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### Bug description I've replicated this with the RStudio default blog template. You can view a repository here https://github.com/JoFrhwld/quarto-name I changed the [`./index.qmd`](https://github.com/JoFrhwld/quarto-name/blob/master/index.qmd) header to have a grid listing: ```yaml # ./index.qmd --- title: "blog-template" listing: contents: posts sort: "date desc" type: grid categories: true sort-ui: false filter-ui: false page-layout: full title-block-banner: true --- ``` [In one post](https://github.com/JoFrhwld/quarto-name/blob/master/posts/welcome/index.qmd), I included an image in the post body. ```yaml # posts/welcome/index.qmd --- title: "Welcome To My Blog" author: "Tristan O'Malley" date: "2023-03-15" categories: [news] --- This is the first post in a Quarto blog. Welcome!  Since this post doesn't specify an explicit `image`, the first image in the post will be used in the listing page of posts. ``` [In the other](https://github.com/JoFrhwld/quarto-name/blob/master/posts/post-with-code/index.qmd), I specified it in the yaml header. ```yaml # posts/post-with-code/index.qmd --- title: "Post With Code" author: "Harlow Malloc" date: "2023-03-18" categories: [news, code, analysis] image: palmerpenguins.png --- ``` The resulting main page looks like so:  #### Version info R: ```r sessionInfo() # R version 4.2.2 (2022-10-31) # Platform: aarch64-apple-darwin20 (64-bit) # Running under: macOS Ventura 13.2.1 quarto::quarto_version() # [1] ‘1.3.280’ ``` Quarto: ```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: 1.3.280 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.2 Path: /opt/homebrew/opt/[email protected]/bin/python3.11 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library knitr: 1.40 rmarkdown: 2.17 [✓] Checking Knitr engine render......OK ``` RStudio: Version 2023.03.0+386 (2023.03.0+386) ### 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.

so if a user links to this page: https://quarto.org/docs/download/tarball.html?version=1.3.290&idPrefix=download-pre but like: https://quarto.org/docs/download/tarball.html Just make it show the latest version.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4967 <div type='discussions-op-text'> ^{Originally posted by **mcanouil** March 25, 2023} The website is great regarding markdown typesetting. In addition to what is already in it, I think it would be really great to also include Quarto CLI commands documentation as some kind of reference page (and/or "man" page). Also, I noticed the `quarto use` command is not at all documented, not even in Quarto CLI itself. <img width="1124" alt="image" src="https://user-images.githubusercontent.com/8896044/227738301-58da899b-4ecb-49fa-95f8-25adaa907bcd.png"> <img width="1124" alt="image" src="https://user-images.githubusercontent.com/8896044/227738347-0e25d47e-44a3-422c-a918-fc2fc2736978.png"> </div>

### Bug description Hello, I'm currently using the version `1.3.290`. I've got a small but specific problem with the code annotation for annotating [VHDL](https://en.wikipedia.org/wiki/VHDL) code. It doesn't seem to detect the `-- <x>`-Snippet and therefore doesn't correctly generate the annotation in the PDF. ````md --- format: pdf --- ```vhdl type state is (S0, S1, S2); signal c_st, n_st : state; p_seq: process (rst, clk) -- <1> begin ... end process; p_com: process (i, c_st) -- <2> begin ... end process; ``` 1. [*Memorizing*]{.underline} 2. [*Memoryless*]{.underline} ```` **Note**: `--` is used for comments in VHDL ## `quarto check` ```cmd [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.290 Path: C:\Users\Joel\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.5 Path: C:/Users/Joel/AppData/Local/Programs/Python/Python310/python.exe Jupyter: 5.1.1 Kernels: python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.2.2 Path: C:/PROGRA~1/R/R-42~1.2 LibPaths: - C:/Users/Joel/AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.2/library knitr: 1.41 rmarkdown: 2.20 [>] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description ### Issue: Inconsistent information between your web page tutorial and the demo file Hi team, There is inconsistent information between your web page tutorial and the demo file (hello.qmd). Please review them. On your [web page](https://quarto.org/docs/get-started/hello/rstudio.html), the [**YAML title**](https://quarto.org/docs/get-started/hello/rstudio.html#yaml-header) was "Hello, Quarto". However, in the demo file (hello.pmd), it was "Penguins, meet Quarto!". Such inconsistency has caused confusion to me (I believe also to others). Please kindly look into this. Thanks. Additional details required: **RStudio IDE version** 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 **Operating system** R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044) **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: 1.3.290 Path: C:\Users\mickeyang\AppData\Local\Programs\Quarto\bin CodePage: 936 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.8.2 Path: C:/Program Files/Python38/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with py -m pip install jupyter [>] Checking R installation...........OK Version: 4.2.0 Path: C:/PROGRA~1/R/R-42~1.0 LibPaths: - C:/Users/mickeyang/AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.0/library knitr: 1.41 rmarkdown: 2.19 [>] Checking Knitr engine render......OK ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description I am having trouble rendering my quarto documents as pdfs similar to issue #4951 . I am unable to install tinytex due to an error. Such weird errors I am not sure if I am even able to properly uninstall. All I can tell there seems to be a folder missing called "win32". I am worried about both install and uninstall because I get errors with both. Can anyone help me install or check my uninstall? ## Main Error ### Technical Specifications **OS Version** Windows 10 **OS Distribution** Windows 10 Home 21H2 Build 19044.2728 **OS "Experience Version":** Windows Feature Experience Pack 120.2212.4190.0 **Rstudio Build version:** RStudio 2022.07.2 Build 576 **Tinytex package version:** 0.44 **Processor:** AMD Ryzen 9 5900X 12-Core Processor 3.70 GHz **RAM:** 64 Gb **Windows and Application Disk:** C:/ with 200 Gb **Primary Document Disk and Large Applications Disk:** D:/ with 3 Tb ### Install Error I the primary error seems to be this OS error 3 error. I have looked in the folder where it is installed and have not found it listed ``` Microsoft Windows [Version 10.0.19044.2728] (c) Microsoft Corporation. All rights reserved. C:\Users\secret\Documents>quarto install tool tinytex Installing tinytex [>] Downloading TinyTex v2023.03.21 [>] Unzipping TinyTeX-v2023.03.21.zip [>] Moving files [>] Verifying tlgpg support ERROR: Error executing 'C:\Users\secret\AppData\Roaming\TinyTeX\bin\win32\tlmgr.bat': The system cannot find the path specified. (os error 3) ``` There is a windows folder but there is no win32 folder. The file its looking for seems to be under a "windows" folder....  ### Output and Error when I try to detect my version of tinytex I get this error when I try to detect my tlmgr. Tinytex does detect something, but its like something is missing.... ``` C:\Users\secret\Documents>tlmgr --version 'tlmgr' is not recognized as an internal or external command, operable program or batch file. ``` ``` tinytex::tlmgr_version() tlmgr revision 66457 (2023-03-08 00:07:12 +0100) tlmgr using installation: C:/Users/OS/AppData/Roaming/TinyTeX TeX Live (https://tug.org/texlive) version 2023 ``` ### Uninstall error I am still not sure if I did this correctly, as the uninstallation produces errors too. ``` tinytex::uninstall_tinytex() tlmgr.pl: no auxiliary texmf trees defined, so nothing removed tlmgr.pl: action conf returned an error; continuing. tlmgr.pl: An error has occurred. See above messages. Exiting. ``` ## Quarto Pdf Rendering Errors ### Test Quarto Document I am not sure how to upload a qmd would be even helpful as this is an installation bug. I did at least test to see if thing were working good enough and this is the error I got. ``` --- title: "test" format: pdf 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). ``` ### Error when I run the template quarto document shown here This is the render I receive constantly when trying to render the above test .qmd ``` processing file: test2.qmd |.............. | 20% ordinary text without R code |............................ | 40% label: unnamed-chunk-1 |.......................................... | 60% ordinary text without R code |........................................................ | 80% label: unnamed-chunk-2 (with options) List of 1 $ echo: logi FALSE |......................................................................| 100% ordinary text without R code output file: test2.knit.md pandoc to: latex output-file: test2.tex standalone: true pdf-engine: xelatex variables: graphics: true tables: true default-image-extension: pdf metadata documentclass: scrartcl classoption: - DIV=11 - numbers=noendperiod papersize: letter header-includes: - '\KOMAoption{captions}{tableheading}' block-headings: true title: test editor: visual running xelatex - 1 No TeX installation was detected. Please run 'quarto install tool tinytex' to install TinyTex. If you prefer, you may install TexLive or another TeX distribution. ``` P.S. I have tried MikeTex on many computer is the past and been very frustrated trying to install or get it even to work. So I would like to avoid manual install of MikeTex as much as humanly possible because I am worried I will mess it up. ### 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 ## Issue Description It seems that using a floating `sidebar` in Quarto sets the `floating` class on the `body` element, which in turn causes bootstrap to not apply `border-top` to `nav-footer` (see below), in turn causing the footer border to not show up. ```css body:not(.floating) .nav-footer { border-top: 1px solid #dee2e6; } ``` We are using custom CSS as a workaround currently (https://github.com/datascijedi/website/pull/79). ## Reproducible Example `_quarto.yml` ```yaml project: type: website output-dir: _site website: sidebar: - title: "Page 1 Sidebar" style: "floating" # style: "docked" border: true collapse-level: 2 align: left contents: - text: "Page 1" file: page1.qmd page-footer: border: true left: "Left Stuff" ``` `page1.qmd` ```md # Page 1 ``` ## Environment Details OS: macOS Ventura 13.2.1 Rendering via CLI with with `quarto preview`. Output of `quarto check`: ``` [✓] Checking Quarto installation......OK Version: 1.1.251 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.16 Path: ... Jupyter: 4.8.1 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description When using the [Matlab kernel](https://github.com/Calysto/matlab_kernel) in a qmd file `````` --- jupyter: matlab --- ```{matlab} fprintf('First line\n') fprintf('Second line\n') fprintf('Third line ') fprintf('in two parts\n') ``` `````` it appears in Quarto's HTML output as  though it should be like in Matlab itself:  The reason is that in the intermediate notebook, there are separate output cells: `````` { "cell_type": "code", "execution_count": 1, "id": "6a87d088", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "First line\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Second line\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Third line " ] }, { "name": "stdout", "output_type": "stream", "text": [ "in two parts\n" ] } ], "source": [ "fprintf('First line\\n')\n", "fprintf('Second line\\n')\n", "fprintf('Third line ')\n", "fprintf('in two parts\\n')" ] } `````` If I have a code cell with the same contents in a regular Jupyter notebook, everything is fine:  The underlying code is `````` { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "First line\n", "Second line\n", "Third line in two parts\n" ] } ], "source": [ "fprintf('First line\\n')\n", "fprintf('Second line\\n')\n", "fprintf('Third line ')\n", "fprintf('in two parts\\n')" ] }, `````` *** My system: Debian GNU/Linux 11.6, kernel 5.10.0-21-amd64 MATLAB 9.13.0.2166757 (R2022b) Update 4 `quarto check`: ```` [✓] Checking Quarto installation......OK Version: 1.2.335 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.5 (Conda) Path: /home/ca/.conda/envs/std/bin/python Jupyter: 4.10.0 Kernels: python3, matlab, matlab_connect [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.0.4 Path: /usr/lib/R LibPaths: - /home/ca/.local/lib/R - /usr/lib/R/site-library - /usr/lib/R/library rmarkdown: 2.11 [✓] Checking Knitr engine render......OK ```` ### 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.

Currently `$code-annotation-higlight-color` and `$code-annotation-higlight-bg` are not described in Quarto's documentation, either on <https://quarto.org/docs/authoring/code-annotation.html> or <https://quarto.org/docs/output-formats/html-themes.html#sass-variables>[^1]. [^1]: Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4960

