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|---|---|
### Bug description
I installed Quarto on Fedora 37 through the tar archive, for any version >=1.2.
When trying to run quarto, e.g. `quarto check` I end up having this error:
```
tcc: error: mprotect failed: did you mean to configure --with-selinux?
```
Quarto works perfectly with version 1.1.251
I don't really know where to start to track where the issue is coming from. | {
"assignee": null,
"comments": 10,
"created_at": "2022-10-24T20:07:03Z",
"creator": "alxsimon",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 3012,
"state": "closed",
"title": "Fedora error with version >=1.2",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3012"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3009
<div type='discussions-op-text'>
<sup>Originally posted by **kbvernon** October 24, 2022</sup>
Is there a way to specify the image title and alt text in the yaml of an about page? The documentation for the about page suggests you can only change image width and shape, but maybe there's information somewhere else about working with images linked in the yaml?
Thanks!</div> | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-10-24T19:33:46Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3010,
"state": "closed",
"title": "Support image-alt / title in about pages",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3010"
} |
### Bug description
Os: Ubuntu 22.04
VScode: 1.72.2
Quarto: 1.1.251
Quarto VScode extension: v1.50.0
Plotly graph shows inside Jupyter Notebook in VSCode, but it does not show in slides when rendering with quarto. - Note: sometimes it shows in slides but not consistent.
[plotly_graphs_jupyter.zip](https://github.com/quarto-dev/quarto-cli/files/9853298/plotly_graphs_jupyter.zip)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-10-24T16:20:00Z",
"creator": "rleyvasal",
"is_pull_request": false,
"labels": [
"jupyter"
],
"locked": false,
"milestone": "v1.3",
"number": 3006,
"state": "closed",
"title": "Plotly output from jupyter notebook not showing on slides VScode + Jupyter + Python + Revealjs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3006"
} |
See complete thread for details, but basically markdown like
```markdown
---
## Test 123
```
creates problems for us in `yaml.ts` `export function readYamlFromMarkdown()`
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3001
<div type='discussions-op-text'>
<sup>Originally posted by **samarzayan** October 24, 2022</sup>
I am getting the following error exactly at the last `:`.
`YAMLError: end of the stream or a document separator is expected at line 7, column 3:`
when I use every callout block, for example:
`:::{.callout-note}`
`Sample note.`
`:::`
I checked online for about 2 hours but had no luck. Someone, please help.
The syntax is correct as per the Quarto [docs](https://quarto.org/docs/authoring/callouts.html).</div> | {
"assignee": "cscheid",
"comments": 4,
"created_at": "2022-10-24T14:07:43Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"enhancement",
"lint"
],
"locked": false,
"milestone": "v1.4",
"number": 3004,
"state": "open",
"title": "Error parsing `---` without whitespace",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3004"
} |
### Bug description
When adding and setting the references and footnotes to be located on the margin within a callout fenced divs, the layout is not longer respected and the divs takes the whole width.
````
---
format: html
reference-location: margin
---
:::{.callout}
Something
:::
:::{.callout}
Something^[Something in the margin]
:::
:::{.callout}
Something[^1]
:::
[^1]: Something in the margin
::::{.callout}
Something
:::{.aside}
Simply something aside for reference
:::
::::
````
<img width="1624" alt="image" src="https://user-images.githubusercontent.com/8896044/197538051-8399e417-3202-456b-9b4e-c713e2345ccb.png">
---
System:
- OS: MacOS Monterey (Apple Silicon)
- IDE: VSCode
- Quarto: v1.2.237
| {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-10-24T13:34:33Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3003,
"state": "closed",
"title": "Margin footnotes/references in callout messes the page layout",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3003"
} |
### Bug description
In order to work around some `hyperref` option issues that exist with using `citeproc` I started to use `natbib` as the latex engine, as per discussion in #2017.
I've just noticed a side-effect of this change now: `natbib` creates a Bibliography section at the end of the document regardless of the placement of the following .qmd references file:
```
# References {.unnumbered}
::: {#refs}
:::
```
In my case, I had placed some appendices after the reference section but when I use `natbib` I get a blank references page, then appendices and then a bibliography section. The HTML output follows the .yml specification, as does the pdf when using the default `citeproc` but the natbib creates it own section.
I don't mind the references/bibliography getting shifted to the end, but the blank references page and use of bibliography instead of reference creates an inconsistency with the HTML version.
I'm not sure if this is a bug or a feature of `natbib` that requires some additional parameters being set in the yaml file.
I'm using window on my computer but the GitLab Pages instance is built in Linux and this happens in both cases. I'm using the latest `quarto` version (1.2.237).
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-10-24T11:20:16Z",
"creator": "jpmorr",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3002,
"state": "closed",
"title": "Using natbib as cite-method creates bibliography at end of document and not at specified location",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3002"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2990
<div type='discussions-op-text'>
<sup>Originally posted by **mcanouil** October 23, 2022</sup>
Hi,
currently, the grid listing has a default height of 150px for top image in the card which causes the image to be "cropped" in nearly all situations.
Instead, I would suggest to not set `height` property but`max-height` to allow responsive scaling of the image without cropping the image.
For example, on the left, manually defined max-height, while on the right it's the default from the grid listing.
<img width="741" alt="Screenshot of a grid listing made with quarto using a three columns layout and showing two cards. On the left a card with an image properly scaled without cropping and on the right a image vertically cropped due to css height property set to 150 pixels" src="https://user-images.githubusercontent.com/8896044/197394786-d40b57a1-bad5-456c-bd76-8c523765f329.png">
A video to show the resizing issue of setting `height`.
https://user-images.githubusercontent.com/8896044/197395474-62bf6851-1f4e-47bc-8f8c-0b067c1e79f4.mov
</div> | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-10-23T20:24:05Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.4",
"number": 2999,
"state": "open",
"title": "Replace default `height` for \"banner image\" in grid listing by `max-height`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2999"
} |
### Bug description
Let me begin by thanking you for the very fine work with RStudio, RMarkdown, and now Quarto. I was using Tex Live with no issues up until 2016, and am now returning to writing documents. I decided to reinstall R, RStudio, and use TinyTex.
Current Windows Operating System: **Windows 10 Pro Version 21H2**
After installing **Rstudio 2022.07.02 Build 576** and beginning my transition to Quarto, I discovered that TinyTex will not install properly on my Windows 10 computer. It appears almost certain that the problem is related to a space in the Windows username, "James Nash".
Below is the code that appears in the Quarto terminal window. As you can see, the installation process misinterprets the path,
chopping it at the space in the username "James Nash." As a result, TinyTex installation fails, and I've been unable to implement the ability to compile to pdf format. I searched for documentation about TinyTex installation issues, but could find nothing.
Can you fix this, or suggest a workaround? Since Windows supports (almost encourages) user names with spaces, this problem will recur. Many thanks,
### Quarto Terminal Record
```Microsoft Windows [Version 10.0.19044.2130]
(c) Microsoft Corporation. All rights reserved.
C:\Users\James Nash\Documents>quarto install tool tinytex
Installing tinytex
[>] Downloading TinyTex v2022.10
(-) Unzipping TinyTeX-v2022.10.zipExpand-Archive : A positional parameter cannot be found that accepts argument
'Nash\AppData\Local\Temp\50c9640e\TinyTeX-v2022.10.zip'.**
At line:1 char:1
+ Expand-Archive C:\Users\James Nash\AppData\Local\Temp\50c9640e\Tin ...
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ CategoryInfo : InvalidArgument: (:) [Expand-Archive], ParameterBindingException
+ FullyQualifiedErrorId : PositionalParameterNotFound,Expand-Archive
[>] Unzipping TinyTeX-v2022.10.zip
[>] Moving files
ERROR: NotFound: The system cannot find the file specified. (os error 2), stat 'C:\Users\James Nash\AppData\Local\Temp\50c9640e\TinyTeX'
C:\Users\James Nash\Documents>quarto tools list
[>] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.10
C:\Users\James Nash\Documents>
```
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-10-23T19:21:12Z",
"creator": "JimInNashville",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2998,
"state": "closed",
"title": "Quarto TinyTex installation fails due to space in Windows username",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2998"
} |
### Bug description
Hi,
the default style of a 1️⃣ markdown table is not the same of 2️⃣ the one generated by code.
I think they should have the same style. Moreover I prefer the code table one.
I'm using quarto 1.2.226.
Distributor ID: Debian
Description: Pengwin
Release: 11
Codename: bullseye
Here a sample code: https://gist.github.com/aborruso/47aa44e894b942d8303abdaad3679674
Thank you
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 15,
"created_at": "2022-10-23T17:10:28Z",
"creator": "aborruso",
"is_pull_request": false,
"labels": [
"documentation",
"enhancement"
],
"locked": false,
"milestone": "v1.3",
"number": 2997,
"state": "closed",
"title": "table default style: not the same for markdown tables and code tables",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2997"
} |
### Bug description
Hi,
First, thanks for this awesome Quarto!
I am trying to render a quarto document containing gt tables and have an issue.
The document does not render if the .qmd file is located in a subdirectory of my project directory (with option execute-dir: project). The document renders well without the gt table or if the document is located at the root of the project directory.
The error is:
Quitting from lines 29-31 (test.qmd)
Error in readLines(con, warn = FALSE) : cannot open the connection
Calls: .main ... -> enumerate_output_formats -> read_utf8 -> readLines
Any idea?
Running Rstudio 2022.07.2 on Windows.
Thanks,
Thomas.
Here is a small code to reproduce:
````
---
title: "Untitled"
format: html
editor: visual
---
## Quarto
Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
## Running Code
When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this:
```{r}
library(gt)
gt(airquality)
```
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 6,
"created_at": "2022-10-23T16:41:21Z",
"creator": "tdemarchin",
"is_pull_request": false,
"labels": [
"bug",
"tables"
],
"locked": false,
"milestone": "v1.2",
"number": 2996,
"state": "closed",
"title": " Rstudio: Quarto file within a subdirectory and gt tables not rendering",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2996"
} |
### Bug description
Hi,
I am trying to create a blog deployed by GitHub Pages. However, the process [you are describing](https://quarto.org/docs/publishing/github-pages.html) is failing when I try to run the `quarto publish` command
Here is what I get in my terminal:
My repo is hosted in this link: https://github.com/msh855/TheQuantEconomist
As a side note, the way I created the `ph-pages` branch is by just creating a new branch from the `main` branch as the documentation on your website was not very clear on how to create `gh-page` branch.
I am using Mac, if this helps. | {
"assignee": null,
"comments": 4,
"created_at": "2022-10-23T16:08:44Z",
"creator": "msh855",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "Future",
"number": 2994,
"state": "open",
"title": "Publish command does not work and authentication fails ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2994"
} |
In reveal.js presentations, the menu item for the PDF Export tool triggers the overview mode rather than a PDF export.
Looking at what I believe is the respective code, it appears to be a simple oversight and probably straightforward to fix:
https://github.com/quarto-dev/quarto-cli/blob/7cc0ced8c9d62a8bc6a3ed8863160f90729b77bf/src/format/reveal/format-reveal-plugin.ts#L438-L442
Weirdly, though, the key binding "e" still works as expected. | {
"assignee": "cderv",
"comments": 10,
"created_at": "2022-10-23T09:29:24Z",
"creator": "awehrfritz",
"is_pull_request": false,
"labels": [
"bug",
"revealjs"
],
"locked": false,
"milestone": "v1.3",
"number": 2988,
"state": "closed",
"title": "Reveal.js PDF Export menu item is broken",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2988"
} |
### Bug description
When I use the `standalone` and `embed-resources` YAML options, Quarto still returns the following warning:
```
[WARNING] Deprecated: --self-contained. use --embed-resources --standalone
```
## Example
````
---
title: "standalone_bug"
format:
html:
standalone: true
embed-resources: true
---
```{r}
1+1
```
````
### Rendering output
```
❯ quarto render standalone_bug.qmd
processing file: standalone_bug.qmd
|....................... | 33%
ordinary text without R code
|............................................... | 67%
label: unnamed-chunk-1
|......................................................................| 100%
ordinary text without R code
output file: standalone_bug.knit.md
pandoc
to: html
output-file: standalone_bug.html
standalone: true
embed-resources: 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: standalone_bug
[WARNING] Deprecated: --self-contained. use --embed-resources --standalone
Output created: standalone_bug.html
```
## System Info
### OS Info
Mac OS Monterey (12.6)
### Quarto Version
```
❯ quarto -V
1.1.251
```
### R Version
```
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-10-22T16:28:14Z",
"creator": "maxdrohde",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2981,
"state": "closed",
"title": "Warning for `--self-contained` when using `--embed-resources --standalone`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2981"
} |
### Bug description
Quarto apparently requires Chrome or Chromium to render graphviz documents, but on Pop_OS 22.04, chromium is only available through flatpak. The search method in puppeteer.ts#findChrome don't find the flatpak installation.
