Datasets:

hamel

/

quarto-issues

like 0

### Bug description I am running Quarto to produce a report in which I mix python with R (using 95% R). When I started trying to use python, I believe that RStudio is not recognizing my python installation and packages: ``` Error in py_call_impl(callable, call_args$unnamed, call_args$named) : ModuleNotFoundError: No module named 'pandas' ``` Any ideas? ### Steps to reproduce --- title: 'Nota Técnica - Índice Socioeconômico dos Estudantes' author: '' format: html: encoding: 'UTF-8' theme: style.css editor: visual lang: pt execute: echo: false warning: false --- ```{python} #| label: load-py-pckgs import pandas as pd import seaborn as sns ``` ### Expected behavior I expected it to load python packages and modules with no problems. ### Actual behavior Error when loading any python package. ### Your environment IDE: RStudio 2022.07.2 Build 576 R version 4.1.0 (2021-05-18) (can't update because of internal packages built with this version) OS: Windows 11 ### Quarto check output `quarto check` gives me: C:\Users\joao.freire\Documents>quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.433 Path: C:\Users\joao.freire\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.11.4 Path: C:/Program Files/Python311/python.exe Jupyter: 5.3.1 Kernels: python3 (/) Checking Jupyter engine render....0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.1.0 Path: C:/Users/joao.freire/Documents/R/R-4.1.0 LibPaths: - C:/Users/joao.freire/Documents/R/R-4.1.0/library knitr: 1.42 rmarkdown: 2.23 [>] Checking Knitr engine render......OK C:\Users\joao.freire\Documents>quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.433 Path: C:\Users\joao.freire\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.11.4 Path: C:/Program Files/Python311/python.exe Jupyter: 5.3.1 Kernels: python3 ``` (\) Checking Jupyter engine render....0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.1.0 Path: C:/Users/joao.freire/Documents/R/R-4.1.0 LibPaths: - C:/Users/joao.freire/Documents/R/R-4.1.0/library knitr: 1.42 rmarkdown: 2.23 [>] Checking Knitr engine render......OK ```

### Bug description Python plots from python chunk are not shown in a quarto-document with knitr engine. However, with the jupytr engine it works. ### Steps to reproduce `````qmd --- title: 'Plots not showing' format: html # engine: jupytr engine: knitr --- ```{python} import statsmodels.api as sm import pandas df = sm.datasets.get_rdataset("Guerry", "HistData").data fm = sm.formula.ols('Lottery ~ Literacy + Wealth + C(Region)', data = df).fit() print(fm.summary()) fig = sm.graphics.influence_plot(fm, criterion="cooks") fig.show() ``` ### Expected behavior The plot should be included in the rendered html file ### Actual behavior The plot is not shown ### Your environment - IDE RStudio: Version 2023.06.0+421 (2023.06.0+421) - MacOS 12.6.2 ### Quarto check output [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.433 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.10 (Conda) Path: /Users/seb/Library/r-miniconda-arm64/bin/python Jupyter: 5.3.0 Kernels: julia-1.8, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.3.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library knitr: 1.43 rmarkdown: 2.22 [✓] Checking Knitr engine render......OK

It seems there is quite a few differences, or rather unsupported customisation using SCSS variables that are possible for a HTML theme but not working withing revealjs format. This could probably be improved. This issue will try to track such improvement - [ ] https://github.com/quarto-dev/quarto-cli/discussions/6087#discussioncomment-6339297 - `$toc-font-size`, `$toc-color` - [ ] https://github.com/quarto-dev/quarto-cli/issues/5038 - https://quarto.org/docs/output-formats/html-themes.html#callouts

### Bug description In a blog where one of the post has this badge ``` [](https://bestpractices.coreinfrastructure.org/projects/1882) ``` the badge is converted to ``` <p><a href="https://bestpractices.coreinfrastructure.org/projects/1882"><img src="https://bestpractices.coreinfrastructure.org/projects/1882/badge.png" class="img-fluid figure-img"></a></p> ``` therefore the image is missing. Interestingly in the post listing (where I would not expect it to be included, other issue #6091), the badge is ``` <a href="./posts/post-with-code/index.html"> <img src="https://bestpractices.coreinfrastructure.org/projects/1882/badge" class="thumnail-image"> </a> ``` It might unusual for a badge to be specified without extension, though. I see it's also done for metacran badges https://github.com/r-lib/usethis/blob/d3614c701b9e2ee6f680a245d3315b1b941f49de/README.Rmd#L21 ### Steps to reproduce https://github.com/maelle/badgeblog/blob/main/posts/post-with-code/index.qmd#L8 ### Expected behavior I would expect no extension to be added to the image in the badge. ### Actual behavior A PNG extension is added. ### Your environment RStudio 2023.03.0+386 "Cherry Blossom" Release (3c53477afb13ab959aeb5b34df1f10c237b256c3, 2023-03-09) for Ubuntu Bionic Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) rstudio/2023.03.0+386 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36 ### Quarto check output ```bash [✓] Checking versions of quarto binary dependencies... Pandoc version 2.19.2: OK Dart Sass version 1.32.8: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.49 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.10 Path: /usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.0 Path: /opt/R/4.2.0/lib/R LibPaths: - /home/maelle/R/x86_64-pc-linux-gnu-library/4.2 - /opt/R/4.2.0/lib/R/library rmarkdown: 2.22 [✓] Checking Knitr engine render......OK ```

### Bug description For a blog with a default post listing, if one of the posts has a badge as only image, the badge is used as image in the listing. I was surprised by this behavior but it might be intended?  ### Steps to reproduce https://github.com/maelle/badgeblog/blob/fadf0dc478982e8fff2f8ec186432de951590875/posts/post-with-code/index.qmd#L8 ### Expected behavior I would expect no image to be used (except for a placeholder image if one was defined). ### Actual behavior _No response_ ### Your environment - RStudio 2023.03.0+386 "Cherry Blossom" Release (3c53477afb13ab959aeb5b34df1f10c237b256c3, 2023-03-09) for Ubuntu Bionic Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) rstudio/2023.03.0+386 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36 ### Quarto check output ```bash [✓] Checking versions of quarto binary dependencies... Pandoc version 2.19.2: OK Dart Sass version 1.32.8: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.49 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.10 Path: /usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.2.0 Path: /opt/R/4.2.0/lib/R LibPaths: - /home/maelle/R/x86_64-pc-linux-gnu-library/4.2 - /opt/R/4.2.0/lib/R/library rmarkdown: 2.22 [✓] Checking Knitr engine render......OK ```

### Bug description *Originally raised [here](https://github.com/quarto-dev/quarto-cli/issues/6015#issuecomment-1616288334) and possibly related but it was suggested to open a new issue. That problem was related to pandoc's handling of docx files and was fixed by pandoc for that format. This maybe a similar problem, IDK.* I was trying to control the overall table width of a kable-generated html table in a website project. I tried to specify `tbl-colwidths` in the chunk but this was ignored. Then I tried the `kable_styling(full_width = FALSE)` which normally does a good job of adjusting overall width and individual column width, but this was also ignored. It appears the settings are ignored or perhaps overridden. At least in the case of `tbl-colwidths` I can see the information passed to the html in the page source but it looks like it is echoed there and not really used (my best guess). ### Steps to reproduce ## _quarto.yml ``` project: title: "test" type: "website" ``` ## test.qmd ```` --- title: "Two Ways to Handle Table Width Using kable; Neither Works" --- @tbl-results1 shows how to control the table column widths; however, the settings seem to be ignored. At the same time, another way to control this with `kable` doesn't work either, see @tbl-results2. ```{r} #| echo: false library("kableExtra") library("magrittr") ``` ```{r} #| label: tbl-results1 #| tbl-cap: "mtcars using colwidths doesn't work." #| tbl-colwidths: [15, 15, 15, 15] kable(mtcars[,1:3]) %>% kable_styling(c("striped", "bordered")) ``` ```{r} #| label: tbl-results2 #| tbl-cap: "mtcars with full_width = FALSE doesn't work." kable(mtcars[,1:3]) %>% kable_styling(c("striped", "bordered"), full_width = FALSE) ``` ```` ### Expected behavior I want the table column widths to shrink to contain the contents w/o a lot of white space, and in turn, this will make the table overall narrower. ### Actual behavior Right now the table occupies the full width with a lot of white space. ### Your environment -IDE: command line -OS: MacOS 12.6.7 ### Quarto check output ```bash [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Users/bryanhanson/Documents/Professional/Research/R_Pkgs/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.2 Path: /usr/local/opt/[email protected]/bin/python3.11 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.3.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library knitr: 1.43 rmarkdown: 2.22 [✓] Checking Knitr engine render......OK ```

### Bug description When using wkhtmltopdf as the pdf engine, the output pdf starts with a line reading: \usepackage{booktabs} \usepackage{caption} \usepackage{longtable} I tried adding these to the YAML and it didn't solve the problem: latex-auto-mk: false latex-auto-install: false ### Steps to reproduce _No response_ ### Expected behavior _No response_ ### Actual behavior _No response_ ### Your environment _No response_ ### Quarto check output _No response_

### Bug description When using relative urls in a quarto document, e.g. `[my link](../../doc.qmd)`, the relative url is resolved to its absolute path in the html output after rendering, e.g. `[my link](https://example.com/stuff/doc.html)`. However in the RSS feed, these relative urls are not resolved to the absolute path. This behavior can be seen in the quarto.org RSS feed. The [W3 RSS validator tool](https://validator.w3.org/feed/check.cgi?url=https%3A%2F%2Fquarto.org%2Fdocs%2Fblog%2Findex.xml) calls out many relative urls in the quarto.org feed. For example, line 49: ``` description should not contain relative URL references: ../../../../docs/output-formats/html-code.html#code-linking (49 occurrences) ``` I use my RSS feed to automate email updates to my subscribers. Since relative urls in the feed are not resolved, internal links in my posts are broken in the email updates. I suppose this would also be problematic in sindication use cases like Rbloggers or pythonBloggers.

### Bug description This is cross-posted from [Expand Plotly output in Quarto HTML document to full screen](https://stackoverflow.com/questions/76591841/expand-plotly-output-in-quarto-html-document-to-full-screen) I would like to make plotly output from a chunk in a Quarto HTML document expandable to a full screen view. `bslib` seems to offer such a solution via card(full_screen = TRUE,...) which is documented at https://rstudio.github.io/bslib/articles/cards.html#filling-outputs I can do this with R Markdown, but it appears that either `bslib` is unable to modify the theme as needed to support this behavior, or some Quarto CSS theming may be overriding desired behavior. When I render the Quarto version, two things are different than desired about the layout: 1. Clicking the "expand" button only expands the plot to the size of the quarto output 2. The "expand" button is rendered as a black bar at the bottom of the graphic instead of the aesthetically pleasing arrows that only appear when the user hovers over the card. ## Unzoomed:  ## Zoomed:  ### Steps to reproduce ````qmd --- title: "Quarto Zoom Plotly" format: html --- ```{r} #| warn: false #| message: false suppressPackageStartupMessages({ library(bslib) library(shiny) library(htmltools) library(plotly) }) card(title = "", full_screen = TRUE, plot_ly(x = diamonds$cut) ) ``` ```` ````qmd --- title: "R Markdown Zoom Plotly" output: html_document: theme: version: 5 --- ```{r warning=FALSE, message=FALSE} #| warn: false #| message: false suppressPackageStartupMessages({ library(bslib) library(shiny) library(htmltools) library(plotly) }) card(title = "", full_screen = TRUE, plot_ly(x = diamonds$cut) ) ``` ```` ### Expected behavior _No response_ ### Actual behavior _No response_ ### Your environment RStudio 2022.12.0+353.pro20 "Elsbeth Geranium" Release (02ace23e263335c78e1df5b0892e48913e5fcecf, 2022-12-15) for Ubuntu Bionic Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/114.0.0.0 Safari/537.36 Ubuntu 20.04 ### Quarto check output Testing against a dev version pulled from the repo today ```bash [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /home/matthew14786/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.16 Path: /opt/python/3.9.16/bin/python3 Jupyter: 5.1.0 Kernels: dash-testing-3.9.16, testvenv, python3, py3.10.9, py3.9.16 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.2 Path: /opt/R/4.2.2/lib/R LibPaths: - /home/matthew14786/R/x86_64-pc-linux-gnu-library/4.2 - /opt/R/4.2.2/lib/R/library knitr: 1.43 rmarkdown: 2.22 [✓] Checking Knitr engine render......OK ```

### Bug description A reminder for a left-behind problem mentioned in #3776. ### Steps to reproduce ````qmd --- title: "QED symbol test" format: pdf: keep-tex: true --- :::{.proof} This is a proof. ::: ```` ### Expected behavior Should produce LaTeX code like this: ```latex \begin{proof} This is a proof. \end{proof} ``` which handle the spacing of QED symbol properly. ### Actual behavior However, Quarto actually produces this ```latex \begin{proof} This is a proof. \end{proof} ``` The empty line inserted before `\end{proof}` causes the QED symbol lies in a new line, instead of the end of the last line of the proof. [Probably helpful](https://tex.stackexchange.com/questions/51781/qed-symbol-on-the-same-page-as-proof) ### Your environment - IDE: vscode - OS: Windows 11 ### Quarto check output ```bash [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.340 Path: C:\Program Files\Quarto\bin CodePage: 936 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....(None) Unable to locate an installed version of Python 3. Install Python 3 from https://www.python.org/downloads/ [>] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ```

### Bug description Using the `quarto-required` argument as described here: https://quarto.org/docs/reference/formats/html.html#format-options doesn't appear to work. ### Steps to reproduce ````qmd --- format: html: quarto-required: ">= 1000.4.375" --- ## Quarto ```` ### Expected behavior I would expect an error to be thrown is the version wasn't satisfied. ### Actual behavior Argument is ignored. ### Your environment - IDE: Version 2023.05.0-daily+206 (2023.05.0-daily+206) - OS: MacOS Ventura 13.4 ### Quarto check output ```bash [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.176 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.7 (Conda) Path: /Users/emilhvitfeldt/miniforge3/bin/python Jupyter: (None) Jupyter is not available in this Python installation. Install with conda install jupyter [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources LibPaths: - /Users/emilhvitfeldt/Library/R/arm64/4.2/library - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library knitr: 1.43 rmarkdown: 2.22 [✓] Checking Knitr engine render......OK- ```

