmd - summary.qmd - references.qmd bibliography: references.bib format: html: theme: cosmo pdf: documentclass: scrreprt ``` Switch to mobile view. A search icon is visible on the right of the collapsed menu, under the navbar which has its own search icon. OS: Kubuntu 20.04 Quarto version: 1.3.282 ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

My addition here to the wish list for quarto crossref (@cscheid :-)): a mechanism for **\tag**ging. For equations, one could keep LaTeX syntax, that is what presumably most users of such a feature already are familiar with. _Originally posted by @ute in https://github.com/quarto-dev/quarto-cli/issues/4136#issuecomment-1556118974_

### Bug description Using Quarto 1.3.340 and macOS. Given the Quarto configuration that declares an output directory: ```yaml project: output-dir: out ``` and a single `index.qmd` file: ````markdown --- title: nothing important --- this is some content. ```` Rendering this content produces the files: ``` ./index_files/ (an empty directory) ./out/index.html ./out/index_files/ ``` There is an `index_files/` directory left behind alongside the `out/` output directory. ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /Applications/RStudio.app/Contents/Resources/app/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description On Windows, when I convert a document to word using quarto 1.4.84, I get the following error:  I don't get this error with quarto 1.3.353. I'm currently in the middle of trying to get a report out. Once I've finished the submission, I will come back to this issue and submit a reproducible example. ### 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.

I found this auditing our crossref issue list: ```` --- title: foo --- ::: {#fig-histograms} ```{r} #| fig-show: hold #| fig-width: 4 #| fig-height: 3 #| layout-nrow: 1 hist(runif(100)) hist(rnorm(100)) ``` This caption is unique ::: ```` On `main`, this .qmd yields: <img width="793" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/285675/6c54f930-5eb7-4c49-bc45-c07dfbb9843f"> Note the weird centering of the code and the bad positioning of the anchor link.

### Bug description I have a markdown file like this: ```` --- title: "Report" date: last-modified --- ```{julia} #| error: true data1 = zeros(3, 3, 3) data2 = zeros(3, 3) data1[:, :, 2] .= 1.0 data2 .= data1 ``` ```{mermaid} %%| echo: false flowchart LR Main(Main) --> lib1(lib1) Main(Main) --> lib2(lib2) Main(Main) --> lib3(lib3) ``` ```` with a `_quarto.yml` like this: ``` project: preview: port: 4200 quarto-required: ">= 1.3.0" jupyter: julia-1.9 execute: output: true echo: true warning: true error: false freeze: auto eval: true cache: true ``` With this version: ``` $ quarto --version 1.3.353 ``` I get this error: ``` error: Module evaluation is still pending but there are no pending ops or dynamic imports. This situation is often caused by unresolved promises. ``` With this version: ``` $ quarto --version 1.4.84 ``` I get this error: ``` error: Top-level await promise never resolved await quarto(quartoArgs, (cmd)=>{ ^ at <anonymous> (file:///C:/Users/USERNAME/AppData/Local/Programs/Quarto/bin/quarto.js:102268:9) ``` This was the same error I was getting in this issue: https://github.com/quarto-dev/quarto-cli/issues/5580 Removing the `{mermaid}` executable block makes the error go away. I'm running this on Windows. ``` $ quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.4.84 Path: C:\Users\USERNAME\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.12 (Conda) Path: C:/Users/USERNAME/Miniconda3/python.exe Jupyter: 5.1.0 Kernels: python3, julia-1.9 [>] Checking Jupyter engine render....OK [>] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### Checklist - [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 file fails to compile with quarto 1.4.84, running under Ubuntu 22.04: ```` --- title: test format: pdf --- ```{r} missing <- function(x) x ``` ```` The error message is ```` processing file: test.qmd |................................... | 67% (unnamed-chunk-1) Quitting from lines 7-8 (test.qmd) Error in missing(options) && inherits(x, c("knit_image_paths", "html_screenshot", : invalid 'x' type in 'x && y' Calls: .main ... process_group.block -> call_block -> block_exec -> eng_r -> unlist -> sew Execution halted ```` The file compiles correctly with an Rmd extension and `output: pdf_document`. [test.zip](https://github.com/quarto-dev/quarto-cli/files/11546182/test.zip) Output of `quarto check`: [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.84 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /usr/bin/python3 Jupyter: 4.9.1 Kernels: ir, python2, python3 (|) Checking Jupyter engine render....[IPKernelApp] WARNING | debugpy_stream undefined, debugging will not be enabled [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.3.0 Path: /usr/lib/R LibPaths: - /data/rmcd/R/x86_64-pc-linux-gnu-library/4.3 - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/lib/R/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Using Quarto 1.3.340 on macOS. Given the Quarto `index.qmd` document: ````markdown 1. Some thing. 2. Another **[`GET /some/arbitrarily/long/thing`](https://example.com/api/reference/some-arbitrarily-long-thing)** thing that you want to know about. 3. Success! ```` When previewed, the link text is ... spaced-out. <img width="714" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/f68aef8a-a9e2-462a-9776-c46b5b688a91"> Workaround: Remove the newline within the fixed-font region. ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /Applications/RStudio.app/Contents/Resources/app/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Using Quarto 1.3.340 on macOS with Safari. Given the Quarto project: ```yaml project: type: website website: sidebar: - title: "important things" collapse-level: 1 contents: - text: "introduction" file: "index.qmd" - section: "R" contents: - text: "overview" file: "r.qmd" - text: "details" file: "details.qmd" ``` and empty `*.qmd` files: ```bash touch index.qmd r.qmd details.qmd ``` When previewed, the sidebar navigation for "R" allows clicking only on the text "R" and the "&gt;" marker. The remainder of the line between the text and marker is not clickable. That region does, however, does activate the "hover" for that line. This short capture shows the text becoming active on hover, but not allowing a click. https://github.com/quarto-dev/quarto-cli/assets/362187/c17a0abb-1e35-4af0-a2e9-a46371154d99 ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /Applications/RStudio.app/Contents/Resources/app/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Using Quarto 1.3.340 on macOS ````markdown * normal text * `code text` * [normal link](https://quarto.org) * [`code link`](https://quarto.org) * [`testthat::test_that`](https://quarto.org) ```` When rendered, the `code link` and `test_that` text do not differ by much; the reader might incorrectly think that there is an underscore for both, or no underscore at all. <img width="233" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/04335054-a801-4da8-a868-afc6cba32635"> ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /Applications/RStudio.app/Contents/Resources/app/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Using Quarto 1.3.340 and macOS Using a Quarto project with the YAML: ```yaml project: type: website website: sidebar: - title: "navigations" contents: - text: "apples, bananas, and cucumbers" file: "index.qmd" - text: "cucumbers salad" file: "cucumbers.qmd" - text: "roasting brussels sprouts" file: "roasting.qmd" ``` Each of `index.qmd`, `cucumbers.qmd`, and `roasting.qmd` are empty files. ```bash touch index.qmd cucumbers.qmd roasting.qmd ``` When rendered, the first heading tends to wrap. When it wraps, the line spacing makes the wrapped line look like a distinct entry, not like text that belongs with the previous line. <img width="277" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/362187/7137835e-9f68-43c5-bc44-35b75210712d"> ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.340 Path: /Applications/RStudio.app/Contents/Resources/app/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 3.6.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/3.6/Resources/library knitr: 1.42.8 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.