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### Bug description Thanks for the great package! I've very much enjoyed using it. My bug is related to [#834](https://github.com/quarto-dev/quarto-cli/issues/834). In the example below, the 4th reference note is still being placed on top of the previous note. ``` --- format: html reference-location: margin --- Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.[^1] Ut enim ad minim veniam, quis nostrud exercitation, Ut enim ad minim veniam, quis nostrud exercitation.[^2] Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation. Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation. Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation.[^3] Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation. Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation.[^4] [^1]: This is citation number 1, Lorem ipsum dolor sit amet [^2]: This is citation number 2, which is even longer. Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet. Ut enim ad minim veniam, quis nostrud exercitation. [^3]: This is citation number 3, which is still placed nicely in the margin. Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. [^4]: The problem is with the position of this last citation, number 4. ```  I'm running Quarto Version: 0.9.603 on R version 4.1.0 in RStudio 2022.02.3+492 for macOS.

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1178 <div type='discussions-op-text'> ^{Originally posted by **fuhrmanator** June 18, 2022} In books it is very useful to refer to a section by its name. The Quarto documentation does this, e.g. the link to "Cross references" on this line: https://github.com/quarto-dev/quarto-web/blob/eed8baacea8448cd2ec60e34250ad2215de6831f/docs/authoring/figures.qmd#L25 But it's done with a hyperlink to an absolute HTML page. Another example is within a page: https://github.com/quarto-dev/quarto-web/blob/eed8baacea8448cd2ec60e34250ad2215de6831f/docs/authoring/cross-references.qmd#L26 There's an anchor generated through `## Options {#options}`. It seems to be HTML-specific. In LaTeX, it's done by `\nameref{sec-blahblah}` and I see that quarto supports this for PDF output. Are there plans to make this work with `@sec-blahblah` for other render destinations (e.g. html)? I'm thinking something like `[caption@sec-blahblah]` as a general solution. </div>

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1191 <div type='discussions-op-text'> ^{Originally posted by **eitsupi** June 21, 2022} The recently made direct-commit feature to gh-branch is great. However, the latest version of quarto seems to generate an error after branch creation because of different rules for URLs to be published in systems that mimic GitHub Pages other than GitHub. Is there any way to disable the validation after publish?</div>

### Bug description I'm trying to figure out an error, but I can't get a sense of what it means at all. I'm using 0.9.603 in VSCode and Python on Windows. This happens when I run `preview` on my `.qmd` file. ``` Starting python3 kernel...Done Executing 'paper.ipynb' Cell 1/7...Done Cell 2/7...Done Cell 3/7...Done Cell 4/7...ERROR: None of the known patterns match for omitted due to data restrictions. ``` Any idea what might be causing this? here's my quarto check: ``` [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /home/am2497/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.7 (Conda) Path: /home/am2497/miniconda3/envs/uganda-uber/bin/python Jupyter: 4.9.1 Kernels: minimod-env, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.0.5 Path: /home/am2497/miniconda3/envs/uganda-uber/lib/R LibPaths: - /home/am2497/miniconda3/envs/uganda-uber/lib/R/library rmarkdown: (None) The rmarkdown package is not available in this R installation. Install with install.packages("rmarkdown") ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description Try rendering the penguins example here: https://github.com/quarto-dev/quarto-web/blob/main/docs/interactive/ojs/examples/penguins.qmd When you view source, note that the first `{ojs}` cell includes braces but subsequent ones do not:  ### Checklist - [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [ ] included a minimal, self-contained, and reproducible example? - [ ] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description I've moved to `quarto` from RMarkdown where it is possible to insert verbatim code chunks, as in this example document: ````` --- title: "rmarkdown" output: html_document --- ````{quarto} --- output: html_document --- ```{r} 2+2 ``` ```` ````` However, in `quarto` this does not work: ````` --- title: "{quarto}" format: html --- ````{verbatim} --- output: html_document --- ```{r} 2+2 ``` ```` ````` When using RStudio to render the `.qmd` document the following warning is generated: ``` In get_engine(options$engine) : Unknown language engine 'quarto' (must be registered via knit_engines$set()). ``` Which suggests if a code chunk is specified in an unknown language engine it defaults to the 'quarto' engine? Conversely, in RMarkdown if you provide an unknown language engine (eg `pretend`) there is an attempt to use that engine ``` Warning message: In get_engine(options$engine) : Unknown language engine 'pretend' (must be registered via knit_engines$set()). ``` ### Version info - Operating System: macOS Monterey - quarto check ``` [✓] Checking Quarto installation......OK Version: 0.9.288 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.12 Path: /usr/local/opt/python@3.9/bin/python3.9 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` - RStudio version `2022.02.3 Build 492` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [x] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description I believe you can put R commands into chunk paramters, this is useful but does give issues when you miss out a space. E.g. ```` --- title: "test" --- ```{r} #| warning: false #| eval:false ``` ```` Which gives the error: processing file: test.rmarkdown Error in yaml::yaml.load(yaml, eval.expr = TRUE) : Scanner error: while scanning a simple key at line 2, column 1 could not find expected ':' at line 3, column 1 Calls: .main ... parse_block -> partition_yaml_options -> <Anonymous> Execution halted I presume that this is because the eval:false line is being interpreted as R rather than YAML, but the error message isn't helpful and had me messing with the top YAML as it didn't mention when code chunk it was referring to. Strangely, dropping the warning line fixes things: ```` --- title: "test" --- ```{r} #| eval:false ``` ```` RStudio: 2022.02.3 Build 492 Windows ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [ ] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

When filling #1186, I upgraded Quarto as usual with `brew upgrade quarto` and I encountered an error while trying to render #1186 again. ``` assertion failed [block != nullptr]: BasicBlock requested for unrecognized address (BuilderBase.h:550 block_for_offset) /Applications/quarto/bin/quarto: line 106: 44356 Trace/BPT trap: 5 "${SCRIPT_PATH}/tools/deno" ${QUARTO_ACTION} ${QUARTO_DENO_OPTIONS} ${QUARTO_DENO_EXTRA_OPTIONS} "${QUARTO_IMPORT_ARGMAP}" "${QUARTO_TARGET}" "$@" ``` I tried to reinstall 0.9.598 (latest: https://formulae.brew.sh/cask/quarto#default) which produced the same result. OS: MacOS arm64

### Bug description I'm running Quarto 0.9.600. When Quarto encounters a YAML error anywhere in the document, it fails with the error message ```{md} ERROR: Render failed due to invalid YAML. ``` Since in-chunk options are handled as YAML, such errors can appear anywhere in the document's source files. If it's been a minute since you've re-rendered the output, the lack of information in the error message can make it challenging to locate the problem in a moderately complex document. ````md --- title: "This document is broken" author: "But where?" --- ```{r} #| include: false 2 + 2 ``` The problem isn't in the previous chunk. Maybe it has to do with @tbl-mtcars? ```{r} #| label: tbl-mtcars #| tbl-cap: "Right here! I'm missing my closing quote knitr::kable(mtcars) ``` ```` So as a feature request/enhancement I'd like to request more informative error messages when the YAML parser gets tripped up. ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description Cross references are not parsed properly when combining figure reference and article reference, i.e., the article reference is missing See: https://github.com/mcanouil/quarto-issues/tree/main/quarto-cli-1186 Possibly related to #1155 Quarto: 0.9.592 (I tried to upgrade to 598 and broke Quarto) OS: MacOS arm64

### Bug description From https://github.com/quarto-dev/quarto-cli/discussions/1182 ````markdown --- format: pdf keep-md: true keep-tex: true --- ```{r} #| label: tbl-md #| tbl-cap: "$\\beta$~1~" knitr::kable(data.frame(x = rnorm(5))) ``` ```{r} #| label: tbl-latex #| tbl-cap: "$\\beta$~1~" knitr::kable(data.frame(x = rnorm(5)), format = "latex") ``` ````  In the first case `kable()` will produce Markdown table, and we will process the code in there, setting the table caption as a Caption element in the AST which will preserve the `$ $` math syntax. https://github.com/quarto-dev/quarto-cli/blob/0501d0708794a5030fc3b3f64dfca23e93200c0a/src/resources/filters/quarto-pre/table-captions.lua#L136-L140 In the second case, the table produced will be LaTeX, and in this case, we'll process there: https://github.com/quarto-dev/quarto-cli/blob/0501d0708794a5030fc3b3f64dfca23e93200c0a/src/resources/filters/quarto-pre/table-captions.lua#L201-L205 We are loosing the `$ $` math syntax when calling `stringify` I believe, so when calling `stringEscape()` the `\beta` will not be correctly parsed as Math. If we want to support Markdown syntax for table caption, we should probably align the two treatment. Using Dev version of Quarto, on Windows 11. ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description The change in our format regex to support custom formats breaks autocompletions because our "complete through prefixes" code doesn't currently support character classes. ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description Here is a (pandoc) markdown test file `test.qmd` ``` # Test $$\begin{equation} 1+2 \end{equation}$$ Some text $$\begin{equation} 3+4 \end{equation}$$ more text $$\begin{equation} 5+6 \end{equation}$$ even more text $$\begin{equation} 7+8 \end{equation}$$ the end. ``` When rendering as html with pandoc `pandoc -t html5 --mathjax -s -o test-pandoc.html test.qmd` it renders correctly.  However when rendering the file to html with quarto ` quarto render test.qmd` `$$` are showing up in the text of the html file  This happens with quarto 0.9.592 and pandoc 2.18 on Mac OS X 10.15.7 . ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description When trying to generate a PDF with the VS extension or e.g. `quarto.cmd preview paper.qmd`, I get the following error, even after installing tinytex as per the instructions. ``` 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. ``` ``` $ quarto.cmd install tool tinytex tinytex is already installed and up to date. ``` Platform: Windows 10 ``` $ quarto.cmd check [>] Checking Quarto installation......OK Version: 0.9.596 Path: C:\Users\luke\AppData\Local\Programs\Quarto\bin\ CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.1 Path: c:/Users/luke/src/cde/cde-stuff/scientific-writing/assignment-4/.venv/Scripts/python.exe Jupyter: 4.10.0 Kernels: python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.1.3 Path: C:/PROGRA~1/R/R-41~1.3 LibPaths: - C:/Program Files/R/R-4.1.3/library rmarkdown: (None) The rmarkdown package is not available in this R installation. Install with install.packages("rmarkdown") ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description ´quarto install tool tinytex´ triggers a download of a package of approx. 200mb. Any interruptions to the connection seem to break the download and require it to be started again. This is noticeable whilst travelling with e.g. train wifi or mobile hotspot.  Platform: Windows 10. quarto cli version: 0.9.596 ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

I'm working on a paper that includes many tables in an appendix section. Some tables are too large to be output on a single portrait-oriented page. A standard practice in my field is to present tables in rotated format — not changing the portrait/landscape orientation of the page, but simply rotating the table. I've looked around the Quarto documentation and can't find any hints as to how I might do this. Any help would be appreciated.

@cscheid For our stable release I wanted to take the final patch release of Deno 1.22 (v1.22.3, we are currently back at 1.22.0). I have so far done the following: - Updates configuration for Deno 1.22.3 - Updates the embedded standard library for quarto run to 0.143.0 (the version that was released with Deno 1.22.3) These commits are on this branch: https://github.com/quarto-dev/quarto-cli/tree/feature/deno-1.22.3 I wasn't exactly sure how to update the vendored stuff though, so hopefully you can do that so I can get schooled on the process. One potential snag point is that the cliffy code has full URL imports of the old std library (0.138.0) so it seems like some additional redirection from 0.138.0 to 0.143.0 might be required? Once you have tests passing and this is ready to merge, let's squash the branch down to a single commit so that we can easily back it out if there are unexpected regressions.