### Bug description Author is render as `true`. ### Steps to reproduce Consider `index.qmd` as ``` --- title: "MWE" author: - name: given: Jane family: Doe email: [email protected] orcid: 0000 attributes: corresponding: true - name: given: Jonh family: Doe orcid: 0000 --- Lorem ipsum ``` and run `quarto render index.qmd --to commonmark --output rendered_index.commonmark`. ### Expected behavior Author is render using `author[].name.literal` from [Author Schema](https://quarto.org/docs/journals/authors.html#author-schema) like ``` # MWE Jane Doe, John Doe Lorem ipsum ``` ### Actual behavior Each author is render as `true`: ``` # MWE truetrue Lorem ipsum ``` ### Your environment - OS: Linux 6.2.12-1-MANJARO ### Quarto check output ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.176 Path: /opt/quarto-1.4.176/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.10 Path: /usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ```

### Bug description If creator provides a valid [author metadata following Author Schema](https://quarto.org/docs/journals/authors.html#author-schema) and convert the `.qmd` file to Markdown, some information in the author metadata is discarted. ### Steps to reproduce Consider the `index.qmd` file: ``` --- title: "MWE" author: - name: given: Jane family: Doe email: [email protected] orcid: 0000 attributes: corresponding: true - name: given: Jonh family: Doe orcid: 0000 --- Lorem ipsum ``` and run `quarto render index.qmd --to markdown --output rendered_index.md`. ### Expected behavior Output is identical to the input: ``` --- title: "MWE" author: - name: given: Jane family: Doe email: [email protected] orcid: 0000 attributes: corresponding: true - name: given: Jonh family: Doe orcid: 0000 --- Lorem ipsum ``` This is what happen when using [Hugo format](https://quarto.org/docs/output-formats/hugo.html). `quarto render index.qmd --to hugo-md --output rendered_index.hugo && diff index.qmd rendered_index.hugo` produces ``` 17c17 < Lorem ipsum \ No newline at end of file --- > Lorem ipsum ``` ### Actual behavior Information in the YAML header is lost: ``` --- author: - family: Doe given: Jane - family: Doe given: Jonh title: MWE toc-title: Table of contents --- Lorem ipsum ``` ### Your environment - OS: Linux 6.2.12-1-MANJARO ### Quarto check output ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.176 Path: /opt/quarto-1.4.176/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.10 Path: /usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ```

### Bug description When I render a qmd file that has inside a [pagebreak](https://quarto.org/docs/authoring/markdown-basics.html#page-breaks), and I render it to docx, I'm not able to open the output and I have this error  ### Steps to reproduce I have tested using this input and running `quarto render test.qmd --to docx -o test.docx`. My OS is Debian 11 and I'm using quarto 1.4.43. ````qmd --- title: "Title" format: docx: toc: false number-sections: false highlight-style: github --- # A title Lorem ipsum {{< pagebreak >}} # Another title Lorem ipsum ```` ### Expected behavior To be able to open a paginated docx. ### Actual behavior Opening the output in office fow win I have this error  ### Your environment My OS is Debian 11 and I'm using quarto 1.4.43. ### Quarto check output ```bash [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.1: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.43 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.2 Path: /usr/bin/python3 Jupyter: 5.1.2 Kernels: bash, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.0.4 Path: /usr/lib/R LibPaths: - /home/aborruso/R/x86_64-pc-linux-gnu-library/4.0 - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/lib/R/library knitr: 1.41 rmarkdown: 2.19 [✓] Checking Knitr engine render......OK ```

Within a Quarto .qmd file the directive that works here in GitHub (see below) and in the Mermaid interactive editor, is ignored when rendering a .qmd file to HTML (from within RStudio under Windows 10). This affects the whole of my website when rebuilt, but was working some/several weeks ago. Is there any quick workaround to get the directive obeyed? e.g., downgrading Quarto to some earlier version?  ``` %%{init: {"htmlLabels": true} }%% flowchart LR A(<i>model formula</i>) --> B[model fit\nfunction] --> C(model fit\nobject) --> D1['diagnostics' plots] AA(<i>observations</i>) --> B C --> D2[query methods] ```` The same code as an embed in this message renders correctly. ```mermaid %%{init: {"htmlLabels": true} }%% flowchart LR A(<i>model formula</i>) --> B[model fit\nfunction] --> C(model fit\nobject) --> D1['diagnostics' plots] AA(<i>observations</i>) --> B C --> D2[query methods] ````

### Bug description First, thank you for your work on this wonderful project!! I am trying to understand whether Observable variables are able to be used within text formatted as code. As part of this, `ojs` code blocks seem not to honor the `output: asis` execution option. ### Steps to reproduce 1. Create a Quarto `.qmd` file with the following contents: ````md --- format: html: code-fold: true toc: true toc-depth: 6 toc-expand: 2 toc-location: right number-sections: true number-depth: 3 toc-title: Contents anchor-sections: true smooth-scroll: true embed-resources: true # Make the file self-contained. execute: freeze: auto # Re-render only when source changes --- ::: {.callout-important title="Enter variables about your project"} ```{ojs} //| echo: false viewof example_variable = Inputs.text({label: "Example variable"}) ``` ::: Here is some example code for you to copy and paste: Test 0: ${example_variable} Test 1: `${example_variable}` Test 2: `ojs example_variable` Test 3: ```{ojs} //| output: asis //| echo: false ` \`\`\` ${example_variable} \`\`\` ` ``` Test 4: ```sh # example using ${example_variable} ``` ```` 2. Render the file as HTML 3. Type "test123" into the input box. ### Expected behavior 1. All tests should replace "example_variable" with `test123`. 2. Test 3 should render code-block-formatted text, rather than a string. ### Actual behavior 1. Quarto does not interpolate variables within non-executed code blocks. (Is there an existing alternative syntax for this?) 2. The output of Test 3 is parsed as a string, rather than as Markdown.  ### Your environment - IDE: VSCode 1.76.0, Quarto plugin 1.88.0 - MacOS Ventura 13.4 ### Quarto check output ```bash $ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.433 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.7.16 (Conda) Path: /Users/<username>/mambaforge/envs/example_project/bin/python Jupyter: 4.12.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ```

As discussed, Quarto currently does not natively provides ways to deal with various images depending on context such as light/dark theme, or small/large screen display. Some related work: - JavaScript: <https://mickael.canouil.fr/posts/2023-05-30-quarto-light-dark/> - GitHub context classes: <https://github.blog/changelog/2021-11-24-specify-theme-context-for-images-in-markdown/> - #3263 and `thematic` R package (<https://rstudio.github.io/thematic/> - #5439 - <https://developer.mozilla.org/fr/docs/Web/CSS/@media/prefers-color-scheme>

### Bug description When running `quarto check` I see the following: ```bash [✓] Checking R installation...........OK Version: 4.3.0 Path: /usr/local/lib/R LibPaths: - /usr/local/lib/R/site-library - /usr/local/lib/R/library - /home/mpollock/R/x86_64-pc-linux-gnu-library/4.0 knitr: 1.43 rmarkdown: 2.22 ``` It knows that I'm running R version 4.3.0, and there exists a `/home/mpollock/R/x86_64-pc-linux-gnu-library/4.3` that RStudio will pick up and use by default. Why does quarto want to use the older 4.0 user library? Within RStudio my default library paths are ```r .libPaths() #> [1] "/home/mpollock/R/x86_64-pc-linux-gnu-library/4.3" #> [2] "/usr/local/lib/R/site-library" #> [3] "/usr/local/lib/R/library" ``` A secondary question is about library path ordering. RStudio will defer to the user library, while quarto appears to prioritize the system library. I can split this into a separate issue if that's useful. ### Steps to reproduce Install multiple versions of R, install packages to the user library path for both. Then run `quarto check` ### Expected behavior Quarto uses the user library path consistent with the R version being used. ### Actual behavior It is using an old user library path. If the old library path is deleted is used no user library path at all. ### Your environment - IDE: RStudio 2023.06.0+421 "Mountain Hydrangea" Release (583b465ecc45e60ee9de085148cd2f9741cc5214, 2023-06-06) for Ubuntu Jammy Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/16.5.1 Safari/605.1.15 - Running via jupyter using and extension of the [rocker/binder:4.3.0](https://rocker-project.org/images/versioned/binder.html) image ### Quarto check output ```bash [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.353 Path: /usr/lib/rstudio-server/bin/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /usr/bin/python3 Jupyter: 5.3.0 Kernels: ir, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.3.0 Path: /usr/local/lib/R LibPaths: - /usr/local/lib/R/site-library - /usr/local/lib/R/library - /home/mpollock/R/x86_64-pc-linux-gnu-library/4.0 knitr: 1.43 rmarkdown: 2.22 ```

### Bug description The link referring to the rsvg-convert package https://quarto.org/docs/prerelease/1.3/pdf.html#svg-images does not resolve to the correct page. ### Steps to reproduce Go to: https://quarto.org/docs/prerelease/1.3/pdf.html#svg-images Click on the link for Windows: https://community.chocolatey.org/packages/r%E2%80%A6 ### Expected behavior URL should link to the correct page. I believe that should be: https://community.chocolatey.org/packages/rsvg-convert ### Actual behavior URL renders the default 'page not found' page. ### Your environment _No response_ ### Quarto check output _No response_

### Bug description Hi, I'm using Quarto + VSCode + Docusaurus to write a thesis and after upgrading to latest version citations stopped working in Docusaurus. The [@somequotation] are not rendering anymore but just remain unchanged in the output. Rendering to PDF still works fine. Please advise. ### Steps to reproduce `abstract.qmd:` ``` --- title: Abstract bibliography: [ref.bib] csl: apa.csl sidebar_position: 1 editor: render-on-save: false --- Example quote: [@circleeconomyCircularityGapReport2022] says blablaba. ``` ### Expected behavior Citation [@circleeconomyCircularityGapReport2022] should be transformed into a reference. ### Actual behavior [@circleeconomyCircularityGapReport2022] remains untransformed. ### Your environment - MacOS Ventura 13.4 (22F66) - Visual Studio Code Version: 1.79.2 Commit: 695af097c7bd098fbf017ce3ac85e09bbc5dda06 Date: 2023-06-14T08:58:52.392Z Electron: 22.5.7 Chromium: 108.0.5359.215 Node.js: 16.17.1 V8: 10.8.168.25-electron.0 OS: Darwin x64 22.5.0 - VSCode Quarto extension v1.88.0 - Zotero 6.0.26 - Docusaurus 2.4.0 ### Quarto check output ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.176 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.9 (Conda) Path: /Users/krishaamer/anaconda3/bin/python Jupyter: 5.2.0 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.3.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library knitr: 1.43 rmarkdown: 2.22 [✓] Checking Knitr engine render......OK ``` ### Quarto preview output ``` quarto preview /Users/krishaamer/Desktop/current/green-filter-research/research/abstract.qmd --no-browser --no-watch-inputs (base) krishaamer@Kriss-MacBook-Pro-2 green-filter-research % quarto preview /Users/krishaamer/Desktop/current/green-filter-research/research/abstract.qmd --no-browser --no-watch-inputs pandoc to: >- markdown_strict+raw_html+all_symbols_escapable+backtick_code_blocks+fenced_code_blocks+space_in_atx_header+intraword_underscores+lists_without_preceding_blankline+shortcut_reference_links+autolink_bare_uris+emoji+footnotes+gfm_auto_identifiers+pipe_tables+strikeout+task_lists+tex_math_dollars+pipe_tables+tex_math_dollars+header_attributes+raw_html+all_symbols_escapable+backtick_code_blocks+fenced_code_blocks+space_in_atx_header+intraword_underscores+lists_without_preceding_blankline+shortcut_reference_links output-file: abstract.md standalone: true default-image-extension: png wrap: none html-math-method: webtex metadata title: Abstract bibliography: - ref.bib csl: apa.csl sidebar_position: 1 editor: render-on-save: false Output created: abstract.md Preparing to preview Watching files for changes Preview service running (7224) > docusaurus > docusaurus start --no-open --port 4027 --host 127.0.0.1 [INFO] Starting the development server... [SUCCESS] Docusaurus website is running at: http://127.0.0.1:4027/ ℹ Compiling Client ✔ Client: Compiled successfully in 2.67s Browse at http://localhost:4027/ client (webpack 5.87.0) compiled successfully ℹ Compiling Client ✔ Client: Compiled successfully in 403.70ms client (webpack 5.87.0) compiled successfully ℹ Compiling Client ✔ Client: Compiled successfully in 242.15ms client (webpack 5.87.0) compiled successfully ```

Takes this qmd `test.qmd` ````markdown --- title: "Test" format: pdf: output-file: pdf.pdf keep-tex: true --- # Test ```` This will produce a `test.tex` and a `pdf.pdf` output. I think it could be better to have the intermediate be renamed to the `output-file` option when provided. 🤔 Opening this issue to track the idea and look into what we can do.

quarto.log.error() doesn't give stack trace.