Steps to reproduce (Debian Linux assumed):
1) Uninstall Chrome/Chromium installed through deb package or `quarto tools install chromium` (this should remove `chromium-browser` from the path.
2) Install chromium using `flatpak install org.chromium.Chromium` (note, run this as user, not root).
3) Verify that chromium runs by executing `flatpak run org.chromium.Chromium`
4) Attempt to use quarto to render `foo.qmd` (attached). This will generate the error.
[foo.qmd.txt](https://github.com/quarto-dev/quarto-cli/files/9844787/foo.qmd.txt)
I'm getting this error with RStudio 2022.07.0+548 "Spotted Wakerobin" Release (34ea3031089fa4e38738a9256d6fa6d70629c822, 2022-07-06) for Ubuntu Jammy
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36 and quarto version 1.0.37
Some quick tests with my machine verify that the command `flatpak info org.chromium.Chromium` can be used to test that chromium is installed using flatpak (and `which flatpak` can be used to test for flatpak. The info command will return an error if chromium is not installed.
If it is installed, it can be launched using `flatpak run org.chromium.Chromium ...` where ... are the usual command line arguments.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 5,
"created_at": "2022-10-22T16:13:44Z",
"creator": "ralmond",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 2980,
"state": "open",
"title": "Quarto deos not find chromium if installed through flatpak",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2980"
} |
### Bug description
## Example 1
````
---
title: "syntax_highlighting_bug"
format:
html:
code-link: false
---
```{r}
f <- function(x){
y <- 1+2+3
z <- (x+y)^2
return(z)
}
```
````
### Output
<img width="872" alt="Screen Shot 2022-10-22 at 10 47 18" src="https://user-images.githubusercontent.com/25734232/197348603-509c9933-2ec6-41b5-9ed4-87724e6f23ed.png">
## Example 2
````
---
title: "syntax_highlighting_bug"
format:
html:
code-link: true
---
```{r}
f <- function(x){
y <- 1+2+3
z <- (x+y)^2
return(z)
}
```
````
### Output
<img width="869" alt="Screen Shot 2022-10-22 at 10 47 31" src="https://user-images.githubusercontent.com/25734232/197348595-f6281796-7cd1-4158-a505-726de2001cdc.png">
## System Info
RStudio 2022.07.2+576 "Spotted Wakerobin" Release (e7373ef832b49b2a9b88162cfe7eac5f22c40b34, 2022-09-06) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 12_6_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
```
❯ quarto -V
1.1.251
```
R version 4.0.5 Patched (2021-06-20 r80990) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-10-22T15:49:21Z",
"creator": "maxdrohde",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2979,
"state": "closed",
"title": "`code-link: true` option removes syntax highlighting",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2979"
} |
### Bug description
I'm using Chrome beta Version 107.0.5304.36 in Debian Linux 12 (testing).
Here's a screenshot of the Getting Started page that I see:
Here's what I see after I click the "Install Quarto" button with a mysterious underscore:
I found a "Download Quarto" page through Google, which also features an undescore button which doesn't go anywhere.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 4,
"created_at": "2022-10-22T12:37:11Z",
"creator": "sswam",
"is_pull_request": false,
"labels": [
"bug",
"documentation"
],
"locked": false,
"milestone": "v1.2",
"number": 2977,
"state": "closed",
"title": "Get Started page, Step 1, Install Quarto button is not working, in Chrome on Debian Linux 12 (testing)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2977"
} |
### Bug description
From @muellerzr and @jph00:
Quarto isn't rendering Mermaid graphs when in a notebook that also uses fastprogress:
In a markdown cell:
```
{mermaid}
flowchart TD
A[Gather Data] --> B[Clean Data]
B --> C[Build `DataLoaders`]
C ==> D[Build a `Learner`]
D ==> E[Train with modern best practices]
E ==> F[Deploy]
F --> A
E ==> C
```
In a code cell (& execute it):
```
from fastprogress.fastprogress import master_bar, progress_bar
mbar = master_bar(list(range(5)))
for i in mbar:
mbar.write([f'Entry {i}', f'Value: {i+1}'], table=True)
```
The error message is:
```
Uncaught ReferenceError: mermaid is not defined
<anonymous> http://localhost:3000/site_libs/quarto-diagram/mermaid-init.js:21
```
Notebook which exhibits this issue on quarto render/preview: https://gist.github.com/muellerzr/2b2384041115d941ca9ec3a9fcf0fd03
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-10-22T10:48:35Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2974,
"state": "closed",
"title": "mermaid not defined error when ipywidgets are present",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2974"
} |
### Bug description
I am attempting to pass a YAML file of execution parameters via the command line option `--execute-params`:
`test.qmd` file:
```
---
title: test
date: now
format: pdf
---
Test document.
```
`test.yml` file:
```
date-format: MMM DD, YYYY HH:mm:ss z
```
Command line:
```
quarto render test.qmd --execute-params test.yml
```
Using this command, I would expect the date to be formatted in the manner specified in the YAML file, but the rendered file uses the default long format. Am I using the command line argument incorrectly, or is there an issue here?
Running macOS version 12.6, and Quarto version 1.1.179.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 6,
"created_at": "2022-10-22T03:12:06Z",
"creator": "connorp",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2971,
"state": "closed",
"title": "Specifying YAML files via the command line",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2971"
} |
### Bug description
Os: Ubuntu 22.04
VScode: 1.72.2
Quarto: 1.1.251
Quarto VScode extension: v1.50.0
`render-on-save: true` on yaml header does not work consistently. Only the first time the notebook is saved with `Ctrl+s` the notebook renders, but as soon as a new cell is added to the notebook and `Ctrl+s` used again, rendering does not work.
# Steps to reproduce
1. Open notebook
2. Ctrl+S - renders the slides without issue
3. Click on yaml header
4. Press keyboard key 'b' - adds empty header below the yaml header
5. Ctrl+S - does not render the slides
# Screenshot of empty cell added below yaml header
# Reproducible example
[slides_quarto_sample_render_on_save.zip](https://github.com/quarto-dev/quarto-cli/files/9840965/slides_quarto_sample_render_on_save.zip)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 10,
"created_at": "2022-10-21T16:59:33Z",
"creator": "rleyvasal",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2967,
"state": "closed",
"title": "`render-on-save: true` does not consistently work VScode + Jupyter + Python + Revealjs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2967"
} |
The bug reported [here](https://github.com/quarto-ext/fontawesome/issues/7) is a quarto bug.
If a snippet of a page gets "transplanted" to a different page because of a listing, then shortcode dependencies that are induced by that snippet need to be carried to the listing page. In this case, it's the `fontawesome` shortcode, but that problem will come up more generally.
We're probably detecting the shortcodes "too early" in the process, before the snippets are included, and so we're missing the snippet contents. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-10-21T15:28:17Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 2966,
"state": "open",
"title": "cross-page shortcode dependencies",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2966"
} |
According to the documentation, Quarto provides format strings for week (W, WW) and year (GGGG) in the ISO year calendar. However, it only provides numeric day strings with Sunday being 0 (d), whereas the ISO week begins with Monday=1 and ends with Sunday=7. It appears one cannot format a proper ISO week date such as 2022-W42-5. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-10-21T12:59:55Z",
"creator": "wiedenhoeft",
"is_pull_request": false,
"labels": [
"enhancement",
"upstream"
],
"locked": false,
"milestone": "v1.4",
"number": 2970,
"state": "open",
"title": "No ISO day",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2970"
} |
### Bug description
Content of tabsets cannot be displayed in rendered Jupyter notebook with python code.
Os: Ubuntu 22.04
VScode: 1.72.2
Quarto: 1.1.251
Quarto VScode extension: v1.50.0
# Code
yaml header in notebook (first cell in raw format):
```yaml
---
title: "Jupyter notebook render"
format:
revealjs:
incremental: true
theme: dark
controls: true
editor:
render-on-save: true
---
```
````markdown
::: {.panel-tabset}
### Tab A
Content for `Tab A`
california_housing.frame.head(5)
### Tab B
Content for `Tab B`
```{python}
fig, ax = plt.subplots(subplot_kw={'projection': 'polar'})
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()
```
:::
````
# Screenshots of Jupyter notebook cells
# Rendered output
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 5,
"created_at": "2022-10-20T19:39:47Z",
"creator": "rleyvasal",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2956,
"state": "closed",
"title": "Tabsets Shown, but content not displayed - VScode + Jupyter + Python + Revealjs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2956"
} |
### Bug description
I am trying to rebuild the vetiver website within a Docker container. Running individual python chunks within the container work fine, but when trying to render the .qmd files I get the following:
```
$ quarto render index.qmd --to html
processing file: index.qmd
|.............. | 20%
ordinary text without R code
|............................ | 40%
label: unnamed-chunk-1
|.......................................... | 60%
ordinary text without R code
|........................................................ | 80%
label: unnamed-chunk-2 (with options)
List of 1
$ engine: chr "python"
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: py_call_impl(callable, dots$args, dots$keywords)
2: builtins$eval(compiled, globals, locals)
3: force(expr)
4: py_capture_output(builtins$eval(compiled, globals, locals))
5: py_compile_eval(snippet, compile_mode)
6: reticulate::eng_python(options)
7: engine(options)
8: in_dir(input_dir(), expr)
9: in_input_dir(engine(options))
10: block_exec(params)
11: call_block(x)
12: process_group.block(group)
13: process_group(group)
14: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
15: process_file(text, output)
16: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
17: rmarkdown::render(input = input, output_format = output_format, knit_root_dir = knit_root_dir, params = params, run_pandoc = FALSE, envir = globalenv())
18: execute(params$input, params$format, params$tempDir, params$libDir, params$dependencies, params$cwd, params$params, params$resourceDir, params$handledLanguages, params$markdown)
19: .main()
An irrecoverable exception occurred. R is aborting now ...
root@d8296102c061:/home/conda/r_miniconda_container#
```
I removed all python chunks from `index.qmd` to see if the error is raised, but it runs fine and then it fails in the next python chunk - the first evaluated python chunk in `getting_started/index.qmd`:
```{python}
from vetiver.data import mtcars
from sklearn import linear_model
car_mod = linear_model.LinearRegression().fit(mtcars.drop(columns="mpg"), mtcars["mpg"])
```
Steps to reproduce:
```
docker pull registry.gitlab.com/arronlacey/r_miniconda_container
docker run --rm -p 8787:8787 registry.gitlab.com/arronlacey/r_miniconda_container
docker exec -it <container name> /bin/bash
git clone https://gitlab.com/arronlacey/r_miniconda_container.git
cd r_miniconda_container
quarto render index.qmd --to html
```
Dockerfile:
```
FROM rocker/r-ver:4.2.1
RUN apt-get update
RUN apt-get install -y --no-install-recommends libxt6
RUN apt-get install nano
ENV S6_VERSION=v2.1.0.2
ENV RSTUDIO_VERSION=2022.07.2+576
ENV DEFAULT_USER=rstudio
ENV PANDOC_VERSION=default
ENV QUARTO_VERSION=default
RUN /rocker_scripts/install_rstudio.sh
RUN /rocker_scripts/install_pandoc.sh
RUN /rocker_scripts/install_quarto.sh
RUN quarto install extension --no-prompt quarto-ext/grouped-tabsets
RUN useradd -u 1001 -g rstudio -m conda
USER conda
WORKDIR /home/conda
ENV PATH="/home/conda/miniconda3/bin:${PATH}"
ARG PATH="/home/conda/miniconda3/bin:${PATH}"
ENV MLFLOW_BIN=/home/conda/miniconda3/bin/mlflow
ENV MLFLOW_PYTHON_BIN=/home/conda/miniconda3/bin/python
RUN wget \
https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
&& bash Miniconda3-latest-Linux-x86_64.sh -b \
&& rm -f Miniconda3-latest-Linux-x86_64.sh
RUN conda --version
USER root
RUN R -q -e 'install.packages(c("reticulate","vetiver","pins","dplyr","checkmate","quarto","gt","tidymodels","randomForest"))'
ENV PATH "$PATH:/root/.local/share/r-miniconda/bin"
RUN R -q -e 'reticulate::py_install(envname="base",c("vetiver","pins","scikit-learn","pandas","nbformat","nbclient"),pip=TRUE)'
ENV USER="rstudio"
CMD ["/usr/lib/rstudio-server/bin/rserver", "--server-daemonize", "0", "--auth-none", "1"]
EXPOSE 8787
CMD ["/init"]
```
Host details:
```
Distributor ID: Ubuntu
Description: Ubuntu 22.04.1 LTS
Release: 22.04
Codename: jammy
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 5,
"created_at": "2022-10-20T11:04:05Z",
"creator": "arronlacey",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro",
"third-party"
],
"locked": false,
"milestone": "v1.3",
"number": 2950,
"state": "closed",
"title": "segfault address 0x1, cause 'memory not mapped'",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2950"
} |
### Bug description
Hi,
First of all thanks for this fantastic tool!