### Bug description Hi, I'm maintainer of Arch Linux package `quarto-cli` (0.9.594 currenly). Few days ago deno was updated there to 1.23.0 With the new Deno version I'm getting half a dozen of errors during the build: ``` ../dist/bin/tools/deno run --unstable --allow-env --allow-read --allow-write --allow-run --allow-net --allow-ffi --importmap=../../src/import_map.json bld.ts prepare-dist --log-level info Using configuration: {"productName":"Quarto","version":"0.9","importmap":"/home/trap000d/src/quarto-cli/src/dev_import_map.json","directoryInfo":{"root":"/home/trap000d/src/quarto-cli","pkg":"/home/trap000d/src/quarto-cli/package","dist":"/home/trap000d/src/quarto-cli/package/dist","share":"/home/trap000d/src/quarto-cli/package/dist/share","src":"/home/trap000d/src/quarto-cli/src","out":"/home/trap000d/src/quarto-cli/package/out","bin":"/home/trap000d/src/quarto-cli/package/dist/bin"}} Moving supporting files Ensuring dir /home/trap000d/src/quarto-cli/package/dist/share exists Copying /home/trap000d/src/quarto-cli/COPYING.md to /home/trap000d/src/quarto-cli/package/dist/share/COPYING.md Ensuring dir /home/trap000d/src/quarto-cli/package/dist/share exists Copying /home/trap000d/src/quarto-cli/COPYRIGHT to /home/trap000d/src/quarto-cli/package/dist/share/COPYRIGHT Ensuring dir /home/trap000d/src/quarto-cli/package/dist exists Copying /home/trap000d/src/quarto-cli/src/resources to /home/trap000d/src/quarto-cli/package/dist/share Ensuring dir /home/trap000d/src/quarto-cli/package/dist/bin exists Copying /home/trap000d/src/quarto-cli/src/resources/vendor to /home/trap000d/src/quarto-cli/package/dist/bin/vendor Creating Deno Bundle /home/trap000d/src/quarto-cli/package/dist/bin/quarto.js ["/home/trap000d/src/quarto-cli/package/dist/bin/tools/deno","bundle","--unstable","--importmap=/home/trap000d/src/quarto-cli/src/dev_import_map.json","/home/trap000d/src/quarto-cli/src/quarto.ts","/home/trap000d/src/quarto-cli/package/dist/bin/quarto.js"] Check file:///home/trap000d/src/quarto-cli/src/quarto.ts error: TS2352 [ERROR]: Conversion of type 'bigint' to type 'number' may be a mistake because neither type sufficiently overlaps with the other. If this was intentional, convert the expression to 'unknown' first. const usizeBytes = dylib.symbols.deno_dom_usize_len() as number; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ at file:///home/trap000d/src/quarto-cli/src/core/deno-dom.ts:61:28 TS2783 [ERROR]: 'type' is specified more than once, so this usage will be overwritten. type: "full", ~~~~~~~~~~~~ at file:///home/trap000d/src/quarto-cli/src/project/types/website/listing/website-listing.ts:245:9 TS2785 [ERROR]: This spread always overwrites this property. ...options[kFeed], ~~~~~~~~~~~~~~~~~ at file:///home/trap000d/src/quarto-cli/src/project/types/website/listing/website-listing.ts:246:9 TS2352 [ERROR]: Conversion of type 'undefined' to type 'string' may be a mistake because neither type sufficiently overlaps with the other. If this was intentional, convert the expression to 'unknown' first. giscusOptions[kGiscusCategoryId] as string, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ at file:///home/trap000d/src/quarto-cli/src/project/types/website/website-giscus.ts:77:13 TS2551 [ERROR]: Property 'sleepSync' does not exist on type 'typeof Deno'. Did you mean 'seekSync'? Deno.sleepSync(3000); ~~~~~~~~~ at file:///home/trap000d/src/quarto-cli/src/project/serve/serve.ts:571:14 'seekSync' is declared here. export function seekSync( ~~~~~~~~ at asset:///lib.deno.ns.d.ts:999:19 TS2564 [ERROR]: Property '[Symbol.toStringTag]' has no initializer and is not definitely assigned in the constructor. readonly [Symbol.toStringTag]: string; ~~~~~~~~~~~~~~~~~~~~ at file:///home/trap000d/src/quarto-cli/src/publish/netlify/api/core/CancelablePromise.ts:25:12 Found 5 errors. ERROR: Failure to bundle /home/trap000d/src/quarto-cli/src/quarto.ts Error: Failure to bundle /home/trap000d/src/quarto-cli/src/quarto.ts at bundle (file:///home/trap000d/src/quarto-cli/package/src/util/deno.ts:38:11) at async prepareDist (file:///home/trap000d/src/quarto-cli/package/src/common/prepare-dist.ts:39:3) at async Command.fn (file:///home/trap000d/src/quarto-cli/package/src/cmd/pkg-cmd.ts:38:5) at async Command.execute (https://deno.land/x/cliffy@v0.24.2/command/command.ts:1275:7) at async quartoBld (file:///home/trap000d/src/quarto-cli/package/src/bld.ts:48:3) at async mainRunner (file:///home/trap000d/src/quarto-cli/src/core/main.ts:39:5) at async file:///home/trap000d/src/quarto-cli/package/src/bld.ts:52:3 ``` After rolling back to old Deno version (1.22.3) all seems OK. As a temporary override I've added "deno <1.23.0" into PKGBUILD. However it's just a matter of time when other distributions (Manjaro of Fedora) will pick up the new Deno. So please take a look occasionally at these errors. Regards. ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1172 <div type='discussions-op-text'> ^{Originally posted by **harrelfe** June 17, 2022} I specify cap-location: margin in my Quarto book yaml. For the few figures that have multiple panels this causes the figures to no longer be rendered in a matrix but rather as larger individual plots. Is there a way to override cap-location for one code chunk? Here's some test code: --- title: "Test" format: html: self-contained: true cap-location: margin --- ```{r} #| label: fig-test #| fig.width: 8 #| fig.height: 8 #| fig.scap: 'Four examples of residual plots' #| fig.cap: 'Using residuals to check some of the assumptions of the simple linear regression model.' #| fig-subcap: #| - "Non-constant $\\sigma^2$, which might call for transforming $y$" #| - "Constant $\\sigma^2$ but systemic failure of the linearity assumption" #| - "Ideal situation of white noise (no trend, constant variance)" #| - "$q-q$ plot demonstrating approximate normality of residuals, for a sample of size $n=50$. Horizontal reference lines are at zero, which is by definition the mean of all residuals." #| layout-ncol: 2 plot(rnorm(20)); plot(runif(20)); hist(rnorm(100)); hist(rexp(100)) ``` </div>

### Bug description At https://datasciencebox.org/, if you switch between pages in the navbar, the `page-footer` jumps/flickers. The page is built via a GitHub action but I observe the same behaviour when rendered with dev-quarto as well. ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1166 <div type='discussions-op-text'> ^{Originally posted by **linogaliana** June 17, 2022} Hi, `callouts` are a really nice feature. I have seen in the doc that currently Jupyter Notebooks are not supported (https://quarto.org/docs/authoring/callouts.html). I totally understand this is not a priority and might be tricky to implement. However, in the future, that would be really cool to also propose boxes for this output format. - As far as I understood discussions in https://github.com/jupyter/notebook/issues/1292 it seems that there exists some features in Jupyter Notebook with some raw HTML `<div>`. Some examples are given [here](https://github.com/jupyter/notebook/issues/1292#issuecomment-570548806) - However, all boxes provided by `quarto` are not supported - Boxes are not as aesthetic as those provided by `quarto` (or jupyterbook). This is of course not a priority (functional boxes would first be great) but this would be cool to a nice box in notebook. I saw that it is possible to embed some styling element directly in the `div` ([see this stackoverflow thread](https://stackoverflow.com/questions/62562105/syntax-highlighting-for-code-blocks-within-alert-box-in-jupyter-for-both-noteboo)) but maybe there's a better way to start - @choldgraf maybe has an opinion on the best way to proceed Once again, I understand that tweaking some notebook features is not a priority. But helping python users generate nice notebooks from quarto could be appreciated</div>

### Bug description This one has me scratching my head! I have an [example notebook on Observable](https://observablehq.com/d/4edbbf49c9c105af) based on the [Synchronised Inputs](https://observablehq.com/@observablehq/synchronized-inputs?collection=@observablehq/inputs) notebook. In my example, each of three buttons sets three sliders to preset values. This example works great in the Observable notebook, but when I try it in Quarto, the buttons won't render unless I disable all of the calls to my `setControls` function but one. The sliders and other element do render, and if I comment out all of the `setControls` calls after the first, all three buttons render too (although of course, only slider is moved by one button). Here's the code as a QMD: ```` --- title: Test --- ```{ojs} // use this to update the other controls when we choose a preset function setControl(input, value) { input.value = value; input.dispatchEvent(new Event("input", {bubbles: true})); return; } ``` ```{ojs} viewof presetButtons = Inputs.button([ [ "Preset A", () => { setControl(viewof sliderRed, 30); setControl(viewof sliderBlue, 50000); setControl(viewof sliderGreen, 1000); } ], [ "Preset B", () => { setControl(viewof sliderRed, 30); setControl(viewof sliderBlue, 16000); setControl(viewof sliderGreen, 2500); } ], [ "Preset C", () => { setControl(viewof sliderRed, 30); setControl(viewof sliderBlue, 16000); setControl(viewof sliderGreen, 8000); } ] ]); ``` #### CONTROLS ```{ojs} viewof sliderGreen = Inputs.range([1000, 10000], { label: html`Green` }); ``` ```{ojs} viewof sliderBlue = Inputs.range([15000, 70000], { label: html`Blue` }); ``` ```{ojs} viewof sliderRed = Inputs.range([0.1, 90], { label: "Red" }); ``` ```` In Quarto, I also get in the Developer Tools console: > Uncaught (in promise) TypeError: Cannot read properties of null (reading 'querySelectorAll') at quarto-ojs-runtime.js:18729:34 > (anonymous) @ quarto-ojs-runtime.js:18729 > Promise.catch (async) > interpret @ quarto-ojs-runtime.js:18714 > interpretFromScriptTags @ quarto-ojs-runtime.js:18759 > (anonymous) @ (index):207 I'm using Quarto `c976d176a` and R 4.1.2 on MacOS 12.3.1. ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description I made a GitHub action to update https://rlille.fr website built with Quarto. I wanted to check the latest updates in Quarto. It appears from the automatic PR (https://github.com/RLille/rlille.fr/pull/8), that now `og:description` and `twitter:description` content are truncated for some reason (It's only 43 characters). You can see the file in the PR below https://github.com/RLille/rlille.fr/pull/8/files#diff-59d7533953135e1ecd90fda6cbbe9f578fb34255fb782d4f072d896ab8465a7eL88 Quarto: 0.9.587 GitHub Action: ubuntu-latest (<https://github.com/RLille/rlille.fr/blob/main/.github/workflows/build.yml>)

### Bug description When using `pptx` as an output format, `mermaid` isn't rendering. A minimal `.qmd` file with an example is below: ```` --- title: "Mermaid not rendering" format: pptx --- ## Mermaid won't render ```{mermaid} graph LR A[Hello] --> B[World] ``` ```` The resulting PowerPoint contains the title of the slide, but not the diagram: [mermaid-pptx.zip](https://github.com/quarto-dev/quarto-cli/files/8914092/mermaid-pptx.zip) I'm running `Ubuntu 20.04.4 LTS` on WSL2. Output from `quarto check`: ``` [✓] Checking Quarto installation......OK Version: 0.9.587 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.10 Path: /usr/bin/python3 Jupyter: 4.10.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.0 Path: /usr/lib/R LibPaths: - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/lib/R/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description I'd like to attach a CSS class or to a code chunk: `hello`, or example, or `hello` and `goodbye`. But in my rendered output, the chunk element appears to get `class="cell h e l l o"` or `class="cell h e l l o g o o d b y e"` (note the spaces). Here's my test example: ```` --- title: "Test doc" format: html: self-contained: true --- Here's a chunk: ```{ojs} //| classes: hello 3 + 3 ``` ```` The output HTML is attached: [_test.html.zip](https://github.com/quarto-dev/quarto-cli/files/8906351/_test.html.zip) My Quarto version is as of commit `a450f1c0f` (about six days ago). My R version is 4.1.2, and RMarkdown is 2.11. My MacOS version is 12.3.1. ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

Consider the following code cells in a quarto-document: ```` ## Welcome {.unnumbered} ```{r} my_list = list(1, 2, 3) typeof(my_list) ``` ```{python} my_list = [1, 2, 3] type(my_list) ``` ```` Would it be possible to add a flag to `quarto` that specifies only _R_ code chunks be written/evaluated? e.g. ```` ## Welcome {.unnumbered} ```{r} my_list = list(1, 2, 3) typeof(my_list) ``` ````

It is not that uncommon to refer to citations within something already in parentheses or to have the citation in parentheses along with a cross reference to a table, figure, or equation. In those cases it can be nice to separate each element by a semi-colon rather than having back to back parentheses e.g. "(Figure 3; Name 2022)" as opposed to "(Figure 3) (Name 2022)". This issue has been raised on [stackoverflow](https://stackoverflow.com/questions/64209134/r-markdown-suppress-parentheses-in-specific-citations), but there was never an accepted answer. Perhaps there could be (or already is) some syntax for this in quarto?