### Bug description I've noticed, the Frontmatter/YAML parser seems to act funny when multiple new lines are inserted between entries, or well anywhere in the frontmatter. When only one new line between entries is used, the parser detects the `pdf` format automatically. ### Steps to reproduce - **Working Version**: Compile the following document ```qmd --- title: "Untitled" format: pdf: pdf-engine: pdflatex --- hello world ``` - **Breaking Behaviour**: Add a new line directly after `---` in the frontmatter ```qmd --- title: "Untitled" format: pdf: pdf-engine: pdflatex --- hello world ``` - **Breaking Behaviour**: Add double new lines anywhere in the frontmatter ```qmd --- title: "Untitled" format: pdf: pdf-engine: pdflatex --- hello world ``` ### Expected behavior Compile the document correctly using the given format (in this case being `pdf`).  ### Actual behavior  Following also breaks the expected behaviour ```qmd --- title: "Untitled" format: pdf: pdf-engine: pdflatex --- ``` ```qmd --- title: "Untitled" format: pdf: pdf-engine: pdflatex --- ``` ```qmd --- title: "Untitled" format: pdf: pdf-engine: pdflatex --- ``` ### Your environment - IDE: VSCode - OS: Windows 10 ### Quarto check output ```bash $ quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.433 Path: C:\Users\Joel\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.5 Path: C:/Users/Joel/AppData/Local/Programs/Python/Python310/python.exe Jupyter: 5.1.1 Kernels: python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.2.2 Path: C:/PROGRA~1/R/R-42~1.2 LibPaths: - C:/Users/Joel/AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.2/library knitr: 1.41 rmarkdown: 2.20 [>] Checking Knitr engine render......OK ```

### Bug description I think I'm facing a bug, but let me know if I'm not doing things right. When outputting to a beamer format, I can't get code block formatting to behave as I would like. Specifically, using the options `code-block-bg`, `code-block-border-left`, and `highlight-style`, I do not get any background color or left border at all. This is despite all 3 of these properties being part of the [beamer options](https://quarto.org/docs/reference/formats/presentations/beamer.html). The same combination of settings works perfectly when outputting to a pdf format, however. ### Steps to reproduce Here is a MWE with the issue: ```` qmd --- title: "Test" format: beamer: code-block-bg: "#f8f8f8" code-block-border-left: "#245ABE" highlight-style: github --- ### Testing code blocks Code block: ```python import numpy as np x = 3 # Defining a variable def best_function(arg1): """ This is a docstring. """ return arg1 best_function(24.8) ``` ```` ### Expected behavior This should produce the following colors (taken from pdf output) -- focusing here only on the code block:  ### Actual behavior When outputting to beamer, I get the following instead:  Also, if I comment out `highlight-style: github`, I get even stranger behavior. The whole block takes on the color of the left border:  ### Your environment - OS: MacOS 13.4.1 - IDE: VSCodium 1.79.2 ### Quarto check output ```bash [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.427 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.12 (Conda) Path: /opt/homebrew/Caskroom/miniforge/base/bin/python Jupyter: 5.3.1 Kernels: julia-0.4, matlab_kernel, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 3.2.4 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/me/Library/R/3.2/library - /Library/Frameworks/R.framework/Versions/3.2/Resources/library knitr: 1.12.3 NOTE: knitr version 1.12.3 is too old. Please upgrade to 1.30 or later. rmarkdown: 0.9.5 The knitr package is outdated in this R installation. Update with update.packages("knitr") ```

### Bug description I can't directly include sass in the chunk to modify my background color. ### Steps to reproduce ````qmd --- format: html engine: knitr --- ```{sass} $body-bg: black !default; ``` ```` ### Your environment - quarto version: 1.4.80

I have noticed that the `Plot` version is a little bit late with [latest observablehq plot version](https://github.com/observablehq/plot/blob/main/CHANGELOG.md#068) https://github.com/quarto-dev/quarto-cli/blob/121d710f7c02f00de0c6f4fa06db83587d751b3a/src/resources/formats/html/ojs/quarto-ojs-runtime.js#L208 0.6.6 and 0.6.7 bring some new nice features like tooltips that would be great for quarto users. Latest Plot version is `0.6.8`. Would you consider updating the version embedded with quarto by default ?

### Bug description If I create a sample blog using command: `$ quarto create-project myblog --type website:blog` then the text in myblog/posts/welcome/index.qmd looks like: ``` --- title: "Welcome To My Blog" author: "Tristan O'Malley" date: "2023-06-23" categories: [news] --- This is the first post in a Quarto blog. Welcome!  Since this post doesn't specify an explicit `image`, the first image in the post will be used in the listing page of posts. ``` As the text in this file describes, thumbnail.jpg is used in the blog listing created in myblog/index.qmd. But if I add an `image-placeholder` option to the listing entry, then thumbnail.jpg is no longer used in the blog listing. It's ignored, and the image specified in the `image-placeholder` option is used in the listing. I think using the `image-placeholder` option should not disable the feature that looks for an image in the blog post body if an image is not specified in the file metadata. The image placeholder image should be a true last resort. ### Steps to reproduce Create a blog project: `$ quarto create-project myblog --type website:blog` Edit myblog/index.qmd so it looks thus: ``` --- title: "myblog" listing: contents: posts sort: "date desc" type: default categories: true sort-ui: false filter-ui: false image-placeholder: profile.jpg page-layout: full title-block-banner: true --- ``` and re-render. ### Expected behavior Quarto should find that thumbnail.jpg is used in the body of the blog post at myblog/posts/welcome/index.qmd and use it in this file's entry in the blog listing. ### Actual behavior Quarto ignores thumbnail.jpg and uses profile.jpg in the listing for the "Welcome To My Blog" entry. ### Your environment Command line. Linux Kubuntu 20.04 ### Quarto check output _No response_

### Bug description Repro repo: https://github.com/mfisher87/sscce-quarto-preview-hot-reload-listing Either use this repo to test, or find details below. When editing a page that is part of listing, `quarto preview` will hot reload. In Quarto `1.3.361` and prior, the edited page was correctly displayed after the hot reload. In Quarto `1.3.427`, the listing page is displayed instead. ### Steps to reproduce * `quarto create-project --type website` * `mkdir listing` * Create `listing/index.md` with barebones `listing` front-matter. * Edit `_quarto.yml` to add a link to `listing/index.md`. * Create `listing/foo.md` with barebones content. Try the following steps with different versions of Quarto * `quarto preview` * Edit `listing/foo.md`, and write. * The browser will refresh automatically. Is the test post displayed, or is the listing page displayed? * In Quarto `1.3.427`, the latter is the case, which is unintuitive to me. In previous versions, the former is the case. I expect the page I edited to be displayed! ### Expected behavior When editing a page, triggering a hot reload by `quarto preview`, I expect to see the page I edited. ### Actual behavior If the edited page is part of a listing, the listing index is displayed instead of the edited page in Quarto 1.3.427. ### Your environment Ubuntu 22 Quarto 1.3.427 ### Quarto check output ```bash $ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.58.3: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.427 Path: /home/robatt/.local/share/miniconda3/envs/itsarobin-homepage/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.4 (Conda) Path: /home/robatt/.local/share/miniconda3/envs/itsarobin-homepage/bin/python Jupyter: 5.3.1 Kernels: python3 (-) Checking Jupyter engine render....0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........(None) Unable to locate an installed version of R. Install R from https://cloud.r-project.org/ ```

### Bug description Today I was running regression tests, and wanted to produce the results in a Quarto document. I used two packages for the same task: broom and easystats. But there is a difference as far as the cross-referencing is concerned. For the tables generated through broom package, one table doesn't display caption. Instead, I can see "?caption" in its place. But if I use easystats set of packages, I can see the correct captions for both the tables. The output of quarto check is as follows: ### Steps to reproduce --- title: "Reprex" editor: visual --- In this document, I am trying to capture how quarto treats two packages `broom` and `easystats` differently for the purpose of cross-referencing. I observed that when I have two tables in a single code chunk, arranged in a single column, there is an issue with cross-referencing. ```{r} library(easystats) library(broom) dummy <- data.frame(y = rnorm(100),x = rpois(100,3)) ``` Now we can create two regression models from this dummy data. ```{r} lm_mod1 <- lm(y~x, data = dummy) lm_mod2 <- lm(x~y, data = dummy) ``` Now let me create two tables using broom ```{r} #| label: tbl-tables-broom #| tbl-cap: "Tables using Broom" #| tbl-subcap: true #| layout-nrow: 2 lm_mod1 |> broom::tidy() lm_mod2 |> broom::tidy() ``` And now similarly, using easystats: ```{r} #| label: tbl-tables-easystats #| tbl-cap: "Tables using Easystats" #| tbl-subcap: true #| layout-nrow: 2 lm_mod1 |> model_parameters() |> display() lm_mod2 |> model_performance() |> display() ``` ### Expected behavior All the four tables (two generated using broom, and two generated using easystats) should have similar captions. ### Actual behavior One table generated through broom package shows "?caption" as the caption. ### Your environment IDE: RStudio 2023.03.1 +446 OS: Windows 10 ### Quarto check output ``` quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.4.163 Path: C:\Users\Maulik\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.11.3 Path: C:/Program Files/Python311/python.exe Jupyter: 5.3.0 Kernels: python3 (-) Checking Jupyter engine render....0.18s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.3.0 Path: C:/PROGRA~1/R/R-43~1.0 LibPaths: - C:/Users/Maulik/AppData/Local/R/win-library/4.3 - C:/Program Files/R/R-4.3.0/library knitr: 1.43 rmarkdown: 2.22 [>] Checking Knitr engine render......OK ```

### Bug description When using CrossRef autocomplete feature for references in VSCode I get this error. ``` Error running filter /Applications/quarto/share/filters/crossref/crossref.lua: /Applications/quarto/share/filters/crossref/crossref.lua:3448: attempt to call a nil value (global 'init_crossref_options') stack traceback: [Error - 01:36:53] Request textDocument/completion failed. Message: Request textDocument/completion failed with message: Command failed: /Applications/quarto/bin/tools/pandoc --defaults defaults.yml Error running filter /Applications/quarto/share/filters/crossref/crossref.lua: /Applications/quarto/share/filters/crossref/crossref.lua:3448: attempt to call a nil value (global 'init_crossref_options') stack traceback: Code: -32603 ``` I guess the bug is caused by a function naming inconsistency in the release version of v1.3.427. [crossref.lua](https://github.com/quarto-dev/quarto-cli/blob/1412f03797ca3446cec67d190b8dbd66fff8e5f5/src/resources/filters/crossref/crossref.lua) ```lua -- chain of filters return { init_crossref_options(), ... } ``` [options.lua](https://github.com/quarto-dev/quarto-cli/blob/1412f03797ca3446cec67d190b8dbd66fff8e5f5/src/resources/filters/crossref/options.lua) ```lua function initCrossrefOptions() return { Meta = function(meta) crossref.options = readFilterOptions(meta, "crossref") -- automatically set maxHeading to 1 if we are in chapters mode, otherwise set to max (7) if crossrefOption("chapters", false) then crossref.maxHeading = 1 else crossref.maxHeading = 7 end end } end ``` The `main` branch is not affected by this issue, only the current release (v1.3) branch. ### Steps to reproduce 1. Use current Quarto version (v1.3.427) 2. Try to use VSCode Intellisense in .qmd file, that tries to lookup a [reference](https://quarto.org/docs/authoring/cross-references.html#references) ### Expected behavior Autocomplete works and no error is shown. ### Actual behavior Autocomplete doesn't work and an error is shown in the output. ### Your environment - IDE: Visual Studio Code 1.79.2 - OS: MacOS Ventura 13.4 ### Quarto check output [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.427 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Applications/Xcode.app/Contents/Developer/usr/bin/python3 Jupyter: 4.11.1 Kernels: python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/justinas/Library/R/arm64/4.2/library - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK

### Bug description Code annotation numbers (in the little circle) appear one line above where they should in the output, in Safari. ### Steps to reproduce The following code, with a comment meant to be on the second line of the r code results in the output below in Safari, where the (1) appears on the first line instead. ````qmd --- title: "Test" format: html --- ```{r} 2 + 1 1 + 1 #<1> ``` 1. Test comment ```` <img width="755" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/2888701/3b581c51-0c86-4d88-9f97-df7143be5eed"> ### Expected behavior In Chrome and Firefox the output is correct, with the above code producing the following output, with the (1) appears correctly on the second line: <img width="636" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/2888701/716843e5-bfd4-4678-a995-5e09c6580bba"> ### Actual behavior The code above results in the following in Safari, where the (1) is on the first line of the R code instead of the second (as above). <img width="755" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/2888701/3b581c51-0c86-4d88-9f97-df7143be5eed"> ### Your environment IDE: Rstudio 2023.06.0+421 OS: macOS Ventura 13.4.1 Safari: Version 16.5.1 (18615.2.9.11.7) ### Quarto check output ```bash quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.361 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter (\) Checking R installation...........Warning message: "~/.Rprofile" is missing a trailing newline [✓] Checking R installation...........OK Version: 4.3.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Users/abraver/Library/CloudStorage/Dropbox/R stuff/bloop/renv/library/R-4.3/aarch64-apple-darwin20 - /Users/abraver/Library/Caches/org.R-project.R/R/renv/sandbox/R-4.3/aarch64-apple-darwin20/84ba8b13 knitr: 1.43 rmarkdown: 2.22 [✓] Checking Knitr engine render......OK ```

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/6006 <div type='discussions-op-text'> ^{Originally posted by **aborruso** June 22, 2023} ### Description Hi, when I render this qmd, the columns width it not the one I have set. How to force it to be `50,30,20`? I'm using quarto 1.4.43 in Debian 11. ````qmd --- title: "UV2" format: docx: toc: false number-sections: false highlight-style: github tbl-colwidths: [50,30,20] --- # test | Question | Reply | Note | | --- | --- | --- | |aMagna sint duis proident do. Laboris Lorem exercitation consectetur quis|a|b| |aMagna sint duis proident do. Laboris Lorem exercitation consectetur quis|a|b| ````  </div>

### Bug description Basically, I had the same issue as the one reported in [#1577](https://github.com/quarto-dev/quarto-cli/issues/1577), i.e., " was able to publish a toy example once using the command line, but have not been able to successfully do so again even when using the same procedure", quoting [@jcblsn](https://github.com/quarto-dev/quarto-cli/issues/1577#issue-1322204864). May I ask how to solve this issue, considering that no solution was mentioned in #1577. The complete error message I had is shown below. ```Shell > quarto publish quarto-pub ? Publish with account: › [email protected] ? Site name: › oatsite2 [✓] Creating quarto-pub site ERROR: API Error: 429 - Too Many Requests Error: API Error: 429 - Too Many Requests at QuartoPubClient.createSite (file:///Applications/quarto/bin/quarto.js:111358:23) at async file:///Applications/quarto/bin/quarto.js:108983:26 at async withSpinner (file:///Applications/quarto/bin/quarto.js:56613:9) at async handlePublish (file:///Applications/quarto/bin/quarto.js:108980:9) at async publishSite (file:///Applications/quarto/bin/quarto.js:121225:38) at async publish5 (file:///Applications/quarto/bin/quarto.js:121443:61) at async doPublish (file:///Applications/quarto/bin/quarto.js:121399:13) at async publishAction (file:///Applications/quarto/bin/quarto.js:121435:13) at async Command.fn (file:///Applications/quarto/bin/quarto.js:121387:9) at async Command.execute (file:///Applications/quarto/bin/quarto.js:8437:13) ``` ### Steps to reproduce 1. I use `quarto create-project oatsite2 --type website` to create a quarto website project. 2. Then, I `CD oatsite2`, and run `quarto publish quarto-pub`. ### Expected behavior I should get the example website published on `quartopub.com`, just as the one I have published here [oatsite](https://oat.quarto.pub/oatsite/). ### Actual behavior I got the following error: ```Shell > quarto publish quarto-pub ? Publish with account: › [email protected] ? Site name: › oatsite2 [✓] Creating quarto-pub site ERROR: API Error: 429 - Too Many Requests Error: API Error: 429 - Too Many Requests at QuartoPubClient.createSite (file:///Applications/quarto/bin/quarto.js:111358:23) at async file:///Applications/quarto/bin/quarto.js:108983:26 at async withSpinner (file:///Applications/quarto/bin/quarto.js:56613:9) at async handlePublish (file:///Applications/quarto/bin/quarto.js:108980:9) at async publishSite (file:///Applications/quarto/bin/quarto.js:121225:38) at async publish5 (file:///Applications/quarto/bin/quarto.js:121443:61) at async doPublish (file:///Applications/quarto/bin/quarto.js:121399:13) at async publishAction (file:///Applications/quarto/bin/quarto.js:121435:13) at async Command.fn (file:///Applications/quarto/bin/quarto.js:121387:9) at async Command.execute (file:///Applications/quarto/bin/quarto.js:8437:13) ``` ### Your environment - IDE: Neovim v0.10.0-dev-532+gc07dceba3-Homebrew - OS: Mac OS Ventura 13.4.1 - Quarto: 1.3.361 ### Quarto check output ```Shell > quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.361 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.8.10 (Conda) Path: /Users/minioat/opt/anaconda3/envs/dl/bin/python Jupyter: 4.7.1 Kernels: julia-1.6, 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/ ```