### Bug description This code renders successfully with Quarto stable ``` --- title: "example of broken link" --- {width="488"} [SOURCE](http://r-statistics.co/Top50-Ggplot2-Visualizations-MasterList-R-Code.html) ``` $ quarto check [>] Checking Quarto installation......OK Version: 1.2.475 Path: C:\Program Files\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....(None) Unable to locate an installed version of Python 3. Install Python 3 from https://www.python.org/downloads/ [>] Checking R installation...........OK Version: 4.2.1 Path: C:/PROGRA~1/R/R-42~1.1 LibPaths: - C:/Users/Apste/AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.1/library rmarkdown: 2.16 -------------------------------------------------- It does not with the Quarto release candidate. I think it has something to do with 'deno,' whatever that is. pandoc to: html output-file: temp.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: example of broken link ERROR: The filename, directory name, or volume label syntax is incorrect. (os error 123), stat 'C:\Users\Apste\Documents\R Projects\http:\r-statistics.co\screenshots\ggplot_masterlist_2.png' Error: The filename, directory name, or volume label syntax is incorrect. (os error 123), stat 'C:\Users\Apste\Documents\R Projects\http:\r-statistics.co\screenshots\ggplot_masterlist_2.png' at Object.statSync (deno:runtime/js/30_fs.js:322:9) at createWalkEntrySync (file:///C:/PROGRA~1/Quarto/bin/quarto.js:2754:23) at expandGlobSync (file:///C:/PROGRA~1/Quarto/bin/quarto.js:2874:25) at expandGlobSync.next (<anonymous>) at expandGlobs (file:///C:/PROGRA~1/Quarto/bin/quarto.js:5786:24) at resolveGlobs (file:///C:/PROGRA~1/Quarto/bin/quarto.js:5862:26) at resolvePathGlobs (file:///C:/PROGRA~1/Quarto/bin/quarto.js:5798:12) at resolveFileResources (file:///C:/PROGRA~1/Quarto/bin/quarto.js:76176:23) at resourceFilesFromFile (file:///C:/PROGRA~1/Quarto/bin/quarto.js:76191:37) at resourceFilesFromRenderedFile (file:///C:/PROGRA~1/Quarto/bin/quarto.js:76185:12) $ quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.290 Path: C:\Program Files\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....(None) Unable to locate an installed version of Python 3. Install Python 3 from https://www.python.org/downloads/ [>] Checking R installation...........OK Version: 4.2.1 Path: C:/PROGRA~1/R/R-42~1.1 LibPaths: - C:/Users/Apste/AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.1/library knitr: 1.42 rmarkdown: 2.16 [>] Checking Knitr engine render......OK 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 ### 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 Desired outcome is to add a title or Figure label and/or figure caption to a mermaid diagram in a qmd file. Quarto documentation shows figure labeling for graphviz dot, but same syntax does not work with mermaid. https://quarto.org/docs/authoring/diagrams.html#figures The outcome of this mermaid issues has support for adding title support to yaml frontmatter. However this does not appear to work with qmd output in Rstudio (get a syntax error). https://github.com/mermaid-js/mermaid/pull/3706 Mac OS Ventura 13.2.1, M1 Pro chip Rstudio Version 2023.030.0+386 ``` quarto check [✓] Checking Quarto installation......OK Version: 1.2.335 Path: /Users/hk/Applications/RStudio.app/Contents/Resources/app/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Applications/Xcode.app/Contents/Developer/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library rmarkdown: 2.16 [✓] Checking Knitr engine render......OK ``` Attached qmd file (renamed .txt in order to upload through github) [MermaidTitle.qmd.txt](https://github.com/quarto-dev/quarto-cli/files/11069292/MermaidTitle.qmd.txt) ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Understood that C4 diagrams have experimental support in mermaid. But wanted to open a ticket noting that their use in RStudio qmd document returns a syntax error in the rendered HTML output. https://mermaid.js.org/syntax/c4c.html ``` C4Context title System Context diagram for Internet Banking System Enterprise_Boundary(b0, "BankBoundary0") { Person(customerA, "Banking Customer A", "A customer of the bank, with personal bank accounts.") Person(customerB, "Banking Customer B") Person_Ext(customerC, "Banking Customer C", "desc") Person(customerD, "Banking Customer D", "A customer of the bank, <br/> with personal bank accounts.") System(SystemAA, "Internet Banking System", "Allows customers to view information about their bank accounts, and make payments.") Enterprise_Boundary(b1, "BankBoundary") { SystemDb_Ext(SystemE, "Mainframe Banking System", "Stores all of the core banking information about customers, accounts, transactions, etc.") System_Boundary(b2, "BankBoundary2") { System(SystemA, "Banking System A") System(SystemB, "Banking System B", "A system of the bank, with personal bank accounts. next line.") } System_Ext(SystemC, "E-mail system", "The internal Microsoft Exchange e-mail system.") SystemDb(SystemD, "Banking System D Database", "A system of the bank, with personal bank accounts.") Boundary(b3, "BankBoundary3", "boundary") { SystemQueue(SystemF, "Banking System F Queue", "A system of the bank.") SystemQueue_Ext(SystemG, "Banking System G Queue", "A system of the bank, with personal bank accounts.") } } } BiRel(customerA, SystemAA, "Uses") BiRel(SystemAA, SystemE, "Uses") Rel(SystemAA, SystemC, "Sends e-mails", "SMTP") Rel(SystemC, customerA, "Sends e-mails to") UpdateElementStyle(customerA, $fontColor="red", $bgColor="grey", $borderColor="red") UpdateRelStyle(customerA, SystemAA, $textColor="blue", $lineColor="blue", $offsetX="5") UpdateRelStyle(SystemAA, SystemE, $textColor="blue", $lineColor="blue", $offsetY="-10") UpdateRelStyle(SystemAA, SystemC, $textColor="blue", $lineColor="blue", $offsetY="-40", $offsetX="-50") UpdateRelStyle(SystemC, customerA, $textColor="red", $lineColor="red", $offsetX="-50", $offsetY="20") UpdateLayoutConfig($c4ShapeInRow="3", $c4BoundaryInRow="1") ``` Mac OS Ventura 13.2.1, M1 Pro chip Rstudio Version 2023.030.0+386 ``` quarto check [✓] Checking Quarto installation......OK Version: 1.2.335 Path: /Users/hk/Applications/RStudio.app/Contents/Resources/app/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Applications/Xcode.app/Contents/Developer/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library rmarkdown: 2.16 [✓] Checking Knitr engine render......OK ``` Attached qmd file (renamed .txt in order to upload through github) [TEMPDiagrams.qmd.txt](https://github.com/quarto-dev/quarto-cli/files/11069225/TEMPDiagrams.qmd.txt) ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Hi, Is it possible to use Python variables in LaTeX expressions similarly to that it is possible for R variables? Namely, the following qmd-file ````` --- title: "Test Knitr" format: html --- ```{r} x <- 1 #Code in R ``` Test: $x= `r x`$ ```{python} y = 1 #Code in Python ``` Test: $y= `python y`$ ````` reproduces the expected line for R `Test: x=1`, but not for Python ``Test: y= `python y` `` (the same is in pdf, btw). I am not sure if it is a bug or if the corresponding feature is not released yet. ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description The quarto works for python based qmd files and also Jupyter, but does not work for R. I tried `quarto check` and it seems that the problem is induced by Quarto not finding R installation. ``` dev-dsk % quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.287 Path: /opt/quarto/1.3.287/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 (Conda) Path: /home/zhakaida/miniconda3/envs/r_hte/bin/python Jupyter: 5.2.0 Kernels: python3, ir, lsm38, r, lsm37, julia-1.8 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` I am in a conda environment, and the R location is : ``` dev-desk % which R ~/miniconda3/envs/r_hte/bin/R ``` and this bin folder is in the PATH ``` % echo $PATH /home/zhakaida/.toolbox/bin:.:/opt/quarto/1.3.287/bin:/local/home/zhakaida/.vscode-server/bin/ee2b180d582a7f601fa6ecfdad8d9fd269ab1884/bin/remote-cli:/home/zhakaida/.toolbox/bin:/home/zhakaida/miniconda3/envs/r_hte/bin:/home/zhakaida/miniconda3/condabin:/usr/local/bin:/usr/bin:/home/zhakaida/bin:/usr/local/sbin:/usr/sbin:/home/zhakaida/bin:/usr/local/texlive/2022/bin/x86_64-linux:/home/zhakaida/programs/julia-1.8.5/bin:/usr/local/texlive/2022/bin/x86_64-linux:/home/zhakaida/programs/julia-1.8.5/bin ``` The system information is: ``` Operating System: Amazon Linux 2 CPE OS Name : cpe:2.3:o:amazon:amazon_linux:2:-:internal Kernel: Linux 5.4.235-151.344.amzn2int.x86_64 Architecture: x86-64 ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

We no longer need to bundle JS now that deno has improved their caching behavior. In addition, `deno bundle` is deprecated and doesn't work with npm specifiers, and is the reason we're stuck with 1.28.2. On top of that, `deno bundle` is causing us continued grief with its bugs in cyclic dependencies. So, let's get rid of it. I think the main complication is figuring out how to build releases, specifically in macOS, where the notarizer is very particular about directory names. We might need to do a little bit of working around that.

Documentation wise it was nice to see this section https://quarto.org/docs/computations/execution-options.html#figure-options which I hadn't found before. Maybe it could be linked in the[ Authoring/Figures/Computations](https://quarto.org/docs/authoring/figures.html#computations) section? _Originally posted by @see24 in https://github.com/quarto-dev/quarto-cli/issues/4933#issuecomment-1483066246_

### Bug description Here is a reprex: ```` --- format: html --- ```{r} 2 + 2 # <1> summary(cars) # <2> ``` 1. Add 2 to 2 2. Summary of `cars` dataset 1. Followed by 2. an enumerated list about something else ```` The result is: <img width="800" alt="Screenshot 2023-03-24 at 12 25 56 PM" src="https://user-images.githubusercontent.com/5965649/227584642-2153531a-c883-4341-b704-1e1ef8ea565e.png"> The enumerated list isn't in the output. And actually there is a warning Quarto emits: ``` WARNING: List item 3 has no corresponding annotation in the code cell (Followed by) WARNING: List item 4 has no corresponding annotation in the code cell (an enumerated list about something else) ``` Adding some text in between the two enumerated lists is the only solution I found so far. I'm using: - Quarto 1.3.287 - RStudio 2023.03.0+386 "Cherry Blossom" Release (3c53477afb13ab959aeb5b34df1f10c237b256c3, 2023-03-09) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.03.0+386 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36 ``` Mines-MacBook-Pro---Posit:quarto-for-academics mine$ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.287 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.1 Path: /usr/local/bin/python3 Jupyter: 4.9.1 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library knitr: 1.42 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Any help? processing file: try.qmd output file: try.knit.md pandoc to: latex output-file: try.tex standalone: true pdf-engine: xelatex variables: graphics: true tables: true default-image-extension: pdf toc: true number-sections: true metadata documentclass: scrartcl classoption: - DIV=11 - numbers=noendperiod papersize: letter header-includes: - '\KOMAoption{captions}{tableheading}' block-headings: true title: My document colorlinks: true 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 The system cannot find the path specified. ### 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.

To avoid users incorrectly filing pandoc issues about quarto bugs, let's explicitly check for pandoc errors and add to that message.

Potential fixes and enhancements to Confluence Publishing for the 1.4 Milestone. - [x] https://github.com/quarto-dev/quarto-cli/issues/4489 - [ ] https://github.com/quarto-dev/quarto-cli/issues/4890 - [ ] https://github.com/quarto-dev/quarto-cli/issues/5151 - [ ] https://github.com/quarto-dev/quarto-cli/issues/4660 - [ ] https://github.com/quarto-dev/quarto-cli/issues/4478

We have currently some scripts that allows to locally run test in parallels. It is based on diving our tests to run in clusters https://github.com/quarto-dev/quarto-cli/blob/main/tests/run-parallel-tests.ts We should be able to leverage this to create buckets of tests to run, and then use some parallel jobs in CI (using matrix of tests to run) with GHA. ## Other context based on initial pre work research Default runners on GHA are 2-cores so limited but concurrent Job is possible, and [the limit depends on the Free or paid plan](https://docs.github.com/en/actions/learn-github-actions/usage-limits-billing-and-administration#usage-limits) - With Free, it is 20 concurrent jobs - With Enterprise, [it will be up-to 500](https://github.blog/changelog/2023-03-09-increased-concurrency-for-2-core-linux-windows-hosted-actions-runners-for-enterprise-plans/) - Pro and Team plans are in between This will cover jobs in a workflow or across workflows However, currently in beta for Team or Enterprise plan, there is now [an offer of larger runners](https://docs.github.com/en/actions/using-github-hosted-runners/using-larger-runners)with max being 64 cores - which would allow us to run parellel tests as on local computer. So I think Github Action can have what we need, but maybe not enough without full Paid plan.

Work for this is being done as a Quarto extension in the `https://github.com/rich-iannone/quarto-email` repository (private for now). The email body will be in a div with class `"email"`. To make this work with the Connect emailing system, the main goal, the filter needs to generate a JSON file in the working directory with specific key names. Connect will be updated to watch for this file; this is close to the blastula/Connect model where R Markdown metadata is captured when certain key-value pairs are present.

## The Big Ol' List of Things To Fix - [ ] ensure format options work across formats (or document where they can't) - #215 - [ ] control numbering of anchor crossrefs - #644 - #1145 - #5614 - [ ] Caption format control for float crossrefs - #645 - [ ] Allow fine-grained control over crossref label formatting - #1095 - #1771 - #2356 - #2439 - #3440 - #4364 - #4532 - #5481 - #5621 - #5652 - [ ] allow arbitrary content as the payload of float crossrefs (e.g. if a third-party library tells us that something is a table, we go along with it) Allow listing captions/labels on executable code blocks and computational tables - [ ] #1084 - [ ] #1556 - [ ] #1580 - [ ] #2297 - [ ] #3397 - [ ] #3600 - [ ] #3601 - [ ] #3770 - [ ] #4168 - [ ] #4171 - [ ] #4517 - [ ] #4637 - [ ] #4776 - [ ] #4938 - [ ] #5101 - [ ] #5161 - [ ] #5383 - [ ] Customizable categories for Float and Block crossreferences - [x] #1655 - [ ] #3323 - [ ] #3979 - [ ] Glossary support - #1697 - [ ] Improve treatment of compound crossreferences - #1706 - #1707 - [ ] `-cap-location` control for all Float crossreferences as well as subfloats - #1829 - #1990 - #2154 - #2196 - #2221 - #3931 - [ ] Page number format control for page regions where collations (list of *) are put - #1889 - [ ] Bookdown text references: in-body captions that can be "included" via references - #1959 - [ ] Crossref collations (list of figures, tables, equations, etc) in non-PDF formats - #2138 - [ ] Crossreferenceable callouts - #2241 - #4863 - [ ] `fig-*` support: layout interaction, non-crossreferenced images - #2251 - #3370 - [ ] Equation numbering, multiple refs in a single block, tags - #2275 - #4136 - [ ] Float crossrefs, subfloats, captions and lack thereof - #2492 - #2551 - #3603 - #3711 - [ ] Book parts should be referenceable - #2571 - #3234 - [ ] Crossref, TOC, `knit_child` interactions - #3178 - [ ] Crossrefs in the content of computational outputs like tables - #3340 - [ ] Short caption support for all Float crossrefs - #3498 - [ ] Be careful about redefining block crossref environments in Beamer and amsmath generally - #3650 - [ ] Be careful about introducing nested LaTeX floats - #3736 - [ ] Allow input code of computational cell to be a listing, and handle it as a decorated code block - #2683 - [ ] Crossref filter and citeproc interaction - #1186 ## Straggler issues - [ ] Check the `crossref` label - [ ] Check the issues that refer to this - [ ] Consistency of CSS class names: "fig" vs "figure", etc.