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1150 <div type='discussions-op-text'> ^{Originally posted by **olivroy** June 14, 2022} It might be a good idea to control table font size In a chunk ```{r} #| tbl-font-size: "80%" knitr::kable(head(mtcars)) ``` Sometimes for large table, it is common that the font size is smaller.</div>

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1149 <div type='discussions-op-text'> ^{Originally posted by **ma-riviere** June 14, 2022} Hello Quarto, I'm wondering if there is a way to make Quarto (or Pandoc) use more threads/cores ? I'm currently compiling a document to HTML (from R), and it takes more than 3 hours. The document is not that long: 2700 lines (more than half of those being text). There are no complex computations (the knitting in itself takes only a few minutes), but once it's done knitting, it will take close to 3 hours to output the HTML document (which is roughly 15MB in size). During that whole time, only ~5% of my CPU is used by the Deno virtual machine, so I was wondering if there was a way to have it use more CPU resources to speed up the process ? Thanks :)</div>

### Bug description It seems that the crossref is not being converted to python notebook format when using `quarto convert`. A MRE is as follows, ````md --- title: Ref in converted `ipynb` --- ```{python} # a code chunk print("See below") ``` $$ E = mc^2 $$ {#eq-example} See an example, @eq-example. ```` This `mre.qmd` file was then converted to a notebook using `quarto convert mre.qmd`. When the converted `ipynb` file is opened, the crossref is not working as expected.  ```bash ❯ quarto check [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /home/julian/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.4 Path: /usr/bin/python3 Jupyter: 4.10.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.1.2 Path: /usr/lib/R LibPaths: - /home/julian/R/x86_64-pc-linux-gnu-library/4.1 - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/lib/R/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` I am running popos (Linux Uhuntu 22.04) ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

I no longer have the prompt (or the preview panel) that ask where to preview the generated HTML file either Windows 10 / MacOS 12.4, while I stil have it within a Docker container running Debian. The settings were not modified (*i.e.*, default). Any idea, how to fix this, if not on quarto-vscode side? <img width="366" alt="Screenshot 2022-06-14 at 15 56 26" src="https://user-images.githubusercontent.com/8896044/173595023-dca363f7-c77e-4dcb-9121-bb8a9982b577.png"> Also, I think path resolution for the preview has a bug when trying to render/preview `subfolder/file.qmd` and setting `_quarto.yml` with `execute-dir: project`. This results in VSCode prompting the user to choose external browser or editor, but in both cases this ends with: ``` ... Output created: index.html Watching files for changes Browse at http:///localhost:6840/subfolder/index.html GET: / (404: Not Found) ``` OS: Windows 10 / MacOS 12.4 VSCode: 1.68 quarto-vscode: 1.24 Quarto: 0.9.573

### Bug description Hello, Somewhere between 0.9.426 and 0.9.580 Quarto has stopped processing multiplexed revealjs presentations correctly and the `*-speaker.html` file is no longer presenting correctly - there's no slides etc it's just a single document, e.g.:  The issue only seems to occur for self-contained presentations only, which I guess is due to the introduction of the following lines in the resulting `*-speaker.html` file (not present in the standard non-speaker html: ```html <script src="presentation-testing_files/libs/clipboard/clipboard.min.js"></script> <script src="presentation-testing_files/libs/quarto-html/tabby.min.js"></script> <script src="presentation-testing_files/libs/quarto-html/popper.min.js"></script> <script src="presentation-testing_files/libs/quarto-html/tippy.umd.min.js"></script> <link href="presentation-testing_files/libs/quarto-html/tippy.css" rel="stylesheet"> <link href="presentation-testing_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet"> <link href="presentation-testing_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"> ``` Obviously, these don't exist for a self-contained presentation so presumably they shouldn't be there in the case of a self-contained presentation. I guess this is the problem but I can't be sure as there's quite a bit different in the `*-speaker.html` files between versions 0.9.426 and 0.9.580. Just to be clear: * non-multiplexed presentations - fine * multiplexed presentations when **not** self-contained - both fine * multiplexed presentations when self-contained - `*-speaker.html` is broken, standard .html is fine Thanks ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [ ] included a minimal, self-contained, and reproducible example? - [ ] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description Rendering a qmd file like the following will leave a file named `qmdfilename_files/figure-docx/mermaid-figure-1.png`. If this is the expected behavior, it would be a good idea to write to .gitignore to exclude these files. ````qmd --- title: "Untitled" format: docx --- ```{mermaid} flowchart LR A[Hard edge] --> B(Round edge) B --> C{Decision} C --> D[Result one] C --> E[Result two] ``` ```` I tested it on Windows and Linux. ```sh $ quarto check [✓] Checking Quarto installation......OK Version: 0.9.580 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.10 Path: /usr/bin/python3 Jupyter: 4.10.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.0 Path: /usr/local/lib/R LibPaths: - /usr/local/lib/R/site-library - /usr/local/lib/R/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description When both `toc: true` and `number-sections: true` are set, the section number is added twice in the ToC, resulting in dead links when one clicks on them in the ToC. Small reproducible example (running under quarto `v0.9.566` and RStudio `2022.02.3 Build 492` on macOS Monterey) ``` --- title: "toc-gfm-numbered-sections" author: "Aymeric Stamm" format: gfm: default html: default editor: visual toc: true number-sections: true --- ## H1 ### Sub-H1 ## H2 ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1140 <div type='discussions-op-text'> ^{Originally posted by **fuhrmanator** June 13, 2022} I'm using SVG a lot in my markdown, and it renders nicely (most of the time) in PDF by way of `rsvg-convert` part of the LaTeX chain: > (rsvg-convert.exe:2516): Pango-WARNING **: couldn't load font "Helvetica Not-Rotated 13.640625", falling back to "Sans Not-Rotated 13.640625", expect ugly output. I'd like to use Inkscape instead, as it does some things better, especially with fonts I've installed in Windows. Is there a way to specify that SVG conversions to PDF should be done using Inkscape? </div>

### Bug description I am unable to use `cat()` to print computed output from in-line R code, even though it works in a code chunk. Example `qmd` file: ````--- title: "test" format: html execute: results: asis --- <!-- nothing shows up --> `r cat("hello")` <!-- prints --> `r "no cat here"` ```{r} cat("hello") # prints ``` ```` Output: <img width="1039" alt="quarto-cat-bug-png" src="https://user-images.githubusercontent.com/13459362/173477280-39f3b5e8-64dc-4209-90ee-f63b96edd064.png"> Output of `quarto check`: ``` [✓] Checking Quarto installation......OK Version: 0.9.579 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.3 (Conda) Path: /Users/joelnitta/miniconda3/bin/python Jupyter: 4.10.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/joelnitta/Dropbox/Jobs/2022/utsunomiya/renv/library/R-4.2/x86_64-apple-darwin17.0 - /Library/Frameworks/R.framework/Versions/4.2/Resources/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` IDE: vs-code v1.67.2 OS: Mac Monterey v12.4 R: v4.2.0 Output of `sessionInfo()`: ``` > sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur/Monterey 10.16 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices datasets utils methods base loaded via a namespace (and not attached): [1] compiler_4.2.0 cli_3.3.0 tools_4.2.0 jsonlite_1.8.0 rlang_1.0.2 [6] renv_0.15.5 ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description Sometime prior to 0.9.577 my book project would generate PlantUML/GraphViz images using pandoc's official diagram filter with no troubles, if I used the `self-contained: true` in the html part of the .yml. It seems to be broken now. Instead of `data:` uri's for the filter-generated SVGs, I get e.g.: ```html <img src="b0a06efeb01f6cbd272bae71a5fa8f954dc5413a.svg" class="img-fluid figure-img"> ``` They're not stored anywhere, so the server records these errors: ```terminal [WARNING] Could not fetch resource b0a06efeb01f6cbd272bae71a5fa8f954dc5413a.svg ``` There's a workaround if I hack the command using `quarto preview --to html --extract-media=_book/images`, but it effectively negates the `self-contained: true` option. To help you with a minimal working example, I created a repo at https://github.com/fuhrmanator/quarto-test ``` quarto check [>] Checking Quarto installation......OK Version: 0.9.577 Path: C:\Users\fuhrm\AppData\Local\Programs\Quarto\bin\ CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.2 Path: C:/Python310/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with py -m pip install jupyter [>] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` Windows 10. ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description When using a footnote inside a figure caption, Quarto crashes. I'm converting a pandoc book to Quarto, and I was previously able to use a footnote inside a caption in Pandoc: ```markdown ![Here's a caption[^1].](images/example.jpg) [^1]: Here's a footnote. ``` But it crashes when I try this in quarto, because (I suspect) the footnote is inside the caption (and maybe something's not being escaped properly?): ``` Latexmk: If appropriate, the -f option can be used to get latexmk to try to force complete processing. Reverting Windows console CPs to (in,out) = (437,65001) Error producing PDF. ! Argument of \caption@ydblarg has an extra }. <inserted text> \par l.794 footnote.}.} ``` I'm running quarto on Windows 10. ```terminal quarto check [>] Checking Quarto installation......OK Version: 0.9.577 Path: C:\Users\fuhrm\AppData\Local\Programs\Quarto\bin\ CodePage: unknown [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.2 Path: C:/Python310/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with py -m pip install jupyter [>] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

I use the dropdown menu in the main navigation to link the related blog posts/listing categories. However, only the first one could automatically refresh the page. Following categories do not automatically refresh the page when clicking and I have to click return to refresh it.