Consider the minimal working example (`mwe.qmd`) below: ``` --- title: MWE author: Raniere Silva --- Awesome. ``` `quarto render mwe.qmd --to markdown` works as expected and produces ``` --- author: - Raniere Silva title: MWE toc-title: Table of contents --- Awesome. ``` Pandoc's `--metadata` argument can be used to change the YAML file. For example, `quarto render mwe.qmd --to markdown --metadata="toc-title:Foo Bar"` produces ``` --- author: - Raniere Silva title: MWE toc-title: Foo Bar --- Awesome. ``` I expect that I could use Pandoc's `--metadata` to enable [citable articles](https://quarto.org/docs/authoring/create-citeable-articles.html) but `quarto render mwe.qmd --to markdown --metadata="citation:true"` produces ``` pandoc --metadata citation:true to: markdown output-file: mwe.md standalone: true default-image-extension: png metadata title: MWE author: Raniere Silva Error running filter /opt/quarto/share/filters/main.lua: /opt/quarto/share/filters/main.lua:1177: attempt to index a boolean value (local 'citationMeta') stack traceback: /opt/quarto/share/filters/main.lua:5261: in field 'Meta' /opt/quarto/share/filters/main.lua:79: in function 'run_emulated_filter' (...tail calls...) /opt/quarto/share/filters/main.lua:74: in function 'run_emulated_filter' /opt/quarto/share/filters/main.lua:566: in local 'callback' /opt/quarto/share/filters/main.lua:577: in upvalue 'run_emulated_filter_chain' /opt/quarto/share/filters/main.lua:610: in function </opt/quarto/share/filters/main.lua:607> ``` I believe this is because > [--metadata](https://pandoc.org/MANUAL.html#option--metadata) affects the metadata of the underlying document (which is accessible from filters and may be printed in some output formats) and metadata values will be escaped when inserted into the template. Is possible to extend `appendix-cite-as` to enable both formats and allow it to be enable by `--metadata`?

kbd styling is among the .scss we need to make available to revealjs as it works for HTML with bootstrap. Related on that topic to * https://github.com/quarto-dev/quarto-cli/issues/5038 And also related to other kbd works * https://github.com/quarto-dev/quarto-cli/issues/5879 * https://github.com/quarto-dev/quarto-cli/issues/5403 ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/6009 <div type='discussions-op-text'> ^{Originally posted by **c-zippel** June 23, 2023} ### Description It'd be neat if keyboard shortcuts produced with the `kbd` shortcode in Reveal presentations were styled similarly to those in HTML documents, with a grey background and outline, rather than as normal slide text. In HTML:  In Reveal:  Thank you for considering this feature request! <details> <summary>.qmd for the screenshots</summary> ```` --- format: html: default revealjs: output-file: revealjs.html --- ## Keyboard Shortcut Here's a keyboard shortcut: {{< kbd Ctrl+S >}} ```` </details> </div>

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/6005 <div type='discussions-op-text'> ^{Originally posted by **jakobarendt** June 22, 2023} ### Description Thank you so much to all for developing the incredibly powerful Quarto! I am currently writing my master's thesis with your software, and I am only starting to grasp what it can do. One thing I have noticed, is that it makes some changes to my `.gitignore` file, when I run `quarto render` for my quarto book project. You have already explained this further in [this answer](https://github.com/quarto-dev/quarto-cli/discussions/575#discussioncomment-2524433). In my case, however, it adds `/.quarto/` as an item to the `.gitignore` file, even though I already have `.quarto` in it. To my understanding of the syntax, the latter is even more "restrictive" than the former in the sense that it always excludes `.quarto` directories/files independently of where are they are stored relative to the `.gitignore` file. I imagine that you still had you reasons for implementing it the way it is now. Why does `quarto render` not acknowledge `.quarto` as a `.gitignore` parameter? Another aspect that I want to mention here is that having `quarto render` acknowledge the more restrictive `.quarto` exclusion would make it more consistent with the R command `usethis::git_vaccinate()`, since there the ignore parameter is also `.quarto`. Quarto version: 1.3.361 Machine: macOS Ventura 13.4</div>

### Bug description I've noticed that fig-width and fig-height, when set in a Python code chunk, only seem to work once. In other words, their first appearance in a code chunk sets their values for all further Python code chunks. Contrast this with R behavior, where each code chunk can have a different width and height. I've seen bug reports for the Jupyter engine, but this is behavior using knitr, I believe. I haven't seen exactly this bug report in the list, but could have missed it. Thanks for your work on Quarto! ### Steps to reproduce ````qmd --- title: "fig-width test" format: html editor_options: chunk_output_type: console --- ## Make a Wide R Plot ```{r} #| fig-width: 8 #| fig-height: 2 plot(x=c(1, 2, 3, 4), y=c(1, 4, 9, 16)) ``` ## Make a Square R Plot ```{r} #| fig-width: 3 #| fig-height: 3 plot(x=c(1, 2, 3, 4), y=c(1, 4, 9, 16)) ``` ## Make a Wide Python Plot ```{python} #| fig-width: 8 #| fig-height: 2 import matplotlib.pyplot as plt plt.plot([1,2,3,4], [1,4,9,16], 'ro') plt.show() ``` ## Make a Square Python Plot ```{python} #| fig-width: 3 #| fig-height: 3 plt.plot([1,2,3,4], [1,4,9,16], 'ro') plt.show() ``` ```` ### Expected behavior All plots should have dimensions set by chunk's fig-width, fig-height. ### Actual behavior After first python chunk, fig-height, fig-width not respected. ### Your environment Quarto Version: 1.3.361 RStudio: 2023.06.0+421 R: 4.3.0 (2023-04-21) Python: Python 3.8.13 (reported by reticulate) Reticulate 1.29 REPL OS: Linux (Ubuntu Jammy) ### Quarto check output [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.361 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.3.0 Path: /usr/lib/R LibPaths: - /home/thatcher/R/x86_64-pc-linux-gnu-library/4.3 - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/lib/R/library knitr: 1.43 rmarkdown: 2.22 [✓] Checking Knitr engine render......OK

### Bug description When I use plotly and crosstalk to create an interactive graph and render it in Quarto, the checkboxes don't show for filter_checkbox. The functionality is there; I can select and deselect the options; however, the actual checkboxes don't show and there is no indication within the crosstalk filter_checkbox which fields have been selected. The titles for the filters are also cut off on the left side. ### Steps to reproduce ````qmd --- title: "Reprex" format: html execute: echo: false warning: false --- ## Reproducible Example ```{r} library(dplyr) library(plotly) library(data.table) library(crosstalk) reprex<-data.frame( "Category" = c("a", "b", "c", "d", "e", "f", "g"), "Today" = seq(1, 7, 1), "Yesterday" = seq(1, 14, 2), "Two.Days.Ago" = seq(3, 9, 1) ) figrepex <- reprex |> setDT() |> melt(id.vars="Category", measure.vars=c("Today", "Yesterday", "Two.Days.Ago"), value.name = "Counts", variable.name="Compare") |> mutate(Compare = factor(Compare, levels=c("Today", "Yesterday", "Two.Days.Ago")) )|> setDF() |> SharedData$new() figrep<-figrepex %>% plot_ly(x = ~Category, y = ~Counts, color = ~Compare, type='bar') bscols( widths = c(3,NA), list( filter_checkbox(id="Compare", label="Compare", sharedData = figrepex, group=~Compare), filter_checkbox(id = "Category", label="Category", sharedData = figrepex, group=~Category) ), figrep ) ``` ```` ### Expected behavior When I run the code, I should see the output with checkboxes visible:  This is obtained from the following code: ```` reprex<-data.frame( "Category" = c("a", "b", "c", "d", "e", "f", "g"), "Today" = seq(1, 7, 1), "Yesterday" = seq(1, 14, 2), "Two.Days.Ago" = seq(3, 9, 1) ) figrepex <- reprex |> setDT() |> melt(id.vars="Category", measure.vars=c("Today", "Yesterday", "Two.Days.Ago"), value.name = "Counts", variable.name="Compare") |> mutate(Compare = factor(Compare, levels=c("Today", "Yesterday", "Two.Days.Ago")) )|> setDF() |> SharedData$new() figrep<-figrepex %>% plot_ly(x = ~Category, y = ~Counts, color = ~Compare, type='bar') bscols( widths = c(3,NA), list( filter_checkbox(id="Compare", label="Compare", sharedData = figrepex, group=~Compare), filter_checkbox(id = "Category", label="Category", sharedData = figrepex, group=~Category) ), figrep ) ```` ### Actual behavior Instead, the checkboxes don't show and the filter headers are chopped off as well:  ### Your environment - IDE: I have replicated this on two different versions of RStudio: RStudio 2023.03.0+386 RStudio 2023.06.0+421 - OS: I have replicated this on laptop running Windows 10 Enterprise (using RStudio 2023.03.0+38) and a server running Windows Server 2019 (running RStudio 2023.06.0+421) ### Quarto check output On the laptop, quarto check gives: [>] Checking Quarto installation......OK Version: 1.2.335 Path: C:\Program Files\RStudio\resources\app\bin\quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.4 Path: C:/.../AppData/Local/Programs/Python/Python310/python.exe Jupyter: 4.10.0 Kernels: python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.2.0 Path: C:/PROGRA~1/R/R-42~1.0 LibPaths: - C:/.../Documents/R/win-library/4.2 - C:/Program Files/R/R-4.2.0/library rmarkdown: 2.21 [>] Checking Knitr engine render......OK On the server, quarto check gives: [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.361 Path: C:\Program Files\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.4 Path: C:/Program Files/Python39/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with py -m pip install jupyter [>] Checking R installation...........OK Version: 4.2.3 Path: C:/PROGRA~1/R/R-42~1.3 LibPaths: - C:/Users/.../AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.3/library knitr: 1.42 rmarkdown: 2.22 [>] Checking Knitr engine render......OK

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/6001 <div type='discussions-op-text'> ^{Originally posted by **thegilpatrick** June 21, 2023} ### Description Updated Quarto to version 1.4.161 and started getting errors when trying to preview this old QMD file. Here is the [QMD file](https://github.com/thegilpatrick/Blog/blob/main/posts/R-TidyCensus/index.qmd) Error in Terminal: ``` PS C:\Users\16615\OneDrive\Desktop\Blog> quarto preview c:/Users/16615/OneDrive/Desktop/Blog/posts/R-TidyCensus/index.qmd --no-browser --no-watch-inputs [1/2] posts\R-TidyCensus\index.qmd processing file: index.qmd output file: index.knit.md Error running filter C:/Users/16615/AppData/Local/Programs/Quarto/share/filters/main.lua: ...615/AppData/Local/Programs/Quarto/share/filters/main.lua:4247: attempt to call a nil value (global 'stringifyTokens') stack traceback: ...615/AppData/Local/Programs/Quarto/share/filters/main.lua:4283: in upvalue 'stringifyTokens' ...615/AppData/Local/Programs/Quarto/share/filters/main.lua:4321: in function <...615/AppData/Local/Programs/Quarto/share/filters/main.lua:4296> (...tail calls...) [C]: in ? [C]: in method 'walk' ...615/AppData/Local/Programs/Quarto/share/filters/main.lua:98: in function 'run_emulated_filter' ...615/AppData/Local/Programs/Quarto/share/filters/main.lua:566: in local 'callback' ...615/AppData/Local/Programs/Quarto/share/filters/main.lua:577: in upvalue 'run_emulated_filter_chain' ...615/AppData/Local/Programs/Quarto/share/filters/main.lua:610: in function <...615/AppData/Local/Programs/Quarto/share/filters/main.lua:607> stack traceback: ...615/AppData/Local/Programs/Quarto/share/filters/main.lua:98: in function 'run_emulated_filter' ...615/AppData/Local/Programs/Quarto/share/filters/main.lua:566: in local 'callback' ...615/AppData/Local/Programs/Quarto/share/filters/main.lua:577: in upvalue 'run_emulated_filter_chain' ...615/AppData/Local/Programs/Quarto/share/filters/main.lua:610: in function <...615/AppData/Local/Programs/Quarto/share/filters/main.lua:607> ```</div>

### Bug description Graphviz diagrams do not behave like other types of figures, their labels do not work, captions work only partially, and positioning in the margin only works in HTML, not in PDF. ### Steps to reproduce ````qmd --- title: Example format: pdf: papersize: a4 fontsize: 9pt geometry: - showframe html: fontsize: 9pt --- Hello world! ```{python} # | label: fig-test # | fig-cap: Beautiful blue bars. # | column: margin # | echo: false import matplotlib.pyplot as plt categories = ["A", "B", "C", "D"] values = [10, 20, 15, 25] plt.figure(figsize=(6, 3)) plt.barh(categories, values) plt.show() ``` ```{dot} // | fig-label: causal-graph-1 // | fig-cap: Causal graph for observational analysis. // | fig-width: 100px // | fig-height: 100px // | column: margin digraph D { {W,X} -> {Y} [color=blue] } ``` ```{dot} // | fig-label: causal-graph-2 // | fig-cap: Causal graph for observational analysis. // | fig-width: 100px // | fig-height: 100px // | column: page digraph D { {W,X} -> {Y} [color=blue] } ``` ```{dot} // | fig-label: causal-graph-3 // | fig-cap: Causal graph for observational analysis. // | fig-width: 100px // | fig-height: 100px // | column: body digraph D { {W,X} -> {Y} [color=blue] } ``` Have a look at @causal-graph-3 and at @fig-test! ```` ### Expected behavior > Diagrams can be treated as figures the same way that images and plot output are. [source](https://quarto.org/docs/authoring/diagrams.html#figures) ### Actual behavior Unfortunately, there are multiple problems with Graphviz diagrams: - They do not respect the `column: margin` attribute for PDF, but they do for HTML. - They are not citable for both HTML and PDF. - The "Figure: ..." prefix is not added to the figure for both HTML and PDF. HTML: <img width="1204" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/46022183/fc0d1a9a-160c-4837-aa3b-b7b7213c9ff7"> PDF: <img width="684" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/46022183/fe0e3c7b-d63e-4a7b-b94d-3908c5168075"> ### Your environment - IDE: latest VSCode, but this is with quarto-cli - OS: MacOS 13.4 ### Quarto check output ```bash [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.361 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.10 Path: /Users/david/Repositories/protest-impact/.venv/bin/python Jupyter: 5.3.0 Kernels: ir, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library knitr: 1.39 rmarkdown: 2.14 [✓] Checking Knitr engine render......OK ```