I have been trying to build a project of *book* type with a cls file for the bibliography. Although the pdf render works well, the html one triggers an error. So as to keep a minimal example, I have tried with the initial files built after the command `quarto create-project mybook --type book` only adding the cls file (official elsevier-harvard.cls) and adding the line `csl: elsevier-harvard.csl` in `_quarto.yml`. The same file works well on a classical project (not book).
The error is
```
File C:.barthelemy_workspace-harvard.csl not found in resource path
ERROR: File C:.barthelemy_workspace-harvard.csl not found in resource path
```
I put in attachment the full log of console output from rendering on a Windows 10 system.
[config.log](https://github.com/quarto-dev/quarto-cli/files/9827341/config.log)
Thanks in advance for your help.
Best regards
JF Barthélémy
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 18,
"created_at": "2022-10-20T07:36:54Z",
"creator": "jfbarthelemy",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "v1.3",
"number": 2945,
"state": "closed",
"title": "Problem with html render of a book with csl file",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2945"
} |
### Bug description
# Issue
Using a different name of the output of a quarto file does not change the name of the additional directory with supporting files.
This happens both in RStudio as well as when calling
```
quarto render reprex.qmd --output test.html
```
# Reprex
```
---
title: "reprex-quarto"
output-file: "test"
output-ext: "html"
---
This will create a
- file `test.html` and a
- directory called `reprex_files` (because I've named the Quarto file `reprex.qmd`)
```
# OS
```
Distributor ID: Ubuntu
Description: Ubuntu 20.04.5 LTS
Release: 20.04
Codename: focal
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-10-20T07:24:29Z",
"creator": "AlbertRapp",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 2944,
"state": "open",
"title": "Files directory does not change name when output is named differently",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2944"
} |
### Bug description
Hello,
I observed that the `::: {.incremental}` syntax create non-incremental bullet list instead of incremental list. In the example belliw, both the .incremental and .non-incremental div return the same non-incremental bullet list.
```
::: {.incremental}
- List element A
- List element B
:::
::: {.nonincremental}
- List element A
- List element B
:::
```
I observed this in html document and MS Word output. The other output format are probably the same. Could this be corrected in a future update? This syntax is used by the _quartostamp_ package which make it useful to quickly insert numbered list.
I'm using RStudio 2022.07.1 Build 554 with the latest version of quarto.
My operating system is Windows 10.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 3,
"created_at": "2022-10-20T07:13:38Z",
"creator": "Pierre9344",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2943,
"state": "closed",
"title": "::: {.incremental} syntax return non-incremental list",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2943"
} |
In a book project, `index.qmd` is required (else you get an error).
The documentation at https://quarto.org/docs/books/book-structure.html doesn't explain how `index.qmd` works in the context of a book project. | {
"assignee": "dragonstyle",
"comments": 4,
"created_at": "2022-10-19T19:56:47Z",
"creator": "fuhrmanator",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.2",
"number": 2941,
"state": "closed",
"title": "Book structure doesn't explain index.qmd",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2941"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2895
<div type='discussions-op-text'>
<sup>Originally posted by **aborruso** October 17, 2022</sup>
Hi,
is there a way to insert an [aside notation](https://quarto.org/docs/authoring/article-layout.html#asides) for a code generated table?
The only way I have found is to use a margin content `{.column-margin}`.
Thank you
</div> | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-10-19T16:36:55Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"bug",
"articles"
],
"locked": false,
"milestone": "v1.3",
"number": 2934,
"state": "closed",
"title": "Span and Div `.aside` elements behave differently (and counterintuitively)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2934"
} |
### Bug description
I'm on Windows 10 running RStudio 2022.07.2 Build 576. I created a new Quarto Project with the following YAML header:
```
---
title: "reprex-quarto"
output-file: "test"
output-ext: "html"
---
```
Per @cscheid request on quarto-dev/quarto-r#89, when I include an `output-file` and `output-ext` in the YAML header of a quarto document, and click the 'Render' button, the corresponding document is created, but sans formatting. In the 'Background Jobs' tab I see an error: `ERROR: The filename, directory name, or volume label syntax is incorrect. (os error 123)`. When I open 'test.html' it looks like this:
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 15,
"created_at": "2022-10-19T16:07:18Z",
"creator": "daranzolin",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro",
"windows"
],
"locked": false,
"milestone": "v1.3",
"number": 2931,
"state": "closed",
"title": "No formatting when specifying 'output-file' and 'output-ext' in YAML header",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2931"
} |
### Bug description
In any quarto project (website, book, etc) with pdf/latex output, if you type something like
```
\(F_{X}(x)=\operatorname{Pr}(X \leq x)\).
```
quarto parses it as
```
(F\_\{X\}(x)=\operatorname{Pr}(X\leq x)).
```
Causing the following error
```
Missing $ inserted.
<inserted text>
$
l.241 ... (F\_\{X\}(x)=\operatorname{Pr}(X
You may need to $ $ around an expression in this file.
see index.log for more information.
```
For html document, here is the final output
The same code in `bookdown` looks like this
The `\( \)` is the "newer" (LaTeX) inline mode of the classic `$ $` (TeX). A discussion about their features is here: https://tex.stackexchange.com/a/513/42627
I think that quarto should be support both ways to guarantee maximum compatibility.
Here is a full qmd example
```
---
title: "Latex inline \( \) doesn't work"
format: pdf
---
\(F_{X}(x)=\operatorname{Pr}(X \leq x)\).
```
My quarto version is ` 1.2.226`.
Best.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 6,
"created_at": "2022-10-18T22:41:01Z",
"creator": "maikol-solis",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2924,
"state": "closed",
"title": "Quarto doesn't parse \\( \\) (inline LaTeX math) correctly with pdf and html documents",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2924"
} |
### Bug description
From #2865, it appears variables stored in `_variables.yml` can only be accessed if a `_quarto.yml` file exists (it can be empty).
The code below produces the following HTML:
<img width="574" alt="image" src="https://user-images.githubusercontent.com/8896044/196536859-4cace025-2dbe-4c44-9154-78b54aa73d3e.png">
While adding an empty `_quarto.yml` produces the following:
<img width="574" alt="image" src="https://user-images.githubusercontent.com/8896044/196537030-3653b619-ac16-49ae-b91f-de37e277463d.png">
The documentation does not really says it's required to have a `_quarto.yml` file (<https://quarto.org/docs/authoring/variables.html#var>) and I would not expect this to be a requirement.
- Quarto document:
````
---
title: "title"
categories:
- "{{< var kws.k1 >}}"
- "{{< var kws.k2 >}}"
abc: def
---
# Header 1
Reading {{< var kws.k1 >}} works!
````
- `_variables.yml`
```
kws:
k1: keyword1
k2: keyword2
k3: keyword3
```
---
Quarto: v1.2.210
OS: MacOS 12
Arch: Apple Silicon
IDE: VSCode
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 5,
"created_at": "2022-10-18T20:30:02Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.2",
"number": 2918,
"state": "closed",
"title": "`_variables.yml` only works if `_quarto.yml` exists",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2918"
} |
Not sure if this is an issue with quarto, the R package gt, pandoc, or something else.
If an R gt table uses the tab_header function, the table will no longer render to docx, although it will render to html and pdf.
The self-contained qmd example below creates a gt table without tab_header, and then one with tab_header. The first table will render to all three formats but the second renders only to html and pdf, but not to docx. Not shown - the table will render to docx if title=NULL, but then it won't have a title, of course. If I alter the second example below to wrap the title in md or html (i.e., title=md("abc") or title=html("abc")) it still will not render to docx.
I also have done this with dev versions of quarto-cli and RStudio but have the same problem.
I don't have great workarounds. I can gtsave the table to a png file and then include it as a picture, or use NULL titles.
Advice welcome on what I can do to work around, and whether I should report this elsewhere.
Many thanks.
**Minimal reproducible example below (a qmd file).**
````
---
format:
html:
theme: cosmo
pdf:
documentclass: scrreprt
docx:
toc: true
---
Show how tab_header affects quarto rendering to docx
Setup:
Windows 11 Pro Build 22623
R-4.2.1
RStudio-2022.07.2-576.exe
quarto-1.1.251-win.msi
```{r}
library(tidyverse)
library(gt)
```
Table without header
```{r}
mtcars |>
gt()
```
Table with header
```{r}
mtcars |>
gt() |>
tab_header(title="abc")
```
````
| {
"assignee": null,
"comments": 4,
"created_at": "2022-10-18T19:02:40Z",
"creator": "donboyd5",
"is_pull_request": false,
"labels": [
"third-party",
"tables"
],
"locked": false,
"milestone": null,
"number": 2916,
"state": "closed",
"title": "Possible bug: R gt tables do not render to docx when tab_header is used with anything other than NULL titles",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2916"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2872
<div type='discussions-op-text'>
<sup>Originally posted by **fredguth** October 15, 2022</sup>
I have been trying to create a Project template for a custom thesis with the Brazilian Academic Standard (ABNT) extending dragonstyle/abnt proof-of-concept.
My problem is that I want to let people write "dedication" and "acknowledgment" pages in the frontmatter by adding qmd files.
Ideally the _quarto.yml would have a `frontmatter` section similar to `chapters`:
``` yaml
...
frontmatter:
- frontmatter/dedication.qmd
- frontmatter/acknowledgments.qmd
- frontmatter/epigraph.qmd
chapters:
- chapters/introduction.qmd
...
````
The table of contents would be rendered between the frontmatter and the body/chapters section.
Extensions like [Quarto Thesis] or [Quarto Titlepages] handle these with `tex` includes and that is how I am dealing with it now. One could also just use metadata and include them in the tex (which I dislike because you end up with a huge yaml file). But I wonder if it would be possible to use the `frontmatter/dedication.qmd` tex output in the `before-body.tex`.
</div> | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-10-18T14:00:48Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"enhancement",
"books"
],
"locked": false,
"milestone": "v1.4",
"number": 2908,
"state": "open",
"title": "Using qmd files in the front matter",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2908"
} |
### Bug description
Hello,
I have noticed that when adding notes to a slide with a plot, the notes seem to shrink the plot, even though the notes are not visible on the slide, which seems non-ideal.