Quarto's custom date format can provide the time zone, but only as UTC offset (e.g. `-6:00`) rather than the time zone name/abbreviation (e.g. `PDT` or `Pacific Daylight Time`). ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description When I widen the browser, the page follows the left side instead of being centered as shown in the attached screenshot. I do not understand under what conditions this occurs, as it does not happen in my other projects.  Source: https://github.com/rocker-org/website/blob/9e36976f182639fefb1921cb472b5410e17c2fbc/images/index.md ```sh $ quarto check [✓] Checking Quarto installation......OK Version: 0.9.577 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.10 Path: /usr/bin/python3 Jupyter: 4.10.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.0 Path: /usr/local/lib/R LibPaths: - /usr/local/lib/R/site-library - /usr/local/lib/R/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description I noticed that the shorcode example is missing in the reference page. Perhaps the behavior of quarto has changed? https://quarto.org/docs/authoring/includes.html  ````md --- title: "Includes" --- ## Overview Includes are a convenient way to re-use content across documents. Includes work for plain markdown content as well as for `.qmd` files with executable code cells (note however that the cells must all use the same engine -- i.e. knitr or jupyter, but not both). To include a file, add the `{{< include >}}` shortcode at the location in your document where you want it included: ``` markdown {{< include _content.qmd >}} ``` ```` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [ ] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description Originally reported by @314a here: https://github.com/quarto-dev/quarto-cli/discussions/1033#discussioncomment-2923301 I started writing a post-render script. The stripped down version should render a file to the output folder specified in the _quarto.yml_ file. The following code works well when running the file "test.ts" with `deno run --allow-run _resources/scripts/test.ts`, but when invoking it as a post-render script, the error message is: ` "Files\Quarto\bin\quarto.js""==""" cannot be processed syntactically at this point.` (there seems to be an issue with the path to the quarto executable. File test.ts: ``` const p = Deno.run({ cmd: ["cmd", " /c ", "quarto", "--version"] }); // create subprocess await p.status(); ``` same holds for running a batch file. The following batch file _batch.cmd_ runs smoothly standalone, but results in the same error, if invoked as a post-render script in quarto. ``` echo check pandoc version: pandoc --version echo check quarto version: quarto --version ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description My issue is that quarto cannot found numpy package if the file is rendered in vs code. Works perfectly RStudio, or if a cell is simple ran, but fails if I try to render the file. I enclose a pic about the error message.  ### Checklist - [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [ ] included a minimal, self-contained, and reproducible example? - [ ] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description # Problem description I am trying to include an RSS feed for my blog listing. This works all fine with the blog setup that you get when you create a new quarto blog from within RStudio. But it breaks if I tweak the landing page. Then, I get ``` ## Error 1 ERROR: PermissionDenied: Zugriff verweigert (os error 5), rename 'C:\Users\Alber\Desktop\feed-test\site_libs' -> 'C:\Users\Alber\Desktop\feed-test\_site\site_libs' ## Error 2 PermissionDenied: Zugriff verweigert (os error 5), stat 'C:\Users\Alber\Desktop\feed-test\_site\blog.feed-full-staged' ``` Note that I have tried operating with admin rights but that did not help. Let me describe a minimal example. # Minimal example that works Create new quarto blog via RStudio. Then modify `index.qmd` and `_quarto.yml` as described in [Quarto docs](https://quarto.org/docs/websites/website-blog.html#rss-feed) to include an RSS feed. ### index.qmd ``` --- title: "feed-test" listing: contents: posts sort: "date desc" type: default categories: true feed: true page-layout: full title-block-banner: true `---` ``` ### _quarto.yml ``` project: type: website website: title: "feed-test" site-url: https://www.myblogexample.io description: 'Great blog' navbar: right: - blog.qmd - icon: github href: https://github.com/ - icon: twitter href: https://twitter.com - icon: rss href: blog.xml format: html: theme: cosmo css: styles.css editor: visual `` ``` # Changes that break the blog Now, I want my blog to have a landing page that is different from the blog listing. So, I renamed * `index.qmd` > `blog.qmd` * `about.qmd` > `index.qmd` This causes `blog.qmd` to not render anymore with one of the above error. Sometimes it renders without a problem but accessing `blog.html` then errors out with the second error (above). # System Information ### OS I am using Windows 10 ### R ``` R version 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) ``` ### RStudio ``` RStudio 2022.02.3 Build 492 © 2009-2022 RStudio, PBC "Prairie Trillium" Release (1db809b8, 2022-05-20) for Windows Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36 ``` ### Quarto ``` Version: 0.9.566 Path: C:\Users\Alber\AppData\Local\Programs\Quarto\bin\ CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.8.2 Path: C:/Users/Alber/AppData/Local/Programs/Python/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: 4.0.3 Path: C:/PROGRA~1/R/R-40~1.3 LibPaths: - C:/Users/Alber/Documents/R/win-library/4.0 - C:/Program Files/R/R-4.0.3/library rmarkdown: 2.13 [>] Checking Knitr engine render......OK ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description Hi, I would like to give a bug report - I use Quarto book to render a source file (`.qmd`) that lives in a **subdirectory**. - I've found that, **plot output** from that particular file is not included if the output format is `docx`. (but HTML output works fine) ## Example I've created [a minimal example repo here](https://github.com/Lightbridge-KS/quarto-book-figpath-bug). `plot(cars)` from [this source file](https://github.com/Lightbridge-KS/quarto-book-figpath-bug/blob/main/subdir/intro.qmd) is not included in [MS Word output](https://github.com/Lightbridge-KS/quarto-book-figpath-bug/blob/main/_book/Quarto-debug-figure-path.docx) (but, [HTML output](https://lightbridge-ks.github.io/quarto-book-figpath-bug/) works fine) The following error msg is generated: ``` [WARNING] Could not fetch resource intro_files/figure-docx/fig-cars-bug-1.png: replacing image with description ``` [**_quarto.yml**](https://github.com/Lightbridge-KS/quarto-book-figpath-bug/blob/main/_quarto.yml) ```yml project: type: book book: title: "Quarto debug figure path" author: "Kittipos Sirivongrungson" date: "6/11/2022" chapters: - index.qmd - subdir/intro.qmd # Figure problem in here bibliography: references.bib format: html: theme: cosmo docx: default ``` ## My Session Info ```shell $ quarto check ``` [✓] Checking Quarto installation......OK Version: 0.9.566 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.7 (Conda) Path: /Users/kittipos/opt/miniconda3/bin/python Jupyter: 4.9.2 Kernels: julia-1.7, julia-1.5, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/kittipos/Desktop/R_Programming/quarto/quarto-book-figpath-bug/renv/library/R-4.2/x86_64-apple-darwin17.0 - /Library/Frameworks/R.framework/Versions/4.2/Resources/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ```r > session_info() ``` ─ Session info ──────────────────────────────────── setting value version R version 4.2.0 (2022-04-22) os macOS Monterey 12.4 system x86_64, darwin17.0 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz Asia/Bangkok date 2022-06-11 rstudio 2022.02.3+492 Prairie Trillium (desktop) pandoc 2.16.2 @ /usr/local/bin/pandoc Your guys did a great job so far. Thank you very much. ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description At least on the about page jolla theme seems to break off at the edges when viewed from smart phones. This is also reproduced when using the desktop browser's developer tools. In this image, the site as displayed with `quarto preview` and in the desktop version of Firefox.  website: https://www.rocker-project.org/ source: https://github.com/rocker-org/website/tree/47ccfc619fffaca5d8caac4db79edeee526e0e46 ``` [✓] Checking Quarto installation......OK Version: 0.9.566 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.10 Path: /usr/bin/python3 Jupyter: 4.10.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.0 Path: /usr/local/lib/R LibPaths: - /usr/local/lib/R/site-library - /usr/local/lib/R/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description Is it possible to add an additional folder when creating a Website at `output-dir`? In blogdown the "static" folder could be exported at `output-dir`

### Bug description I have the following listing yaml: ``` title: "Hello" image: "hello.jpg" image-alt: "Image's alt text" ``` The rendered listing page is the following: <img width="875" alt="Screen Shot 2022-06-10 at 4 30 42 PM" src="https://user-images.githubusercontent.com/5965649/173146466-bcd036ff-79ba-4f55-9624-eb2cac2c6728.png"> Removing the single quote fixes the issue: ``` title: "Hello" image: "hello.jpg" image-alt: "Image alt text" ``` <img width="873" alt="Screen Shot 2022-06-10 at 4 31 04 PM" src="https://user-images.githubusercontent.com/5965649/173146532-3c38746a-d6b2-4381-89af-c7450628fa52.png"> I'm running dev-Quarto (just updated). ``` Mines-MacBook-Pro-2:quarto-website mine$ quarto check [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Users/mine/Desktop/RStudio/quarto-cli/package/dist/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: 4.1.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.1/Resources/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` RStudio version: RStudio 2022.06.0-daily+421 "Spotted Wakerobin" Daily (2572293ae6f54278ae07e0cd10b29a370c69104c, 2022-05-19) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 12_4_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36 OS: macOS 12.4 ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [x] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description ## The issue I believe I found a bug where shared metadata for posts is not shown on listing page of a website, but it is shown on the individual posts. ## Description and minimal example I have a website containing a listing page with the following structure: ```default |- documents/ |-- index.qmd |-- posts/ |--- _metadata.yml |--- post-1/index.md |--- ... |--- post-100/index.md ``` Inside `_metadata.yml` I've specified some default options for the posts: ```default date: last-modified author: Michael ``` When I preview the site and visit the pages for these posts, I can see that the params in `_metadata.yml` have been passed through. **However**, when I visit the `documents` listing page on the site the default date and author are not showing up for the list items. My `index.qmd` file looks like this: ```default --- title: Documents listing: sort: "date desc" contents: "posts" type: "table" page-size: 30 sort-ui: true filter-ui: true categories: true feed: false field-display-names: author: "Author(s)" date: Last modified page-layout: full title-block-banner: "#EDF3F9" title-block-banner-color: body search: true --- ``` Here is a screenshot to clarify. Posts where the date and author have had their values filled manually show that metadata on the listing page, but posts where I'm using the defaults don't show the metadata on the listing page.  ## Quarto Check Using OSX: ```default quarto check [✓] Checking Quarto installation......OK Version: 0.9.563 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.1 (Conda) Path: /Users/Michael/Library/r-miniconda/envs/r-reticulate-mne/bin/python Jupyter: 4.7.0 Kernels: ir, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.1.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/Michael/Library/R/4.1/library - /Library/Frameworks/R.framework/Versions/4.1/Resources/library rmarkdown: 2.13 [✓] Checking Knitr engine render......OK ``` ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description I'm running into the following error `LaTeX Error: Not in outer par mode` when trying to render a `.qmd` as a `pdf`. The problem only occurs when using `fig-align:` together with `#| fig-cap:`. Removing one or the other option solves the issue. Below is a reproducible example. `````` --- format: pdf execute: echo: false warning: false fig-format: pdf fig-align: center --- ```{r} #| fig-cap: foo plot(1) ``` `````` Probably related to the following issue https://github.com/quarto-dev/quarto-cli/issues/462#issue-1180525040. I'm using Quarto v. 0.9.549 in RStudio v. 4.2.0, running on macOS Monterey. ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

When I render PDF, I want to keep .aux files so that I can do cross referencing using external document with {xr}. The option `keep-tex: true` only keeps .tex files.

It looks like the way `code-link: true` works is through this R script https://github.com/quarto-dev/quarto-cli/blob/f30845bb322ec9bbfcb4b5e6e12887aa902f5fcc/src/resources/rmd/rmd.R If I uninstall one of the dependencies you use there, say, jsonlite, and try and run `quarto render` then I get: ```r [ 1/15] posts/2022-03-11-using-vs-code-to-debug-r-packages-with-c-code/index.qmd Error in loadNamespace(x) : there is no package called ‘jsonlite’ Calls: .main ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted WARNING: Unable to perform code-link (code-link requires R and the downlit package) ``` So the error message from R is right but the warning from quarto is a little off. Maybe there should be some kind of up front check for all of the dependencies required to run that script? Like xfun, knitr, rmarkdown, htmltools, etc. Run with quarto 0.9.344

### Bug description Twitter and open cards aren't properly copying the image file as a resource for images that are only referenced by the twitter/opengraph metadata. We need to contribute the image to the resources when we add in the website-meta post processor. ### Checklist - [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [ ] included a minimal, self-contained, and reproducible example? - [ ] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description Jupyter notebooks wrap dataframe column heading text as needed. When rendering in Quarto the wrap is not maintained so the headers (and the tables) trail off the side of the page. Quarto version: 0.09.495 OS: Windows 11 Pro 22000.675 Input: ``` title: "Wrap Text Column Heading" title-block-style: default format: pdf ``` ``` import pandas as pd data = {'Long Header Text 1': [3, 2, 1, 0], 'Long Header Text 2': ['a', 'b', 'c', 'd'], 'Long Header Text 3': ['a', 'b', 'c', 'd'], 'Long Header Text 4': ['a', 'b', 'c', 'd'], 'Long Header Text 5': ['a', 'b', 'c', 'd'], 'Long Header Text 6': ['a', 'b', 'c', 'd'], 'Long Header Text 7': ['a', 'b', 'c', 'd'], 'Long Header Text 8': ['a', 'b', 'c', 'd'], 'Long Header Text 9': ['a', 'b', 'c', 'd']} pd.DataFrame.from_dict(data) ``` Notebook output:  Quarto output:  ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [X] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

Dataframe headings (produced from a Jupyter/python code cell) show greek symbols:  When I use Quarto to render the pdf, column headings are shown with the Latex command:  I would like the Quarto output to display the Greek symbols. Do you know how I can do this? Quarto version: 0.09.495