### Bug description Consider the following `hello.qmd` file: ```qmd --- title: Hello format: revealjs: width: 1600 height: 900 --- ## Hello Hello^[Hello<br>hello] ``` The document was rendered using `quarto render hello.qmd`. In the HTML output, the footnote was displayed in full: <img width="1948" alt="quart_html" src="https://github.com/quarto-dev/quarto-cli/assets/10522520/8867d06b-67d1-4845-97b2-da49dbf86873"> However, if I print the HTML to PDF in Google Chrome according to the documentation [here](https://quarto.org/docs/presentations/revealjs/presenting.html#print-to-pdf), the footnote was clipped: <img width="1388" alt="quarto_pdf" src="https://github.com/quarto-dev/quarto-cli/assets/10522520/8d773a93-ffd3-4b3a-a197-77f66350b39e"> Note that there was also a blank page in the printed PDF, which echoed the discussion in #3997. Currently, a workaround is to use a different PDF converter such as `decktape`, which solved both the footnote display issue as well as the trailing-blank-page issue. Thank you for your help in advance. ### Steps to reproduce _No response_ ### Expected behavior _No response_ ### Actual behavior _No response_ ### Your environment - IDE: Visual Studio Code 1.79.2 (Universal) - OS: macOS 13.4 - Quarto: 1.3.361 - Google Chrome: 114.0.5735.133 (Official Build) (arm64) ### Quarto check output ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.361 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.4 Path: /opt/homebrew/opt/[email protected]/bin/python3.11 Jupyter: 5.3.0 Kernels: ir, julia-1.9 NOTE: No Jupyter kernel for Python found [✓] Checking R installation...........OK Version: 4.3.1 Path: /opt/homebrew/Cellar/r/4.3.1/lib/R LibPaths: - /opt/homebrew/lib/R/4.3/site-library - /opt/homebrew/Cellar/r/4.3.1/lib/R/library knitr: 1.43 rmarkdown: 2.22 [✓] Checking Knitr engine render......OK ```

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5993 <div type='discussions-op-text'> ^{Originally posted by **rgaiacs** June 21, 2023} ### Description I have a Git remote source named `quarto`: ``` $ git remote -v quarto [email protected]:gesiscss/orc2.git (fetch) quarto [email protected]:gesiscss/orc2.git (push) ``` Executing `quarto publish gh-pages` produces the follow prompt ``` ? Publish site to undefined using gh-pages? (Y/n) › ``` Will be great if the prompt get information of other remote sources.</div>

### Bug description Hi, I am including a observable plot in a html document. I am used to set in the yaml as: ```` --- format: html: code-fold: true execute: eval: true echo: true message: false warning: false output: true include: false --- ```` and selectively set the include option to true where I need it. However, doing so, the ojs chunks does not appear when adding the //|include option, the same working perfectly when yaml include option set to true. I have also tried the `{ojs, include=TRUE}` like mermaid syntax, and all combination in between them. Seems that the yaml option overwrite the local one? ### Steps to reproduce ```` ```{r} library(palmerpenguins) ojs_define(data = penguins) ``` ```{ojs} //| panel: sidebar //| include: true viewof bill_length_min = Inputs.range( [32, 50], {value: 32, step: 1, label: "Bill length (min):"} ) viewof islands = Inputs.checkbox( ["Torgersen", "Biscoe", "Dream"], { value: ["Torgersen", "Biscoe", "Dream"], label: "Islands:" } ) ``` ::: {.panel-tabset} ## Graph ```{ojs} //| include: true Plot.plot({ facet: {data: filtered, x: "sex", y: "island"}, color: { legend: true }, marks: [ Plot.frame({ strokeOpacity: 0.1 }), Plot.dot(filtered, { x: "body_mass_g", y: "bill_length_mm", stroke: "species", tip: true }) ] }) ``` ## Data ```{ojs} //| include: true Inputs.table(filtered, { columns: [ "body_mass_g", "flipper_length_mm", "species","bill_length_mm" ]}) ``` ::: ```{ojs} filtered = transpose(data).filter(function(penguin) { return bill_length_min < penguin.bill_length_mm && islands.includes(penguin.island); }) ``` ```` ### Expected behavior The ojs chunk should appear in the rendered doc when yaml option is false and chunk option are true ### Actual behavior the ojs chunk does not appear, only the two empty tabsets ### Your environment My settings: ```` version R version 4.3.0 (2023-04-21 ucrt) os Windows 10 x64 (build 19045) system x86_64, mingw32 ui RStudio language EN collate French_France.utf8 ctype French_France.utf8 tz Europe/Paris date 2023-06-21 rstudio 2023.06.0+421 Mountain Hydrangea (desktop) pandoc 3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown) quarto : "1.3.361" ```` ### Quarto check output ```` [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.361 Path: C:\Users\lehuen201\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.11.4 Path: C:/Python311/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with py -m pip install jupyter [>] Checking R installation...........OK Version: 4.3.0 Path: C:/Users/lehuen201/AppData/Local/Programs/R/R-4.3.0 LibPaths: - C:/Users/lehuen201/AppData/Local/Programs/R/R-4.3.0/library knitr: 1.43 rmarkdown: 2.22 [>] Checking Knitr engine render......OK ````

### Bug description When rendering a .ipynb file to html the resultant html file has some code like: requirejs.config({ paths: { 'plotly': ['https://cdn.plot.ly/plotly-2.12.1.min'] } }); But https://cdn.plot.ly/plotly-2.12.1.min no longer exists. The plots are no longer being generated. I was able to fudge by editing the html with different location of plotly: cdnjs.cloudflare.com/ajax/libs/plotly.js/2.24.2/plotly Has plotly moved its repository for the library and quarto needs to be updated? ### Steps to reproduce _No response_ ### Expected behavior _No response_ ### Actual behavior _No response_ ### Your environment _No response_ ### Quarto check output _No response_

### Bug description I have a document that will show a plot when rendered to html but when I publish the document to quarto pub it disapears. I also noticed this issue is occurring on the quarto [website](https://quarto.org/docs/interactive/widgets/jupyter.html). Is this just a browser issue (google chrome) with my computer or is the plot properly rendering on other browsers/computers. As seen in the photo there is a blank space where the plot should be. Any help would be appreciated. thanks.  ### Steps to reproduce _No response_ ### Expected behavior _No response_ ### Actual behavior _No response_ ### Your environment _No response_ ### Quarto check output _No response_

### Bug description Like #5964 https://models-on-a-plane.pages.dev/ The navbar at top includes an external link to calcwithdec.dev, which doesn't open in a new window, despite `link-external-newwindow: true` in `_quarto.yml` ### Steps to reproduce _No response_ ### Expected behavior External link should open in a new window/tab ### Actual behavior Opens in existing tab, taking user away from website. ### Your environment OS: Ubuntu ### Quarto check output ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.151 Path: /opt/quarto/bin ```

### Bug description Hello, I want to use functionality from the shinyjs package in an interactive Quarto document, namely conditionally hiding/disabling action buttons. I can see from shinyjs documentation that it should be compatible with markdown documents when specifying the argument `rmd=TRUE` in `shinyjs::useShinyjs(rmd = TRUE)`. However in the simple reprex below the show/hide functionality does not work. I tried the same thing with the disable/enable functions which also did not work. ### Steps to reproduce ````qmd --- format: html server: shiny --- ```{r, include=FALSE} library(shiny) library(shinyjs) ``` ```{r} shinyjs::useShinyjs(rmd = TRUE) shinyjs::hidden(actionButton("HiddenButton", "I was hidden")) actionButton("ShowButton", "Show Button") textOutput("text") ``` ```{r} #| context: server library(shiny) library(shinyjs) shinyjs::useShinyjs(rmd = TRUE) observeEvent(input$ShowButton, { showElement("HiddenButton") }) observeEvent(input$HiddenButton, { output$text <- renderText("Hidden button activated") }) ``` ```` ### Expected behavior The action button with ID "HiddenButton" should be hidden when the document is rendered and revealed when the button "ShowButton" is clicked. ### Actual behavior Button is not hidden ### Your environment -IDE: RStudio 2023.06.0+421 -OS: Windows 10 64bit ### Quarto check output ``` $ quarto check A new release of Deno is available: 1.28.2 → 1.34.3 Run `deno upgrade` to install it. [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.330 Path: C:\Users\bblack\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.9.0 Path: C:/Program Files/Python39/python.exe Jupyter: 4.7.1 Kernels: ir NOTE: No Jupyter kernel for Python found [>] Checking R installation...........OK Version: 4.2.2 Path: C:/Users/bblack/AppData/Local/Programs/R/R-4.2.2 LibPaths: - C:/Users/bblack/AppData/Local/Programs/R/R-4.2.2/library knitr: 1.43 rmarkdown: 2.21 [>] Checking Knitr engine render......OK ```

### Description I'm suggesting that it could be useful to map a few additional CSS variables from Yaml to the CSS `:root` variables. Currently, there are already some variables defined such as: ``` :root { --quarto-body-bg: #ffffff; --quarto-body-color: #212529; --quarto-text-muted: #6c757d; --quarto-border-color: #dee2e6; --quarto-border-width: 1px; --quarto-border-radius: 0.25rem; --quarto-font-monospace: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace; } ``` and, for example, the document's [fontcolor, monofont, linkcolor, etc, can be set in the Yaml](https://quarto.org/docs/output-formats/html-themes.html#basic-options). I believe it would be useful to add a couple of such mappings, for example to define a "accent" / "highlighting" colour, as a minimal theming system. It's common for a document to have one main colour (black font), and another colour for titles, buttons, etc. This kind of logic is used in other systems, such as Beamer themes or ggplot2 themes. Colour palettes can even be derived from this parent element by CSS transformations, e.g. ``` color: color-mix(in srgb, var(--quarto-highlight) 20%, transparent); ``` to create a semi-transparent, lighter shade. I'm not sure how many of these mappings might make sense – presumably just very few, otherwise it'll get too complicated to follow the possible interactions between Bootstrap and (S)CSS variables.

If both the `pdfcrop` binary and Ghostscript are available on the system, Quarto crops figures in PDF output regardless of the relevant chunk option. Tested on Ubuntu 22.04 with Quarto 1.3.361. I've tried to disable cropping without success by - setting the chunk option (in YAML format) `crop: false` - setting the chunk option (in YAML format) `fig-crop: false` - setting `knitr.opts_chunk.crop: false` in `_quarto.yml`. - setting `knitr.opts_chunk.fig_crop: false` in `_quarto.yml`. - setting `format.pdf.crop: false` in `_quarto.yml`. - setting `format.pdf.fig_crop: false` in `_quarto.yml`. - running `knitr::opts_chunk$set(crop = FALSE)` in a chunk before the figure chunks. - running `knitr::opts_chunk$set(fig_crop = FALSE)` in a chunk before the figure chunks. The only way that actually disabled PDF figure cropping was running `knitr::knit_hooks$set(crop = function(...){})` in a chunk before the figure chunks. Note that I'm a bit confused about the correct name of the cropping chunk option on the knitr side of things: While the *R Markdown Cookbook* [mentions a `crop` chunk option](https://bookdown.org/yihui/rmarkdown-cookbook/crop-plot.html) (same what the [Quarto sources seem to refer to](https://github.com/quarto-dev/quarto-cli/blob/c8fb73c433215926d1b8b18f39e29bc1a215e33d/src/resources/rmd/execute.R#L277-L281)), the *R Markdown: The Definitive Guide* [mentions a `fig_crop` chunk option](https://bookdown.org/yihui/rmarkdown/pdf-document.html#figure-options-1). Quarto seems to ignore both of them. _Originally posted by @salim-b in https://github.com/quarto-dev/quarto-cli/discussions/2917#discussioncomment-6224496_

See #5950 for a use case. We should be encouraging users to try `tinytex` before reporting a latex bug, since we've been having a number of issues with incompatible system installations of texlive etc.