### Bug description A markdown table does not have a horizontal scrollbar after rendering from a QMD document. I tried my best in the docs and on Google Search and in other Github issues. As seen below, the same table written in code blocks get a horizontal scrollbar automatically. Is there any hack of doing so? Win 10 ``` >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: 1.3.283 Path: C:\quarto\bin CodePage: 65001 [>] Checking basic markdown render....OK ``` ### The markdown table code I used. ```md | **CustomerKey** | **GeographyKey** | **CustomerAlternateKey** | **Title** | **FirstName** | **MiddleName** | **LastName** | **NameStyle** | **BirthDate** | **MaritalStatus** | **Suffix** | **Gender** | **EmailAddress** | **YearlyIncome** | **TotalChildren** | **NumberChildrenAtHome** | **EnglishEducation** | **SpanishEducation** | **FrenchEducation** | **EnglishOccupation** | **SpanishOccupation** | **FrenchOccupation** | **HouseOwnerFlag** | **NumberCarsOwned** | **AddressLine1** | **AddressLine2** | **Phone** | **DateFirstPurchase** | **CommuteDistance** | |-----------------|------------------|--------------------------|-----------|---------------|----------------|--------------|---------------|---------------|-------------------|------------|------------|----------------------------------|------------------|-------------------|--------------------------|----------------------|----------------------|---------------------|-----------------------|-----------------------|----------------------|--------------------|---------------------|---------------------|------------------|---------------------|-----------------------|---------------------| | 11000 | 26 | AW00011000 | | Jon | V | Yang | 0 | 1970-04-08 | M | | M | jon24\@adventure-works.com | \$90,000.00 | 2 | 0 | Bachelors | Licenciatura | Bac + 4 | Professional | Profesional | Cadre | 1 | 0 | 3761 N. 14th St | | 1 (11) 500 555-0162 | 2005-07-22 | 1-2 Miles | | 11001 | 37 | AW00011001 | | Eugene | L | Huang | 0 | 1969-05-14 | S | | M | eugene10\@adventure-works.com | \$60,000.00 | 3 | 3 | Bachelors | Licenciatura | Bac + 4 | Professional | Profesional | Cadre | 0 | 1 | 2243 W St. | | 1 (11) 500 555-0110 | 2005-07-18 | 0-1 Miles | | 11002 | 31 | AW00011002 | | Ruben | | Torres | 0 | 1969-08-12 | M | | M | ruben35\@adventure-works.com | \$60,000.00 | 3 | 3 | Bachelors | Licenciatura | Bac + 4 | Professional | Profesional | Cadre | 1 | 1 | 5844 Linden Land | | 1 (11) 500 555-0184 | 2005-07-10 | 2-5 Miles | | 11003 | 11 | AW00011003 | | Christy | | Zhu | 0 | 1972-02-15 | S | | F | christy12\@adventure-works.com | \$70,000.00 | 0 | 0 | Bachelors | Licenciatura | Bac + 4 | Professional | Profesional | Cadre | 0 | 1 | 1825 Village Pl. | | 1 (11) 500 555-0162 | 2005-07-01 | 5-10 Miles | | 11004 | 19 | AW00011004 | | Elizabeth | | Johnson | 0 | 1972-08-08 | S | | F | elizabeth5\@adventure-works.com | \$80,000.00 | 5 | 5 | Bachelors | Licenciatura | Bac + 4 | Professional | Profesional | Cadre | 1 | 4 | 7553 Harness Circle | | 1 (11) 500 555-0131 | 2005-07-26 | 1-2 Miles | | 11005 | 22 | AW00011005 | | Julio | | Ruiz | 0 | 1969-08-05 | S | | M | julio1\@adventure-works.com | \$70,000.00 | 0 | 0 | Bachelors | Licenciatura | Bac + 4 | Professional | Profesional | Cadre | 1 | 1 | 7305 Humphrey Drive | | 1 (11) 500 555-0151 | 2005-07-02 | 5-10 Miles | | 11006 | 8 | AW00011006 | | Janet | G | Alvarez | 0 | 1969-12-06 | S | | F | janet9\@adventure-works.com | \$70,000.00 | 0 | 0 | Bachelors | Licenciatura | Bac + 4 | Professional | Profesional | Cadre | 1 | 1 | 2612 Berry Dr | | 1 (11) 500 555-0184 | 2005-07-27 | 5-10 Miles | | 11007 | 40 | AW00011007 | | Marco | | Mehta | 0 | 1968-05-09 | M | | M | marco14\@adventure-works.com | \$60,000.00 | 3 | 3 | Bachelors | Licenciatura | Bac + 4 | Professional | Profesional | Cadre | 1 | 2 | 942 Brook Street | | 1 (11) 500 555-0126 | 2005-07-12 | 0-1 Miles | | 11008 | 32 | AW00011008 | | Rob | | Verhoff | 0 | 1968-07-07 | S | | F | rob4\@adventure-works.com | \$60,000.00 | 4 | 4 | Bachelors | Licenciatura | Bac + 4 | Professional | Profesional | Cadre | 1 | 3 | 624 Peabody Road | | 1 (11) 500 555-0164 | 2005-07-28 | 10+ Miles | | 11009 | 25 | AW00011009 | | Shannon | C | Carlson | 0 | 1968-04-01 | S | | M | shannon38\@adventure-works.com | \$70,000.00 | 0 | 0 | Bachelors | Licenciatura | Bac + 4 | Professional | Profesional | Cadre | 0 | 1 | 3839 Northgate Road | | 1 (11) 500 555-0110 | 2005-07-30 | 5-10 Miles | | 11010 | 22 | AW00011010 | | Jacquelyn | C | Suarez | 0 | 1968-02-06 | S | | F | jacquelyn20\@adventure-works.com | \$70,000.00 | 0 | 0 | Bachelors | Licenciatura | Bac + 4 | Professional | Profesional | Cadre | 0 | 1 | 7800 Corrinne Court | | 1 (11) 500 555-0169 | 2005-07-17 | 5-10 Miles | | 11011 | 22 | AW00011011 | | Curtis | | Lu | 0 | 1967-11-04 | M | | M | curtis9\@adventure-works.com | \$60,000.00 | 4 | 4 | Bachelors | Licenciatura | Bac + 4 | Professional | Profesional | Cadre | 1 | 4 | 1224 Shoenic | | 1 (11) 500 555-0117 | 2005-07-02 | 10+ Miles | | 11012 | 611 | AW00011012 | | Lauren | M | Walker | 0 | 1972-01-18 | M | | F | lauren41\@adventure-works.com | \$100,000.00 | 2 | 0 | Bachelors | Licenciatura | Bac + 4 | Management | Gestión | Direction | 1 | 2 | 4785 Scott Street | | 717-555-0164 | 2007-09-17 | 1-2 Miles | | 11013 | 543 | AW00011013 | | Ian | M | Jenkins | 0 | 1972-08-06 | M | | M | ian47\@adventure-works.com | \$100,000.00 | 2 | 0 | Bachelors | Licenciatura | Bac + 4 | Management | Gestión | Direction | 1 | 3 | 7902 Hudson Ave. | | 817-555-0185 | 2007-10-15 | 0-1 Miles | | 11014 | 634 | AW00011014 | | Sydney | | Bennett | 0 | 1972-05-09 | S | | F | sydney23\@adventure-works.com | \$100,000.00 | 3 | 0 | Bachelors | Licenciatura | Bac + 4 | Management | Gestión | Direction | 0 | 3 | 9011 Tank Drive | | 431-555-0156 | 2007-09-24 | 1-2 Miles | ``` ### The final render  ### 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.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3249 <div type='discussions-op-text'> ^{Originally posted by **jmgirard** November 8, 2022} I am hosting a Quarto website on Github Pages using the "docs" method. I have a custom domain and thus need to have a `docs/CNAME` file in my project. However, it seems that quarto is removing this file whenever I render via `quarto render`. Is there a way to tell quarto to keep this CNAME file? I tried the `website: site-url` option but that didn't seem to do it.</div> This is also from https://github.com/quarto-dev/quarto-actions/issues/73

### Bug description updating existing packages finding package for tikzfill.image.sty compilation failed- no matching packages LaTeX Error: File `tikzfill.image.sty' not found. Type X to quit or <RETURN> to proceed, or enter new name. (Default extension: sty) Enter file name: ! Emergency stop. <read *> l.24 ^^M see test.log for more information. <img width="618" alt="code_test_renderpdf_revealjs" src="https://user-images.githubusercontent.com/39628456/227474508-820a9878-4b9f-43e9-a385-29b814d19a05.png"> ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Hi, I've just started getting what appears to be an error with table crossref.lua. This appeared all of a sudden (within the last two weeks). I'm on Mac OS 13.2.1 (22D68), with Quarto v1.78.0 through VSCode 1.76.2. I think everything is updated (R ver 4.2.3) and it worked just a couple of weeks ago and now the render to .docx fails with: Error running filter /Applications/quarto/share/filters/crossref/crossref.lua: table expected, got Inline I'm using the gt() (very. ‘0.6.0’) package for the table I am rendering. Any help would be appreciated. Quarto check below Thanks quarto check [✓] Checking Quarto installation......OK Version: 1.2.313 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Applications/Xcode.app/Contents/Developer/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/noble/Library/R/arm64/4.2/library - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library rmarkdown: 2.20.1 [✓] Checking Knitr engine render......OK Reproducible Example. .qmd file: ````markdown --- title: "test" crossref: fig-title: 'Figure' fig-labels: arabic title-delim: "-" fig-prefix: "Figure" tbl-labels: "Table" --- @tbl-tabs1 ```{r} #| label: tbl-tabs1 #| tbl-cap: Test install.packages("tidyverse"); library(tidyverse) install.packages("gt"); library(gt) tabs1 <- data.frame(matrix(rnorm(5*11, 0, 2), ncol = 5, nrow = 11)) gt(tabs1) %>% fmt_number(columns = 2:5, decimals = 2) %>% tab_row_group(label = "Fixed Effects", rows = 1:7) %>% tab_row_group(label = "Random Effects", rows = 8:11) %>% tab_style(style = list(cell_text(weight = "bold")), locations = list(cells_column_labels(), cells_row_groups())) %>% opt_table_lines(extent = "none") %>% tab_style(style = cell_borders(sides = c("top", "bottom")), locations = list(cells_column_labels())) %>% tab_style(style = cell_borders(sides = "bottom", weight = px(2)), locations = cells_body(rows = 7)) ``` ```` Which results in a VSCode error: ```` Error running filter /Applications/quarto/share/filters/crossref/crossref.lua: table expected, got Inline as well as an Error in RStudio (2023.03.0+386 (2023.03.0+386)). Error running filter /Applications/quarto/share/filters/crossref/crossref.lua: PandocLuaError "all choices failed\n\twhile retrieving stringifyable element" stack traceback: /Applications/quarto/share/filters/crossref/crossref.lua:2660: in function 'processRawTable' /Applications/quarto/share/filters/crossref/crossref.lua:2484: in local 'fn' /Applications/quarto/share/filters/crossref/crossref.lua:1239: in function </Applications/quarto/share/filters/crossref/crossref.lua:1233> ```` ### 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 After upgrading from v. 0.9.515 to v. 1.3.282, a previously working book project failed to render via quarto preview with message "property name number-depth is invalid" Option "number-depth" is still included in the guide as a valid option for a book project. Kubuntu 20.04 To reproduce: Create a new book project: ```` $ quarto create-project mybook --type book ```` Edit generated _quarto.yml to add "number-depth" option: ```` project: type: book book: title: "mybook" author: "Norah Jones" date: "3/23/2023" number-depth: 0 chapters: - index.qmd - intro.qmd - summary.qmd - references.qmd bibliography: references.bib format: html: theme: cosmo pdf: documentclass: scrreprt ```` Start quarto preview: ```` $ quarto preview mybook ERROR: Project _quarto.yml validation failed. In file mybook/_quarto.yml (line 8, columns 3--15) property name number-depth is invalid 7: date: "3/23/2023" 8: number-depth: 0 ~~~~~~~~~~~~~ 9: chapters: ℹ The error happened in location book:number-depth. Error: Project _quarto.yml validation failed. In file mybook/_quarto.yml (line 8, columns 3--15) property name number-depth is invalid 7: date: "3/23/2023" 8: number-depth: 0 ~~~~~~~~~~~~~ 9: chapters: ℹ The error happened in location book:number-depth. at readAndValidateYamlFromFile (file:///opt/quarto/bin/quarto.js:20541:15) at async file:///opt/quarto/bin/quarto.js:60660:26 at async projectContext (file:///opt/quarto/bin/quarto.js:60515:26) at async serveProject (file:///opt/quarto/bin/quarto.js:107564:19) at async Command.fn (file:///opt/quarto/bin/quarto.js:108162:13) at async Command.execute (file:///opt/quarto/bin/quarto.js:8437:13) at async quarto (file:///opt/quarto/bin/quarto.js:127272:5) at async file:///opt/quarto/bin/quarto.js:127290:9 ```` quarto check output: ```` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.282 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.10 Path: /usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.1 Path: /usr/lib/R LibPaths: - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/lib/R/library knitr: 1.37 rmarkdown: 2.11 [✓] Checking Knitr engine render......OK ```` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] 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 Similar to #4934, the collapsed sidebar items have invalid ARIA attributes and should be buttons rather than links, and the chevron should be combined with the text so that it has a clear label. Here's the [axe issue description ](https://axe.deque.com/issues/72e98c34-2809-4c7a-9520-dc5d820f02b4)using the [Quarto guide page](https://quarto.org/docs/guide/) as an example. The summary of the problem from Gary: > this is a disclosure button that shows/hides a list of links. With vision you can tell that pretty easily, but having that programmatically indicated with the use of corresponding HTML elements (or at least roles) is essential for someone who can't see it. @gtritchie described his approach for fixing this: > If I was fixing the left-nav, at a minimum, I'd want to: > * combine the label and the chevron into a single disclosure control (one tabstop), either link or button, with `aria-expanded`; no reason for them to be separate things when you're tabbing through the page (or navigating with screen reader) > * in addition to `aria-expanded`, could also have `aria-controls` on the disclosure pointing at the list it controls, but as far as I know no screen reader uses that information for anything so it's not essential > * the links inside the expanded region should be list items in an unordered list (and the list should be named to match its parent using either `aria-labelledby="[id]"` or by duplicating the parent's label in an `aria-label` on the list > * this gives a screen reader user much more context; it tells them that these are the things that got exposed when they expanded the item, and tells them how many there are, and which one they are on, etc.