### Bug description When pasting a piece of text from MSWord in visual mode, some extra lines are included. Linebreaks are also added in the text (at a given width). When pasting the same piece of text in source mode, the result is as expected with no lines or linebreaks added. This seems to be true on Win11 and MacOS, with the latest RStudio (492) installed. ### Checklist - [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [ ] included a minimal, self-contained, and reproducible example? - [ ] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Bug description Hello, I used the following to install TinyTex in a VSCode terminal on Windows 10.0.19044: ``` quarto tools install tinytex ``` Which outputted: ``` Installing tinytex [>] Downloading TinyTex v2022.05 [>] Unzipping TinyTeX-v2022.05.zip [>] Moving files [>] Verifying tlgpg support [>] Default Repository: https://ctan.math.illinois.edu/systems/texlive/tlnet/ [>] Updating paths ERROR: suggestUserBinPaths not currently supported on Windows ``` When I try to render a qmd to PDF I get the error: ``` running xelatex - 1 No TeX installation was detected. Please run 'quarto tools install tinytex' to install TinyTex. If you prefer, you may install TexLive or another TeX distribution. ``` Which is weird because I can see the TinyTex folder sitting in C:\Users\myname\AppData\Roaming which as far as I can tell is the intended behaviour? And when I try to re-install TinyTex using the first command it will abort and say there already is a TinyTex installation. quarto check: ``` [>] Checking Quarto installation......OK Version: 0.9.393 Path: C:\Users\myname\AppData\Local\Programs\Quarto\bin\ CodePage: unknown [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.4 Path: C:/Users/myname/scoop/apps/python/current/python.exe Jupyter: 4.10.0 Kernels: python3 [>] Checking Jupyter engine render....OK ``` It looks like TinyTex can't be found whilst rendering? I'm completely clueless about LaTeX installations so I tried following the recommended installation.. ### Checklist - [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [ ] included a minimal, self-contained, and reproducible example? - [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1112 <div type='discussions-op-text'> ^{Originally posted by **arnaudgallou** June 9, 2022} I can't manage to capitalize a cross-reference by changing the syntax of the inline reference as explained in the [documentation](https://quarto.org/docs/authoring/cross-references.html#references). Below is an [example](https://github.com/arnaudgallou/dummy-qmd/blob/main/crossrefs/crossrefs.qmd) with the resulting output being visible [here](https://github.com/arnaudgallou/dummy-qmd/blob/main/crossrefs/crossrefs.md). ``` --- title: Cross references editor_options: markdown: wrap: sentence format: gfm crossref: title-delim: . fig-title: Fig. fig-prefix: fig. eq-prefix: eq. fig-format: svg --- ## Figures {{< include ../_figure.qmd >}} **single plot** @fig-foo @Fig-foo **faceted plot** [@fig-foo]A **supplementary plot** Fig. S[-@fig-foo] ## Equations $$\alpha=2$$ {#eq-a} @eq-a @Eq-a ``` I'm using Quarto v. 0.9.549 on RStudio v. 4.2.0, running on macOS Monterey.</div>

### Bug description Is it possible to include Quarto templates in an R Package, as is possible for R Markdown? I've tried following the same methodology as for R Markdown, i.e. I added template resources to inst/quarto/templates, but that doesn't seem to work. I'm working in RStudio, and I'm expecting to select the template as from the "New R Markdown", shown here:  I'm not seeing the same capability with "New Quarto Document" after updating my package with template material:  RStudio Version: RStudio 2022.02.3+492 "Prairie Trillium" Release (1db809b8323ba0a87c148d16eb84efe39a8e7785, 2022-05-20) for Windows Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36 ### Checklist - [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [ ] included a minimal, self-contained, and reproducible example? - [ ] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

**OS:** Pop!_OS 22.04 LTS x86_64 **Quarto version:** 0.9.550 Minimal example to reproduce error: ```sh quarto create-project mybook --type book ``` Add conditional content to bottom of intro.qmd: ``` # Introduction This is a book created from markdown and executable code. See @knuth84 for additional discussion of literate programming. ::: {.content-visible when-format="html"} Will only appear in HTML. ::: ``` Render book: ```sh quarto render --to all ``` Encountered error: ```sh Error running filter /opt/quarto/share/filters/quarto-pre/quarto-pre.lua: /opt/quarto/share/filters/quarto-pre/quarto-pre.lua:217: attempt to call a nil value (field 'formatMatches') stack traceback: /opt/quarto/share/filters/quarto-pre/quarto-pre.lua:233: in function 'handleVisible' (...tail calls...) ``` Output of `quarto check` ``` [✓] Checking Quarto installation......OK Version: 0.9.550 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.7 (Conda) Path: /home/bjorn/miniconda3/bin/python Jupyter: 4.9.2 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.0 Path: /usr/lib/R LibPaths: - /home/bjorn/R/x86_64-pc-linux-gnu-library/4.2 - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/lib/R/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` The last version (that I know of) that did **not** produce an error was 0.9.426

It would be nice to have the option to show the listing `image` in the actual post as a featured image. This would require getting the sizing and layout correct and I imagine two types of images might be needed: a square one for listing and a rectangular one as a banner on post page.

Good morning, I am working on a Python/Django tutorial and I decided to use Quarto to generate the necessary commands. At the moment of generating the tutorial I get the following error   `error: Uncaught (in promise) Error: Is a directory (os error 21) return parse6(new TextDecoder("utf-8").decode(await Deno.readFile(filepath))); ^ at async Object.readFile (deno:runtime/js/40_read_file.js:24:20) at async parseFileAsync (file:///opt/quarto/bin/quarto.js:22537:55) at async config (file:///opt/quarto/bin/quarto.js:22514:18) at async Object.dotenv (file:///opt/quarto/bin/quarto.js:22616:28) at async file:///opt/quarto/bin/quarto.js:92983:23` Previously I installed Jupyter Notebook but it does not run.

There seems to be a nonsensical tile mixed in with the HTML site listing page (https://quarto.org/docs/websites/website-listings.html). Note that it may disappear if I am editing files while `quarto preview` is running. ## `type: grid`  ## `type: default`  - Ubuntu 20.04 - quarto 0.9.545 source: https://github.com/rocker-org/website/blob/4b4675886c633b68fd05472eaa6ff2b16dcf0b22/use/index.md ## Checklist When filing a _bug report_, please check the boxes below to confirm that you have provided us with the information we need. Have you: - [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [x] included a minimal, self-contained, and reproducible example? - [x] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [x] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

I think we should add some more description in the pages as currently we get not so nice cards when sharing links. Example on https://community.rstudio.com  @dragonstyle does description needs to be set on a per `.qmd` basis for this ? Should we set one global as discussed in https://github.com/quarto-dev/quarto-web/discussions/200 ? Once in one of the tool, we added a feature to generate a defaut `description` based on page content (getting all the text and creating automatically a summary with the first N words / character. Not sure if this is a feature that would be interesting to have.

Look at the second aside, before and after switching to Visual mode https://user-images.githubusercontent.com/19150088/172512228-b2469cdb-9a3e-44b7-b497-b01bdc497878.mov Original code in the qmd: ``` --- title: "2022-05-23_locale-revisited" editor_options: chunk_output_type: console --- # Intro [Hadley is the one who recognized that viewing data frames from this angle opens up powerful new workflows that are especially useful for data analysis.]{.aside} [[Hadley](https://hadley.nz) is the one who recognized that viewing data frames from this angle opens up powerful new workflows that are especially useful for data analysis.]{.aside} [A person, [Hadley](https://hadley.nz), is the one who recognized that viewing data frames from this angle opens up powerful new workflows that are especially useful for data analysis.]{.aside} ``` RStudio 2022.06.0-daily+490 "Spotted Wakerobin" Daily (6c526a3d2ada5e2327136ad0f8a568cdb9a2ca07, 2022-06-07) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 12_2_1) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36 quarto 0.9.344

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1086 <div type='discussions-op-text'> ^{Originally posted by **fitzchivalrik** June 7, 2022} I am in the process of porting my latex template for my thesis to quarto, using the `book` template. When using `appendices` in the `book` yaml, quarto inserts `\addcontentsline{toc}{part}{Appendices}` right after `\appendix`. Unfortunately, this does not adhere to the style guide I need to use. It would be great if this was configurable (`appendix-style: none` does not seem to affect this). Related, I think the produced hyperlink is incorrect, as clicking on `Appendices` in the toc in the PDF moves to the section before the first appendix, however, I am unsure if this is not an error in my setup. ```yaml book: chapters: - index.qmd appendices: # <- - appendix/first.qmd ``` https://github.com/quarto-dev/quarto-cli/blob/5a889b6316be4abcde8b0c3c5d4e4c2f58e4bbd4/src/resources/filters/quarto-pre/book-numbering.lua#L26-L32 Thanks for the software and your work, having one code base to produce a beautiful book-website _and_ PDF is really great.</div>

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1088 <div type='discussions-op-text'> ^{Originally posted by **arnaudgallou** June 7, 2022} Here're a few suggestions/recommendations for possible improvements. I couldn't find easy solutions in the documentation to do what follows so I assume no proper solutions already exist. ### Cross referencing 1. Being able to customize the text of the link when referencing a particular panels in a composite plot (e.g. generated by `ggplot::facet_grid()` or `ggplot::facet_wrap()`). The idea would be to have something that looks like [Fig. 1A]() or [Fig. 1A-B](). I'm currently using `[@fig-x]A-B` which produces [Fig. 1]()A-B but the unlinked plot tag looks ugly when the `ref-hyperlink` option is `true`. I was thinking to have something like `@fig-x{A}` or `@fig-x{A-B}` to append some text to the text link. 2. Somewhat similar to the first point. I'm missing a more flexible way to customize the prefix of supplementary figue/table refs. At the moment, using the `fig-prefix` option adds a space between the prefix and label. A solution could be to have no space as default prefix separator so that `fig-prefix: "Fig. S"` would produce Fig. Sx and add a space in the prefix if need be `fig-prefix: "fig. "`. Alternatively, we could have a yaml option to set the prefix separator. Currently using `Fig. S[-@fig-x]` which has the same ugly look when enabling hyperlinks. 3. Adding a `x-title-template` option for figures and tables to customize the text of figure/table titles easily and with more control. We could imagine something with a placeholder for the labelling. E.g. `fig-title-template: "**Fig. S{label}.**"` would produce **Fig. S1.** I can more or less do that with `title-delim` and `fig-title`, although I don't find it very convenient. However, I cannot figure out an easy way to have the `fig-labels` bold. Besides, I have the same spacing problem as mentioned in point 2 for supplementary figures/tables. 4. I'm missing an easy-to-use system for cross referencing between the supplementary materials and main text. Not sure what would be a simple solution for that because I assume cross references are generated during the rendering process. Ideally, I would imagine adding a yaml option in the main text file to link all references from a specific document (e.g. `appendix: supplementary.qmd`) and have a new tag for supplementary figures/tables (e.g. `@fig-supp-x`) for easy cross referencing in the main text. 5. Adding a way to have a cross reference and citation within the same pair of brackets. E.g.: `blah blah Foo (1999; Fig. 1)`. Probably quite specific and not very common so not sure how relevant it is. ### Text layout 1. Adding a yaml option to align figure/table captions to the left/right/center. This can easily be done with some css but such a trivial thing should be done with a yaml option in my opinion. 2. Adding a yaml option to justify the text of the document. Same as above, can easily be done with a line of css but having a yaml option to do it would make sense to me. ### Other In RStudio, that would be great to have the possibility to open a file that was included in a document using the `{{< include >}}` shortcode by clicking on it in the visual markdown editor. E.g.: ``` {{< include _file.qmd >}} # click the shortcode tag to open _file.qmd in a new tab ``` </div>

The last version 0.9.542 for mac OS do not show all the information in the yaml for the author. Fails to display: link to author url affiliation link to affiliation url orcid

When a gt table, that has a [`rowname_col`](https://gt.rstudio.com/reference/gt.html) specified, is included in a knitr code chunk that *also* has a `tbl-cap` set, rendering the document to PDF fails with the following error: <details><summary>Terminal output</summary> ``` processing file: t.qmd |....................... | 33% ordinary text without R code |............................................... | 67% label: tbl-one (with options) List of 2 $ tbl-cap: chr "A table" $ echo : chr "fenced" |......................................................................| 100% ordinary text without R code output file: t.knit.md pandoc to: latex output-file: t.tex standalone: true pdf-engine: xelatex variables: graphics: true tables: true default-image-extension: pdf filters: - crossref metadata documentclass: scrartcl classoption: - DIV=11 - numbers=noendperiod papersize: letter header-includes: - '\KOMAoption{captions}{tableheading}' block-headings: true keep-md: true keep-tex: true 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 Misplaced \noalign. \caption ->\noalign {\global \@captionabovetrue }\scr@caption l.213 \caption {\label{tbl-one}A table }\tabularnewline see t.log for more information. ``` </details Reproducible example (that creates above output): - Source file: [`t.qmd`](https://salim-b.gitlab.io/adhoc/t.qmd) - Render command: `quarto render t.qmd --to=pdf --metadata=keep-md:true --metadata=keep-tex:true` - Intermediate Markdown file: [`t.md`](https://salim-b.gitlab.io/adhoc/t.md) - Intermediate TeX file: [`t.tex`](https://salim-b.gitlab.io/adhoc/t.tex) - Log file: [`t.log`](https://salim-b.gitlab.io/adhoc/t.log) Note that gt sets `rowname_col = "rowname"` by default when a column named `rowname` is present in the input data, so removing the explicit `rowname_col = "rowname"` in the example above results in the same error. Also `mtcars |> gt::gt(rownames_to_stub = TRUE)` has the same result (since it produces the same table). When either `rowname_col` is set to an inexistent column name (resulting in ommitting the table stub that would otherwise contain the row names), *or* the `tbl-cap` chunk option is removed, the PDF renders fine. ## System details - Quarto 0.9.535 - R 4.2.0 - Latest TinyTeX providing `XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex 2022.6.7)` - Ubuntu 20.04 ## Checklist When filing a _bug report_, please check the boxes below to confirm that you have provided us with the information we need. Have you: - [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [x] included a minimal, self-contained, and reproducible example? - [x] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [x] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