Here's a toy example, I'm using RStudio 2022.07.0 Build 548 on Windows 11:
````
---
title: "Slide notes affect plot size"
format: revealjs
---
## This is a slide without notes
```{r}
library(ggplot2)
data <- data.frame(x = rnorm(100),
y = rnorm(100))
ggplot(data, aes(x = x, y = y)) +
geom_point()
```
## This is a slide with notes
```{r}
library(ggplot2)
data <- data.frame(x = rnorm(100),
y = rnorm(100))
ggplot(data, aes(x = x, y = y)) +
geom_point()
```
::: notes
- This is a note
:::
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 3,
"created_at": "2022-10-18T09:20:07Z",
"creator": "drcaprosser",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro",
"revealjs"
],
"locked": false,
"milestone": "v1.3",
"number": 2904,
"state": "closed",
"title": "Revealjs slide notes affect plot size",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2904"
} |
### Bug description
Poor search usability.
> What is the title text?
> I don't know :-p that's my point
> Everything either says decision or documentation
I am on Windows. The screenshot is on an iPhone.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 9,
"created_at": "2022-10-18T07:04:33Z",
"creator": "fire",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2902,
"state": "closed",
"title": "Poor search usability for Quatro sites.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2902"
} |
It would be great to be able to give a qmd file as an abstract instead of having to write everything in the frontmatter!
| {
"assignee": null,
"comments": 2,
"created_at": "2022-10-17T21:32:38Z",
"creator": "lcnbr",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 2897,
"state": "open",
"title": "Abstract as file",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2897"
} |
### Bug description
There seems to be no way to have an aknowledgement section in a book. Ideally, this comes before the toc, and could either be directly in the metadata, or provided in a file. Probably even more generally it would be nice to be able to put things in the front, main and back matter explicitly.
| {
"assignee": null,
"comments": 1,
"created_at": "2022-10-17T21:26:37Z",
"creator": "lcnbr",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": null,
"number": 2896,
"state": "closed",
"title": "thanks in book",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2896"
} |
Hi,
I don't think the `link-citations` YAML parameter is documented anywhere and I think it is necessary to enable in order to get hyperlinked things, at least in PDF, in my testing.
The use of `colorlinks` and the `*color` set of parameters had no apparent affect unless `link-citations: true`, like with R Markdown. I found this out through some trial and error. | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-10-17T20:07:04Z",
"creator": "mattwarkentin",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2893,
"state": "closed",
"title": "`link-citations` not documented anywhere",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2893"
} |
### Bug description
### Details
RStudio 2022.07.2+576 "Spotted Wakerobin" Release (e7373ef832b49b2a9b88162cfe7eac5f22c40b34, 2022-09-06) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 12_6_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
### Example
When using interactivity with Altair, the selections are offset from the pointer. This issue only occurs with reveal.js, not HTML reports.
https://user-images.githubusercontent.com/25734232/196245078-568e0b11-f1eb-419f-ab9a-8b826a562d94.mp4
### Code
````
---
title: "altair_selection_bug"
format: revealjs
jupyter: python3
---
```{python}
# From here: https://altair-viz.github.io/gallery/interactive_brush.html
import altair as alt
from vega_datasets import data
source = data.cars()
brush = alt.selection(type='interval')
alt.Chart(source).mark_point().encode(
x='Horsepower:Q',
y='Miles_per_Gallon:Q',
color=alt.condition(brush, 'Cylinders:O', alt.value('grey')),
).add_selection(brush)
```
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 6,
"created_at": "2022-10-17T17:29:44Z",
"creator": "maxdrohde",
"is_pull_request": false,
"labels": [
"bug",
"third-party"
],
"locked": false,
"milestone": "v1.4",
"number": 2891,
"state": "open",
"title": "Altair interactive selection doesn't work well with reveal.js",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2891"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2844
<div type='discussions-op-text'>
<sup>Originally posted by **zeileis** October 13, 2022</sup>
In quarto 1.1251, when using one of the [theorem divs](https://quarto.org/docs/authoring/cross-references.html#theorems-and-proofs) with just a list (itemized or enumerated), then in HTML output the theorem title becomes the first list element. Only if there is a paragraph prior to the list, it is handled correctly. Example:
```
::: {#def-twothings-plain}
## Plain list
1. First things first.
2. Second thoughts.
:::
::: {#def-twothings-plus}
## List plus intro paragraph
This is about two things.
1. First things first.
2. Second thoughts.
:::
```
Rendered to HTML:
Rendered to PDF it is a bit better but also not ideal:
I guess this may be related to the earlier discussion https://github.com/quarto-dev/quarto-cli/discussions/1925 and corresponding fix https://github.com/quarto-dev/quarto-cli/issues/1926.
One can work around the problem by including something like a non-breaking space only in the first paragraph but it would be nice to have having to do this.</div> | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-10-17T15:12:39Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2886,
"state": "closed",
"title": "theorem environments containing just a list",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2886"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2868
<div type='discussions-op-text'>
<sup>Originally posted by **aborruso** October 15, 2022</sup>
Hi,
it would be great to have in quarto for vega-lite, something like the Mermaid diagrams.
To write something like
````
``` {vega-lite}
{
"data": {
"values": [
{"a": "C", "b": 2}, {"a": "C", "b": 7}, {"a": "C", "b": 4},
{"a": "D", "b": 1}, {"a": "D", "b": 2}, {"a": "D", "b": 6},
{"a": "E", "b": 8}, {"a": "E", "b": 4}, {"a": "E", "b": 7}
]
},
"mark": "point",
"encoding": {
"x": {"field": "a", "type": "nominal"}
}
}
```
````
to get
Thank you</div> | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-10-17T15:08:49Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 2885,
"state": "open",
"title": "Add vega-lite as embedding object",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2885"
} |
### Bug description
When hitting refresh on a HTML file generated from Quarto, margin footnotes from much earlier show up at the top of the screen, even if the text they correspond to is long gone.
https://user-images.githubusercontent.com/13658517/196154621-519e78b8-463f-46b2-ac2e-82537b6ab85d.mov
Footnotes in the margin are generated with `reference-location: margin` in the preamble.
I provide [an example](https://github.com/quarto-dev/quarto-cli/files/9799403/test.md), tested on Chromium and Firefox.
**Configuration**
MacOS Monterey 12.4 MacBook Pro (14 pouces, 2021)
RStudio 2022.07.2+576 "Spotted Wakerobin" Release (e7373ef832b49b2a9b88162cfe7eac5f22c40b34, 2022-09-06) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 12_4_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 3,
"created_at": "2022-10-17T10:27:39Z",
"creator": "katossky",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2883,
"state": "closed",
"title": "Margin footnotes pile up at top of screen on page refresh (even though calling number is not visible)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2883"
} |
### Bug description
For a blog listing page, the sort date is not working properly when I try to combine a directory listing with a metadata listing. Here's my listing page config, that pulls in all of the posts in the current working directly and has one additional item that's specified as metadata:
````md
---
title: "Blog"
listing:
contents:
- "."
- title: "My special blog post, with an external link"
date: "2022-10-16"
author: Brian Kent
categories: [interviews]
description: "I recently sat down with John Doe to talk about data science."
href: https://www.johndoedatascience.com/interviews/briankent
sort: "date desc"
type: default
---
````
I expected all of the listing items to be sorted globally, but the metadata item is not (and ends up at the bottom). When I inspect the page source, I see that the items specified by directory have dates that have been converted to epoch milliseconds, while the metadata listing item has not been converted and remains a string.
So, for example, one of the regular blog posts has a date "2021-01-09" and the corresponding html div has `data-listing-date-sort=1610172000000`
```html
<div class="quarto-post image-right" data-index="23" data-categories="" data-listing-date-sort="1610172000000" data-listing-file-modified-sort="1665932827072" data-listing-reading-time-sort="2.67">
...
</div>
```
But the ad hoc, metadata-based listing item---which has date "2022-10-16"---has a div that looks like this
```html
<div class="quarto-post image-right" data-index="24" data-categories="interviews" data-listing-date-sort="2022-10-16" data-listing-file-modified-sort="null">
...
</div>
```
So the date just hasn't been converted to epoch milliseconds.
I'm using Ubuntu 20.04.5 with Quarto version 1.1.251. I also installed the latest Quarto pre-release 1.2.219 and see the same issue.
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-10-16T20:45:50Z",
"creator": "bpkent",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2880,
"state": "closed",
"title": "Blog listing from metadata not sorted correctly with other listing items (date not converted to epoch milliseconds)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2880"
} |
### Bug description
It seems I can't get tables to be fullwidth in the pdf output no matter what I try:
```
+---------------+---------------+--------------------+
| Fruit | Price | Advantages |
+===============+===============+====================+
| Bananas | $1.34 | - built-in wrapper |
| | | - bright color |
+---------------+---------------+--------------------+
| Oranges | $2.10 | - cures scurvy |
| | | - tasty |
+---------------+---------------+--------------------+
: Sample grid table. {.column-page-right}
```
this does not work in the pdf output
| {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-10-16T19:12:27Z",
"creator": "lcnbr",
"is_pull_request": false,
"labels": [
"bug",
"articles"
],
"locked": false,
"milestone": "v1.4",
"number": 2878,
"state": "open",
"title": "column-body-right not applied to table",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2878"
} |
### Bug description
When I include an anonymous figure without extension i.e. ``, and I have the default extensions set for pdf and html output in a book I get the following error
```
Error running filter /opt/quarto/share/filters/quarto-post/quarto-post.lua:
/opt/quarto/share/filters/quarto-post/quarto-post.lua:2277: attempt to index a nil value (field 'attr')
stack traceback:
/opt/quarto/share/filters/quarto-post/quarto-post.lua:1119: in function </opt/quarto/share/filters/quarto-post/quarto-post.lua:1113>
```
my _quarto.yml has the following shape:
```
project:
type: book
book:
title: "mwebib"
author: "Jane Doe"
date: "10/10/2022"
chapters:
- index.qmd
- intro.qmd
- summary.qmd
- references.qmd
bibliography: references.bib
format:
html:
theme: cosmo
cite-method: citeproc
default-image-extension: svg
pdf:
documentclass: scrreprt
cite-method: biblatex
default-image-extension: tex
```
| {
"assignee": "cscheid",
"comments": 7,
"created_at": "2022-10-16T16:32:30Z",
"creator": "lcnbr",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "v1.3",
"number": 2877,
"state": "closed",
"title": "Anonymous figure and default-image-extensions don't work together",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2877"
} |
### Bug description
When I used RMarkdown following tex code used to yield equation numbers and I could get references. But in Quarto it seems to be no longer possible. My .qmd file is part of a Quarto Book. Neither preview nor render made a difference.
> \begin{gather}
> \max z = 3x_{1} + 2x_{2} \label{eq:obj.fun} \\
> s.t. \nonumber \\
> 2x_{1} + x_{2} \le 100 \label{eq:finishing.constraint} \\
> x_{1} + x_{2} \le 80 \label{eq:carpentry.constraint}\\
> x_{1} \le 40 \label{eq:demand.constraint}\\
> x_{1},x_{2} \ge 0 \\
> \end{gather}
>
> See \ref{eq:obj.fun}
I saw this [cross references](https://quarto.org/docs/authoring/cross-references.html#equations) section on Quarto but having too many dollar signs is hard on readability. Is there a way to get numbering back?
My RStudio version is 2022.07.1 Build 554 on MacOS Monterey 12.2.1
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 5,
"created_at": "2022-10-15T16:47:04Z",
"creator": "berkorbay",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 2870,
"state": "closed",
"title": "Equation numbering for \"gather\" is not working.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2870"
} |
Hi,
in that code page there is a note about "Code line numbers", but it's not rendered in [the manual](https://quarto.org/docs/output-formats/html-code.html).