### Bug description Collapsed callouts when rendered use an invalid/inaccessible pattern where the ARIA attribute `aria-expanded="false"` is invalid [link to [axe DevTools issue found](https://axe.deque.com/issues/1b566527-127f-4660-acb1-4a7e61e0a018) when attached qmd is rendered]. From discussion with @gtritchie, they should use the disclosure pattern and be buttons: > Yes, disclosures should be buttons. Currently this is just a `<div>` with no role, which is what Axe is flagging. The pattern to implement is this: https://www.w3.org/WAI/ARIA/apg/patterns/disclosure/ These also need to be keyboard operable. You can't tab to them. Buttons should operate with both spacebar and enter key. I can't seem to attach the actual qmd, so here it is in a gist [collapsed-callout.qmd](https://gist.github.com/batpigandme/481fa863efc13ac705d29a1ddd96d5c5) Quarto check output ``` [✓] Checking Quarto installation......OK Version: 1.2.475 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.11 (Conda) Path: /opt/homebrew/Caskroom/miniconda/base/bin/python Jupyter: 4.10.0 Kernels: python3 (|) Checking Jupyter engine render....Unable to load extension: pydevd_plugins.extensions.types.pydevd_plugin_pandas_types Unable to load extension: pydevd_plugins.extensions.types.pydevd_plugin_pandas_types [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.2 Path: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources LibPaths: - /Users/maraaverick/Library/R/arm64/4.2/library - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library rmarkdown: 2.20.1 [✓] Checking Knitr engine render......OK ``` OS independent ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description I would like the out-width to equal the fig-width that I have specified in inches in a code chunk. In the documentation it says "[By default figures are displayed using their actual size](https://quarto.org/docs/authoring/figures.html#figure-sizing)" but this does not happen when I have set the dpi of my figure to be larger than the default. I would like the out-width to be equal to the fig-width in terms of the actual space it takes up on my screen rather than the current behaviour where it is much larger if I have set a larger than default dpi. Currently I can only get this outcome by setting all 4 of fig-width, fig-height, out-width and out-height. If the default needs to stay the same could there be a way to set a yaml option that ties out-width to fig-width? ````md --- title: "Dpi in Yaml" format: html fig-dpi: 300 --- ## no options The figure is created with a size that fits the output space. ```{r} plot(mtcars[1:4]) ``` ## fig-height and fig-width specified If fig-height and fig-width are small relative to the output space the figure will be expanded to fill it. Eg the font size is too large. ```{r} #| fig-width: 3 #| fig-height: 3 plot(mtcars[1:4]) ``` ## out-height and out-width specified Only by setting all 4 can I get a figure that is displayed as the size created it with. Despite this statement in quarto docs "[By default figures are displayed using their actual size](https://quarto.org/docs/authoring/figures.html#figure-sizing)" ```{r} #| fig-width: 3 #| fig-height: 3 #| out-width: 3in #| out-height: 3in plot(mtcars[1:4]) ``` ```` RStudio version 2023.03.0+386 Windows 10 Checking Quarto installation......OK Version: 1.2.335 Path: C:\Program Files\RStudio\resources\app\bin\quarto\bin CodePage: 1252 ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Quarto is failing to find the R installation on my machine. This fails from within R studio and when run from a shell. R is in the PATH and works as expected. R works fine within RStudio and compilation with RMarkdown also works. ``` E:\>set QUARTO_LOG_LEVEL=DEBUG E:\>quarto check [>] Checking Quarto installation......OK Version: 1.2.335 Path: C:\Program Files\RStudio\resources\app\bin\quarto\bin CodePage: 1252 Loaded deno-dom-native (-) Checking basic markdown render....[trace] Parsed [Plain [Str "long"]] at line 1 [trace] Parsed [Plain [Str "en"]] at line 1 [trace] Parsed [Plain [Str "true"]] at line 1 [trace] Parsed [Plain [Str "1.2.335"]] at line 1 [trace] Parsed [Plain [Str "Title"]] at line 1 [trace] Parsed [Plain [Str "Table",Space,Str "of",Space,Str "contents"]] at line 1 [trace] Parsed [] at line 5 [trace] Parsed [Header 2 ("header",[],[]) [Str "Header"]] at line 8 Loaded deno-dom-native [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.6 Path: C:/Program Files/Python39/python.exe Jupyter: 5.3.0 Kernels: python3 (-) Checking Jupyter engine render....Loaded deno-dom-native (/) Checking Jupyter engine render....[trace] Parsed [Plain [Str "long"]] at line 1 [trace] Parsed [Plain [Str "en"]] at line 1 [trace] Parsed [Plain [Str "true"]] at line 1 [trace] Parsed [Plain [Str "1.2.335"]] at line 1 [trace] Parsed [Plain [Str "Title"]] at line 1 [trace] Parsed [Plain [Str "Table",Space,Str "of",Space,Str "contents"]] at line 1 [trace] Parsed [] at line 4 [trace] Parsed [Header 2 ("header",[],[]) [Str "Header"]] at line 6 [trace] Parsed [CodeBlock ("",["python","cell-code"],[]) "1 + 1"] at line 11 [trace] Parsed [CodeBlock ("",[],[]) "2"] at line 15 [trace] Parsed [Div ("",["cell-output","cell-output-display"],[("execution_ at line 16 [trace] Parsed [Div ("",["cell"],[("execution_count","1")]) [CodeBlock ("", at line 20 Loaded deno-dom-native [>] 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/ ``` So this fails. but R is definitely there and works. ``` C:\>where R C:\Users\andrewss\AppData\Local\Programs\R\R-4.2.3\bin\x64\R.exe C:\>R --version R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see https://www.gnu.org/licenses/. ``` This even fails if I explicitly set QUARTO_R ``` C:\>set QUARTO_R="C:\Users\andrewss\AppData\Local\Programs\R\R-4.2.3\bin\x64\R.exe" C:\>echo %QUARTO_R% "C:\Users\andrewss\AppData\Local\Programs\R\R-4.2.3\bin\x64\R.exe" C:\>quarto check [>] Checking Quarto installation......OK Version: 1.2.335 Path: C:\Program Files\RStudio\resources\app\bin\quarto\bin CodePage: 1252 [Removed non-R stuff] [>] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` There are no files relating to R in the quarto log directory. ``` C:\Users\andrewss\AppData\Local\quarto\logs>dir Volume in drive C has no label. Volume Serial Number is 0A21-80E0 Directory of C:\Users\andrewss\AppData\Local\quarto\logs 22/03/2023 10:10 <DIR> . 22/03/2023 10:10 <DIR> .. 22/03/2023 10:10 0 jupyter-kernel.log 1 File(s) 0 bytes 2 Dir(s) 59,993,976,832 bytes free ``` If it matters, the version of RStudio is 2023.03.0 OS is Windows10. ### 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.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3615 <div type='discussions-op-text'> ^{Originally posted by **michielvdmeulen** December 9, 2022} I'm trying to serve a blog on a non-root path, but despite following the instructions in the [documentation](https://quarto.org/docs/websites/website-navigation.html#non-root-site-paths) I can't get it to work. My situation is identical to that in the docs, apart from different url naming of course, so something like this: URL: https://example.com/mysite/ _quarto.yml: ``` website: title: "My Site" site-path: "/mysite/" ``` When I render the site with and without the `site-path` option and compare the generated `index.html` file in the `_site` folder, both are exactly identical - even when I have completely deleted and re-rendered the content. In fact, only the `_site\site_libs\quarto-nav\quarto-nav.js` file has one line difference:  Apparently, this is either not enough or is not picked up on the server side. I'm using the latest Quarto version (1.2.269). Does someone have an idea what could be wrong? Any help would be highly appreciated!</div>


### Bug description Setting custom text via code-summary doesn't seem to be working for OJS code chunks. ````md --- title: "repr" --- This is R code. ```{r} #| code-fold: true #| code-summary: "My text" 1 + 1 ``` This is Python code. ```{python} #| code-fold: true #| code-summary: "My text" 1 + 1 ``` This is OJS code. ```{ojs} //| code-fold: true //| code-summary: "My text" 1 + 1 ``` End. ```` <img width="426" alt="repr" src="https://user-images.githubusercontent.com/90334727/227147052-1068b58c-efab-4b3e-a483-a7946b467da2.png"> Mac Ventura 13.1 / RStudio v.2023.03.0+386 / `quarto check`: ``` [✓] Checking Quarto installation......OK Version: 1.2.475 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.9 (Conda) Path: /Users/themoon/miniconda3/bin/python Jupyter: (None) Jupyter is not available in this Python installation. Install with conda install jupyter [✓] Checking R installation...........OK Version: 4.2.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/themoon/Documents/twopoints/renv/library/R-4.2/aarch64-apple-darwin20 - /Users/themoon/Documents/twopoints/renv/sandbox/R-4.2/aarch64-apple-darwin20/84ba8b13 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.