From the documentation site: > Note that for Jupyter, the cache for a document is invalidated if *any* of the code blocks change. For Knitr, invalidation occurs on a per-cell basis. (emphasis added) It would be great it adding or modifying 1 python cell only invalidates the cache for that specific cell, rather than re-executing *all* code cells. This would be really nice if you wanted to say add a new plotting cell but don't want to rerun expensive computations in previous cells I'm not sure if this is a limitation of `jupyter-cache` or if there are plans to support this in the future. Or maybe allow usage or incorporation of a different caching library, e.g. like [ipycache](https://github.com/rossant/ipycache)

Hi, Hope you are well :) The GitHub Action generated page does not display author and date. First image. But the local RStudio generated page renders normally. Second image. <hr> <img width="713" alt="Screen Shot 2022-06-07 at 18 57 56" src="https://user-images.githubusercontent.com/7208830/172427690-7104be8c-c825-470e-a820-7a84d2a61527.png"> <hr> <img width="760" alt="Screen Shot 2022-06-07 at 18 55 00" src="https://user-images.githubusercontent.com/7208830/172427695-e928b70a-65f5-473b-aaff-6055b8649d67.png"> <hr> Local configuration: ``` (base) Serdars-iMac:patolojiatlasi.github.io serdarbalci$ quarto check [✓] Checking Quarto installation......OK Version: 0.9.495 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.12 (Conda) Path: /Users/serdarbalci/miniconda3/bin/python Jupyter: (None) Jupyter is not available in this Python installation. Install with conda install jupyter [✓] Checking R installation...........OK Version: 4.1.3 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/serdarbalci/Documents/GitHub/patolojiatlasi.github.io/renv/library/R-4.1/aarch64-apple-darwin20 - /private/var/folders/cd/2ybg5n514bdfsg2n2wnsspmw0000gn/T/Rtmp7cEqH7/renv-system-library rmarkdown: 2.13 [✓] Checking Knitr engine render......OK ``` GitHub Action file: https://github.com/patolojiatlasi/patolojiatlasi.github.io/blob/main/.github/workflows/Quarto-Render-Bilingual-Book-Push-Tweet-Updates.yml#L46

Dear list members, The last version 0.9.536 for Mac OS do not display the author information specified in the yaml. ``` --- title: "Visualizando datos en escala de Likert" subtitle: Como visualizar datos en escala de Likert image: "likert.png" author: - name: Manuel Spínola url: http://www.icomvis.una.ac.cr/index.php/manuel affiliation: ICOMVIS - UNA affiliation-url: http://www.icomvis.una.ac.cr/ orcid: 0000-0002-7839-1908 date: 2022-06-07 citation: true toc: true toc-title: Tabla de contenido toc-location: left toc-depth: 4 bibliography: references.bib lang: es draft: false categories: - "Escala Likert" - "Visualización de datos" --- ```

<!-- Welcome to the quarto GitHub repo! We are always happy to hear feedback from our users. To file a _bug report_, please follow these instructions carefully: <https://yihui.org/issue/#bug-reports> Also, please complete and keep the checklist below in your issue. This helps you know what to check for opening a good issue report. It also helps know that you've have done the common steps that can solve your potential issue. At last, if you have posted the same issue elsewhere, please mention it here, with a link to the other issue. --> Hello Developer: yaml settings are as follows, but in the web site when toc no number, while a single document will show the number. ``` format: html: toc: true number-sections: true ```  

Hi! I'm having issues with subfigures produced by plotly. It seems like the fig-subcap option is not recognized. Instead, the caption is placed to the top right of the figure instead of formatted correctly at the bottom. ## reprex Here's a minimal example to see the difference. ```` ```{r setup, include=FALSE} data(mtcars) ``` ```{r} #| layout-nrow: 1 #| fig-cap: "Plotting mtcars dataset with ggplot2" #| fig-subcap: #| - "wt vs mpg" #| - "mpg vs wt" #| label: fig-mtcars mtcars |> ggplot2::ggplot(ggplot2::aes(wt, mpg)) + ggplot2::geom_point() mtcars |> ggplot2::ggplot(ggplot2::aes(mpg, wt)) + ggplot2::geom_point() ``` ```{r} #| layout-nrow: 1 #| fig-cap: "Plotting mtcars dataset with plotly" #| fig-subcap: #| - "wt vs mpg" #| - "mpg vs wt" #| label: fig-mtcars-plotly mtcars |> plotly::plot_ly(x = ~wt, y = ~mpg, type = "scatter", mode = "markers") mtcars |> plotly::plot_ly(x = ~mpg, y = ~wt, type = "scatter", mode = "markers") ``` ```` ## Tested with - quarto 0.9.535 - RStudio 2022.06.0-daily+435 "Spotted Wakerobin" Daily (d0717845d82ddf7467f7061734570f6db215da72, 2022-05-22) for Windows Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36 - R 4.2.0 - plotly 4.10.0 ## quarto check output ```` [>] Checking Quarto installation......OK Version: 0.9.535 Path: C:\Users\XYZ\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/XYZ/R/win-library - C:/Program Files/R/R-4.2.0/library rmarkdown: 2.14 [>] Checking Knitr engine render......OK ```` ## Checklist When filing a _bug report_, please check the boxes below to confirm that you have provided us with the information we need. Have you: - [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [x] included a minimal, self-contained, and reproducible example? - [x] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

I'm not sure if this is the best place to ask this, but for some reason after installing the latest version of `quarto` from the website, I'm unable to render or build any documents that contain python cells. If I try using an older version, it no longer works either. I'm not sure if I screwed up something by simply downloading and running the latest `.pkg` file for macOS, but the output of `quarto render` or `quarto serve` no longer work with the following `lua` errors: Using this example from the documentation website (and swapping out to my jupyter kernel, I've tried several I know work outside of quarto): ``` --- title: "matplotlib demo" format: html: code-fold: true jupyter: base --- For a demonstration of a line plot on a polar axis, see @fig-polar. ```{python} #| label: fig-polar #| fig-cap: "A line plot on a polar axis" import numpy as np import matplotlib.pyplot as plt r = np.arange(0, 2, 0.01) theta = 2 * np.pi * r fig, ax = plt.subplots( subplot_kw = {'projection': 'polar'} ) ax.plot(theta, r) ax.set_rticks([0.5, 1, 1.5, 2]) ax.grid(True) plt.show() ``` ``` quarto render test.qmd Error running filter /Users/Esh/Documents/pyprojects/quarto-cli/src/resources/filters/quarto-post/quarto-post.lua: ...ts/quarto-cli/src/resources/filters/quarto-post/book.lua:11: attempt to index a nil value (field 'attr') stack traceback: ...i/src/resources/filters/quarto-post/../common/pandoc.lua:50: in function <...i/src/resources/filters/quarto-post/../common/pandoc.lua:44> ``` I've tried installing from the website, removing that version, installing the homebrew version, uninstalling the homebrew version, and building from this git repo locally (that's the last version I tested in the snippet above), but no version works anymore. Is there an installation "side-effect" that I need to reset before upgrading/reinstalling `quarto`? I've also tried updating my `pandoc` via homebrew and it's currently at: ``` pandoc 2.12 Compiled with pandoc-types 1.22, texmath 0.12.1.1, skylighting 0.10.4, citeproc 0.3.0.8, ipynb 0.1.0.1 User data directory: /Users/Esh/.local/share/pandoc Copyright (C) 2006-2021 John MacFarlane. Web: https://pandoc.org This is free software; see the source for copying conditions. There is no warranty, not even for merchantability or fitness for a particular purpose. ``` Here's the output of `quarto check`. I don't have an R install and because I'm not using R and prior to updating ,when things worked I didn't have R installed either. ``` [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Users/Esh/Documents/pyprojects/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.5 (Conda) Path: /Users/Esh/anaconda3/bin/python Jupyter: 4.9.2 Kernels: pymer4, utilz, py-feat, collab_filter, quarto, base [✓] 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'm on macOS 12.3.1, currently using the development build of `quarto` but this started when I installed 0.9.533

It seems that `quarto` wants tables to be the way `kable` makes them (piped/markdown style), not the JS chunks produced by, say, `DT::datatable`. `datatable` produces output, but captions and cross-referencing are ignored. Small example: ``` --- title: "test" format: html execute: echo: false --- ```{r} library(knitr) library(DT) d <- iris[1:20,] ``` # kable @tbl-kable comes here. ```{r} #| tbl-cap: "kable {#tbl-kable}" kable(d) ``` # DT::datatable @tbl-datatable comes here. ```{r} #| tab-cap: "datatable {#tbl-datatable}" datatable(d) ``` ``` Unexpected output in final html is shown in attached screenshot. Many thanks for looking into this. ## Sys info: ``` MacBook-Pro-4:results jackman$ quarto check [✓] Checking Quarto installation......OK Version: 0.9.528 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.10 Path: /usr/local/bin/python3 Jupyter: 4.10.0 Kernels: julia-0.6, python3 (-) Checking Jupyter engine render....2022-06-07 14:10:55,569 - traitlets - WARNING - Kernel Provisioning: The 'local-provisioner' is not found. This is likely due to the presence of multiple jupyter_client distributions and a previous distribution is being used as the source for entrypoints - which does not include 'local-provisioner'. That distribution should be removed such that only the version-appropriate distribution remains (version >= 7). Until then, a 'local-provisioner' entrypoint will be automatically constructed and used. The candidate distribution locations are: ['/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/jupyter_client-7.3.2.dist-info'] [✓] Checking Jupyter engine render....OK (/) Checking R installation...........Loadi <img width="1001" alt="Screen Shot 2022-06-07 at 2 25 14 pm" src="https://user-images.githubusercontent.com/963653/172295722-9a0b57b8-8ef7-4a92-bcca-2258acb9bc9c.png"> ng .Rprofile for the current workflowr project This is workflowr version 1.7.0 Run ?workflowr for help getting started [✓] Checking R installation...........OK Version: 4.3.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/jackman/Library/R/arm64/4.3/library - /Library/Frameworks/R.framework/Versions/4.3/Resources/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` <img width="1001" alt="Screen Shot 2022-06-07 at 2 25 14 pm" src="https://user-images.githubusercontent.com/963653/172295846-4d713479-b0e8-4683-b085-17dad61548ca.png">

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/712 <div type='discussions-op-text'> ^{Originally posted by **bbartholdy** April 22, 2022} Hi all, I would like to be able to have my references at the end of each chapter, and only the references that were used in the chapter. It's possible to do this for the HTML output with the `reference-location: section` yaml option, but this doesn't seem to carry over to the PDF output. I have also tried using `::: {#refs} :::` at the end of each chapter, but that prints the whole bibliography for the entire book. Is there an easy option to do this that I missed in the documentation? If not, I can also submit an issue for a feature request.</div>

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/409 <div type='discussions-op-text'> ^{Originally posted by **nurfatimaj** March 12, 2022} Is it possible to use other icon packs, such as [Academicons](https://jpswalsh.github.io/academicons/)? </div>

## Checklist When filing a _bug report_, please check the boxes below to confirm that you have provided us with the information we need. Have you: - [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [x] included a minimal, self-contained, and reproducible example? - [x] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [x] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? ## Issue The `linestretch` options described in https://quarto.org/docs/output-formats/html-themes.html#basic-options must be a string, not a numeric. ## Reprex ``` format: html: linestretch: 2 # causes error, must be a string ``` causes ``` In file book/_quarto.yml (line 104, columns 18--21) Key linestretch has value 1.7, which must be a string 104: linestretch: 1.7 ~~~ ✖ The value 1.7 is number. ℹ The error happened in location format:html:linestretch. ```

From https://github.com/rstudio/rstudio-pro/issues/3485, it seems that we still download some deno libraries dynamically when importing the vendored puppeteer library. This is probably a bug in our conversion of the `deno vendor` output.