### Bug description I have encountered a problem when using Quarto in RStudio. When I attempt to parse a YAML file, I get an error message indicating a bad indentation of a mapping entry at line 9, column 8. The specific error message is YAMLError: bad indentation of a mapping entry at line 9, column 8: toc: true. I have tried various combinations of indents and spaces, but the error persists. I am unsure about what has gone wrong. ### Steps to reproduce --- title: "Challenge 9 " author: "Zhongyue Lin" description: "Creating a function" date: "6/19/2023" format: html: df-print: paged toc: true code-copy: true code-tools: true categories: - challenge_9 --- ERROR: YAMLError: bad indentation of a mapping entry at line 9, column 8: toc: true ^ YAMLError: bad indentation of a mapping entry at line 9, column 8: toc: true ^ at generateError (file:///Applications/quarto/bin/quarto.js:10719:12) at throwError (file:///Applications/quarto/bin/quarto.js:10722:11) at readBlockMapping (file:///Applications/quarto/bin/quarto.js:11361:20) at composeNode (file:///Applications/quarto/bin/quarto.js:11528:84) at readBlockMapping (file:///Applications/quarto/bin/quarto.js:11346:17) at composeNode (file:///Applications/quarto/bin/quarto.js:11528:84) at readDocument (file:///Applications/quarto/bin/quarto.js:11642:5) at loadDocuments (file:///Applications/quarto/bin/quarto.js:11679:9) at load (file:///Applications/quarto/bin/quarto.js:11684:23) at parse3 (file:///Applications/quarto/bin/quarto.js:11694:12) ### Expected behavior I expect the YAML file to be parsed correctly without any errors. ### Actual behavior I expect the YAML file to be parsed correctly without any errors. ### Your environment IDE: RStudio 2023.06.0+421 OS: macOS Monterey, Version 12.6 quarto --version 1.3.361 ### Quarto check output [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.361 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.13 (Conda) Path: /Users/leo/opt/anaconda3/bin/python Jupyter: 4.11.1 Kernels: python3, julia-1.8, matlab, matlab_connect, ir [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library knitr: 1.42 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK

### Bug description Hello there, I am trying to print my revealjs presentation, but when I press `E` to enter Print View mode, two slide titles appear above my first slide and I can't print it. My current workaround is to print only slides 3-21. Any idea on what is happening?  ### Steps to reproduce Presentation: https://baarthur.github.io/29iioa_slides/src/iioa_slide.html#/title-slide Code: https://github.com/baarthur/29iioa_slides/blob/main/src/iioa_slide.qmd ### Expected behavior _No response_ ### Actual behavior _No response_ ### Your environment _No response_ ### Quarto check output [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK NOTE: Deno version 1.33.2 is too old. Please upgrade to 1.33.1 or later. [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.60 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.9.6 Path: /Library/Developer/CommandLineTools/usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.3.0 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library knitr: 1.43 rmarkdown: 2.22 [✓] Checking Knitr engine render......OK

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5895 <div type='discussions-op-text'> ^{Originally posted by **pipme** June 12, 2023} ### Description This question is related to #290 . `backref=true` seems not working for generating backlinks in the output pdf. A minimal reproducible example is below: `index.qmd` file: ```qmd --- title: "Start Blogging with Quarto" date: "2023-06-10" bibliography: [local.bib] format: html: default pdf: cite-method: biblatex biblatexoptions: - "backend=biber" - "backref=true" keep-tex: true --- For testing backref. [@navarro2022] ``` With a `local.bib` file: ``` @online{navarro2022, author = {Navarro, Danielle}, title = {Porting a Distill Blog to Quarto}, date = {2022-04-20}, url = {https://blog.djnavarro.net/posts/2022-04-20_porting-to-quarto}, langid = {en} } ``` The command I used is `quarto preview index.qmd --to pdf`. --- Apart from the above question for generating backlinks in pdf, **can we do the same thing for HTML**? i.e., adding back links in the reference list to go back to some specific locations of the HTML where the article got cited. It would be something like the footnote backlink I guess, which is a nice feature. Thanks! ### Additional information Quarto version: 1.3.361 MacOS: 13.4 (22F66) Xelatex: ``` XeTeX 3.141592653-2.6-0.999995 (TeX Live 2023) kpathsea version 6.3.5 Copyright 2023 SIL International, Jonathan Kew and Khaled Hosny. There is NO warranty. Redistribution of this software is covered by the terms of both the XeTeX copyright and the Lesser GNU General Public License. For more information about these matters, see the file named COPYING and the XeTeX source. Primary author of XeTeX: Jonathan Kew. Compiled with ICU version 72.1; using 72.1 Compiled with zlib version 1.2.13; using 1.2.13 Compiled with FreeType2 version 2.13.0; using 2.13.0 Compiled with Graphite2 version 1.3.14; using 1.3.14 Compiled with HarfBuzz version 7.0.1; using 7.0.1 Compiled with libpng version 1.6.39; using 1.6.39 Compiled with pplib version v2.05 less toxic i hope Using Mac OS X Core Text and Cocoa frameworks ``` biber version: 2.19 Terminal output log: ```zsh ❯ quarto preview index.qmd --to pdf pandoc to: latex output-file: index.tex standalone: true pdf-engine: xelatex variables: graphics: true tables: true default-image-extension: pdf cite-method: biblatex metadata documentclass: scrartcl classoption: - DIV=11 - numbers=noendperiod papersize: letter header-includes: - '\KOMAoption{captions}{tableheading}' block-headings: true title: Start Blogging with Quarto date: '2023-06-10' bibliography: - local.bib biblatexoptions: - backend=biber - backref=true running xelatex - 1 This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode generating bibliography INFO - This is Biber 2.19 INFO - Logfile is 'index.blg' INFO - Reading 'index.bcf' INFO - Found 1 citekeys in bib section 0 INFO - Processing section 0 INFO - Looking for bibtex file 'local.bib' for section 0 INFO - LaTeX decoding ... INFO - Found BibTeX data source 'local.bib' INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable' INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized' INFO - Sorting list 'nty/global//global/global' of type 'entry' with template 'nty' and locale 'en-US' INFO - No sort tailoring available for locale 'en-US' INFO - Writing 'index.bbl' with encoding 'UTF-8' INFO - Output to index.bbl running xelatex - 2 This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode Output created: index.pdf Watching files for changes Browse at http://localhost:3243/web/viewer.html ``` </div>

In a github action rendering, there will be a checkout at each rendering. This implies that the last modified date of each file will be the same as the git checkout date. This is because of the fact that git does not store last modified date information. There are workaround to restore date of file to last commit date for the files: * https://github.com/BenLubar/git-last-modified * https://stackoverflow.com/questions/21735435/git-clone-changes-file-modification-time/55609950#55609950 Maybe we could try be clever when inside a git project, or leverage the `_freeze` state for project to store information. ### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5899 <div type='discussions-op-text'> ^{Originally posted by **adityam** June 13, 2023} ### Description I am using github actions to publish my website. 1. Website: https://adityam.github.io/stochastic-control/ 2. Github action: https://github.com/adityam/stochastic-control/blob/quarto/.github/workflows/quarto-render.yml In `_quarto.yml`, I have set ``` format: html: published-title: Updated date: last-modified ``` but all my pages have today's date. I suspect that the last modified date is coming from the date the date when github CI clones the repo (and hence today's date) rather than when the file was checked into the repo (which is the true last-modified date). Is it possible to somehow use the date when the file was last committed to git, for example, similar to [what is available for hugo](https://gohugo.io/variables/git/) </div>

### Bug description Hi, I really like the repo actions! I have a draft website here where I use them: https://models-on-a-plane.pages.dev/ In the footer there is a link to calculang on GitHub, which opens in a new window, due to `link-external-newwindow: true`. The Edit this page, View Source and Report an issue links alongside them ("Repo actions links") don't follow the same behaviour. ### Steps to reproduce https://gitlab.com/declann/models-on-a-plane `_quarto.yml` has: ``` repo-url: https://gitlab.com/declann/models-on-a-plane issue-url: https://gitlab.com/declann/models-on-a-plane/-/issues repo-actions: - edit - source - issue ``` and also `link-external-newwindow: true` ### Expected behavior Repo actions links should obey `link-external-newwindow` i.e. open in a new window whenever set to true ### Actual behavior Repo actions links take the user away from website ### Your environment _No response_ ### Quarto check output ``` [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.4.151 Path: /opt/quarto/bin ```

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5896 <div type='discussions-op-text'> ^{Originally posted by **pipme** June 12, 2023} ### Description In mobile view, I can't find the links to other formats like revealjs, pdf etc, neither table of contents. Is it a bug or intended behaviours? For example, https://pipme.github.io/posts/2023-06-11-Quarto-tips/index-gist.html in the desktop:  While in mobile Chrome: <img src='https://github.com/quarto-dev/quarto-cli/assets/30783979/38e8a46d-29e2-45c7-bd54-5c23ab7cb3ed' width="200px" /> </div>

### Bug description Wide tables do not stretch beyond the body column in PDFs. <img width="658" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/46022183/5737a017-205d-4fb6-99d1-8829ef4d2443"> (For HTML, it is working:) <img width="684" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/46022183/6ec77415-a8bd-48bc-b4b1-52a2945de0fb"> ### Steps to reproduce ````qmd --- title: Example format: pdf: papersize: a4 fontsize: 9pt geometry: - showframe html: fontsize: 9pt --- ```{python} # | label: tbl-official-overview # | tbl-cap: Official overview. # | column: page # | echo: false from IPython.display import Markdown import pandas as pd md = pd.read_csv("table.csv", sep=";").to_markdown(index=False) print("\n".join(md.split("\n")[:4])) Markdown(md) ``` ```` `table.csv`: ````csv region;city;kpop;cap?;reg?;obs?;2015;2016;2017;2018;2019;2020;2021;2022 Baden-Württemberg;Karlsruhe;283; ;x; ; ; ; ; ; ; ;490;467 Bayern;München;1,260;x;x; ; ; ; ;1,145;1,170;1,364;1,983;1,169 Berlin;Berlin;3,426;x;x;x; ; ; ;4,290;5,405;5,890;6,207;6,442 Brandenburg;Potsdam;182;x;x; ; ; ; ; ;214;238;287;326 Bremen;Bremen;546;x; ; ; ; ; ; ;654;631;623;721 Hamburg;–;–; ; ; ; ; ; ; ; ; ; ; Hessen;Wiesbaden;278;x;x; ; ; ; ; ;159;235;304;256 Mecklenburg-Vorpommern;–;–; ; ; ; ; ; ; ; ; ; ; Niedersachsen;–;–; ; ; ; ; ; ; ; ; ; ; Nordrhein-Westfalen;Köln;963; ;x; ; ; ; ;1,037; ; ; ;1,551 Nordrhein-Westfalen;Wuppertal;360; ;x; ; ; ; ; ; ; ; ;209 Rheinland-Pfalz;Mainz;217;x;x; ; ; ; ;255;248;305;312;411 Saarland;–;–; ; ; ; ; ; ; ; ; ; ; Sachsen;Dresden;556;x;x; ; ; ; ; ; ;164;292;405 Sachsen-Anhalt;Magdeburg;235;x;x;x;215;167;135;175;222;312;411;435 Schleswig-Holstein;Kiel;246;x;x; ; ; ; ; ; ; ;272;341 Thüringen;Erfurt;213;x; ; ; ; ; ; ;305;285;331;351 ;sum;8,771;10;11;2;215;167;135;6,902;8,377;9,424;11,512;13,084 ```` Markdown that is produced as intermediate step: ````md | region | city | kpop | cap? | reg? | obs? | 2015 | 2016 | 2017 | 2018 | 2019 | 2020 | 2021 | 2022 | |:-----------------------|:----------|:-------|:-------|:--------|:--------|:-------|:-------|:-------|:-------|:-------|:-------|:-------|:-------| | Baden-Württemberg | Karlsruhe | 283 | | x | | | | | | | | 490 | 467 | | Bayern | München | 1,260 | x | x | | | | | 1,145 | 1,170 | 1,364 | 1,983 | 1,169 | | Berlin | Berlin | 3,426 | x | x | x | | | | 4,290 | 5,405 | 5,890 | 6,207 | 6,442 | | Brandenburg | Potsdam | 182 | x | x | | | | | | 214 | 238 | 287 | 326 | | Bremen | Bremen | 546 | x | | | | | | | 654 | 631 | 623 | 721 | | Hamburg | – | – | | | | | | | | | | | | | Hessen | Wiesbaden | 278 | x | x | | | | | | 159 | 235 | 304 | 256 | | Mecklenburg-Vorpommern | – | – | | | | | | | | | | | | | Niedersachsen | – | – | | | | | | | | | | | | | Nordrhein-Westfalen | Köln | 963 | | x | | | | | 1,037 | | | | 1,551 | | Nordrhein-Westfalen | Wuppertal | 360 | | x | | | | | | | | | 209 | | Rheinland-Pfalz | Mainz | 217 | x | x | | | | | 255 | 248 | 305 | 312 | 411 | | Saarland | – | – | | | | | | | | | | | | | Sachsen | Dresden | 556 | x | x | | | | | | | 164 | 292 | 405 | | Sachsen-Anhalt | Magdeburg | 235 | x | x | x | 215 | 167 | 135 | 175 | 222 | 312 | 411 | 435 | | Schleswig-Holstein | Kiel | 246 | x | x | | | | | | | | 272 | 341 | | Thüringen | Erfurt | 213 | x | | | | | | | 305 | 285 | 331 | 351 | | | sum | 8,771 | 10 | 11 | 2 | 215 | 167 | 135 | 6,902 | 8,377 | 9,424 | 11,512 | 13,084 | ```` The rendered table (just to show that the Markdown is correct): | region | city | kpop | cap? | reg? | obs? | 2015 | 2016 | 2017 | 2018 | 2019 | 2020 | 2021 | 2022 | |:-----------------------|:----------|:-------|:-------|:--------|:--------|:-------|:-------|:-------|:-------|:-------|:-------|:-------|:-------| | Baden-Württemberg | Karlsruhe | 283 | | x | | | | | | | | 490 | 467 | | Bayern | München | 1,260 | x | x | | | | | 1,145 | 1,170 | 1,364 | 1,983 | 1,169 | | Berlin | Berlin | 3,426 | x | x | x | | | | 4,290 | 5,405 | 5,890 | 6,207 | 6,442 | | Brandenburg | Potsdam | 182 | x | x | | | | | | 214 | 238 | 287 | 326 | | Bremen | Bremen | 546 | x | | | | | | | 654 | 631 | 623 | 721 | | Hamburg | – | – | | | | | | | | | | | | | Hessen | Wiesbaden | 278 | x | x | | | | | | 159 | 235 | 304 | 256 | | Mecklenburg-Vorpommern | – | – | | | | | | | | | | | | | Niedersachsen | – | – | | | | | | | | | | | | | Nordrhein-Westfalen | Köln | 963 | | x | | | | | 1,037 | | | | 1,551 | | Nordrhein-Westfalen | Wuppertal | 360 | | x | | | | | | | | | 209 | | Rheinland-Pfalz | Mainz | 217 | x | x | | | | | 255 | 248 | 305 | 312 | 411 | | Saarland | – | – | | | | | | | | | | | | | Sachsen | Dresden | 556 | x | x | | | | | | | 164 | 292 | 405 | | Sachsen-Anhalt | Magdeburg | 235 | x | x | x | 215 | 167 | 135 | 175 | 222 | 312 | 411 | 435 | | Schleswig-Holstein | Kiel | 246 | x | x | | | | | | | | 272 | 341 | | Thüringen | Erfurt | 213 | x | | | | | | | 305 | 285 | 331 | 351 | | | sum | 8,771 | 10 | 11 | 2 | 215 | 167 | 135 | 6,902 | 8,377 | 9,424 | 11,512 | 13,084 | ### Expected behavior The table should fill both the body column and the margin. ### Actual behavior In the PDF, the table only fills the body column. The table caption is too far at the left. In the HTML, things work. https://quarto.org/docs/authoring/article-layout.html#pdflatex-layout states that PDF does not support all layout options in PDF, but to my understanding this one should work. ### Your environment - IDE: VSCode, but this is an issue with quarto-cli - OS: MacOS 13.4 ### Quarto check output [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.361 Path: /Applications/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.10 Path: /Users/david/Repositories/protest-impact/.venv/bin/python Jupyter: 5.3.0 Kernels: ir, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library knitr: 1.39 rmarkdown: 2.14 [✓] Checking Knitr engine render......OK