Is it normal?
| {
"assignee": null,
"comments": 1,
"created_at": "2022-10-15T08:15:46Z",
"creator": "aborruso",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2867,
"state": "closed",
"title": "HTML Code Blocks page: text not rendered in the current version of the manual",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2867"
} |
### Bug description
A while ago I rendered qmd files with the following Python code:
```python
import geopandas
world = geopandas.read_file(geopandas.datasets.get_path('naturalearth_lowres'))
world = world[(world.pop_est>0) & (world.name!="Antarctica")]
world['gdp_per_cap'] = round((world.gdp_md_est * 1e6) / world.pop_est, 2)
world.explore(
column="gdp_per_cap", # make choropleth based on "BoroName" column
popup=True, # show all values in popup (on click)
# tiles="CartoDB positron", # use "CartoDB positron" tiles
cmap="viridis", # use "Set1" matplotlib colormap
style_kwds=dict(color="black") # use black outline
)
```
and worked just fine giving me the following:
Now it renders like this
Looking at the generated md file I noticed that it used to be an iframe with encoded html using the `data-html` tag. Now it generates an iframe with `srcdoc` and the output is not url-encoded
I'm using the latest stable release `1.1.251` and when it worked I was using `0.9.345`
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-10-15T06:47:08Z",
"creator": "betolink",
"is_pull_request": false,
"labels": [
"bug",
"third-party"
],
"locked": false,
"milestone": "v1.4",
"number": 2866,
"state": "open",
"title": "Geopandas output not rendered correctly",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2866"
} |
### Bug description
# Issue
When using `quarto publish gh-pages` to push to _private_ GitHub Pages, the tool get stuck on "Deploying gh-pages branch to website", despite the updated GitHub Pages is deployed and live.
# Example
```sh
$ quarto publish gh-pages
? Publish site to https://example-org.github.io/quarto-book-test/ using gh-pages? (Y/n) › Yes
Switched to a new branch 'gh-pages'
[gh-pages (root-commit) b53766a] Initializing gh-pages branch
...
Preparing worktree (resetting branch 'gh-pages'; was at b53766a)
Branch 'gh-pages' set up to track remote branch 'gh-pages' from 'origin'.
HEAD is now at b53766a Initializing gh-pages branch
[gh-pages dd3779a] Built site for gh-pages
23 files changed, 5334 insertions(+)
...
origin [email protected]:example-org/quarto-book-test.git (fetch)
origin [email protected]:example-org/quarto-book-test.git (push)
X11 forwarding request failed on channel 0
To github.com:example-org/quarto-book-test.git
b53766a..dd3779a HEAD -> gh-pages
(/) Deploying gh-pages branch to website (this may take a few minutes)
```
The latter progress updater never completes. I had to hit <kbd>Ctrl-C</kbd>.
# Troubleshooting
My best guess is that the tool is polling the wrong URL, because _private_ GitHub Pages uses a "random" `*.pages.github.io` URL for security reasons, e.g. <https://upgraded-spork-34abee09.pages.github.io/>. This is explained at <https://docs.github.com/en/enterprise-cloud@latest/pages/getting-started-with-github-pages/changing-the-visibility-of-your-github-pages-site#about-subdomains-for-privately-published-sites>.
# Session info
This is on Ubuntu 20.04 running:
```sh
$ quarto --version
1.2.215
```
I'm pushing to a _private_ repository configured to use _private_ GitHub Pages. This is hosted under a GitHub Enterprise Cloud plan.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 8,
"created_at": "2022-10-14T20:40:07Z",
"creator": "HenrikBengtsson",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 2864,
"state": "open",
"title": "GitHub Pages: `quarto publish gh-pages` stalls at \"deploying gh-pages ...\" for _private_ GitHub Pages",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2864"
} |
### Bug description
```{ojs}
viewof date = Inputs.date()
```
returns a "TypeError: Inputs.date is not a function"
I am using the Visual Studio Code Extension.
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 4,
"created_at": "2022-10-14T19:10:19Z",
"creator": "scottfranz",
"is_pull_request": false,
"labels": [
"enhancement",
"good-first-issue",
"ojs-engine"
],
"locked": false,
"milestone": "v1.3",
"number": 2863,
"state": "closed",
"title": "Improve styling of OJS's date input in quarto",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2863"
} |
### Bug description
I have a very simple `qmd` file (add three backticks to close chunk at end):
````
---
format: pdf
---
```{r}
#| warning: false
#| message: false
library(tidyverse) ##load for plotting
ggplot(data = starwars %>% drop_na()) +
geom_point(mapping = aes(x = height, y = mass)) +
annotate("text", x = 150, y = 750,
label = "Annotation to show it is not a font issue.")
labs(caption = "A caption that gets cropped.")
# add three backticks here to close chunk... having trouble getting markdown to work right here
```
````
In the below picture, you can see that the plot displays correctly on the left-hand side, but gets cropped improperly for pdf output (previewed on the right-hand side); the axis labels and ticks are gone.
I am using dev Quarto version 1.2.209 (needed a different bug to be fixed). I cannot seem to downgrade Quarto to see if bug is in the current release. Windows 10, RSTUDIO 2022.07.9 Build 548.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 5,
"created_at": "2022-10-14T17:59:34Z",
"creator": "flyaflya",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 2861,
"state": "closed",
"title": "PDF is cropping ggplot figures",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2861"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2850
<div type='discussions-op-text'>
<sup>Originally posted by **pat-alt** October 14, 2022</sup>
Currently Jupyter kernels need to be specified on a per-document basis. In other words, specifying the Jupyter kernel in `_quarto.yml` or `_metadata.yml` has no effect: see this [example](https://github.com/pat-alt/quarto-example/tree/main/project-wide-jupyter-kernel) where the kernel defaults to the default kernel `julia-1.6` for the [document](https://github.com/pat-alt/quarto-example/blob/main/project-wide-jupyter-kernel/doc-without-specified-kernel.md) without `jupyter` explicitly declared in the YAML header. Is this a deliberate design choice? Is there anything that speaks against specifying kernels for multiple documents?
**Background**: I'm using Quarto to document my Julia packages. Being able to to control the Julia version for all my docs at once would give me a way to check locally if all code chunks execute successfully for that version. </div> | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-10-14T14:42:34Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"jupyter"
],
"locked": false,
"milestone": "v1.2",
"number": 2853,
"state": "closed",
"title": "Option to specify project-wide `jupyter:` kernel",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2853"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2829
<div type='discussions-op-text'>
<sup>Originally posted by **fradav** October 13, 2022</sup>
Hi all,
Visual Studio Code already supports running “in-editor” cells on remote jupyter just by specifying an url to a jupyter server directly
As for quarto, my understanding is it isn’t possible. There are use cases where it would be very practical or even necessary to edit/render everything but jupyter cells by a locally installed quarto, and also render jupyter cells in a remote server, who sometimes doesn’t even offer the possibility to run or install quarto (Jupyterhub containerized instances for example).
I am a member of the staff of an online journal centered on reproductible research and we use quarto as the mandatory format and tooling for submissions. We would like to offer our authors and editors the possibility to run computations inside article submissions on external (possibly heavily equipped, cluster-like or with gpu) computational ressources, and let authors/editors handle the editing/rendering on their local computers.
Regards,
</div> | {
"assignee": null,
"comments": 1,
"created_at": "2022-10-14T14:28:17Z",
"creator": "fradav",
"is_pull_request": false,
"labels": [],
"locked": true,
"milestone": null,
"number": 2852,
"state": "closed",
"title": "Remote jupyter server for cell rendering (like vscode already supports)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2852"
} |
### Bug description
Hi,
I'm re-render a quarto [book](https://github.com/camilogarciabotero/biocomp-book) with the latest version (99.99) commit 8c2b10dc4.
And got the following error:
```
ERROR: Failed to generate bibliography, rendering failed with code 1
pandoc: /Users/camilogarcia/Documents/Teaching/BiologyCourses/BI0487/Lectures/biocomp-book/Users/camilogarcia/Documents/Teaching/BiologyCourses/BI0487/Lectures/biocomp-book/references.bib: openBinaryFile: does not exist (No such file or directory)
Error: Failed to generate bibliography, rendering failed with code 1
pandoc: /Users/camilogarcia/Documents/Teaching/BiologyCourses/BI0487/Lectures/biocomp-book/Users/camilogarcia/Documents/Teaching/BiologyCourses/BI0487/Lectures/biocomp-book/references.bib: openBinaryFile: does not exist (No such file or directory)
at renderToCSLJSON (file:///Users/camilogarcia/Applications/quarto-cli/src/core/bibliography.ts:99:13)
at async bibliographyCslJson (file:///Users/camilogarcia/Applications/quarto-cli/src/core/bibliography.ts:22:24)
at async googleScholarReferences (file:///Users/camilogarcia/Applications/quarto-cli/src/format/html/format-html-meta.ts:241:22)
at async file:///Users/camilogarcia/Applications/quarto-cli/src/format/html/format-html-meta.ts:42:33
at async file:///Users/camilogarcia/Applications/quarto-cli/src/command/render/render.ts:392:24
at async withTimingAsync (file:///Users/camilogarcia/Applications/quarto-cli/src/core/timing.ts:50:20)
at async runHtmlPostprocessors (file:///Users/camilogarcia/Applications/quarto-cli/src/command/render/render.ts:383:5)
at async renderPandoc (file:///Users/camilogarcia/Applications/quarto-cli/src/command/render/render.ts:169:33)
at async Object.onRender (file:///Users/camilogarcia/Applications/quarto-cli/src/project/types/book/book-render.ts:214:28)
at async renderFiles (file:///Users/camilogarcia/Applications/quarto-cli/src/command/render/render-files.ts:482:11)
```
I'm on macOS:
```
'c.
,xNMM. ----------------------
.OMMMMo OS: macOS 12.6 21G115 x86_64
OMMM0,
.;loddo:' loolloddol;. Kernel: 21.6.0
cKMMMMMMMMMMNWMMMMMMMMMM0: Uptime: 1 day, 23 hours, 46 mins
.KMMMMMMMMMMMMMMMMMMMMMMMWd. Packages: 211 (brew)
XMMMMMMMMMMMMMMMMMMMMMMMX. Shell: zsh 5.8.1
;MMMMMMMMMMMMMMMMMMMMMMMM: Resolution: 1440x900, 1920x1080
:MMMMMMMMMMMMMMMMMMMMMMMM: DE: Aqua
.MMMMMMMMMMMMMMMMMMMMMMMMX. WM: Rectangle
kMMMMMMMMMMMMMMMMMMMMMMMMWd. Terminal: iTerm2
.XMMMMMMMMMMMMMMMMMMMMMMMMMMk Terminal Font: JetBrainsMono-Regular 18
.XMMMMMMMMMMMMMMMMMMMMMMMMK. CPU: Intel i5-8257U (8) @ 1.40GHz
kMMMMMMMMMMMMMMMMMMMMMMd GPU: Intel Iris Plus Graphics 645
;KMMMMMMMWXXWMMMMMMMk. Memory: 6236MiB / 8192MiB
.cooc,. .,coo:.
```
It looks like the `references.bib` file path is being wrongly generated in the function `renderToCSLJSON ` probably in the `cmd.push(join(Deno.cwd(),join(dir,biblio)));` line.
```
export async function renderToCSLJSON(
dir: string,
biblios: string[],
): Promise<CSL[]> {
const bibloEntries = [];
for (const biblio of biblios) {
const cmd = [pandocBinaryPath()];
cmd.push(join(Deno.cwd(), join(dir, biblio)));
cmd.push("-t");
cmd.push("csljson");
cmd.push("--citeproc");
const result = await execProcess(
{ cmd, stdout: "piped", stderr: "piped", cwd: dir },
);
if (result.success) {
if (result.stdout) {
const entries = JSON.parse(result.stdout);
bibloEntries.push(...entries);
}
} else {
throw new Error(
`Failed to generate bibliography, rendering failed with code ${result.code}\n${result.stderr}`,
);
}
}
return bibloEntries;
}
```
Thanks!
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 6,
"created_at": "2022-10-14T14:24:24Z",
"creator": "camilogarciabotero",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2851,
"state": "closed",
"title": "ERROR: Failed to generate bibliography in Quarto 99.9.9",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2851"
} |
### Bug description
I observe some unexpected behaviour when trying to use quarto project profiles: while the content in the body (defined with `:::{.content-visible when-profile="advanced"} ... :::` is correctly shown or hidden, the title and output-dir that should change are ignored.