Hi, In HTML documents, setting the `apperance="minimal"` or `icon=false` attribute on a callout does not suppress the icon when the callout doesn't contain a header. Same goes for setting `callout-appearance: minimal` or `callout-icon: false` in the global options. This issue does not occur in PDF documents. Reprex: ``` --- title: "Callout Icons" format: html --- ::: {.callout-warning appearance="minimal"} This is a callout without a heading. The icon is not suppressed. ::: ::: {.callout-warning appearance="minimal"} # This callout has a heading. The icon is suppressed as expected. ::: ``` <details> <summary>Session Info</summary> ``` R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044), RStudio 2022.2.0.443 Locale: LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C LC_TIME=English_United States.utf8 Package version: base64enc_0.1.3 bslib_0.3.1 cli_3.3.0 compiler_4.2.0 digest_0.6.29 evaluate_0.15 fastmap_1.1.0 fs_1.5.2 glue_1.6.2 graphics_4.2.0 grDevices_4.2.0 highr_0.9 htmltools_0.5.2 jquerylib_0.1.4 jsonlite_1.8.0 knitr_1.39 later_1.3.0 magrittr_2.0.3 methods_4.2.0 processx_3.5.3 ps_1.7.0 quarto_1.1 R6_2.5.1 rappdirs_0.3.3 Rcpp_1.0.8.3 rlang_1.0.2 rmarkdown_2.14 rstudioapi_0.13 sass_0.4.1 stats_4.2.0 stringi_1.7.6 stringr_1.4.0 tinytex_0.39 tools_4.2.0 utils_4.2.0 xfun_0.31 yaml_2.3.5 ``` </details> <details> <summary>Quarto Check</summary> I'm not sure why the check could not locate R. I can run R code chunks in Quarto documents just fine. ``` [>] Checking Quarto installation......OK Version: 0.9.510 Path: C:\Users\czippel\AppData\Local\Programs\Quarto\bin\ CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.11 (Conda) Path: C:/Users/czippel/Anaconda3/python.exe Jupyter: 4.9.2 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/ ``` </details> <!-- Welcome to the quarto GitHub repo! We are always happy to hear feedback from our users. To file a _bug report_, please follow these instructions carefully: <https://yihui.org/issue/#bug-reports> Also, please complete and keep the checklist below in your issue. This helps you know what to check for opening a good issue report. It also helps know that you've have done the common steps that can solve your potential issue. At last, if you have posted the same issue elsewhere, please mention it here, with a link to the other issue. --> ## Checklist When filing a _bug report_, please check the boxes below to confirm that you have provided us with the information we need. Have you: - [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [x] included a minimal, self-contained, and reproducible example? - [x] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [x] upgraded to the latest version (including your versions of R, the RStudio IDE, and relevant R packages)?

Asides formatted using the very nice markdown link syntax `[An aside]{.aside} ` break the XeLaTeX stage of pdf rendering. Rendering a file containing the following: ``` --- title: "Aside bug" --- Some standard text. [An aside]{.aside} ``` Works fine for HTML but gives ``` compilation failed- error Undefined control sequence. l.151 Some standard text. {\marginnote {\begin{footnotesize}An ``` after `quarto render --to pdf aside_bug.qmd`. Updating the file to manually use the `marginnote` package like this ``` --- title: "Aside bug" format: pdf: include-in-header: text: \usepackage{marginnote} --- Some standard text. [An aside]{.aside} ``` renders the aside in the existing margin. That is almost what I wanted, I would have liked the larger margin set when using `::: {.column-margin}` but in contrast to the HTML rendering which now puts the de-emphasised text in between paragraphs. It would be useful to me if this could 1. put the aside in the extended margin 2. do so without interrupting the flow of other paragraphs as `::: {.column-margin}` appears to, for example between bullet points. . This is using - Quarto 0.9.520 - Ubuntu 20.04 in WSL2 on Windows 11 - TinyTex The HTML behaviour appears to be changing. When I first ran into this problem `[An aside]{.aside} ` rendered `An aside` in the margin while `::: {.aside}` put the aside between paragraphs in the main body. With this version both calls put the aside between paragraphs. ## Checklist When filing a _bug report_, please check the boxes below to confirm that you have provided us with the information we need. Have you: - [ x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [ x] included a minimal, self-contained, and reproducible example? - [ x] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [ x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [ x] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ x] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages?

## Checklist When filing a _bug report_, please check the boxes below to confirm that you have provided us with the information we need. Have you: - [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [x] included a minimal, self-contained, and reproducible example? - [x] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [x] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? ## Issue References listed at the same hierarchy level as a part are getting grouped within the last "Part" instead of appearing at the same level (in the Toc).  ## Reprex 1. `quarto create-project mybook --type book` 2. Adjust `_quarto.yml` with content below 3. `quarto render --to pdf` ``` project: type: book book: title: "mybook" author: "Jane Doe" date: "6/6/2022" chapters: - index.qmd - part: intro.qmd chapters: - summary.qmd - references.qmd bibliography: references.bib format: pdf: documentclass: book ``` ## Metadata ``` quarto check [✓] Checking Quarto installation......OK Version: 0.9.515 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.13 Path: /opt/homebrew/opt/python@3.9/bin/python3.9 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/pjs/Library/R/arm64/4.2/library - /opt/R/4.2.0-arm64/Resources/site-library - /opt/R/4.2.0-arm64/Resources/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ```

It's a minor issue, but I was wondering if there is a way to define a static picture (png or svg) as a fallback option for an iframe in a reveal.js presentation? Sometimes it could be that some external policy is blocking the loading of the iframe and it would be nice to have something instead on the slide then. My use case would be displaying my personal webpage at the end of the presentation (with an iframe it would always show the up-to-date version). `{background-iframe="https://page.com/"}`

## Checklist When filing a _bug report_, please check the boxes below to confirm that you have provided us with the information we need. Have you: - [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [x] included a minimal, self-contained, and reproducible example? - [x] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [x] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? ## Issue When creating a PDF with class `srcbook`, the main authors are not taken from `_quarto.yml` but instead from the last `.qmd` rendered. ## Reprex 1. Create book project via `quarto create-project mybook --type book` 2. Add the following header to `summary.qmd` ``` --- author: - test --- ``` 3. `quarto render --to pdf` Now the author in the resulting pdf is "test" rather than "Jane Doe" (which is set in `_quarto.yml`). ## Metadata ``` quarto check [✓] Checking Quarto installation......OK Version: 0.9.515 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.13 Path: /opt/homebrew/opt/python@3.9/bin/python3.9 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/pjs/Library/R/arm64/4.2/library - /opt/R/4.2.0-arm64/Resources/site-library - /opt/R/4.2.0-arm64/Resources/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ```

It would be very helpful if Quarto had a way to streamline the process of adding academic publications to a page. Something similar to the example below: https://research-group.netlify.app/publication/

`revealjs` prioritizes the default syntax highlighting theme even when a value for `highlight-style` is provided, since it places this css for the default highlighting theme in the `<head>` portion of the document. It is especially noticeable for a highlighting theme like `espresso` where the two highlighting themes "mix". Minimal example: ```` --- format: revealjs: execute: echo: true highlight-style: espresso --- ## Title ```{r} rep("dog", 2) ``` ```{r} sum(1, 3) ``` ```` css from default syntax highlighting theme in the `<head>`, which is clashing with `slides_files/libs/quarto-html/quarto-syntax-highlighting.css`: ```css code span.al { color: #ff0000; font-weight: bold; } /* Alert */ code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */ code span.at { color: #7d9029; } /* Attribute */ code span.bn { color: #40a070; } /* BaseN */ code span.bu { } /* BuiltIn */ code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */ code span.ch { color: #4070a0; } /* Char */ code span.cn { color: #880000; } /* Constant */ code span.co { color: #60a0b0; font-style: italic; } /* Comment */ code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */ code span.do { color: #ba2121; font-style: italic; } /* Documentation */ code span.dt { color: #902000; } /* DataType */ code span.dv { color: #40a070; } /* DecVal */ code span.er { color: #ff0000; font-weight: bold; } /* Error */ code span.ex { } /* Extension */ code span.fl { color: #40a070; } /* Float */ code span.fu { color: #06287e; } /* Function */ code span.im { } /* Import */ code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */ code span.kw { color: #007020; font-weight: bold; } /* Keyword */ code span.op { color: #666666; } /* Operator */ code span.ot { color: #007020; } /* Other */ code span.pp { color: #bc7a00; } /* Preprocessor */ code span.sc { color: #4070a0; } /* SpecialChar */ code span.ss { color: #bb6688; } /* SpecialString */ code span.st { color: #4070a0; } /* String */ code span.va { color: #19177c; } /* Variable */ code span.vs { color: #4070a0; } /* VerbatimString */ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */ ``` Output:  Going into the browser's developer tools to delete the above css results in the following correct highlighting:  I don't encounter this issue when the output is `format: html`. ## Checklist When filing a _bug report_, please check the boxes below to confirm that you have provided us with the information we need. Have you: - [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [x] included a minimal, self-contained, and reproducible example? - [x] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? ``` PS C:\Users\Adam> quarto check [>] Checking Quarto installation......OK Version: 0.9.515 Path: C:\Users\Adam\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: 4.1.3 Path: C:/PROGRA~1/R/R-41~1.3 LibPaths: - C:/Users/Adam/Documents/R/win-library/4.1 - C:/Program Files/R/R-4.1.3/library rmarkdown: 2.14 [>] Checking Knitr engine render......OK ``` - [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? - [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well. - [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? Not on the latest version of R... ``` - Session info ---------------------------------------------------------------------------------------------------------------------------------------------------- setting value version R version 4.1.3 (2022-03-10) os Windows 10 x64 (build 19043) system x86_64, mingw32 ui RStudio language (EN) collate English_Canada.1252 ctype English_Canada.1252 tz America/New_York date 2022-06-05 rstudio 2022.02.3+492 Prairie Trillium (desktop) pandoc 2.17.1.1 @ C:/Program Files/RStudio/bin/quarto/bin/ (via rmarkdown) - Packages -------------------------------------------------------------------------------------------------------------------------------------------------------- package * version date (UTC) lib source knitr 1.39 2022-04-26 [1] CRAN (R 4.1.3) quarto 1.1 2022-01-06 [1] CRAN (R 4.1.3) rmarkdown 2.14 2022-04-25 [1] CRAN (R 4.1.3) [1] C:/Users/Adam/Documents/R/win-library/4.1 [2] C:/Program Files/R/R-4.1.3/library ------------------------------------------------------------------------------------------------------------------------------------------------------------------- ```

## Checklist - [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [x] included a minimal, self-contained, and reproducible example? - [x] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? ``` $ quarto check [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Users/david/quarto-cli/package/dist/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...........OK Version: 4.2.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` - [x ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog? `RStudio 2022.02.3+492 "Prairie Trillium" Release (1db809b8323ba0a87c148d16eb84efe39a8e7785, 2022-05-16) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 11_2_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36` - [x ] documented which operating system you're running? If on Linux, please provide the specific distribution as well. MacOS Big Sur - [x ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? Using Quarto from github master. ## Bug The example below uses `knitr::asis_output()` to write an HTML table. This is meant to simulate an R table package doing the same thing. It works fine, and captions and labels are injected by quarto. If I also use `htmltools::htmlPreserve()`, then the table is still shown, but captions are not shown and labels do not resolve. ```` --- title: "Untitled" format: html --- # Without htmlPreserve Reference to @tbl-label. ```{r} #| tbl-cap: "My caption without htmlPreserve" #| label: tbl-label knitr::asis_output("<table><tr><td>A table</td></tr></table>") ``` # With htmlPreserve Reference to @tbl-label-preserve. ```{r} #| tbl-cap: "My caption with htmlPreserve" #| label: tbl-label-preserve knitr::asis_output(htmltools::htmlPreserve("<table><tr><td>A table</td></tr></table>")) ``` ````

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1066 <div type='discussions-op-text'> ^{Originally posted by **eitsupi** June 4, 2022} Recent update (e.g. v0.9.515) seems to show repo-actions on about pages too. Is it possible to turn off repo-actions only on certain pages because it breaks the symmetrical layout?  Source code is here. https://github.com/eitsupi/rocker-website/tree/976b4ba897ef3fddd8cbe4266d3f8c1900d8c5fb</div>

I'd like to move qmd files (book chapters) to a subdirectory as shown in `_quarto.yml`: ``` book: title: "This is my title from the YAML" author: "Jane Doe" date: "6/2/2022" chapters: - index.qmd - frontmatter/cover.qmd - frontmatter/acknowledgements.qmd - abstract.qmd - toc.qmd ``` Both `cover.qmd` and `acknowledgements.qmd` seem to be read just fine from the `frontmatter/` directory. When I move `index.qmd` I then get a rendering error:  Does this mean that `index.qmd` and `_quarto.yml` need to be in the same directory?