### Bug description When rendering an HTML document, if `reference-location` is set to "margin" and a footnote is added to a section title, the section title would be misplaced to the left of the page, e.g.,  ### Steps to reproduce ````qmd --- title: "Minimum reproducible example" format: html: reference-location: "margin" --- ## Section title with notes ^[some notes] some text ## Section title without notes some text ```` ### Expected behavior I expect the section title to be aligned with those without footnotes. ### Actual behavior The section title is misplaced to the left of the page; see the following screenshot:  ### Your environment - IDE: RStudio 2023.06.0+441 - OS: Ubuntu 22.04 ### Quarto check output [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 1.3.361 Path: /opt/quarto/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.6 Path: /usr/bin/python3 Jupyter: (None) Jupyter is not available in this Python installation. Install with python3 -m pip install jupyter [✓] Checking R installation...........OK Version: 4.3.0 Path: /usr/lib/R LibPaths: - /home/nick/R/x86_64-pc-linux-gnu-library/4.3 - /usr/local/lib/R/site-library - /usr/lib/R/site-library - /usr/lib/R/library knitr: 1.42 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK

### Bug description Including subcabs in a multi-table layout produces cross-refs and well formatted tables. But omitting subcabs leaves the cross-ref unresolved *and* horizontal scroll-bars on the tables where there wasn't previously. ### Steps to reproduce ````qmd --- title: results format: html --- Refer to @tbl-fenced. ```{r} #| label: tbl-fenced #| tbl-cap: "Two tables" #| layout-ncol: 2 gt::gt(mtcars[1:10, ]) gt::gt(mtcars[11:19, ]) ``` ```` ### Expected behavior Multi-table layout should have a cross-ref even if it lacks `tbl-subcap`s and tables should not have horizontal scroll bars. ### Actual behavior The cross ref is not resolved, and the tables have horizontal scrollbars ### Your environment - Neovim 0.10 - Windows 10 (19044) ### Quarto check output ``` C:\Users\walki\Desktop>quarto check A new release of Deno is available: 1.28.2 → 1.34.3 Run `deno upgrade` to install it. [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.361 Path: C:\Users\walki\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.11.1 Path: C:/Users/walki/AppData/Local/Programs/Python/Python311/python.exe Jupyter: 5.3.0 Kernels: ir, python3 (-) Checking Jupyter engine render....0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.2.1 Path: C:/PROGRA~1/R/R-42~1.1 LibPaths: - C:/Users/walki/AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.1/library knitr: 1.42 rmarkdown: 2.21 [>] Checking Knitr engine render......OK ```

### Bug description Hello, In the HTML format, with simple callouts without titles, there is a blank space to the right of the icon and above the callout body text where a title would be:  Simple callouts without an icon and other types of callouts look as expected without titles. I've only looked at HTML so not sure if the same issue occurs in other formats. This appears to be new in the pre-release version (I'm using Quarto 1.4.275, the latest available as of this writing). With Quarto 1.3.361, that same callout looked like this:  Thanks very much! ### Steps to reproduce ````qmd --- format: html --- ::: {.callout-caution appearance="simple"} A simple callout with no title ::: Simple callouts without icons and other types of callouts look as expected without titles: ::: {.callout-caution appearance="simple" icon="false"} A simple callout with no title or icon ::: ::: {.callout-caution appearance="default"} A default callout with no title ::: ::: {.callout-caution appearance="minimal"} A minimal callout with no title ::: ::: {.callout-caution icon="false"} A default callout with no title or icon ::: ```` ### Expected behavior I expected the body text of the callout to appear beside the callout icon. ### Actual behavior The body text of the callout is below a blank space to the left of the icon where the callout title (if it were present) would be. ### Your environment - IDE: RStudio 2023.03.1 Build 446 - OS: Windows 10 Pro ### Quarto check output ```bash C:\Users\czippel\Documents>quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.4.151 Path: C:\Users\czippel\AppData\Local\Programs\Quarto\bin CodePage: unknown [>] Checking basic markdown render....OK [>] Checking Python 3 installation....(None) Unable to locate an installed version of Python 3. Install Python 3 from https://www.python.org/downloads/ [>] Checking R installation...........OK Version: 4.3.0 Path: C:/Users/czippel/AppData/Local/Programs/R/R-4.3.0 LibPaths: - C:/Users/czippel/AppData/Local/Programs/R/R-4.3.0/library knitr: 1.43 rmarkdown: 2.22 [>] Checking Knitr engine render......OK ```

### Feature description With the `_quarto.yml` file, different profiles can be created for, e.g., `proofing` and `production` versions of the same document. This is useful for parallel compilation, since builds of the two versions are independent. However, the `_variables.yml` file does not support the profile mechanism, meaning that if you have different variables for `proofing` and `production`, you still need to sequential compile runs. Proposed solution: make `_variables.yml` behave the same way as `_quarto.yml` w.r.t. the profile. ### Steps to reproduce _No response_ ### Expected behavior _No response_ ### Actual behavior _No response_ ### Your environment _No response_ ### Quarto check output _No response_

### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/5948 <div type='discussions-op-text'> ^{Originally posted by **uskovgs** June 16, 2023} ### Description Hi! I wanted to bring to your attention an error I noticed on your website, specifically in [Table 2](https://quarto.org/docs/authoring/tables.html#tbl-planet-measures) of the documentation. The Sun and the Moon are not classified as planets. The Sun is a star, while the Moon is Earth's natural satellite. Additionally, I have observed that the masses listed in the table are also incorrect. Errors have been fixed in the code below. ```python #| label: tbl-planet-measures #| tbl-cap: Planets from IPython.display import Markdown from tabulate import tabulate table = [["Sun",696000,1.989e30], ["Earth",6371,5.972e24], ["Moon",1737,7.34e22], ["Mars",3390,6.39e23]] Markdown(tabulate( table, headers=["Astronomical object","R (km)", "mass (kg)"] )) ``` </div>

### Bug description On Fedora 38, when setting `dev: svg` with the pdf format, the svg generated from rendering has size 0, and throws an error at the `rsvg-convert` step: ``` Error reading SVG test_files/figure-pdf/unnamed-chunk-1-1.svg: XML parse error: Input file is too short ERROR: Failed when attempting to convert a SVG to a PDF for output. An error occurred while attempting to run rsvg-convert. Error code 1 ``` The generated svg file in `_files/figure-pdf/unnamed-chunk-1-1.svg` is empty. ### Steps to reproduce test.qmd: ```` --- format: pdf --- ```{r} #| dev: svg plot(cars) ``` ```` ### Expected behavior Should generate a valid svg file, which is then converted to pdf and put in `_files/mediabag` ### Actual behavior Produces an empty svg file and an error. ### Your environment - IDE: NVim v0.10.0 - OS: Fedora 38 This does not occur on Ubuntu, and replicates on a clean Fedora installation. ### Quarto check output [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /home/wojtek/bin/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.3 Path: /usr/bin/python3 Jupyter: 5.3.0 Kernels: python3, octave, julia-1.9 (/) Checking Jupyter engine render....0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. 0.00s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.3.0 Path: /opt/R/4.3.0/lib64/R LibPaths: - /home/wojtek/R/x86_64-pc-linux-gnu-library/4.3 - /opt/R/4.3.0/lib64/R/library rmarkdown: 2.22 [✓] Checking Knitr engine render......OK

### Bug description `quarto render index.qmd --to pdf,html` fails with `ERROR: Unknown format pdf,html` - but [it seems that should work](https://stackoverflow.com/a/73256116). ### Steps to reproduce I suppose you could reproduce with any document, but try: ``` git clone https://github.com/matthew-brett/test-quarto cd test-quarto quarto render index.qmd --to pdf,html ``` ### Expected behavior Quarto should render the given document or directory to both PDF and HTML formats. ### Actual behavior ``` ERROR: Unknown format pdf,html Stack trace: at resolveFormats (file:///Users/mb312/dev_trees/quarto-cli/src/command/render/render-contexts.ts:591:13) at eventLoopTick (ext:core/01_core.js:181:11) at async renderContexts (file:///Users/mb312/dev_trees/quarto-cli/src/command/render/render-contexts.ts:231:19) at async Object.bookIncrementalRenderAll [as incrementalRenderAll] (file:///Users/mb312/dev_trees/quarto-cli/src/project/types/book/book-render.ts:646:22) at async renderProject (file:///Users/mb312/dev_trees/quarto-cli/src/command/render/project.ts:120:5) at async Command.fn (file:///Users/mb312/dev_trees/quarto-cli/src/command/render/cmd.ts:212:26) at async Command.execute (file:///Users/mb312/dev_trees/quarto-cli/src/vendor/deno.land/x/[email protected]/command/command.ts:1790:7) at async quarto (file:///Users/mb312/dev_trees/quarto-cli/src/quarto.ts:135:3) at async file:///Users/mb312/dev_trees/quarto-cli/src/quarto.ts:167:5 ``` ### Your environment Macos Ventura 13.4 Latest `quarto-cli` commit 1f3581304 ### Quarto check output ``` $ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Users/mb312/dev_trees/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.11 Path: /Users/mb312/.virtualenvs/resampling-with/bin/python3 Jupyter: 5.3.0 Kernels: python3, ir [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.3.0 Path: /opt/homebrew/Cellar/r/4.3.0_1/lib/R LibPaths: - /Users/mb312/Library/R/arm64/4.3/library - /opt/homebrew/lib/R/4.3/site-library - /opt/homebrew/Cellar/r/4.3.0_1/lib/R/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ```