I've set up a project with:
`quarto create-project test-proj`
and added the following files following [the steps here](https://quarto.org/docs/projects/profiles.html#profile-configuration):
<details><summary> test-proj.qmd </summary>
```
## Quarto
Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
:::{.content-visible when-profile="advanced"}
## only in advanced
Some text
:::
```
</details>
<details><summary> _quarto.yml </summary>
```
project:
title: "my website"
type: website
```
</details>
<details><summary> _quarto_advanced.yml </summary>
```
project:
title: "My Website (Advanced)"
output-dir: _site-advanced
```
</details>
Observation:
- using `quarto render` creates a subdirectory `_site` with `test-proj.html` and the title "my website" with the correct content in body
- using `quarto render --profile advanced` overwrites test-proj.html in the `_site` subdirectory and keeps the old title "my website" (unexpected) - but the content in the body (## only in advanced - Some text) is shown as expected
Thus somehow the `output-dir:`and the `title`is not being used from the `_quarto-advanced.yml ` - I am not sure if this is a bug or if I am not applying it correctly - thanks
<details> <summary> Sessioninfo & quarto check </summary>
RStudio: 2022.07.0 Build 548
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
```
[✓] Checking Quarto installation......OK
Version: 1.2.210
Path: /Applications/quarto/bin
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....OK
Version: 3.9.5
Path: /usr/local/opt/[email protected]/bin/python3.9
Jupyter: 4.7.1
Kernels: python3
[✓] Checking Jupyter engine render....OK
[✓] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Versions/4.2/Resources
LibPaths:
- /Users/cb/Library/R/4.0/library
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: (None)
The rmarkdown package is not available in this R installation.
Install with install.packages("rmarkdown")
```
</details>
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 4,
"created_at": "2022-10-13T18:48:24Z",
"creator": "cathblatter",
"is_pull_request": false,
"labels": [
"bug",
"needs-discussion"
],
"locked": false,
"milestone": null,
"number": 2840,
"state": "closed",
"title": "Project profiles ignoring output-dir in _quarto-advanced.yml",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2840"
} |
panel-tabset worked yesterday, but not today. Is this a new bug? Slides with panel-tabset render properly locally, but do not render properly when building a website | {
"assignee": null,
"comments": 2,
"created_at": "2022-10-13T15:43:59Z",
"creator": "marierivers",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": "v1.3",
"number": 2835,
"state": "closed",
"title": "panel-tabset doesn't seem to be working today",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2835"
} |
### Bug description
Using Quarto 1.2.209 rendered on macOS from the CLI; this is the Quarto version included in one of the most recent RStudio dailies.
Quarto with revealjs sees the revealjs style used rather than the default task-list style injected into the document. This is because the `.reveal ul` scoped CSS is preferred over the top-level CSS injected by Quarto+Pandoc.
````markdown
---
title: task list with reveal
format: revealjs
---
## tasks
- [x] wake up
- [ ] brush teeth
- [ ] drink coffee
````
As rendered, you can see both the original list icons and the check-boxes as rendered on Safari. Only the check-boxes should be displayed and they should be more prominent.
<img width="395" alt="image" src="https://user-images.githubusercontent.com/362187/195606696-965bcc97-1c2f-4830-85d4-0f7879ac6a08.png">
I am locally using these override styles; they're imperfect, but an improvement.
```css
.reveal ul.task-list{list-style: none;}
.reveal ul.task-list li input[type="checkbox"] {
width: 2em;
height: 2em;
margin: 0 1em 0.5em -1.6em;
vertical-align: middle;
}
.reveal ul.task-list li input[type="checkbox"][disabled] {
outline:1px solid lightgrey;
}
.reveal ul.task-list li input[type="checkbox"][disabled][checked] {
outline:2px solid green;
}
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 10,
"created_at": "2022-10-13T13:17:13Z",
"creator": "aronatkins",
"is_pull_request": false,
"labels": [
"bug",
"upstream"
],
"locked": false,
"milestone": "v1.4",
"number": 2834,
"state": "open",
"title": "revealjs ul style preferred to task-list style",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2834"
} |
- Consider adding utility function for listing templates to read metadata
- Consider adding native filtering to listing descriptors
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2828
<div type='discussions-op-text'>
<sup>Originally posted by **mllg** October 13, 2022</sup>
I have a folder `publications` which contains a `qmd` for multiple publications. Each `qmd` file comes with meta data about the publication in the front matter. I can now easily list all publications, e.g. with
```yaml
listing:
contents:
- "publications/*.qmd"
```
I now want to provide a different view on this listing, i.e. restrict the listing to include only publications of a specific author. I can do this with a custom listing and an ejs template which filters on pattern `"NAME"`:
```ejs
<ul class="pub-list list">
<% for (const item of items) { %>
<% if(item.author.match("NAME") ){ %>
<li <%= metadataAttrs(item) %>>
<span class="listing-title"><%= item.title %>.</span>
</li>
<% } %>
<% } %>
</ul>
```
I'm wondering if there is a way to
1. retrieve the `"NAME"` pattern from the meta data of the page which is contains the listing, or
2. a different way to pass down variables to ejs templates?
</div> | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-10-13T12:48:21Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 2833,
"state": "closed",
"title": "Filtering items of listings based on meta data",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2833"
} |
### Bug description
When both `code-tools` and `link-external-newwindow` are enabled, the buttons in the code tools are marked as external links and clicking on them leads to new empty windows opened.
Also, although when the source code link is truly external link, the link is not opened in a new tab, but is redirected in the current tab. Again, there's still a new tab opened but it is empty.
I'm using Quarto-1.1.251 on Manjaro (Arch Linux).
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 6,
"created_at": "2022-10-13T10:48:25Z",
"creator": "singuyenmai",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2830,
"state": "closed",
"title": "Buttons in code tools are treated as external links when `link-external-newwindow` enabled",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2830"
} |
## I think I opened this in the wrong forum - apologies
### Bug description
Windows 10
R version 4.1.1 (2021-08-10)
R Studio 2022.07.1 Build 554
Quarto 1.1.251
New to Quarto, but have some experience in R Markdown. When rendering a .qmd (via render button) as an HTML file the preview returns 'Not Found' regardless of whether preview is set to the viewer pane or window. This happens only when I have set the `output-dir:` in the `_quarto.yml` to a sub-directory. The problem doesn't occur when no `output-dir:` is set and the file.qmd is saved to the project directory. I am able open the file manually from the sub-directory and it works fine - the problem only appears to be the preview.
Looking at the Background Jobs tab I can see the following:
Watching files for changes
Browse at http://localhost:4476/new_doc_3.html
GET: /docs/notebooks/new_doc_3.html (404: Not Found)
I can't seem to attach the .qmd or .yml files as requested in the Checklist below.
The .qmd file is just the default text/format when initiating a new Quarto document.
Here is my YAML:
project:
output-dir: docs/notebooks
execute:
echo: false
eval: false
message: false
warning: false
format:
html:
embed-resources: true
number-sections: true
number-depth: 3
toc: true
toc-location: left
toc-depth: 4
code-overflow: wrap
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 0,
"created_at": "2022-10-13T00:17:00Z",
"creator": "RobTour",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2827,
"state": "closed",
"title": "Quarto preview in viewer pane (or browser) returns Not Found when output-dir: set to sub-directory",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2827"
} |
### Bug description
For revealjs formatted presentation, the color of links and the page numbers in the footer are not controlled as expected by the CSS variable `$linkColor`.
Expected behavior:
`$linkColor` and `$linkColorHover` should apply to links in the footer and the page numbers
Observed behavior:
Footer link color is changed with a different CSS variable called `$link-color`
Page number color is not affected by `$link-color` or `$linkColor`, but is affected by `$linkColorHover`
Reprex here:
https://github.com/kmasiello/reprex-footer-link
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-10-12T17:52:09Z",
"creator": "kmasiello",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2820,
"state": "closed",
"title": "revealjs presentation - inconsistent handling of css link colors for body / footer elements",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2820"
} |
I was going to request a feature but it turns out the following already works:
```
---
title: Title
author: John Doe
lang: fr
language: translations.yml
---
Text.
```
and in `translations.yml`:
```
de:
title-block-author-single: Autor
fr:
title-block-author-single: Auteur
```
Specifying `lang: fr` or `lang: de` picks up the right value from `translations.yml`, and `lang: en` uses the non-customized English as expected.
I don't think the documentation mentions that translations can be customized for different languages like this. I find it very useful (see use case in https://github.com/quarto-dev/quarto-cli/discussions/2796 ). Is this officially supported, and if yes would you like a PR for the documentation? | {
"assignee": "jjallaire",
"comments": 2,
"created_at": "2022-10-12T08:16:05Z",
"creator": "knuesel",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2812,
"state": "closed",
"title": "Document language-specific custom translations",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2812"
} |
### Bug description
Hello,
The logo-href of the website/navbar option doesn't work.
For example, if I create a new website template with
```bash
quarto create-project mysite --type website
```
Then modify the _quarto.yml file like so:
```
project:
type: website
website:
title: "mysite"
navbar:
logo-href: about.qmd
left:
- href: index.qmd
text: Home
format:
html:
theme: cosmo
css: styles.css
toc: true
```
The index.qmd content still shows up when I click on the title in the upper navbar (rather than the contents of about.qmd).
I am using the latest pre-release build of quarto 1.2.207. I am simply using the command line (no R studio) on Ubuntu 20.04.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-10-11T23:40:28Z",
"creator": "d-chambers",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2810,
"state": "closed",
"title": "Logo-href doesn't work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2810"
} |
We should offer a better error message than this: https://github.com/quarto-dev/quarto-cli/discussions/2763#discussioncomment-3854662 | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-10-11T21:56:04Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"yaml-validation"
],
"locked": false,
"milestone": "v1.2",
"number": 2808,
"state": "closed",
"title": "catch `!` in yaml parse error messages",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2808"
} |
### Bug description
I've recently just updated quarto and I'm now unable to render pdfs. Instead I get a rather cryptic error message that I'm not able to directly relate to anything. Only thing that has changed since my last successful usage is my quarto version. Here's the current error message:
```
Error running filter C:/Users/xxxxx/AppData/Local/Programs/Quarto/share/filters/quarto-pre/quarto-pre.lua:
.../Programs/Quarto/share/filters/quarto-pre/quarto-pre.lua:2003: attempt to index a nil value (global 'path')
stack traceback:
.../Programs/Quarto/share/filters/quarto-pre/quarto-pre.lua:1974: in local 'fn'
.../Programs/Quarto/share/filters/quarto-pre/quarto-pre.lua:4807: in function <.../Programs/Quarto/share/filters/quarto-pre/quarto-pre.lua:4801>
```
This only affects pdf rendering, html rendering is still working fine.
```
>quarto check
[>] Checking Quarto installation......OK
Version: 1.2.198
Path: C:\Users\jpmor\AppData\Local\Programs\Quarto\bin
CodePage: unknown
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.9.13 (Conda)
Path: C:/Users/xxxxx/anaconda3/python.exe
Jupyter: 4.11.1
Kernels: julia-1.4, julia-1.6, julia-1.7, juliapro_v1.5.4-1-1.5, pycharm-20203b08, python3, iota
[>] Checking Jupyter engine render....OK
[>] Checking R installation...........OK
Version: 4.1.3
Path: C:/PROGRA~1/R/R-41~1.3
LibPaths:
- C:/Users/xxxxx/OneDrive/Documents/R/win-library/4.1
- C:/Program Files/R/R-4.1.3/library
rmarkdown: 2.14
[>] Checking Knitr engine render......OK
```
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 4,
"created_at": "2022-10-11T19:34:33Z",
"creator": "jpmorr",
"is_pull_request": false,
"labels": [
"bug",
"open-pr"
],
"locked": false,
"milestone": null,
"number": 2803,
"state": "closed",
"title": "Quarto unable to render PDF - lua filter error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2803"
} |
### Bug description
**Background**
When I render documents with Python code chunks the incorrect python interpreter is being used. I would like quarto to execute the code chunks using my virtual environment, but instead it is using a different python interpreter.