The [existing docs for custom AST nodes](https://quarto.org/docs/prerelease/1.3/ast.html) need fleshing out. Probably more changes coming that will need docs that live in the same space.

````markdown --- title: Callout padding format: html --- ::: {.callout-note} # Title ## Another header There is no padding here ::: # Document Header Content ::: {.callout-note} # Title There is correct padding here ::: ::: {.callout-note} # Title Something first ## Sub header There is correct padding here ::: ```` In this example we have several cases. If you render that you'll notice that there is no padding applied on the callout that start with a header.  I believe this is because of `section-divs: true` because there will be not `<div class="callout-body-container callout-body">` - it will be merged in the section header `<section id="another-header" class="level2 callout-body-container callout-body">` The classes are added to the section directly so the CSS does not apply https://github.com/quarto-dev/quarto-cli/blob/2246187f1aa0c4bee2b68c677b8efa55a0f8c779/src/resources/formats/html/bootstrap/_bootstrap-rules.scss#L1298-L1301 Either we should just tweak the CSS to support content wrapped in `section` or tweak the body in our Lua filter. I believe only changing the CSS rule is fine. I let you decide @cscheid

### Bug description Im encountering an odd problem when rendering documents into HTML. First a bit of background. Im using the kernel nbstata to use Stata directly with quarto and VScode. So far I have no problems, running code, or getting outputs. However, any now and then, when I display the output straight from Stata, something odd happens. My QMD file is as follows: ``` --- title: "Untitled" format: html: default ipynb: default pdf: default jupyter: nbstata --- ``` First setup ```{stata} clear ssc instal jwdid set linesize 250 set seed 111 set sortseed 111 set obs 100 // <- 100 units gen id = _n gen ai = rchi2(2) // determines When would units receive treatment gen g = runiformint(2,10) replace g = 0 if g>9 // never treated expand 10 // <-T=10 bysort id:gen t=_n gen event = max(0,t-g) gen aux = runiform()*2 bysort t:gen at = aux[1] // Determines Time fixed effect gen te = (1-g/10)+(1-event/10) // Treatment effect but vanishes with time gen eit= rnormal() gen trt = (t>=g)*(g>0) gen teff = te * trt gen y = ai + at + te * trt + eit ``` then 2 regressions ```{stata} qui: jwdid y, ivar(i) tvar(t) gvar(g) estat simple ``` but also ```{stata} qui: jwdid y, ivar(i) tvar(t) gvar(g) never estat simple ``` Everything runs correctly, but when looking at the output in HTML, i get two different behaviors. 1. Everything is fine, and produces the following: ``` ------------------------------------------------------------------------------ | Delta-method | Coefficient std. err. z P>|z| [95% conf. interval] -------------+---------------------------------------------------------------- _at | (2 vs 1) | 1.543749 .1567784 9.85 0.000 1.236469 1.851029 ------------------------------------------------------------------------------ ``` 2. For no reason that I can understand, it also produces the following: ``` ------------------------------------------------------------------------------ | Delta-method | Coefficient std. err. z P>|z| [95% conf. interval] -------------+---------------------------------------------------------------- _at | (2 vs 1) | 1.458058 .1494798 9.75 0.000 1.165083 1.751033 ------------------------------------------------------------------------------ ``` Notice the second line, there is a misalignment, compared to the first line. Exploring the HTML files, the same commands and outcome produce two different things: When things are correctly rendered ```html <div class="cell-output cell-output-stdout"> <pre><code>------------------------------------------------------------------------------ | Delta-method | Coefficient std. err. z P&gt;|z| [95% conf. interval] -------------+---------------------------------------------------------------- _at | (2 vs 1) | 1.543749 .1567784 9.85 0.000 1.236469 1.851029 ------------------------------------------------------------------------------</code></pre> </div> ``` when things are not correctly rendered ```html <pre><code>------------------------------------------------------------------------------</code></pre> </div> <div class="cell-output cell-output-stdout"> <pre><code> | Delta-method | Coefficient std. err. z P&gt;|z| [95% conf. interval]</code></pre> </div> <div class="cell-output cell-output-stdout"> <pre><code>-------------+---------------------------------------------------------------- _at | (2 vs 1) |</code></pre> </div> <div class="cell-output cell-output-stdout"> <pre><code> 1.458058 .1494798 9.75 0.000 1.165083 1.751033 ------------------------------------------------------------------------------</code></pre> ``` Do you think its something to do with the kernel,? or at the rendering step? ### 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.

This was reported by @mine-cetinkaya-rundel ````markdown --- title: "Untitled" format: gfm toc: true --- # A header # With ending dot. # With a.dot in the middle ```` will render to ````markdown # Untitled - [A header](#a-header) - [With ending dot.](#with-ending-dot.) - [With a.dot in the middle](#with-a.dot-in-the-middle) # A header # With ending dot. # With a.dot in the middle ```` The dots are not removed from the identifier produced in TOC. Pasting this markdown in Github will have unfunctional TOC This is because in Pandoc `gfm_auto_identifiers` which remove the punctuation like on Github is only a **reader** extensions - see https://github.com/jgm/pandoc/issues/8709 This means that setting `toc: true` with GFM format does not work really - I think we could add `+gfm_auto_identifiers` to the reader extension `markdown` so that we produce valid TOC - if that is possible...

if we see `credentialless` in the raw params, we should pass it along. ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4913 <div type='discussions-op-text'> ^{Originally posted by **coatless** March 21, 2023} Right now, the video short code `{{ video }}` provides a standard iframe that automatically assumes the pages default headers. https://github.com/quarto-dev/quarto-cli/blob/b0d668e4287f74f5208b510f37414a3341d7973b/src/resources/extensions/quarto/video/video.lua#L81 https://github.com/quarto-dev/quarto-cli/blob/b0d668e4287f74f5208b510f37414a3341d7973b/src/resources/extensions/quarto/video/video.lua#L108 https://github.com/quarto-dev/quarto-cli/blob/b0d668e4287f74f5208b510f37414a3341d7973b/src/resources/extensions/quarto/video/video.lua#L124 Would it be possible to have the short-code support or set by default a `credentialless` state? e.g. ``` <iframe credentialless src="https://example.com"> ``` The `credentialles` state is important for [Cross-Origin-Embedder-Policy (COEP)](https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/Cross-Origin-Embedder-Policy) environments. For [webR](https://docs.r-wasm.org/webr/latest/serving.html) startup and package installs, we need to set the COOP and COEP headers to significantly speed up the availability of in the browser R editor. We're running into issues with the iframe because when we turn on COEP, then any embedded lecture video from YouTube using the video shortcode is blocked with `"youtube refused to connect."`  By having the `<iframe>` tag include `credentialless`, the iframe is loaded from a different, empty context. In particular, it is loaded without cookies. This allows for the removal of the COEP restriction for just the video will allow the entire page to still fall under the custom COOP and COEP headers. For more background, please see: - Background on `iframe-credentialless` set: <https://developer.chrome.com/blog/iframe-credentialless/> - Initial Proposal: <https://github.com/camillelamy/explainers/blob/main/anonymous_iframes.md> Where the issue arose: https://github.com/coatless/quarto-webr/issues/8</div>

### Bug description When creating a website with posts and a listing page, if the author of a post as a long name, the name gets squished and loses white space between words on the listing page. For example, this is what the listing page looks like for the two posts copied below.  <details><summary>Post 1 code</summary> ``` --- title: "Post 1" subtitle: "The first post" author: "An author with a long name" --- This is a blog post written by someone with a long name. ``` </details> <details><summary>Post 2 code</summary> ``` --- title: "Post 2" subtitle: "The second post" author: "Short name" --- This is a blog post written by someone with a short name. ``` </details> <details><summary>system details</summary> Windows 10 RStudio 2023.03.0 Build 386 ``` $ 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: 1.3.280 Path: C:\Users\mherman\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....(None) Unable to locate an installed version of Python 3. Install Python 3 from https://www.python.org/downloads/ [>] Checking R installation...........OK Version: 4.2.0 Path: C:/PROGRA~1/R/R-42~1.0 LibPaths: - C:/Users/mherman/r-library/4.1 - C:/Program Files/R/R-4.2.0/library knitr: 1.42 rmarkdown: 2.20 [>] Checking Knitr engine render......OK ``` </details> ### Checklist - [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Hello, I've recently been struggling with compiling a Quarto-Document to PDF and I don't know why it behaves the way it does. I've installed TinyTex using the installation prompt `quarto install tinytex --update-path` and when trying to compile following document... ```qmd --- title: "Untitled" format: pdf pdf-engine: pdflatex --- This is just a test ``` ...it outputs this silly little message: ```output $ quarto preview c:/dev/quarto/test.qmd --no-browser --no-watch-inputs pandoc to: latex output-file: test.tex standalone: true pdf-engine: pdflatex variables: graphics: true tables: true default-image-extension: pdf metadata documentclass: scrartcl classoption: - DIV=11 - numbers=noendperiod papersize: letter header-includes: - '\KOMAoption{captions}{tableheading}' block-headings: true title: Untitled running pdflatex - 1 command pdflatex not found, attempting install finding package for pdflatex > 1 package to install > installing pdflatex (1 of 1) ERROR: tlmgr returned a non zero status code The system cannot find the path specified. ``` I don't know why it's trying to install pdflatex with the _tlmgr_, even though it's already installed and shouldn't be installed via tlmgr...  Things I've tested so far: - Deleting TinyTex manually and reinstalling it through Quarto -> still same issue - Compile the generated tex-file directly with `pdflatex` -> worked fine - Compile via CMD & VSCode -> both failing # Some more information ## Quarto ``` [>] Checking Quarto installation......OK Version: 1.2.335 Path: C:\Program Files\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.4 Path: C:/Users/joelv/AppData/Local/Programs/Python/Python310/python.exe Jupyter: 4.9.2 Kernels: python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.2.2 Path: C:/PROGRA~1/R/R-4.2.2 LibPaths: - C:/Users/joelv/AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.2/library rmarkdown: 2.20 [>] Checking Knitr engine render......OK ``` ## Latex / Pdflatex ``` [>] pdflatex --version pdfTeX 3.141592653-2.6-1.40.25 (TeX Live 2023) kpathsea version 6.3.5 Copyright 2023 Han The Thanh (pdfTeX) et al. There is NO warranty. Redistribution of this software is covered by the terms of both the pdfTeX copyright and the Lesser GNU General Public License. For more information about these matters, see the file named COPYING and the pdfTeX source. Primary author of pdfTeX: Han The Thanh (pdfTeX) et al. Compiled with libpng 1.6.39; using libpng 1.6.39 Compiled with zlib 1.2.13; using zlib 1.2.13 Compiled with xpdf version 4.04 [>] latex --version pdfTeX 3.141592653-2.6-1.40.25 (TeX Live 2023) kpathsea version 6.3.5 Copyright 2023 Han The Thanh (pdfTeX) et al. There is NO warranty. Redistribution of this software is covered by the terms of both the pdfTeX copyright and the Lesser GNU General Public License. For more information about these matters, see the file named COPYING and the pdfTeX source. Primary author of pdfTeX: Han The Thanh (pdfTeX) et al. Compiled with libpng 1.6.39; using libpng 1.6.39 Compiled with zlib 1.2.13; using zlib 1.2.13 Compiled with xpdf version 4.04 ``` ## Windows I'm using a XPS13 9370 ``` [>] systeminfo | findstr /B /C:"OS" OS Name: Microsoft Windows 10 Pro OS Version: 10.0.19045 N/A Build 19045 OS Manufacturer: Microsoft Corporation OS Configuration: Standalone Workstation OS Build Type: Multiprocessor Free ``` ### 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 ### Bug description Quarto 1.2.335 on Mac OS X 12.6.1 seems to render a list only, if there is an empty line before the list. So the following quarto file `test.qmd` will not render the list ``` --- title: "Introduction to markdown lists" subtitle: "" author: Mark Down date: 2023-01-02 --- ## Introduction to lists This is an example of a list - first item - second item - third item ``` To make this example work as expected ( see [babelmark](https://babelmark.github.io/?text=a+list%0A-+item+1%0A-+item+2) ), one has to add an empty line before the list like ``` This is an example of a list - first item - second item - third item ``` One could argue this is just a documentation bug, because it is not mentioned in https://quarto.org/docs/authoring/markdown-basics.html#lists . However it leads to inconsistent behaviour when rendering iPython notebooks with quarto. The following notebook `test.ipynb` ``` { "cells": [ { "cell_type": "raw", "metadata": {}, "source": [ "---\n", "title: \"Introduction to markdown lists\"\n", "subtitle: \"\"\n", "author: Mark Down\n", "date: 2023-01-02\n", "---" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Introduction to lists\n", "\n", "This is an example of a list\n", "- first item \n", "- second item\n", "- thrid item" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "name": "python", "version": "3.10.6" }, "orig_nbformat": 4, "vscode": { "interpreter": { "hash": "b0fa6594d8f4cbf19f97940f81e996739fb7646882a419484c72d19e05852a7e" } } }, "nbformat": 4, "nbformat_minor": 2 } ``` will render the list correctly when using ``` jupyter nbconvert --execute --to html test.ipynb ``` However it will not render the list when using ``` quarto render test.ipynb --execute ``` This inconsistent behaviour is annoying for users, because it means one has to change the markdown dialect inside jupyter notebooks when one wants to use quarto for rendering. I understand quarto is using pandoc under the hood, so this behaviour probably cannot be changed easily. But maybe an option in the preamble could be given when rendering jupyter notebooks, to let quarto select the correct renderer for a given jupyter notebook. P.S. ``` ❯ quarto check [✓] Checking Quarto installation......OK Version: 1.2.335 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /Users/<username>/.local/share/virtualenvs/test2-O5T_d_dR/bin/python3 Jupyter: 5.3.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.1 Path: /opt/homebrew/Cellar/r/4.2.1_2/lib/R LibPaths: - /opt/homebrew/Cellar/r/4.2.1_2/lib/R/library rmarkdown: (None) The rmarkdown package is not available in this R installation. Install with install.packages("rmarkdown") ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [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.

TeX Live 2023 is out, and now new TinyTeX release is built. One of the change is `win32/` directory becomes `windows/` directory. I believe our code should adapt to that like `tinyTexBinDir()` for example. Still adapting **tinytex** R package to this change. cc @dragonstyle