### Bug description I have a book with a couple of prefaces : https://resampling-stats.github.io/resampling-with/python-book . I want the chapter numbers to start at the first chapter, so the preface pages are `.unnumbered`. I want one preface to crossreference the other, but the links are mislabeled in HTML, and fail to resolve in PDF. Is there a way of doing these crossreferences? See below for a minimal reproducer. ### Steps to reproduce ``` git clone https://github.com/matthew-brett/test-quarto cd test-quarto quarto render . --to html ``` In the HTML rendering you will see that the crossreferences to the unnumbered prefaces resolve correctly to the page, but get labeled with "Chapter 1" and "Chapter 2", although the contents give no number to the prefaces, and label the first (subsequent) chapter with 2. For PDF rendering: ``` quarto render . --to pdf ``` I get: ``` WARNING (/Users/mb312/dev_trees/quarto-cli/src/resources/filters/./crossref/refs.lua:110) Unable to resolve crossref @sec-pre1 WARNING (/Users/mb312/dev_trees/quarto-cli/src/resources/filters/./crossref/refs.lua:110) Unable to resolve crossref @sec-pre2 WARNING (/Users/mb312/dev_trees/quarto-cli/src/resources/filters/./crossref/refs.lua:110) Unable to resolve crossref @sec-pre2 WARNING (/Users/mb312/dev_trees/quarto-cli/src/resources/filters/./crossref/refs.lua:110) Unable to resolve crossref @sec-pre1 WARNING (/Users/mb312/dev_trees/quarto-cli/src/resources/filters/./crossref/refs.lua:110) Unable to resolve crossref @sec-pre1 ``` and indeed, the references to the preface unnumbered sections appear as e.g. `?@sec-pre1.` etc. ### Expected behavior The cross-references should resolve to the correct location rather than failing, in the PDF build. In both cases, the cross-reference label could be the unnumbered document title plus numbering or even section title, as in (in my reproducer) `Preface 2; section 1` or even `Preface 2; Preface 2 subsection`. ### Actual behavior See above. Cross-reference to unnumbered sections fails with warning in PDF build. In HTML build, cross-references point to the correct document and location, but as mislabeled with e.g. "Chapter 1" or "Chapter 2" when the contents give other documents as being chapter 1 and chapter 2. ### Your environment Macos Ventura 12.4 Latest quarto-cli commit 1f3581304 ### Quarto check output ``` $ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Users/mb312/dev_trees/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.10.11 Path: /Users/mb312/.virtualenvs/resampling-with/bin/python3 Jupyter: 5.3.0 Kernels: python3, ir [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.3.0 Path: /opt/homebrew/Cellar/r/4.3.0_1/lib/R LibPaths: - /Users/mb312/Library/R/arm64/4.3/library - /opt/homebrew/lib/R/4.3/site-library - /opt/homebrew/Cellar/r/4.3.0_1/lib/R/library knitr: 1.42 rmarkdown: 2.21 [✓] Checking Knitr engine render......OK ```

```markdown --- title: Test including figure in docx format: html keep-md: true --- {#fig-elephant width=650} ``` (`elephant.png` is from our website, but any image will cause issue) `quarto render` on this doc, and process is stuck at ````powershell > quarto render test2.qmd Quarto version: 99.9.9 Loaded deno-dom-native Windows: Using code page 1252 pandoc --verbose --trace to: html output-file: test2.html standalone: true section-divs: true html-math-method: mathjax wrap: none default-image-extension: png metadata document-css: false link-citations: true date-format: long lang: en title: Test including figure in docx [INFO] Loaded C:\Users\chris\AppData\Local\Temp\quarto-session378b8c77\17dd0693\0dc0abb2\template.patched from C:\Users\chris\AppData\Local\Temp\quarto-session378b8c77\17dd0693\0dc0abb2\template.patched [INFO] Loaded C:\Users\chris\AppData\Local\Temp\quarto-session378b8c77\17dd0693\0dc0abb2\metadata.html from C:\Users\chris\AppData\Local\Temp\quarto-session378b8c77\17dd0693\0dc0abb2\metadata.html [INFO] Loaded C:\Users\chris\AppData\Local\Temp\quarto-session378b8c77\17dd0693\0dc0abb2\styles.html from C:\Users\chris\AppData\Local\Temp\quarto-session378b8c77\17dd0693\0dc0abb2\styles.html [INFO] Loaded C:\Users\chris\AppData\Local\Temp\quarto-session378b8c77\17dd0693\0dc0abb2\title-block.html from C:\Users\chris\AppData\Local\Temp\quarto-session378b8c77\17dd0693\0dc0abb2\title-block.html [INFO] Loaded C:\Users\chris\AppData\Local\Temp\quarto-session378b8c77\17dd0693\0dc0abb2\title-metadata.html from C:\Users\chris\AppData\Local\Temp\quarto-session378b8c77\17dd0693\0dc0abb2\title-metadata.html [INFO] Loaded C:\Users\chris\AppData\Local\Temp\quarto-session378b8c77\17dd0693\0dc0abb2\title-block.html from C:\Users\chris\AppData\Local\Temp\quarto-session378b8c77\17dd0693\0dc0abb2\title-block.html [INFO] Loaded C:\Users\chris\AppData\Local\Temp\quarto-session378b8c77\17dd0693\0dc0abb2\title-metadata.html from C:\Users\chris\AppData\Local\Temp\quarto-session378b8c77\17dd0693\0dc0abb2\title-metadata.html [INFO] Loaded C:\Users\chris\AppData\Local\Temp\quarto-session378b8c77\17dd0693\0dc0abb2\toc.html from C:\Users\chris\AppData\Local\Temp\quarto-session378b8c77\17dd0693\0dc0abb2\toc.html [trace] Parsed [Plain [Str "long"]] at line 1 [trace] Parsed [Plain [Str "en"]] at line 1 [trace] Parsed [Plain [Str "true"]] at line 1 [trace] Parsed [Plain [Str "99.9.9"]] at line 1 [trace] Parsed [Plain [Str "Test",Space,Str "including",Space,Str "figure", at line 1 [trace] Parsed [Plain [Str "Table",Space,Str "of",Space,Str "contents"]] at line 1 [trace] Parsed [] at line 5 [trace] Parsed [Figure ("fig-elephant",[],[]) (Caption Nothing [Plain [Str at line 8 [INFO] Running filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/main.lua [INFO] Completed filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/main.lua in 46 ms ^CTerminer le programme de commandes (O/N) ? O ```` Took me sometime to find as I tried a few things. * Trying to use the tracing feature gave me the hint of infinite loop as the trace created is more than 2 Gb (!!) * I ended up running a git bisect to find where it happens, to understand why. Culprit is https://github.com/quarto-dev/quarto-cli/commit/553fec5f3c421a8c0e9a533ef47d76c6f002e437#diff-a86a3d2ddd41304881ed9f8418b10f3e960315213da5cf51b76a687c88ef1e50R53 (👋 @dragonstyle ) Running a debug mode in VSCODE showed me the difference in here https://github.com/quarto-dev/quarto-cli/blob/1f3581304d2d1112ae22cd970e7c176d8be15600/src/core/path.ts#L275-L276 we were looking for `expandGlobs("elephant.png")` but after the commit, we are looking for `expandGlobs("**\elephant.png")` The difference is small in the commit but the strict mode was removed https://github.com/quarto-dev/quarto-cli/blob/9402ca9ad15b8c693fcc2c7691df3becb3d3631e/src/command/render/resources.ts#L54-L56 So this mode was setting smartGlob to FALSE https://github.com/quarto-dev/quarto-cli/blob/1f3581304d2d1112ae22cd970e7c176d8be15600/src/core/path.ts#L209-L226 but now, it is set to TRUE and we end up going into any `if(smartGlob)` Hope it makes it clear. I can detail more and show what happens. @dragonstyle any insight why remove the strict mode and then change the smartGlob value ? It does not explain the infinite loop but it is related to ``` expandGlobs("**\elephant.png") ``` on Windows

### Bug description I'm creating an article in Quarto and using the `section-title-footnotes:` option in YAML to change the default "Footnotes" title to "References". This customisation works as intended in the Quarto preview on my local machine using VSCode, but when deployed to live site (using GH Actions and GH Pages) the "Footnotes" title reverts to the default. ### Steps to reproduce Truncated version of article follows: ````qmd --- title: "The road to reproducible research: hazards to avoid and tools to get you there safely" description: | The road to reproducibility can be a tricky one to navigate, as Davit Svanidze discovered when he set about making his bachelor's thesis reproducible. If you are thinking of walking a similar path, start here. In this case study, Svanidze and colleagues map their journey, beginning to end -- signposting hazards to avoid and software, tools, and approaches to help you along the way. categories: - Deep learning - Reproducibility - Coding - Collaboration author: Davit Svanidze, Andre Python, et al. date: 06/15/2023 toc: true image: images/computer-intro.png image-alt: A young man sits in front of a computer keyboard, surrounded by monitors and books and with computer cables covering various surfaces. section-title-footnotes: References --- ## Davit’s journey towards reproducibility ### More power, please The focus of my bachelor's thesis was to better understand the initial spread of Covid-19 in China using deep learning algorithms. I was keen to make my work reproducible, but not only for my own sake. The "reproducibility crisis" is a well-documented problem in science as a whole,[^1] [^2] [^3] [^4] with studies suggesting that around one-third of social science studies published between the years 2010 and 2015 in top journals like *Nature* and *Science* could not be reproduced.[^5] Results that cannot be reproduced are not necessarily “wrong”. But, if findings cannot be reproduced, we cannot be sure of their validity. [^1]: Peng, Roger D. 2011. "Reproducible Research in Computational Science." *Science* 334 (6060): 1226--1227. [^2]: Ioannidis, John P. A., Sander Greenland, Mark A. Hlatky, Muin J. Khoury, Malcolm R. Macleod, David Moher, Kenneth F. Schulz, and Robert Tibshirani. 2014. "Increasing Value and Reducing Waste in Research Design, Conduct, and Analysis." *The Lancet* 383 (9912): 166--175. [^3]: Open Science Collaboration. 2015. "Estimating the Reproducibility of Psychological Science." *Science* 349 (6251): aac4716. [^4]: Baker, Monya. 2016. "Reproducibility Crisis?" *Nature* 533 (26): 353--366. [^5]: Camerer, Colin F., Anna Dreber, Felix Holzmeister, Teck-Hua Ho, Jürgen Huber, Magnus Johannesson, Michael Kirchler, Gideon Nave, Brian A. Nosek, Thomas Pfeiffer, *et al*. 2018. "Evaluating the Replicability of Social Science Experiments in *Nature* and *Science* between 2010 and 2015." *Nature Human Behaviour* 2: 637--644. ```` ### Expected behavior  ### Actual behavior  Live version here: https://realworlddatascience.net/case-studies/posts/2023/06/15/road-to-reproducible-research.html ### Your environment - IDE: VSCode, 1.79.1 - OS: Windows 10 Home, version 22H2, OS build 19045.3086 ### Quarto check output ```bash [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.1: OK Dart Sass version 1.55.0: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.3.319 Path: C:\Users\...\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.10.5 Path: C:/Users/btarr/AppData/Local/Programs/Python/Python310/python.exe Jupyter: 4.10.0 Kernels: python3 [>] Checking Jupyter engine render....OK [>] Checking R installation...........OK Version: 4.2.3 Path: C:/PROGRA~1/R/R-42~1.3 LibPaths: - C:/Users/.../AppData/Local/R/win-library/4.2 - C:/Program Files/R/R-4.2.3/library knitr: 1.42 rmarkdown: 2.20 [>] Checking Knitr engine render......OK ```

### Bug description ``` Quitting from lines 101-107 [XYZ] (xyz.qmd) Error in `add_html_caption()`: ! unbenutztes Argument (xfun::grep_sub("^[^<]*<[^>]+aria-labelledby[ ]*=[ ]*\"([^\"]+)\".*$", "\\1", x)) Backtrace: 1. global .main() 2. execute(...) 3. rmarkdown::render(...) 4. knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 5. knitr:::process_file(text, output) ... 14. sew(res, options) 15. knitr:::sew.list(x, options, ...) 16. base::lapply(x, sew, options, ...) 17. FUN(X[[i]], ...) 18. knitr:::sew.knit_asis(x, options, ...) Ausführung angehalten Fehler in close_connection() : konnte Funktion "close_connection" nicht finden Ruft auf: <Anonymous> -> <Anonymous> ``` ### Steps to reproduce I got a simple html document with knnitr engine (under R). There is this code block that does not render: ``` {r} #| label: "XYZ" #| include: true #| echo: true library(plotly) plot_ly(economics, x = ~pop) ``` ### Expected behavior Should render properly. ### Actual behavior _No response_ ### Your environment ``` R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so; LAPACK version 3.8.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 LC_MONETARY=de_DE.UTF-8 [6] LC_MESSAGES=de_DE.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C time zone: Europe/Berlin tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices datasets utils methods base loaded via a namespace (and not attached): [1] vctrs_0.6.2 knitr_1.43 httr_1.4.6 cli_3.6.1 xfun_0.39 rlang_1.1.1 purrr_1.0.1 [8] renv_0.17.3 generics_0.1.3 jsonlite_1.8.5 data.table_1.14.8 glue_1.6.2 colorspace_2.1-0 htmltools_0.5.5 [15] scales_1.2.1 fansi_1.0.4 grid_4.3.0 munsell_0.5.0 tibble_3.2.1 fastmap_1.1.1 yaml_2.3.7 [22] lifecycle_1.0.3 compiler_4.3.0 dplyr_1.1.2 htmlwidgets_1.6.2 pkgconfig_2.0.3 tidyr_1.3.0 rstudioapi_0.14 [29] plotly_4.10.2 digest_0.6.31 viridisLite_0.4.2 R6_2.5.1 tidyselect_1.2.0 utf8_1.2.3 pillar_1.9.0 [36] magrittr_2.0.3 tools_4.3.0 gtable_0.3.3 lazyeval_0.2.2 ggplot2_3.4.2 ``` ### Quarto check output _No response_

### Bug description Dropbox URL is change from June 2023. Please someone tell me how to embed the video to website. This is the link. https://www.dropbox.com/scl/fi/4vrzdjnk7i0wuihl3pzud/Video.mp4?dl=0&rlkey=6ckf190r0jiljtnech4bym1b0 ### Steps to reproduce - Upload a video to dropbox - Copy the Share URL `https://www.dropbox.com/s/s7cffdll62ojsy1/local-video.mp4?dl=0` - Use the video shortcode to load this mp4 via VideoJS `{{< video https://www.dropbox.com/s/s7cffdll62ojsy1/local-video.mp4?dl=0 >}}` ### Expected behavior - As before the video loads via the VideoJS snippet. ### Actual behavior - The video doesn't load and shows a `The media could not be loaded, either because the server or network failed or because the format is not supported.` error. ### Your environment Mac ### Quarto check output ``` ❯ quarto check [✓] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [✓] Checking versions of quarto dependencies......OK [✓] Checking Quarto installation......OK Version: 99.9.9 Path: /Users/amanning/projects/github/quarto/quarto-cli/package/dist/bin [✓] Checking basic markdown render....OK [✓] Checking Python 3 installation....OK Version: 3.11.2 Path: /Library/Frameworks/Python.framework/Versions/3.11/bin/python3 Jupyter: 5.2.0 Kernels: julia-1.8, julia-1.7, python3 [✓] Checking Jupyter engine render....OK [✓] Checking R installation...........OK Version: 4.2.1 Path: /Library/Frameworks/R.framework/Resources LibPaths: - /Library/Frameworks/R.framework/Versions/4.2/Resources/library knitr: 1.42 rmarkdown: 2.20 [✓] Checking Knitr engine render......OK ```

### Bug description Hi there, I noticed that my Quarto site's name is wrong in Google search results. The site name is circled here in green:  ### Steps to reproduce When I google for things on the Shiny website, which has a site name of "Shiny," sometimes it says "Shiny app" or "R Shiny," which is especially disappointing because its real name is "Shiny for R." Here is a Google result for "shiny posit" <img width="741" alt="Screenshot 2023-06-14 at 4 44 22 PM" src="https://github.com/quarto-dev/quarto-cli/assets/5993637/68ed757f-2ad8-4fc4-91a4-6d612e638969"> ### Expected behavior That site name on Google should just be "Shiny". The [Open Graph](https://ogp.me/#optional) website says the meta property should be: `<meta property="og:site_name" content="Shiny">` ### Actual behavior What Quarto creates from the _quarto.yml file is: `<meta property="og:site-name" content="Shiny">` I think this might be as simple as changing the dash in "og:site-name" to and underscore "og:site_name" ### Your environment _No response_ ### Quarto check output _No response_

### Bug description When rendering a book project to html `quarto render --to html`, the search bar seems to yield no results.  When previewing the book project `quarto preview`, the search bar does show results.  ### Steps to reproduce In `RStudio`: `New Project...` > `New Directory` > `Quarto Book` > testbook > `Create Project` Then, render the document using `quarto render --to html`. Open the index.html file and typing 's' for example leads to no results. Preview the document using `quarto preview`. In the browser, typing 's' does show results. ### Expected behavior Results should show in both cases. ### Actual behavior No results whatsoever for a rendered .html file. ### Your environment - IDE: RStudio 2023.06.0+421 - OS: Windows 10 64 bit ### Quarto check output ```bash $ quarto check [>] Checking versions of quarto binary dependencies... Pandoc version 3.1.2: OK Dart Sass version 1.55.0: OK Deno version 1.33.2: OK [>] Checking versions of quarto dependencies......OK [>] Checking Quarto installation......OK Version: 1.4.146 Path: C:\Users\Li Yong\AppData\Local\Programs\Quarto\bin CodePage: 1252 [>] Checking basic markdown render....OK [>] Checking Python 3 installation....OK Version: 3.11.4 Path: C:/Users/Li Yong/AppData/Local/Programs/Python/Python311/python.exe Jupyter: (None) Jupyter is not available in this Python installation. Install with py -m pip install jupyter [>] Checking R installation...........OK Version: 4.1.0 Path: C:/PROGRA~1/R/R-41~1.0 LibPaths: - E:/Documenten/R/win-library/4.1 - C:/Program Files/R/R-4.1.0/library knitr: 1.39 rmarkdown: 2.14 [>] Checking Knitr engine render......OK ```

I have seen this  `book` and `manuscript` should be separated. right ? We probably have something in our YAML schema...

We have this in _bootstrap-rules.scss ```scss .table > thead { border-top-width: 1px; border-top-color: $table-border-color; border-bottom: 1px solid $table-group-separator-color; } ``` But because (I think?) the declaration for `$table-group-separator-color` has `!default` in it in `_variables.scss`: ```scss $table-group-separator-color: currentColor !default; ``` ... this causes our resulting CSS to be invalid: <img width="495" alt="image" src="https://github.com/quarto-dev/quarto-cli/assets/285675/a3a477b0-d6d5-4f08-8de8-e94256c52560">