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1054 <div type='discussions-op-text'> ^{Originally posted by **harrelfe** June 3, 2022} In the following the link to a web page works but the tooltip is ignored: --- title: "Test" format: html --- ``` ```{mermaid} flowchart TD A[this] --> B[that] click A "https://hbiostat.org" "label" click B callback "Tooltip for B" ``` ``` I tried adding the following after the yaml as suggested on the `mermaid` web site (mainly to try `securityLevel`), to no effect: ``` <script> var callback = function(){ alert('A callback was triggered'); } var config = { startOnLoad:true, flowchart:{ useMaxWidth:true, htmlLabels:true, curve:'cardinal', }, securityLevel:'loose', }; mermaid.initialize(config); </script> ``` </div>

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1058 <div type='discussions-op-text'> ^{Originally posted by **bryanhanson** June 3, 2022} I am using [Goatcounter](https://goatcounter.com) for web page analytics. I just figured out after a month that it is not working. Goatcounter says to put this on the page so it will be tracked: ``` <script data-goatcounter="https://chemospec.goatcounter.com/count" async src="//gc.zgo.at/count.js"></script> ``` So I put in my `_quarto.yml` the following: ``` website: body-footer: <script data-goatcounter="https://chemospec.goatcounter.com/count" async src="//gc.zgo.at/count.js"></script> ``` But when the `body-footer` entry is actually put on the page Quarto changes it just a bit: ``` <script data-goatcounter="https://chemospec.goatcounter.com/count" async="" src="../..//gc.zgo.at/count.js"></script> ``` Any suggestions for doing this differently? Or is there a bug in how `body-footer` is being parsed? Full repo is [here](https://github.com/bryanhanson/CSR) Last updated around 3 May using then-current Quarto. However, I don't see any discussion of `body-footer` in either issues or discussions that I can find since that time. </div>

Hey! I am writing a book using Quarto. And I wanted a simple way to reference a chapter or a part of the book. I could just use the Section reference (#sec-...), to reference the first section of the Chapter, so the reader could get to the beggining of the chapter. But the rendered result (like "Section 9.1") would give the impression to the reader, that I am discussing the subject only in that specific Section, when I am actually using a entire Chapter to do so. As an example, at a specific point of the book, I wanted to reference a chapter like this: ``` You can use the `write()` method, which is described latter in the @chp-import-export. ``` This markdown code could result, for example, in something like this: ``` <p>You can use the <code>write()</code> method, which is described latter in the <a href="09-import.html">Chapter<span>9</span></a>.</p> ``` This way, the reader can understand that he should read all the Chapter 9, to fully understand the `write()` method, and not just a specific section. So the idea, is to add simple keys to reference a part or chapter, like `#chp-` for Chapters, and `#prt-` for Parts, so that, they could be rendered differently that section references (`#sec-`) or figure references (`#fig-`). I do not know if the HTML code above makes sense with Quarto directives for cross-references, but, I think it translates well the intention.

When creating a figure div with [subfigures](https://quarto.org/docs/authoring/figures.html#subfigures), the `id` attribute of the *main* figure div is lost in HTML output **as soon as `layout-ncol` is specified**, resulting in broken hyperlinks. Consider the following reproducible example: - Source file: [`t.qmd`](https://salim-b.gitlab.io/adhoc/t.qmd) - Render command: `quarto render t.qmd --to=html --metadata=keep-md:true` - Intermediate Markdown file: [`t.md`](https://salim-b.gitlab.io/adhoc/t.md) - Final HTML file: [`t.html`](https://salim-b.gitlab.io/adhoc/t.html) PDF/LaTeX output is not affected by this bug (i.e. all figure cross-reference links work fine). Using latest Quato release from GitHub, v0.9.514. <!-- Welcome to the quarto GitHub repo! We are always happy to hear feedback from our users. To file a _bug report_, please follow these instructions carefully: <https://yihui.org/issue/#bug-reports> Also, please complete and keep the checklist below in your issue. This helps you know what to check for opening a good issue report. It also helps know that you've have done the common steps that can solve your potential issue. At last, if you have posted the same issue elsewhere, please mention it here, with a link to the other issue. --> ## Checklist When filing a _bug report_, please check the boxes below to confirm that you have provided us with the information we need. Have you: - [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [x] included a minimal, self-contained, and reproducible example? - [x] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [x] upgraded to the latest version (including your versions of R, the RStudio IDE, and relevant R packages)?

<!-- Welcome to the quarto GitHub repo! We are always happy to hear feedback from our users. To file a _bug report_, please follow these instructions carefully: <https://yihui.org/issue/#bug-reports> Also, please complete and keep the checklist below in your issue. This helps you know what to check for opening a good issue report. It also helps know that you've have done the common steps that can solve your potential issue. At last, if you have posted the same issue elsewhere, please mention it here, with a link to the other issue. --> ## Task ```bash tree quarto/ . ├── _quarto.yml ├── code │   └── quarto.qmd ├── data │   └── names.csv ├── quarto.Rproj └── renv.lock ``` Set `execute-dir: project` in `_quarto.yml`. Read file `data/names.csv` from `code/quarto.qmd`, interactively. → Reproducible example: [quarto.zip](https://github.com/quarto-dev/quarto-cli/files/8837360/quarto.zip) ## Expected result `data/names.csv` is read when running the code chunk interactively. ## Error ``` Error: './data/names.csv' does not exist in current working directory ('/Users/xxx/quarto/code'). ``` However, rendering the `.qmd` file works fine. ## Session info ``` R version 4.2.0 (2022-04-22) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.4, RStudio 2022.2.3.492 Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8 Package version: askpass_1.1 assertthat_0.2.1 backports_1.4.1 base64enc_0.1.3 bit_4.0.4 bit64_4.0.5 blob_1.2.3 broom_0.8.0 bslib_0.3.1 callr_3.7.0 cellranger_1.1.0 cli_3.3.0 clipr_0.8.0 colorspace_2.0-3 compiler_4.2.0 cpp11_0.4.2 crayon_1.5.1 curl_4.3.2 data.table_1.14.2 DBI_1.1.2 dbplyr_2.1.1 digest_0.6.29 dplyr_1.0.9 dtplyr_1.2.1 ellipsis_0.3.2 evaluate_0.15 fansi_1.0.3 farver_2.1.0 fastmap_1.1.0 forcats_0.5.1 fs_1.5.2 gargle_1.2.0 generics_0.1.2 ggplot2_3.3.6 glue_1.6.2 googledrive_2.0.0 googlesheets4_1.0.0 graphics_4.2.0 grDevices_4.2.0 grid_4.2.0 gtable_0.3.0 haven_2.5.0 highr_0.9 hms_1.1.1 htmltools_0.5.2 httr_1.4.3 ids_1.0.1 isoband_0.2.5 jquerylib_0.1.4 jsonlite_1.8.0 knitr_1.39 labeling_0.4.2 lattice_0.20.45 lifecycle_1.0.1 lubridate_1.8.0 magrittr_2.0.3 MASS_7.3.57 Matrix_1.4.1 methods_4.2.0 mgcv_1.8.40 mime_0.12 modelr_0.1.8 munsell_0.5.0 nlme_3.1.157 openssl_2.0.2 parallel_4.2.0 pillar_1.7.0 pkgconfig_2.0.3 prettyunits_1.1.1 processx_3.5.3 progress_1.2.2 ps_1.7.0 purrr_0.3.4 R6_2.5.1 rappdirs_0.3.3 RColorBrewer_1.1.3 readr_2.1.2 readxl_1.4.0 rematch_1.0.1 rematch2_2.1.2 renv_0.15.5 reprex_2.0.1 rlang_1.0.2 rmarkdown_2.14 rstudioapi_0.13 rvest_1.0.2 sass_0.4.1 scales_1.2.0 selectr_0.4.2 splines_4.2.0 stats_4.2.0 stringi_1.7.6 stringr_1.4.0 sys_3.4 tibble_3.1.7 tidyr_1.2.0 tidyselect_1.1.2 tidyverse_1.3.1 tinytex_0.39 tools_4.2.0 tzdb_0.3.0 utf8_1.2.2 utils_4.2.0 uuid_1.1.0 vctrs_0.4.1 viridisLite_0.4.0 vroom_1.5.7 withr_2.5.0 xfun_0.31 xml2_1.3.3 yaml_2.3.5 ``` ## Quarto check output ``` [✓] Checking Quarto installation......OK Version: 0.9.501 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.13 Path: /opt/homebrew/opt/python@3.9/bin/python3.9 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/ste/Library/Caches/org.R-project.R/R/renv/library/tidygam-a6f3cf04/R-4.2/aarch64-apple-darwin20 - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ``` ## Checklist When filing a _bug report_, please check the boxes below to confirm that you have provided us with the information we need. Have you: - [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [x] included a minimal, self-contained, and reproducible example? - [x] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue? - [x] upgraded to the latest version (including your versions of R, the RStudio IDE, and relevant R packages)?

It would be great to add an option to enable the output of a code chunk to be scrollable, and to be able to set the max height of the visible output. The idea would be to be able to set that at the site, document or code chunk level. Currently, we are able to set that at the site level using the following CSS entry: ```yaml .cell-output-stdout { overflow-y: scroll; max-height: 300px; } ```

I have a qmd file named `appendix_cmd.qmd`: ```qmd # Appendices {.unnumbered} \appendix ``` which does not translate to ``` \part*{Appendices} ``` but to ``` \part{Appendices} ``` In my `_quarto.yml` I do have something like: ```yml book: title: "This is my title from the YAML" output-file: "some_book" author: "Jane Doe" date: "6/2/2022" chapters: - index.qmd - cover.qmd - acknowledgements.qmd - abstract.qmd - toc.qmd - abbreviations.qmd - mainmatter.qmd - introduction.qmd - part: part1.qmd chapters: - chp01.qmd - chp02.qmd - part: part2.qmd chapters: - chp03.qmd - discussion.qmd - conclusion.qmd - bibliography.qmd - part: appendix_cmd.qmd chapters: - appendix.qmd - colophon.qmd ``` Is there a way to get unnumbered book parts?

I am writing a PDF book using LaTeX. I have my chapters indicated in `_quarto.yml`: ``` book: title: "This is a title" author: "Jane Doe" date: "6/2/2022" chapters: - index.qmd - cover.qmd - acknowledgements.qmd - resumo.qmd - abstract.qmd - toc.qmd - abbreviations.qmd - mainmatter.qmd - introduction.qmd - discussion.qmd - conclusion.qmd - bibliography.qmd ``` Is there a way to get rid of `index.qmd`? I understand that if the output format is HTML it makes more sense to always have such a file. Currently I just keep this file to avoid the error: 

Hello, I tried to run some simple `ojs` code in `.qmd` under RStudio IDE but it's showing an error message:  `hello.qmd` (https://quarto.org/docs/get-started/hello/rstudio.html) is rendered correctly without any error, but if I try to run `ojs` related code it keeps showing the above error message. I've checked that Quarto preview is enabled, and both Quarto (quarto-0.9.462-win) and RStudio (v2022.2.2.485) are installed under C:\Program Files.