### Bug description Quarto 1.2.335 on Mac OS X 12.6.1 seems to render a list only, if there is an empty line before the list. So the following quarto file `test.qmd` will not render the list ``` --- title: "Introduction to markdown lists" subtitle: "" author: Mark Down date: 2023-01-02 --- ## Introduction to lists This is an example of a list - first item - second item - third item ``` To make this example work as expected ( see [babelmark](https://babelmark.github.io/?text=a+list%0A-+item+1%0A-+item+2) ), one has to add an empty line before the list like ``` This is an example of a list - first item - second item - third item ``` One could argue this is just a documentation bug, because it is not mentioned in https://quarto.org/docs/authoring/markdown-basics.html#lists . However it leads to inconsistent behaviour when rendering iPython notebooks with quarto. The following notebook `test.ipynb` ``` { "cells": [ { "cell_type": "raw", "metadata": {}, "source": [ "---\n", "title: \"Introduction to markdown lists\"\n", "subtitle: \"\"\n", "author: Mark Down\n", "date: 2023-01-02\n", "---" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Introduction to lists\n", "\n", "This is an example of a list\n", "- first item \n", "- second item\n", "- thrid item" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "name": "python", "version": "3.10.6" }, "orig_nbformat": 4, "vscode": { "interpreter": { "hash": "b0fa6594d8f4cbf19f97940f81e996739fb7646882a419484c72d19e05852a7e" } } }, "nbformat": 4, "nbformat_minor": 2 } ``` will render the list correctly when using ``` jupyter nbconvert --execute --to html test.ipynb ``` However it will not render the list when using ``` quarto render test.ipynb --execute ``` This inconsistent behaviour is annoying for users, because it means one has to change the markdown dialect inside jupyter notebooks when one wants to use quarto for rendering. I understand quarto is using pandoc under the hood, so this behaviour probably cannot be changed easily. But maybe an option in the preamble could be given when rendering jupyter notebooks, to let quarto select the correct renderer for a given jupyter notebook. P.S. ``` ❯ quarto check [✓] Checking Quarto installation......OK Version: 1.2.335 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /Users/<username>/.local/share/virtualenvs/test2-O5T_d_dR/bin/python3 Jupyter: 5.3.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.1 Path: /opt/homebrew/Cellar/r/4.2.1_2/lib/R LibPaths: - /opt/homebrew/Cellar/r/4.2.1_2/lib/R/library rmarkdown: (None) The rmarkdown package is not available in this R installation. Install with install.packages("rmarkdown") ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [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 a web site project, a page with ``` --- title: "Data Visualization" listing: - id: methods contents: listing-contents.yml type: table --- Lorem ipsum :::{#methods} ::: ``` and `listing-contents.yml` as ``` - `awesome.md` ``` gives the error ``` Unexpected listing contents in file /tmp/quarto/gallery/data_visualization/network_visualisation/listing-contents.yml. The array may only contain listing items, not paths or other types of data. ``` But embedding the YAML into the Markdown works without problem: ``` --- title: "Network Visualization" listing: - id: methods contents: - "awesome.md" type: table --- :::{.column-screen} Lorem ipsum :::{#methods} ::: ::: ``` The pages that I want to include in the list is in directories above the file with the listing. # Environment `uname -a` returns ``` Linux 5b7bffab04a5 6.2.7-2-MANJARO #1 SMP PREEMPT_DYNAMIC Sat Mar 18 17:15:16 UTC 2023 x86_64 GNU/Linux ``` `quarto check` returns ``` [✓] 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: 1.3.280 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....(None) Unable to locate an installed version of Python 3. Install Python 3 from https://www.python.org/downloads/ [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description I have a blog that has the following directory structure: ```markdown $ tree . ├── 404.qmd ├── _quarto.qmd ├── blog │ ├── index.qmd │ ├── welcome-to-my-blog │ │ └── index.qmd │ └── writing-papers-with-markdown │ └── index.qmd └── index.qmd ``` When visiting the page for `welcome-to-my-blog`, there's current no way for a user to go back up just one level: <img width="1512" alt="image" src="https://user-images.githubusercontent.com/1813121/226499488-9ad6688d-789d-40f4-a459-ed99861e5ac5.png"> It is possible for users to click on the `logo` icon to go to the home level though. It would be nice if this could be made to be like this instead: <img width="1512" alt="image" src="https://user-images.githubusercontent.com/1813121/226500063-93a2144b-41e9-4603-9fb7-56eb7a38f88d.png"> where `~` was clickable to get to the root level and `blog` was clickable to blog folder level. Ideally it would be customizable with what text we'd want to show there. You wouldn't need to add `/` like I have in the screenshot, users can probably customize that with css before and after selectors. Users can always hide this by setting `display: none`. What are your thoughts? I'm using `title: false` in the `navbar` but adding a link to the `logo` in the `_quarto.yml` for the screenshots above: ``` website: title: "kdheepak" favicon: ./_quarto/favicon.svg search: location: navbar site-url: https://kdheepak.com repo-url: https://github.com/kdheepak/kdheepak.github.io repo-actions: [edit, issue] open-graph: true twitter-card: true sidebar: alignment: left style: docked navbar: title: false logo: _quarto/favicon.svg collapse: false search: true pinned: false right: - icon: github href: https://github.com/kdheepak aria-label: GitHub - icon: rss href: index.xml aria-label: RSS ``` ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description When installing the quarto pkg file for MacOS, the current default installation requires root. Is there a reason this was chosen as the default? I'd like to propose changing it such that it installs just for one user by default. Users can opt-in to choosing to install it for all users (i.e. with root) if they'd like. ### 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.

`code-line-numbers` is an unclear name for using with Reveal.js to do highlighting, particularly since `code-line-numbers` does other important things to the output. IMO this deserves its own argument, e.g. `code-line-highlighting`, or at least an alias along those lines

### Bug description I can't use `. . .` with or near headers ```markdown --- title: "Untitled" format: revealjs editor: visual --- ## This doesn't work . . . ### hello . . . ### there ## This also doesn't work ### A bit of preamble . . . now something to reveal . . . and a bit more ## I expect these to work the same as this slide . . . hello . . . there ``` I expected the first two slides to behave like the third. ```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: 1.3.280 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.9 Path: /opt/homebrew/opt/[email protected]/bin/python3.10 Jupyter: 5.2.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/malcolmbarrett/Library/R/arm64/4.2/library - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library knitr: 1.42 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ``` On MacOS Montery ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Hi all, I am trying to adapt some of my old RMD templates, and I have a strange issue. When I render a .qmd file to DOCX, the `flextable` package complains that `pandoc version >= 2 required for printing flextable in docx` The thing is, quarto reports that `quarto pandoc --version` is `pandoc 2.19.2` I've tried reinstalling the package, and fiddling around, but to no avail. I know the easy solution would be to not use `flextable` but it's embedded in all of my fancy templates. Interestingly, this works just fine in RStudio with the original RMarkdown version of the file. It seems to fail with any .qmd file: ``` --- title: test output: docx: default --- {r} library(flextable) library(readr) flextable(read_csv("a.csv") ) ``` Quarto is Version: 1.2.247 ### 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.

A container Epic for reveal-js issues that have been collecting. Some of these issues may need refinement and research into scope before scheduling work to the 1.4 Milestone. Some of these issues may need to be re-assigned as we learn more about them. https://github.com/quarto-dev/quarto-cli/issues?q=is%3Aopen+is%3Aissue+label%3Arevealjs+milestone%3Av1.4 - [ ] https://github.com/quarto-dev/quarto-cli/issues/4834 - [ ] https://github.com/quarto-dev/quarto-cli/issues/4493 - [ ] https://github.com/quarto-dev/quarto-cli/issues/4795 - [ ] https://github.com/quarto-dev/quarto-cli/issues/4677 - [ ] https://github.com/quarto-dev/quarto-cli/issues/4530 - [ ] https://github.com/quarto-dev/quarto-cli/issues/4258 - [ ] https://github.com/quarto-dev/quarto-cli/issues/1952 - [ ] https://github.com/quarto-dev/quarto-cli/issues/4738 - [ ] https://github.com/quarto-dev/quarto-cli/issues/4233 - [ ] https://github.com/quarto-dev/quarto-cli/issues/4193 - [ ] https://github.com/quarto-dev/quarto-cli/issues/4185 - [ ] https://github.com/quarto-dev/quarto-cli/issues/3997 - [ ] https://github.com/quarto-dev/quarto-cli/issues/2399 - [ ] https://github.com/quarto-dev/quarto-cli/issues/1952 - [ ] https://github.com/quarto-dev/quarto-cli/issues/1823 - [ ] https://github.com/quarto-dev/quarto-cli/issues/1883 - [ ] https://github.com/quarto-dev/quarto-cli/issues/2743 - [ ] https://github.com/quarto-dev/quarto-cli/issues/2728 - [ ] https://github.com/quarto-dev/quarto-cli/issues/5038 More to be added...

Some thoughts on where 1.3 highlight will live in the "Release Candidate" website: **Bold** indicates a new page/section: * [Confluence](https://quarto.org/docs/prerelease/1.3/confluence.html) -> Guide/Publishing/**Confluence** Also add to list of options on https://quarto.org/docs/publishing/ Do we also need an entry for `confluence-html` in https://quarto.org/docs/output-formats/all-formats.html? * [Multi-format](https://quarto.org/docs/prerelease/1.3/multi-format.html) -> * [Guide/Documents/HTML/HTML Basics # **Multi-format Links**](https://quarto.org/docs/output-formats/html-basics.html) ? * Or, Guide/Documents/HTML/**Multi Format Links**? * [Embedding Notebook Output](https://quarto.org/docs/prerelease/1.3/embed.html) -> * Guide/Advanced/**Embed Jupyter Cells** (like includes) * [Guide/Computations/Python](https://quarto.org/docs/computations/python.html)? Not really right, since this mostly focuses on executable code. * Guide/Authoring/**Jupyter Cells** (like embedding videos) * Add to list of [native shortcodes](https://quarto.org/docs/extensions/shortcodes.html) * [Article Grid Customization](https://quarto.org/docs/prerelease/1.3/grid.html) -> * Guide/Documents/HTML/**HTML Layout** * Or, add to [Guide/Advanced/Page Layout](https://quarto.org/docs/output-formats/page-layout.html) * [Code Annotation](https://quarto.org/docs/prerelease/1.3/code-annotation.html) -> New Annotating Code section in: * [Guide/Documents/HTML/HTML Code Blocks](https://quarto.org/docs/output-formats/html-code.html) * Guide/Documents/PDF/PDF Basics? * Guide/Documents/MS Word/Word Basics? * A link from [Guide/Authoring/Markdown Basics#Source Code](https://quarto.org/docs/authoring/markdown-basics.html#source-code)? * [AsciiDoc Books](https://quarto.org/docs/prerelease/1.3/asciidoc-books.html) -> ? No equivalent for other book formats * Add to [list of Books formats](https://quarto.org/docs/books/) * Add to [list of All formats](https://quarto.org/docs/output-formats/all-formats.html#documents) * [Website Navigation Improvements](https://quarto.org/docs/prerelease/1.3/website-nav.html) - Navbar Tools -> [Guide/Websites/Website Navigation#Top Navigation](https://quarto.org/docs/websites/website-navigation.html#top-navigation) - Responsive Navbar and Sidebar content: doesn't need to live anywhere else? * [Mermaid Diagram Theming](https://quarto.org/docs/prerelease/1.3/mermaid.html) -> Guide/Authoring/Diagrams#**Mermaid Theming** * [PDF: SVG and Remote Images](https://quarto.org/docs/prerelease/1.3/pdf.html#filenames-with-modifiers) * SVG Images * Remote Images * Filename with modifiers These don't really feel at home anywhere. More like, things you hope would work, now do. * [kbd Shortcode](https://quarto.org/docs/prerelease/1.3/kbd.html) -> ? (Doesn't feel big enough for it's own page in Guide/Authoring) * Add to list of [native shortcodes](https://quarto.org/docs/extensions/shortcodes.html) * [Extensions: Quarto AST]() -> Somewhere in Extensions/ * [Extensions/Creating Extensions](https://quarto.org/docs/extensions/creating.html) * [Extensions/Creating Extensions/Filters](https://quarto.org/docs/extensions/filters.html) * [Extensions: HTML Tables](https://quarto.org/docs/prerelease/1.3/tables.html) ? Feels a bit different - more like guidelines for authors that want there tables to work with Quarto.

The docs now mention: ``` quarto create project confluence ``` but don't make use of this template structure. Rewrite this section to use the template project from the start.

### Bug description To reporoduce: * `quarto create project confluence` * Publish to a public space * On warning about permissions, answer: No Result: An error (see below) Expected: Some kind of message that indicates I cancelled publishing, e.g. "Publishing aborted by user" ``` ? Space or Parent Page URL: › https://cwickham.atlassian.net/wiki/spaces/QTS [✓] Verifying... ? We've detected that your account is not able to manage the permissions for this destination. Published pages will be directly editable within the Confluence web editor. This means that if you republish the page from Quarto, you may be overwriting the web edits. We recommend that you establish a clear policy about how this published page will be revised. Are you sure you want to continue? (y/n) › No ERROR: Error at verifyOrWarnManagePermissions (file:///Users/wickhamc/Documents/posit/quarto-cli/src/publish/confluence/confluence-verify.ts:82:13) at async Object.publish (file:///Users/wickhamc/Documents/posit/quarto-cli/src/publish/confluence/confluence.ts:263:3) at async publishSite (file:///Users/wickhamc/Documents/posit/quarto-cli/src/publish/publish.ts:114:36) at async publish (file:///Users/wickhamc/Documents/posit/quarto-cli/src/command/publish/cmd.ts:276:9) at async doPublish (file:///Users/wickhamc/Documents/posit/quarto-cli/src/command/publish/cmd.ts:196:7) at async publishAction (file:///Users/wickhamc/Documents/posit/quarto-cli/src/command/publish/cmd.ts:259:7) at async Command.fn (file:///Users/wickhamc/Documents/posit/quarto-cli/src/command/publish/cmd.ts:154:11) at async Command.execute (file:///Users/wickhamc/Documents/posit/quarto-cli/src/vendor/deno.land/x/[email protected]/command/command.ts:1790:7) at async quarto (file:///Users/wickhamc/Documents/posit/quarto-cli/src/quarto.ts:119:3) at async file:///Users/wickhamc/Documents/posit/quarto-cli/src/quarto.ts:151:5 ``` ``` > quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Users/wickhamc/Documents/posit/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.2 Path: /usr/local/bin/python3 Jupyter: 5.2.0 Kernels: python3 (\) Checking Jupyter engine render....0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/wickhamc/R/4.2 - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library knitr: 1.40 rmarkdown: 2.16 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description I'm trying to create an extension with custom formats, as described here <https://quarto.org/docs/extensions/formats.html>. The second example on that page refers to several custom formats with the same name, `acm-pdf` and `acm-html`. Similar to that, I would like to have custom formats called `document-docx`, `document-html`, and `document-pdf`. So I ran, in the same folder, ``` quarto create extension format:docx quarto create extension format:html quarto create extension format:pdf ``` answering the question for the extension name always with "document". However, the second time I got `ERROR: The file /home/ca/Code/quarto/document/_extensions/document/_extension.yml already exists.` It appears that I cannot create different custom formats with same name but different bases within the same folder, because the created subfolder does not contain the base name suffix. The page mentions under "Example: Revealjs": > Note that the format suffix (revealjs) is excluded from the directory name (this is to account for the possibility of multiple formats e.g. lexconf-revealjs, lexconf-pptx, etc.) This seems to suggest that it should be possible to put the different custom formats even into the same *subfolder*, called "document" in my case – but I don't know how to achieve that. - Is it indeed possible to put the different custom formats into the same subfolder? In that case, there would be a bug in `quarto create extension`. - If not, wouldn't it make more sense to include the suffix in the subfolder name? In that case, the behaviour of `quarto create extension` should be changed. - Is it okay to rename the created subfolders, or do I need to wrap each of them in yet another subfolder? `quarto check`: ``` [✓] Checking Quarto installation......OK Version: 1.2.335 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.2 Path: /usr/bin/python3 Jupyter: 4.9.1 Kernels: python3 (|) Checking Jupyter engine render....Traceback (most recent call last): File "/opt/quarto/share/jupyter/jupyter.py", line 21, in <module> from notebook import notebook_execute, RestartKernel File "/opt/quarto/share/jupyter/notebook.py", line 17, in <module> import nbformat ModuleNotFoundError: No module named 'nbformat' [✓] Checking Jupyter engine render....OK ``` Debian GNU/Linux 11.6 ### 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. - [x] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

The natural syntax is a span: ``` This is some content. [this is some HTML content]{.content-visible when-format="html"} ``` The technical complication is that AST blocks currently declare one of Block or Inline (and it might be hard to make a version of this that intelligently knows its context). If we accept the syntax `{.inline-visible when-format="html"}`, then this is simple enough. We could then add `block-visible` and `block-hidden` for uniformity, and alias content-visible to block-visible. ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4886 <div type='discussions-op-text'> ^{Originally posted by **r-cheologist** March 18, 2023} Consider a `*.qml` file like this: Profile-dependent content follows: ::: {.content-visible when-profile="MYPROFILE"} Content requiring `--profile MYPROFILE` to be added to a `render` call :::: ::: {.content-visible when-profile="MYPROFILE"} More content requiring `--profile MYPROFILE` to be added to a `render` call :::: This introduces extra hspace between the two containers, which prevents fine grained (non-paragraph spanning) use for example for profiles used for translation into different natural languages. Can this be prevented? </div>