**System details**
- Quarto: 1.1.113
- Operating System: M1 mac, macOS Monterey 12.6
**Reprex**
Create and activate a virtual environment:
```bash
python -m venv .venv
source .venv/bin/activate
which python
# /Users/samedwardes/tmp/quarto-env-reprex/.venv/bin/python
python -m pip install jupyter
```
Check quarto:
```bash
quarto check
# [✓] Checking Quarto installation......OK
# Version: 1.1.113
# Path: /Applications/quarto/bin
#
# [✓] Checking basic markdown render....OK
#
# [✓] Checking Python 3 installation....OK
# Version: 3.10.4
# Path: /Users/samedwardes/tmp/quarto-env-reprex/.venv/bin/python3
# Jupyter: 4.11.1
# Kernels: python3, connectapi-kernel, my-project-kernel, connectapi
#
# [✓] Checking Jupyter engine render....OK
#
# [✓] Checking R installation...........OK
# Version: 4.2.1
# Path: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources
# LibPaths:
# - /Users/samedwardes/Library/R/arm64/4.2/library
# - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
# rmarkdown: 2.16
#
# [✓] Checking Knitr engine render......OK
```
Create a new document `example.qmd`:
````markdown
---
title: Virtual environment
---
Python code chunk:
```{python}
import sys
print(sys.executable)
```
````
Then render it:
```bash
quarto render example.qmd --output -
# Executing 'example.ipynb'
# Cell 1/1...Done
#
# pandoc --output /var/folders/v9/fyndz9rs2hs34xwbs1rtmqtm0000gn/T/quarto-session0e5cab67/6e2ffbde/35950ad9.md
# to: markdown
# standalone: true
# default-image-extension: png
#
# metadata
# title: Virtual environment
#
# ---
# title: Virtual environment
# toc-title: Table of contents
# ---
#
# Python code chunk:
#
# ::: {.cell execution_count="1"}
# ``` {.python .cell-code}
# import sys
#
# print(sys.executable)
# ```
#
# ::: {.cell-output .cell-output-stdout}
# /Users/samedwardes/.virtualenvs/py3912/bin/python
# :::
# :::
```
As you can see in the example above, `sys.executable` returns `/Users/samedwardes/.virtualenvs/py3912/bin/python` as opposed to `/Users/samedwardes/tmp/quarto-env-reprex/.venv/bin/python` which is what I was expecting.
**related issues**
- https://github.com/quarto-dev/quarto-web/pull/431
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 11,
"created_at": "2022-10-11T19:18:57Z",
"creator": "SamEdwardes",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro",
"windows"
],
"locked": false,
"milestone": "v1.3",
"number": 2801,
"state": "closed",
"title": "Quarto not using python interpreter from virtual environment",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2801"
} |
Referring to an earlier closed issue #1131
I found an additional bug. ( Similar to the earlier problem generating blog.xml. I see more errors when adding a new listing app.qmd in _quarto.yml
```
(aiking) rahuketu@DESKTOP-OAN2697:/mnt/d/rahuketu/programming/portfolio$ rm -rf /m
media/ mnt/
(aiking) rahuketu@DESKTOP-OAN2697:/mnt/d/rahuketu/programming/portfolio$ rm -rf /mnt/d/rahuketu/programming/portfolio/_site/app
app.feed-full-staged app.html app-listing.json
(aiking) rahuketu@DESKTOP-OAN2697:/mnt/d/rahuketu/programming/portfolio$ rm -rf /mnt/d/rahuketu/programming/portfolio/_site/app.
app.feed-full-staged app.html
(aiking) rahuketu@DESKTOP-OAN2697:/mnt/d/rahuketu/programming/portfolio$ rm -rf /mnt/d/rahuketu/programming/portfolio/_site/app.feed-full-staged
(aiking) rahuketu@DESKTOP-OAN2697:/mnt/d/rahuketu/programming/portfolio$ quarto render
custom2qmd.py
app.qmd
blog.qmd
index.qmd
posts/welcome/index.qmd
[]
app.qmd
blog.qmd
index.qmd
posts/welcome/index.qmd
[1/4] app.qmd
[2/4] blog.qmd
[3/4] index.qmd
[4/4] posts/welcome/index.qmd
WARNING: Unable to generate feed 'app.xml'
ERROR: NotFound: No such file or directory (os error 2), remove '/mnt/d/rahuketu/programming/portfolio/_site/app.feed-full-staged'
(aiking) rahuketu@DESKTOP-OAN2697:/mnt/d/rahuketu/programming/portfolio$ quarto --version
1.1.251
(aiking) rahuketu@DESKTOP-OAN2697:/mnt/d/rahuketu/programming/portfolio$
[1/4] app.qmd
[2/4] blog.qmd
[3/4] index.qmd
[4/4] posts/welcome/index.qmd
WARNING: Unable to generate feed 'app.xml'
ERROR: NotFound: No such file or directory (os error 2), remove '/mnt/d/rahuketu/programming/portfolio/_site/app.feed-full-staged'
```
_Originally posted by @Rahuketu86 in https://github.com/quarto-dev/quarto-cli/issues/1131#issuecomment-1242609040_
| {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-10-11T18:57:12Z",
"creator": "Rahuketu86",
"is_pull_request": false,
"labels": [
"file-systems"
],
"locked": false,
"milestone": "v1.4",
"number": 2800,
"state": "open",
"title": "WSL Rendering: Additional Bug related to #1131",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2800"
} |
### Bug description
```
$ quarto -V
1.2.161
$ quarto preview test-prez.qmd --no-execute
```
example-inline.qmd
```
---
format: html
---
Here is an inline eval, the first three numbers are `r 1:3`
If evaluated, the above should read:
> Here is an inline eval, the first three numbers are 1, 2, 3
```
```
Running on OSX 12.6
Apple M1 Pro
$mode
[1] "desktop"
$version
[1] ‘2022.11.0.203’
$long_version
[1] "2022.11.0-daily+203"
$release_name
[1] "Elsbeth Geranium"
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 0,
"created_at": "2022-10-11T18:28:22Z",
"creator": "jthomasmock",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 2799,
"state": "open",
"title": "quarto preview file.qmd --no-execute still evaluates inline code",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2799"
} |
### Bug description
Not sure if this qualifies as bug or feature request: running `quarto preview` on a file such as
```
---
title: Title
---
Text.
{{< include b.qmd >}}
```
the preview is updated when this file is changed, but not when the included `b.qmd` is changed.
Tested with quarto 1.1.251 and 1.2.203 on Pop!_OS 22.04.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-10-11T12:24:24Z",
"creator": "knuesel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 2795,
"state": "open",
"title": "Preview not updated on changes to included files",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2795"
} |
### Bug description
For example with `a.md` containing
```
---
title: Titre
date: now
---
Bonjour.
```
rendering with `quarto render a.md -M lang=fr` produces:
The "DATE DE PUBLICATION" is correctly localized, but the date itself is in English.
Tested with quarto 1.1.251 and 1.2.203 on Pop!_OS 22.04.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-10-11T12:15:49Z",
"creator": "knuesel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2794,
"state": "closed",
"title": "Wrong date locale when setting lang from command-line",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2794"
} |
### Bug description
For example the file `a.md`:
```
---
title: Title
---
Text.
```
rendered with `quarto render a.md -M author=Someone` shows no author in the output, while the author is shown when using `pandoc a.md -o a.html -s -M author=Someone`.
Tested with quarto 1.1.251 and 1.2.203 on Pop!_OS 22.04.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-10-11T12:08:29Z",
"creator": "knuesel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2793,
"state": "closed",
"title": "Cannot set author from command-line",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2793"
} |
I used the `margin-footer`option with an image.
Works well on the index and list pages, but if I go deeper, the image link is wrong. (.md files are in a folder called recipes_md)
the browser looks at http://localhost:7037/recipes_md/img/fondlogo.png
instead of http://localhost:7037/img/fondlogo.png | {
"assignee": null,
"comments": 1,
"created_at": "2022-10-11T10:40:40Z",
"creator": "jcolomb",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": null,
"number": 2797,
"state": "closed",
"title": "margin-footer image: get relative links bad when files in a folder",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2797"
} |
### Bug description
I am trying to run code that works fine in Spyder python 3.9
When I run it in quarto I cannot figure out why I am getting this indentation error
Another issue is when I try to preview/double click on my main data sheet imported from excel in the environment panel I get this error:
The raw source code is pasted below
```{python}
import matplotlib.patches as mpatches
NumSubjects=data['No. Subjects'].astype('str').str.split().str.get(0).str.extract('(\d+)', expand=False).astype(float)
bins=np.histogram(NumSubjects, bins=[0,10,20,50,100, 500] )
ind=np.digitize(NumSubjects, [0,10,20,50,100, 500])
stack=[]
for rn in range(1,len(bins[0])+1):
stack.append([data['Male'].loc[ind==rn].dropna().astype('str').str.extract('(\d+)').astype(float).sum()[0],data['Female'].loc[ind==rn].dropna().astype('str').str.extract('(\d+)').astype(float).sum()[0]])
```
Thank you
version 2022.07.2 Build 576
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-10-11T01:45:39Z",
"creator": "GraceEMc",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "v1.3",
"number": 2789,
"state": "closed",
"title": "Can't fix/find python indentation error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2789"
} |
### Bug description
Quarto version: 1.1.189
System: WSL (Windows 10) with Ubuntu terminal
The added subscription is not loaded in post pages as it does in the main blog page.
I'm adding `margin-header: subscribe.html ` under `website` section in `_quarto.yml`.
In the posts, only the filename "subscribe.html" appears instead of loading the file! You can see this in the screenshot below. You can check the HTML code from the Developer inspect tool.
FYI, the main blog page works fine as can be seen below.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-10-10T18:19:37Z",
"creator": "e-alizadeh",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2787,
"state": "closed",
"title": "Subscribe doesn't show up in the posts ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2787"
} |
### Bug description
Using `fig-align` within a chunk breaks dynamically generated tabsets (`results: asis`).
I left the `knitr: opts_chunk: fig.align:center` in the example because that's what I was originally using which generated this issue.
This might be the same issue with #1456 where the `html` has the `data-layout="center"` divs, but I don't see alignment being set.
````qmd
---
format: html
# knitr:
# opts_chunk:
# fig.align: center
---
## tabset (ok)
::: {.panel-tabset}
### a
```{r}
plot(1:10)
```
### b
```{r}
plot(10:1)
```
:::
## tabset fig-align (ok)
::: {.panel-tabset}
### a
```{r}
#| fig-align: center
plot(1:10)
```
### b
```{r}
#| fig-align: center
plot(10:1)
```
:::
## tabset asis (ok)
::: {.panel-tabset}
```{r}
#| results: asis
writeLines("### a")
plot(1:10)
writeLines("\n")
writeLines("### b")
plot(10:1)
writeLines("\n")
```
:::
## tabset asis fig-align (not ok)
::: {.panel-tabset}
```{r}
#| results: asis
#| fig-align: center
writeLines("### a")
plot(1:10)
writeLines("\n")
writeLines("### b")
plot(10:1)
writeLines("\n")
```
:::
````
<details>
<summary>Image</summary>
</details>
<details>
<summary>Session information</summary>
``` r
quarto::quarto_version()
#> [1] '1.1.251'
devtools::session_info(info = "platform")
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.1 (2022-06-23 ucrt)
#> os Windows 10 x64 (build 19044)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.utf8
#> ctype English_United States.utf8
#> tz America/New_York
#> date 2022-10-10
#> pandoc 2.19.2 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> ──────────────────────────────────────────────────────────────────────────────
rstudioapi::versionInfo()
#> $citation
#>
#> To cite RStudio in publications use:
#>
#> RStudio Team (2022). RStudio: Integrated Development Environment for R. RStudio, PBC, Boston, MA URL http://www.rstudio.com/.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {RStudio: Integrated Development Environment for R},
#> author = {{RStudio Team}},
#> organization = {RStudio, PBC},
#> address = {Boston, MA},
#> year = {2022},
#> url = {http://www.rstudio.com/},
#> }
#>
#>
#> $mode
#> [1] "desktop"
#>
#> $version
#> [1] ‘2022.7.2.576’
#>
#> $long_version
#> [1] "2022.07.2+576"
#>
#> $release_name
#> [1] "Spotted Wakerobin"
```
</details>
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-10-10T16:19:23Z",
"creator": "jmbarbone",
"is_pull_request": false,
"labels": [
"bug",
"wontfix"
],
"locked": false,
"milestone": "v1.3",
"number": 2784,
"state": "closed",
"title": "`fig-align` and `results: asis` break tabsets",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2784"
} |
### Bug description
Hello there, and before anything, thanks for the terrific work.