### Bug description I would like to use Mermaid diagrams in Quarto pdf. But when I run the following simple example, it returns an error. Here is some reproducible code: ``` --- format: pdf --- ```{mermaid} flowchart LR A[Hard edge] --> B(Round edge) B --> C{Decision} C --> D[Result one] C --> E[Result two] ``` This is the error: `ERROR: No inspectable targets` So I was wondering if it is possible to use Mermaid diagrams in a Quarto pdf document? Thanks in advance! *** I am using the following: - RStudio/2022.12.0+353 - running on a Mac system *** Output of quarto check: ``` [✓] Checking Quarto installation......OK Version: 1.0.35 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.5 (Conda) Path: /Users/quinten/opt/miniconda3/bin/python Jupyter: 5.1.1 Kernels: julia-1.8, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.2 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ``` *** Please note: I also ask a question about this on [Stackoverflow](https://stackoverflow.com/questions/75746323/mermaid-in-pdf-quarto). ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description For my personal blog, these are all the options I had that are currently not present in my quarto version of the blog: ``` <link rel="canonical" href="https://kdheepak.com/blog/{metadata.slug}" /> <meta name="robots" content="index, follow" /> <meta property="og:type" content="article" /> <meta property="og:url" content="https://kdheepak.com/blog/{metadata.slug}" /> <meta property="og:published_time" content={metadata.date} /> <meta property="og:site_name" content={metadata.title} /> <link rel="alternate" type="application/rss+xml" title="RSS" href="/index.xml" /> ``` The `canonical` link was referenced in this discussion (https://github.com/quarto-dev/quarto-cli/discussions/3976) but I don't see how you could do it using `includes` because the url data isn't available to us as a user. Also, as far as I can tell the twitter and opengraph metadata are being added in post processing in typescript, so template partials or any other method is not available for users to add this manually. Is that correct? I think I would be able to write a `post-render` script to add all this but that seems unnecessary and I think Quarto should just do this for all users, OR make an option available for users to do it. ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description When using the [extended author name schema](https://quarto.org/docs/journals/authors.html#author-schema), authors’ names get rendered as [object Object] on listing pages. I’ve set up an example (https://github.com/JoFrhwld/quarto-name) using the default quarto blog template in RStudio, but adjusting the authors names like so ```yaml author: - name: given: "Harlow" family: "Malloc" ``` and ```yaml author: - name: given: "Tristan" family: "O'Malley" literal: "Tristan O'Malley" ``` Both posts appear with “[object Object]” as the author name on the listing page. ### Quarto & RStudio Versions I’ve only run this reproducible example on RStudio Workbench with Quarto v1.0.36. But you can see a live example here, which was built with Quarto v1.3.264 - url: https://lingmethodshub.github.io/content/python/ - post source: https://github.com/LingMethodsHub/Speaker-Diarization-for-Linguistics/blob/main/index.ipynb ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Currently, if two chunks have the same label, the error the user gets back is not that informative. ```r Calls: .main ... process_file -> split_file -> lapply -> FUN -> parse_block 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) 6. knitr:::split_file(lines = text) 7. base::lapply(...) 8. knitr (local) FUN(X[[i]], ...) 9. knitr:::parse_block(g[-1], g[1], params.src, markdown_mode) Execution halted Error in `processx::run(quarto_bin, args, echo = TRUE)`: ! System command 'quarto' failed --- Exit status: 1 stdout & stderr: <printed> --- ``` I actually had to change from `.qmd` to `.Rmd`, and then I got an informative error message about chunk labels being duplicated. I observed this issue on macOS and with Quarto version `1.3.275`. --- To reproduce this error, create `.qmd` file with two chunks that have the same label and try to render the document. ### 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.

Thanks for the report, but please don't open copies of issues on different repositories :) I've answered your question on the quarto-web issue. _Originally posted by @cscheid in https://github.com/quarto-dev/quarto-cli/issues/4130#issuecomment-1406850760_ I tried to find the answer in quarto-web but can't see issue section. Can you post the link please?

Hi I navigated the documentation to see if it was possible but couldn't find anything about it. I want to make a quarto website with various technical reports/preprints/...... involving multiple authors and I'd like to know if I can have a centralised author/affilitation file so that I can reuse the information for different page instead of having to copy paste it everywhere. Cheers

### Bug description It seems that code blocks as well as the resulting table are placed in the margin. - OS: Ubuntu 22.04 - Quarto Dev version (latest commit) ````qmd --- title: test format: html: self-contained: true engine: knitr --- ```{r} #| echo: false library(DBI) con <- dbConnect(RSQLite::SQLite(), ":memory:") dbWriteTable(con, "mtcars", mtcars) ``` ```{r, chunk-one} #| column: margin mtcars |> dplyr::select(cyl) |> head(5) |> knitr::kable() ``` ```{sql} #| column: margin #| connection: con select cyl from mtcars limit 5 ``` ```{r, chunk-one} #| column: margin ``` ````  ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4861 <div type='discussions-op-text'> ^{Originally posted by **KaiWaldrant** March 16, 2023} I was making a bug issue about the tabset-panel inconsistency in border-colors used when I found out it was actually an issue with the themes or rather as i think about it a combination of quarto and the themes used. You can find a demo of the issue here: https://github.com/KaiWaldrant/quarto-panel-tabset-border When using `.tabset-panel` quarto adds a `border-color` for the div with a class `tab-content`. When using a theme like 'simplex' for light-mode and 'darkly' for dark-mode. This will come in conflict as both of those themes do not have a border-color for the `tab-content` class. I am unsure how to classify this issue and where to post it</div>

### Bug description When rendering with quarto 1.2 to pdf, the conditional div does not change anything. In quarto 1.3.272 however right margins are way too large. When commenting out the div part, or removing the .column-screen everything works as expected. HMTL rendering is OK. ``` --- title: problème with .column-screen format: html: theme: cosmo pdf: documentclass: scrreprt classoption: - DIV=12 papersize: a4 fontsize: 10pt --- ## Introduction blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla blabla :::{.content-visible when-format="HTML} ::::{.column-screen} Hello :::: ::: ``` ### 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. A new release of Deno is available: 1.28.2 → 1.31.3 Run `deno upgrade` to install it. [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.272 Path: C:\Users\timbe\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....(None) Unable to locate an installed version of Python 3. Install Python 3 from https://www.python.org/downloads/ [>] Checking R installation...........OK Version: 4.2.3 Path: C:/PROGRA~1/R/R-42~1.3 LibPaths: - C:/Users/timbe/RLibs/4.2.3 - C:/Program Files/R/R-4.2.3/library knitr: 1.42 rmarkdown: 2.20 [>] Checking Knitr engine render......OK OS windows 11, Rstudio 2023.03.0 Build 386 Same problem on macos

### Bug description # Example [test.zip](https://github.com/quarto-dev/quarto-cli/files/11000206/test.zip) # OS Linux - Arch # Quarto check ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.272 Path: /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 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/ ``` ### 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 Website shows up. But there is no graph.   [Quarto-ErrorCode-Github.docx](https://github.com/quarto-dev/quarto-cli/files/10997892/Quarto-ErrorCode-Github.docx) _No response_ ### Checklist - [x ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] 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.

See #4862

- Is the heavy left border a little too strong / intense- should it be reduced? - Should we consider adding other styles of callouts (a couple of alternatives to consider) **Suggestions**  **Material**  **Distill** 

- Should top border be responsive to the presence and position of a table caption or should it always be consistently present? - Should we reduce the intensity of the 'striping' background color of tables? We're currently taking the bootstrap default.

### Bug description The following code in a .qmd document ```tex <!-- Problem --> ``abc" \(123\) ``def" <!-- Problem --> ``abc" ``def" <!-- No problem --> ``abc" ``def" ``` produces (when rendered with the R-code `quarto::quarto_render("mydocument.qmd")` the following TeX code ```tex \texttt{abc"\ \textbackslash{}(123\textbackslash{})}def'' \texttt{abc"}def'' ``abc'' ``def'' ``` and this in turn produces the following PDF  I have no idea what is happening, but Overleaf does not have this problem, so I think this is a Quarto problem. ### Computer setup RStudio version: 2022.12.0 Build 353 Operating system: Windows 10 ```bash $ quarto check [>] Checking Quarto installation......OK Version: 1.2.269 Path: C:\Users\xxxxx\AppData\Local\Programs\RStudio\resources\app\bin\quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.11.2 Path: C:/Users/xxxxx/AppData/Local/Programs/Python/Python311/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with py -m pip install jupyter [>] Checking R installation...........OK Version: 4.2.2 Path: C:/PROGRA~1/R/R-42~1.2 LibPaths: - C:/Program Files/R/R-4.2.2/library rmarkdown: 2.20 [>] 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. ---- ## EDIT RMarkdown also has this problem, so the problem is likely on `knitr`, I will post the issue there. I was too quick to blame Quarto for this :P I will keep the issue here until it gets resolved in case someone else has the same problem.

Steps To Reproduce Description: As seen in debugging #4846. Steps to Reproduce: - Publish a simple document confluence - Use verbose logging `quarto publish confluence hello-world.qmd --log-level debug` - Use this domain `https://x.y/` Expected Result: - Complete error is shown in verbose logging Actual Result: - Error is not logged only the message `server doesnt exist`

### Bug description Hello, Thanks for releasing another great version of Quarto. Excited to make use of Confluence publishing. i tried the minimal example using my custom confluence hosted domain but unfortunately, ``` quarto publish confluence qtr.qmd ? Confluence Domain: › https://x.y/ (\) Verifying...Sending fatal alert BadCertificate [✓] Verifying... ERROR: https://x.y/ doesn't exist Error: https://x.y/ doesn't exist at verifyLocationExists (file:///Applications/quarto/bin/quarto.js:110729:15) at async withSpinner (file:///Applications/quarto/bin/quarto.js:56753:9) at async verifyWithSpinner (file:///Applications/quarto/bin/quarto.js:110707:12) at async verifyLocation (file:///Applications/quarto/bin/quarto.js:110720:12) at async Object.promptAndAuthorizeToken [as authorizeToken] (file:///Applications/quarto/bin/quarto.js:123813:5) at async resolveAccount (file:///Applications/quarto/bin/quarto.js:125466:21) at async doPublish (file:///Applications/quarto/bin/quarto.js:125764:65) at async publishAction (file:///Applications/quarto/bin/quarto.js:125802:13) at async Command.fn (file:///Applications/quarto/bin/quarto.js:125754:9) at async Command.execute (file:///Applications/quarto/bin/quarto.js:8437:13) ``` Given i'm not the adminstrator, what can I do? I can confirm this space works since i've successfully used the Rmarkdown [confluence. plugin](https://engineering.linecorp.com/en/blog/conflr-published) (which takes domain, username, password for uploads) Much appreciated Saptarshi Output of `quarto check` ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.272 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.13 Path: /opt/homebrew/opt/[email protected]/bin/python3.9 Jupyter: 4.11.1 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.0 Path: /opt/homebrew/Cellar/r/4.2.0/lib/R LibPaths: - /opt/homebrew/lib/R/4.2/site-library - /opt/homebrew/Cellar/r/4.2.0/lib/R/library knitr: 1.39 rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

This would help diagnose latex issues.

### Bug description OS-specific keyboard shortcuts seem to fail with HTML but not PDF (using the example in the [pre-release docs](https://quarto.org/docs/prerelease/1.3/kbd.html)). PDF: ```md --- format: pdf --- To print, press {{< kbd Shift-Ctrl-P >}}. To open an existing new project, press {{< kbd mac=Shift-Command-O win=Shift-Control-O linux=Shift-Ctrl-L >}}. ```  HTML: ```md --- format: html --- To print, press {{< kbd Shift-Ctrl-P >}}. To open an existing new project, press {{< kbd mac=Shift-Command-O win=Shift-Control-O linux=Shift-Ctrl-L >}}. ```  Note that this is also the case in the pre-release docs:  --- RStudio 2022.12.0+353 "Elsbeth Geranium" Release (7d165dcfc1b6d300eb247738db2c7076234f6ef0, 2022-12-03) for Windows Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2022.12.0+353 Chrome/102.0.5005.167 Electron/19.1.3 Safari/537.36 Windows 10 x64 (build 19044) ``` > 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: 1.3.271 Path: C:\Users\etienne\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....(None) Unable to locate an installed version of Python 3. Install Python 3 from https://www.python.org/downloads/ [>] Checking R installation...........OK Version: 4.2.2 Path: C:/R LibPaths: - C:/Users/etienne/AppData/Local/R/win-library/4.2 - C:/R/library knitr: 1.42 rmarkdown: 2.20 [>] Checking Knitr engine render......OK ``` ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

We use Lua patterns everywhere, but pandoc ships with lpeg and (lpeg.re) specifically. We should _definitely_ switch to those. (cc @cderv: lpeg is a great parsing engine, it turns out, and lpeg.re is a regex engine with `|` inside it :))

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4822 <div type='discussions-op-text'> ^{Originally posted by **itepifanio** March 14, 2023} Quarto provides [pre and post rendering](https://quarto.org/docs/projects/scripts.html#pre-and-post-render) features but it doesn't extend when live previewing the documents. I have a script that reads `yaml` content and outputs `.qmd` files used in a Quarto website. I was trying to add a custom watcher for the `yaml` files, this way, when a `yaml` file changes the `.qmd` files the Quarto live previewing would refresh. My solution was running Quarto as a subprocess and creating the custom watcher. A pre rendering that works with live previewing would make my life easier because I would be able to run the `yaml` watcher script without working with subprocessing.</div>

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4837 <div type='discussions-op-text'> ^{Originally posted by **galachad** March 15, 2023} Currently, it's not possible to define a custom js hypothesis client. It should be possible to set the `https://hypothes.is/embed.js` to a custom url e.g. https://custom-hypothesis-client.internal/boot.js https://github.com/quarto-dev/quarto-cli/blob/main/src/resources/formats/html/hypothesis/hypothesis.ejs#L6 Thank you for implementing this. </div>

This came up through discussion in https://github.com/quarto-dev/quarto-cli/discussions/4761 by @coatless through the use case of webr Quarto extension (https://github.com/coatless/quarto-webr) Main question is : > Is there a way to register engine requirements or options in a quarto extension, e.g. `_extension.yaml`? Opening this issue to track idea and discussion. Below some thoughts on all this to consider (long writing to write all my thoughts for later reference) ----------- `webr` extension syntax used is inspired by shinylive extension ````markdown --- title: "Testing" format: html filters: - webr --- ```{webr} 1 + 1 ``` ```` When this is run with `engine: knitr` for example, there will be some interaction * A warning ```r Warning message: In get_engine(options$engine) : Unknown language engine 'webr' (must be registered via knit_engines$set()). ``` * A chunk processing by knitr which will lead to different output in intermediate .md file (because Quarto adds the `.cell-code` class for example to wrap knitr results . **jupyter** ``` [trace] Parsed [CodeBlock ("",["{webr}"],[]) "1 + 1 "] at line 12 [trace] Parsed [CodeBlock ("",["{webr}"],[]) "message(\"hello\")"] at line 17 ``` **knitr** ``` [trace] Parsed [CodeBlock ("",["webr","cell-code"],[]) "message(\"hello\")" at line 20 [trace] Parsed [Div ("",["cell"],[]) [CodeBlock ("",["webr","cell-code"],[] at line 23 ``` We don't have those issue with our internal cell handler because we define a custom knitr engine for those and specific processing (no wrapping). Behind this usecase, there is the generic question of How to use Quarto extension to define a `CodeBlock` handler in Lua and have it to play well with the rest ? @jjallaire I know we discussed in the past the Quarto Extension for custom engine and it was not something straightfoward to consider because best integration would mean some typescript processing as we do for `ojs`, `mermaid` and `dot`. However, it seems there is a need to something, maybe just tooling, for Quarto extension that would define specific `CodeBlock` processing. Two use case for now `shinylive` and `webr`. More thoughts on the current context based on my answer https://github.com/quarto-dev/quarto-cli/discussions/4761#discussioncomment-5319569 Using standard Pandoc fenced code attribute syntax prevent any processing by **knitr**. This means something like ````markdown ```{.webr} 1 + 1 ``` ```` knitr will not parse and process this part of the code, and then Lua filter can target using `el.attr.classes:includes("webr")`. As notes `shinylive` uses `shinylive-python` as cell engine name. Using dash `-` makes knitr also not see that as a knitr engine to process. This is an easy solution to make distinction between computation (or internal) cell handlers and Lua based ones. Supports for YAML comments as option is a question though, and this is where `shinylive` solves this by using [typescript](https://github.com/rstudio/shinylive/blob/main/src/scripts/codeblock-to-json.ts) for [parsing comments too](https://github.com/rstudio/shinylive/blob/main/src/parse-codeblock.ts) called from [Lua directly](https://github.com/quarto-ext/shinylive/blob/e5ac95392fd40483f58294ec2ff22944b393eb95/_extensions/quarto-ext/shinylive/shinylive.lua#L71-L76) This shows that probably some tooling is necessary in Quarto Lua API if we want to help with this pattern. OTOH, best would probably be to use common cell handler syntax like ````markdown ```{webr} 1 + 1 ``` ```` This requires probably a way to indicate to computation engines like knitr to skip the parsing and processing of such cells - exactly what we do for `ojs`, `mermaid` and `dot`. Currently [we tell knitr to output those cells as is](https://github.com/quarto-dev/quarto-cli/blob/9debd347ae6b053fd2e445cffb25f7cdec94d082/src/resources/rmd/execute.R#L45-L68). Making that possible directly from extension configuration would allow to say to computation engine from the extension to pass through the code block. Anyhow, some challenges are: * What pattern do we want to promote for this ? * Cell handler be done exclusively from Lua as shinylive and webr as of now ? * or maybe some pre-processing defined by extension that would run as part of quarto render typescript pre processing ? * What helpers tooling could be necessary in Quarto Lua API for extension developer ? * How does this integrate and behave correctly with YAML intelligence for options as comments and existing computation engine, with their own cell engine ?

### Bug description When rendering a plotly plot with quarto it is not correctly scaled according to given width & height arguments passed to the ggplotly scale. This has also been tested for Rmarkdown and there the behavior is as expected. Scaling of the plot output happens on the basis of the width & height arguments. Rstudio version: RStudio 2022.12.0+353.pro20 "Elsbeth Geranium" Release (02ace23e263335c78e1df5b0892e48913e5fcecf, 2022-12-15) for Ubuntu Bionic Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/111.0.0.0 Safari/537.36 Edg/111.0.1661.41 Quarto version: 1.2.280 Quarto example: ````markdown --- title: "Quarto" author: "dkmanl" format: html: embed-resources: true --- ```{r} #| label: packages #| results: hide #| echo: true #| message: false library(tidyverse) library(plotly) ``` ```{r} #| label: data #| echo: true df <- mtcars |> rownames_to_column("model") ``` ```{r} #| label: plot #| echo: true plot <- df |> ggplot(aes(x = mpg, y = hp, color = model)) + geom_point() plotly_width <- 1000 plotly_height <- 600 plot |> ggplotly(width = plotly_width, height = plotly_height) ``` ```` Rmarkdown example: ````markdown --- title: "Rmarkdown" author: "dkmanl" output: html_document --- ```{r, label=packages, results='hide', message=FALSE, echo=TRUE} library(tidyverse) library(plotly) ``` ```{r, label=data, echo=TRUE} df <- mtcars |> rownames_to_column("model") ``` ```{r, label=plot, echo=TRUE} plot <- df |> ggplot(aes(x = mpg, y = hp, color = model)) + geom_point() plotly_width <- 1000 plotly_height <- 600 plot |> ggplotly(width = plotly_width, height = plotly_height) ``` ```` Quarto check: ``` [✓] Checking Quarto installation......OK Version: 1.2.280 Path: /opt/quarto/v1.2.280/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.7 Path: /opt/python/3.10.7/bin/python3 Jupyter: 5.1.3 Kernels: python3, py3.7.7, py3.10.7 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.2 Path: /opt/R/4.2.2/lib/R LibPaths: 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.

**Use case:** It's nice to get feedback on docs/blog from people outside of the dev team (e.g. #os-dev-rel, or #quarto), but it's a big ask to have people outside the team render the docs locally to review a PR. Related issue in quarto-dev/quarto-actions#33

### Bug description Why does the font get smaller after a section is introduced with a title slide using a level 1 header (#) in a revealjs presentation with `{.smaller}` applied globally? I am using RStudio 2022.07.1 and Quarto Version: 1.2.335 Thanks ```` --- title: "test" format: revealjs: smaller: true --- ## Slide 1 This text is normal # New section ## Slide 2 This text is smaller. ```` ``` sessionInfo()``` R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) Matrix products: default locale: [1] LC_COLLATE=English_New Zealand.utf8 LC_CTYPE=English_New Zealand.utf8 LC_MONETARY=English_New Zealand.utf8 [4] LC_NUMERIC=C LC_TIME=English_New Zealand.utf8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] fansi_1.0.3 utf8_1.2.2 dplyr_1.1.0 R6_2.5.1 lifecycle_1.0.3 magrittr_2.0.3 pillar_1.8.1 [8] rlang_1.0.6 cli_3.4.1 rstudioapi_0.14 vctrs_0.5.2 generics_0.1.3 ellipsis_0.3.2 tools_4.2.0 [15] glue_1.6.2 rsconnect_0.8.29 compiler_4.2.0 pkgconfig_2.0.3 tidyselect_1.2.0 tibble_3.1.7 C:\Users\javiera\OneDrive - Cawthron\UA\Stats course\Quarto>quarto check [>] Checking Quarto installation......OK Version: 1.2.335 Path: C:\Users\javiera\AppData\Local\Apps\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.7 (Conda) Path: C:/Users/javiera/Miniconda3/python.exe Jupyter: 5.2.0 Kernels: python3 (|) Checking Jupyter engine render....2023-03-15 18:39:23,598 - traitlets - ERROR - DLL load failed while importing _sqlite3: The specified module could not be found. Traceback (most recent call last): File "C:\Users\javiera\Miniconda3\lib\site-packages\traitlets\traitlets.py", line 656, in get value = obj._trait_values[self.name] KeyError: 'kernel_dirs' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\javiera\Miniconda3\lib\site-packages\jupyter_client\manager.py", line 85, in wrapper out = await method(self, *args, **kwargs) File "C:\Users\javiera\Miniconda3\lib\site-packages\jupyter_client\manager.py", line 397, in _async_start_kernel kernel_cmd, kw = await self._async_pre_start_kernel(**kw) File "C:\Users\javiera\Miniconda3\lib\site-packages\jupyter_client\manager.py", line 359, in _async_pre_start_kernel self.kernel_spec, File "C:\Users\javiera\Miniconda3\lib\site-packages\jupyter_client\manager.py", line 182, in kernel_spec self._kernel_spec = self.kernel_spec_manager.get_kernel_spec(self.kernel_name) File "C:\Users\javiera\Miniconda3\lib\site-packages\jupyter_client\kernelspec.py", line 284, in get_kernel_spec resource_dir = self._find_spec_directory(kernel_name.lower()) File "C:\Users\javiera\Miniconda3\lib\site-packages\jupyter_client\kernelspec.py", line 259, in _find_spec_directory for kernel_dir in [kd for kd in self.kernel_dirs if os.path.isdir(kd)]: File "C:\Users\javiera\Miniconda3\lib\site-packages\traitlets\traitlets.py", line 703, in __get__ return self.get(obj, cls) File "C:\Users\javiera\Miniconda3\lib\site-packages\traitlets\traitlets.py", line 659, in get default = obj.trait_defaults(self.name) File "C:\Users\javiera\Miniconda3\lib\site-packages\traitlets\traitlets.py", line 1872, in trait_defaults return self._get_trait_default_generator(names[0])(self) File "C:\Users\javiera\Miniconda3\lib\site-packages\jupyter_client\kernelspec.py", line 199, in _kernel_dirs_default from IPython.paths import get_ipython_dir File "C:\Users\javiera\Miniconda3\lib\site-packages\IPython\__init__.py", line 53, in <module> from .terminal.embed import embed File "C:\Users\javiera\Miniconda3\lib\site-packages\IPython\terminal\embed.py", line 15, in <module> from IPython.core.interactiveshell import DummyMod, InteractiveShell File "C:\Users\javiera\Miniconda3\lib\site-packages\IPython\core\interactiveshell.py", line 73, in <module> from IPython.core.history import HistoryManager File "C:\Users\javiera\Miniconda3\lib\site-packages\IPython\core\history.py", line 11, in <module> import sqlite3 File "C:\Users\javiera\Miniconda3\lib\sqlite3\__init__.py", line 23, in <module> from sqlite3.dbapi2 import * File "C:\Users\javiera\Miniconda3\lib\sqlite3\dbapi2.py", line 27, in <module> from _sqlite3 import * ImportError: DLL load failed while importing _sqlite3: The specified module could not be found. DLL load failed while importing _sqlite3: The specified module could not be found. [>] Checking Jupyter engine render....OK ### Checklist - [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [X] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4756 <div type='discussions-op-text'> ^{Originally posted by **giorgiopaulon** March 10, 2023} I am interested in exporting a Quarto table to a .pdf document. The only resources I found suggest to use the following ```{r} #| tbl-cap: !expr sprintf("A caption with some math, $\\gamma \\geq 0.5$, ($N = %s$)", nrow(iris)) head(iris) %>% flextable() ``` However, this results in the following  </div>

### Bug description I am getting an error while installing quarto on macOS Ventura 13.2.1: _**The Installer encountered an error that caused the installation to fail. Contact the software manufacturer for assistance**_. I have tried to install it by running a command in a terminal: _sudo installer -pkg ~/Downloads/quarto-1.2.335-macos.pkg -target /Applications_. Still getting an error: installer: Package name is Quarto installer: Upgrading at base path / installer: The upgrade failed. (The Installer encountered an error that caused the installation to fail. Contact the software manufacturer for assistance. An error occurred while extracting files from the package “quarto-1.2.335-macos.pkg”.) ### 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.

(Comes from https://github.com/quarto-dev/quarto-cli/discussions/4092#discussioncomment-4950816) Currently comment letters are managed in multiple files and the same modification must be made to each. I registered for PRQL in #4147, but did not realize that I needed to register in the following files, so it appears that code annotations are not available for PRQL at this time. https://github.com/quarto-dev/quarto-cli/blob/94a815fa510272ed55843cde80ad20cac2e6c2bc/src/resources/jupyter/notebook.py#L528-L571 https://github.com/quarto-dev/quarto-cli/blob/94a815fa510272ed55843cde80ad20cac2e6c2bc/src/core/jupyter/jupyter.ts#L1009-L1052 https://github.com/quarto-dev/quarto-cli/blob/94a815fa510272ed55843cde80ad20cac2e6c2bc/src/resources/filters/quarto-pre/code-annotation.lua#L6-L55 https://github.com/quarto-dev/quarto-cli/blob/94a815fa510272ed55843cde80ad20cac2e6c2bc/src/resources/rmd/hooks.R#L818-L863 https://github.com/quarto-dev/quarto-cli/blob/94a815fa510272ed55843cde80ad20cac2e6c2bc/src/core/lib/partition-cell-options.ts#L310-L354 It would be great if these codes were automatically updated from a single definition file and if there were written instructions for registering new languages.

### Bug description # Version `1.3.264` # Possible Issue IJulia decided to move the location of python # Workaround Use `QUARTO_PYTHON=~/.julia/conda/3/x86_64/bin/python` # OS Linux - Arch ### Checklist - [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 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 provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description Right now `giscus` uses a light theme by default even when a dark theme is toggled. <img width="1045" alt="image" src="https://user-images.githubusercontent.com/1813121/224907905-db32d0e6-0f75-4d84-ba55-bc40df8f6c03.png"> ### Checklist - [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue. - [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report. - [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. - [ ] Please provide the output of `quarto check` so we know which version of quarto and its dependencies you're running.

### Bug description I think when linking to the source file, it would be nice if the `code-tools: source: repo` linked to exact commit for that file on GitHub. For my personal blog, I used to do something like this: ```typescript const commit = child_process .spawnSync("git", ["log", "-n", "1", "--pretty=format:%H", "--", `${filename}`]) .stdout.toString(); metadata.source = `https://github.com/kdheepak/blog/blob/${commit}/${filename}`; ``` ### 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.

I noticed that on the website, the area of a code block where you would normally specify a programming language has random characters instead. It seems like this is the case throughout the website. I also checked on another device just to be sure that it wasn't a weird browser issue, but I'm still seeing it. 

### Bug description There are a few places on the docs website where the code chunk language is not correct. It appears to be a random (?) string of letters instead of the actual language for the code chunk. These are the places where I've seen the problem: - At [Authoring > Diagrams](https://quarto.org/docs/authoring/diagrams.html#overview)  - At [Authoring > Figures > Cross-references](https://quarto.org/docs/authoring/figures.html#cross-references)  ### 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.

I'm getting the compilation error below on one file (w5-digital-imageworlds.qmd) when trying to publish to GH Pages. All other files render correctly, and the file in question has the same YAML as the other files: --- title: "W5: Digital Imageworlds" toc: false format-links: false --- The file is in a directory below the root directory called <modules>, and the .html, .pdf, .tex, and .log files are all rendering in that directory (unlike the other .qmd files). It seems to be some kind of LaTex error. I reinstalled TinyTex but received the same error. Terminal output: ``` digital-culture-sp23 on  main [!?] took 1m 54s 867ms ➜ quarto publish gh-pages ? Update site at https://mroberts1.github.io/digital-culture-sp23/? (Y/n) › Yes From https://github.com/mroberts1/digital-culture-sp23 * branch gh-pages -> FETCH_HEAD Rendering for publish: [1/6] resources/mastodon.qmd running xelatex - 1 This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode running xelatex - 2 This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode [2/6] index.qmd [WARNING] This document format requires a nonempty <title> element. Defaulting to 'quarto-input5fa0eafc' as the title. To specify a title, use 'title' in metadata or --metadata title="...". running xelatex - 1 This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode running xelatex - 2 This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode [3/6] modules/w5-digital-imageworlds.qmd running xelatex - 1 This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode updating tlmgr updating existing packages compilation failed- error LaTeX Error: Cannot determine size of graphic in w5-digital-imageworlds_files/mediabag/ally-icon-indicator-low-circle.b7cd3e0c1511a1080fd322790193604f.svg (no BoundingBox). See the LaTeX manual or LaTeX Companion for explanation. Type H <return> for immediate help. ... l.164 ...cle.b7cd3e0c1511a1080fd322790193604f.svg} \href{https://canvas.emers... see /Users/dokoissho/GitHub/rstudio/digital-culture-sp23/modules/w5-digital-imageworlds.log for more information. ```

### Bug description After updating to the latest pre-release v1.3.260, I've encountered an issue with post `feature.jpg`s no longer additionally showing up in the respective listing page. This set-up had been working okay in an earlier release. Reprex: _quarto.yml: ```` project: type: website website: title: "reprex" navbar: left: - text: Projects href: project/index.qmd - about.qmd ```` project/index.qmd: ```` --- title: "Projects" listing: id: listing contents: . --- ```` project/project1/index.qmd ```` --- title: "reprex" ---  ```` RStudio: Version 2022.12.0+353 (2022.12.0+353) macOS: 13.2.1 (22D68) ### 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.

The following v1 APIs are now deprecated in favor of their 2.0 versions. We should upgrade them if we can: - get Space - get Content - create Content - update Content - get Content by Id - delete Content - get Attachments - get Content for Space

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4792 <div type='discussions-op-text'> ^{Originally posted by **franzeder** March 13, 2023} How can I add a licence (e.g., CC BY-NC) to a quarto book? I would like to print this licence (maybe including the respective figures) at my Quarto Book Website ([https://www.politik-wissenschaft.at/](https://www.politik-wissenschaft.at/)) next to the DOI. How can I do that? </div>

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4787 <div type='discussions-op-text'> ^{Originally posted by **kdheepak** March 12, 2023} By adding a `index.xsl` with appropriate styling, you can make the RSS feed the same style as the webpage. You'll need to add the following to the `index.xml` file. ``` <?xml-stylesheet type="text/xsl" media="screen" href="/index.xsl"?> ``` Here's an example of a `index.xsl` file: ``` <?xml version="1.0" encoding="UTF-8" ?> <xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:atom="http://www.w3.org/2005/Atom" xmlns:dc="http://purl.org/dc/elements/1.1/" version="1.0" > <xsl:output method="xml" /> <xsl:template match="/"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en"> <head> <meta charset="UTF-8" /> <meta name="viewport" content="width=device-width" /> <title><xsl:value-of select="rss/channel/title" /> (RSS)</title> <link rel="stylesheet" href="/_quarto/style.css" /> <link href="/site_libs/quarto-html/tippy.css" rel="stylesheet"/> <link href="/site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"/> <script src="/site_libs/bootstrap/bootstrap.min.js"></script> <link href="/site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet"/> <link href="/site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light"/> <link rel="icon" href="/favicon.svg" /> </head> <body> <article> <header> <h1> <abbr title="Really Simple Syndication">RSS</abbr> feed for <a> <xsl:attribute name="href"> <xsl:value-of select="rss/channel/link" /> </xsl:attribute> <xsl:value-of select="rss/channel/title" /> </a> </h1> </header> <section> <p>You may use the <acronym title="Uniform Resource Locater" >URL</acronym> of this document or copy the address below and paste it for any RSS purposes. <br /> <label for="address">RSS address: </label> <input style="width:300px"> <xsl:attribute name="id">address</xsl:attribute> <xsl:attribute name="spellcheck">false</xsl:attribute> <xsl:attribute name="value"> <xsl:value-of select="rss/channel/atom:link[@rel='self']/@href" /> </xsl:attribute> </input> </p> <p>New to feeds? You can find out more about the RSS file format at <a href="http://en.wikipedia.org/wiki/RSS_(file_format)" >Wikipedia's RSS entry</a> or by clicking <a target="_blank" href="https://duckduckgo.com/?q=how+to+get+started+with+rss+feeds" >here</a> to search on the web to learn more.</p> <h3>Recent blogs:</h3> <xsl:for-each select="rss/channel/item"> <p> <a> <xsl:attribute name="href"><xsl:value-of select="link" /></xsl:attribute><xsl:value-of select="title" /> </a> </p> </xsl:for-each> </section> </article> </body> </html> </xsl:template> </xsl:stylesheet> ``` I haven't fixed the styling for my page yet, but this is what the `index.xml` page would look like with some styling: <img width="1253" alt="image" src="https://user-images.githubusercontent.com/1813121/224585335-a06eda62-de3a-47ca-b4c9-0e7985918568.png"> It'd be ideal if this was autogenerated.</div>

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4522 <div type='discussions-op-text'> ^{Originally posted by **gdietl** February 24, 2023} With quarto, it is possible to generate tables with R or Python. Is there also a way to generate tables with Julia? I've tried using PrettyTables.jl and producing an output in markdown format. However, the output is not correctly interpreted by Quarto, even note wenn setting "output: asis".</div>

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4779 <div type='discussions-op-text'> ^{Originally posted by **kdheepak** March 12, 2023} ### Bug description Currently, when running `quarto preview` for a while and editing multiple pages, there's lots of output on `stdout`. If I accidentally close the tab with the preview (and if I'm not able to reopen it because it's been a while), I'm not able to go back to the terminal and see the URL where the preview server is hosting the code. I have to either try to scroll all the way up (sometimes this has exceeded my scrollback buffer) or I have to restart `quarto preview` (which before using `freeze` and `cache` took a long time to execute). One of these options would solve it for me - Either show the URL after updates, or allow the user to press a key that prints out the URL. </div>