I'm in a situation where I don't think that quarto is working as intendend. I want to use [hugo shortcodes](https://gohugo.io/content-management/shortcodes/) inside a quarto document and this feature is documented on the [quarto website](https://quarto.org/docs/output-formats/hugo.html#shortcodes). However, when I am trying to use this feature, the quotes inside the shortcodes are transformed into smart quotes which breaks the code.
Here is an example quarto document, `test.qmd`.
```
---
format: hugo
---
{{< figure src="/media/spf13.jpg" title="Steve Francia" >}}
{{{< figure src="/media/spf13.jpg" title="Steve Francia" >}}}
```
And here is the rendered `test.md` document.
```
---
format: hugo
---
{{< figure src=“/media/spf13.jpg” title=“Steve Francia” >}}
{{< figure src=“/media/spf13.jpg” title=“Steve Francia” >}}
```
I am almost certain that I had not this problem before (looking back to some old rendered files). I run Quarto version 1.2.188 on a Win11 computer.
Let me know if I can be of any help!
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-10-10T13:34:55Z",
"creator": "cedricbatailler",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2783,
"state": "closed",
"title": "`quarto render` breaks hugo shortcodes by turning quotes into smart quotes",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2783"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2768
<div type='discussions-op-text'>
<sup>Originally posted by **cadojo** October 9, 2022</sup>
I don't think this exists already — a `--draft` option for the `quarto preview` command would be an awesome way to preview the website with draft blog posts included!</div> | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-10-10T13:13:45Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 2781,
"state": "open",
"title": "Draft Preview Mode",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2781"
} |
### Bug description
Code blocks rendered as html partially hidden by scroll bar, example:
<img width="776" alt="image" src="https://user-images.githubusercontent.com/32404415/194864066-dd7d451b-92cc-49a6-bd74-cb4407eb437d.png">
quarto --version
1.1.251
browser:
Name Firefox
Version 105.0.2
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-10-10T12:15:47Z",
"creator": "miwojc",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 2779,
"state": "open",
"title": "Code blocks rendered as html partially hidden by scroll bar",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2779"
} |
### Bug description
Working in [the same rocker-based devcontainer](https://github.com/360-info/quarto-scaffold/tree/test-container) I set up for #2716, I'm finding that attempting to preview a file or project gives me:
```shell
$ quarto preview
Preparing to preview
ERROR: Function not implemented (os error 38)
```
I should note that the first preview successfully renders files (provided the container has enough memory, as per #2716!) first - the problem appears to be specifically with the preview step.
(The devcontainer is based on the `rocker/tidyverse:4.2.1` image, which uses Ubuntu 20.04 and Quarto 1.1.189. Like #2716, I'm running it from an M1 Mac, so it's emulating the `x86_64` image rather than using a native `arm64` one.)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 9,
"created_at": "2022-10-10T00:38:23Z",
"creator": "jimjam-slam",
"is_pull_request": false,
"labels": [
"bug",
"third-party",
"file-systems"
],
"locked": false,
"milestone": "v1.4",
"number": 2771,
"state": "closed",
"title": "Preview in Docker container: function not implemented (os error 38)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2771"
} |
### Bug description
When writing a book and using biblatex for the pdf bibliography, the latex automatically generates the section called bibliography. However, if I also am generating a website, this uses citeproc with a user setup section, called e.g. references. Thus the PDF version has both a references section (devoid of content) and a bibliography after this. How can I either not have a heading in biblatex or use citeproc with numbers? Additionally, if I go the biblatex route and have margin content enabled, how could I remove it for the autogenerated bibliography section, such that the bibliography can span the full width of the document?
| {
"assignee": "dragonstyle",
"comments": 6,
"created_at": "2022-10-09T21:14:53Z",
"creator": "lcnbr",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2770,
"state": "closed",
"title": "Biblatex extra header",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2770"
} |
### Bug description
When I use `echo: fenced` block option and have multiple tables in the block, the second table loses the sub-caption and the bold formatting of the header row. With `echo: true` everything is fine.
Here is a minimal example
```` md
---
title: results
format: html
---
```{r}
#| echo: fenced
#| label: tbl-fenced
#| tbl-cap: "Two tables"
#| tbl-subcap:
#| - tab1
#| - tab2
gt::gt(head(mtcars))
gt::gt(head(mtcars))
```
````
quarto --version 1.2.198
Ubuntu 18.04.6 LTS
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for Ubuntu Bionic
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 4,
"created_at": "2022-10-09T18:38:52Z",
"creator": "richardjtelford",
"is_pull_request": false,
"labels": [
"bug",
"lint",
"ast"
],
"locked": false,
"milestone": "v1.4",
"number": 2769,
"state": "open",
"title": "formatting problems with multiple tables and echo: fenced",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2769"
} |
### Bug description
Having
``` qmd
---
resource-path: .
---
```
in the file, executing `quarto render main.qmd` results in
```
pandoc
to: html
output-file: main.html
standalone: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
resource-path: .
metadata
document-css: false
link-citations: true
date-format: long
lang: en
Aeson exception:
Error in $: parsing [] failed, expected Array, but encountered String
```
Note the last two lines. `quarto pandoc` doesn't raise this exception.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-10-08T20:49:49Z",
"creator": "jakubkaczor",
"is_pull_request": false,
"labels": [
"bug",
"yaml-validation"
],
"locked": false,
"milestone": "v1.2",
"number": 2765,
"state": "closed",
"title": "Changing `resource-path` raises error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2765"
} |
### Bug description
I have a [chicago-fullnote-bibliography.csl](https://www.zotero.org/styles/chicago-fullnote-bibliography-16th-edition) file placed in ~/.local/share/pandoc/csl/ directory. I can convert the following file with `pandoc` and also with `quarto pandoc`, but using `render` or `preview` subcommands raises “File chicago-fullnote-bibliography.csl not found in resource path”.
``` qmd
---
references:
- type: article-journal
id: WatsonCrick1953
author:
- family: Watson
given: J. D.
- family: Crick
given: F. H. C.
issued:
date-parts:
- - 1953
- 4
- 25
title: 'Molecular structure of nucleic acids: a structure for
deoxyribose nucleic acid'
title-short: Molecular structure of nucleic acids
container-title: Nature
volume: 171
issue: 4356
page: 737-738
DOI: 10.1038/171737a0
URL: https://www.nature.com/articles/171737a0
language: en-GB
csl: chicago-fullnote-bibliography
---
Test[@WatsonCrick1953].
```
I am not sure if it is a bug or if it's intended, but as Quarto uses pandoc under the hood, I think the expected behavior is so that pandoc can find files in its data-dir, that is ~/.local/share/pandoc. I am running quarto 1.1.251 on Arch Linux.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 6,
"created_at": "2022-10-08T20:11:25Z",
"creator": "jakubkaczor",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2764,
"state": "closed",
"title": "Allow pandoc find CSL files",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2764"
} |
### Bug description
Using the `layout` attribute outside of a code chunk is ignored unless `result: asis` is also specified.
````qmd
---
format: html
---
## in chunk
The `layout` attribute works fine inside chunk
```{r}
#| layout-nrow: 1
plot(1:10)
plot(10:1)
```
## outside
The `layout` attribute seems to be ignored
::: {layout-nrow=1}
```{r}
plot(1:10)
plot(10:1)
```
:::
## `results: asis`
Unless `results: asis`?
::: {layout-nrow=1}
```{r foo}
#| results: asis
plot(1:10)
plot(10:1)
```
:::
````
quarto version v1.1.251
```
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.1 (2022-06-23 ucrt)
os Windows 10 x64 (build 19044)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.utf8
ctype English_United States.utf8
tz America/New_York
date 2022-10-07
rstudio 2022.07.1+554 Spotted Wakerobin (desktop)
pandoc 2.18 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown)
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-10-07T19:25:07Z",
"creator": "jmbarbone",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "v1.3",
"number": 2761,
"state": "closed",
"title": "`layout` attribute outside of code chunk doesn't work without `result: asis`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2761"
} |
I am reporting this on behalf of @sharvitomar
> i have been trying to update my RStudio/install Quarto. The process so far has not been successful. RStudio help tab's Check for updates option tells me that the current version is upto date. While installing Quarto from the website, i faced some version conflicts and after resolving I still couldn't find Quarto option in the New Project. I then tried to install the new version of RStudio and R. Currently due to some OS incompatibility, it is crashing.
@sharvitomar -- Please provide your OS and RStudio information. | {
"assignee": null,
"comments": 4,
"created_at": "2022-10-07T15:53:13Z",
"creator": "jooyoungseo",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2760,
"state": "closed",
"title": "Quarto project does not appear even after updating RStudio",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2760"
} |
### Bug description
When we use sub folder name in bibliography keyword in _quarto.yml, we get error.
For example:
`bibliography: references.bib`
works, but
`bibliography: bibFilesAndDocuments/references.bib`
gives following error:
```
File bibFilesAndDocuments.bib not found in resource path
ERROR: File bibFilesAndDocuments.bib not found in resource path
```
I am using Windows 10 with Quarto version 1.1.251
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-10-06T20:34:46Z",
"creator": "ati-ozgur",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 2755,
"state": "closed",
"title": "using subfolders in bibliography does not work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2755"
} |
When rendering citation data for a citable article, a perfectly valid (pandoc) CSL YAML construct inside a citation: element, such as
author:
- family: Doe
given: Jane
is ignored, with an empty author = {} appearing in the BibLaTeX data.
Originated in #2723 | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-10-06T18:20:53Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 2753,
"state": "closed",
"title": "Citation author doesn't allow structures names",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2753"
} |
We currently output HTML and BibLaTeX formatted citations, it would be nice to provide a tabset which includes those + other formats like CSL-JSON, CSL-YAML, BibTeX, etc... | {
"assignee": null,
"comments": 1,
"created_at": "2022-10-06T17:59:39Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"enhancement",
"good-first-issue"
],
"locked": false,
"milestone": "v1.4",
"number": 2752,
"state": "open",
"title": "Add support for multiple citation formats in Appendices",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2752"
} |
### Bug description
I am trying to get the author email to show up in the output of a Quarto file (using RStudio 2022.07.2 on Windows 10 with a version of Quarto I got off the website with the past week (I see v1.1.251 now, might be the same).
The default option below did not seem to work.
```yaml
---
title: "title"
author:
- name: "Name"
email: "[email protected]"
format: html
editor: visual
---
```
Next, I tried to use a lua filter from Pandoc based on what is described [here](https://github.com/quarto-dev/quarto-cli/issues/287#issuecomment-1116392282)), but this doesn't seem to be working for me either.
Pandoc option
```yaml
---
title: "title"
author:
- name: "Name"
correspondence: "yes"
email: "[email protected]"
format: html
editor: visual
filters:
- build/scholarly-metadata.lua
- build/author-info-blocks.lua
- quarto
---
```
I also tried using `true` for correspondence and that doesn't work either.
I copied the `scholarly-metadata.lua` and `author-info-blocks.lua` files from pandoc's github [repository ](https://github.com/pandoc/lua-filters)to a subfolder of the directory that the `qmd` file is in.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 6,
"created_at": "2022-10-06T17:58:02Z",
"creator": "jmh530",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2751,
"state": "closed",
"title": "Author email not showing up",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2751"
} |
### Bug description
Publishing a qmd file with format `hugo`, the `last-modified `date is showing the published date ("March 19, 2022") rather than the date the qmd was last updated (October 6, 2022).
---
date: 2022-03-19
date-format: long
format: hugo
lastmod: last-modified
---
<img width="142" alt="image" src="https://user-images.githubusercontent.com/32419319/194310851-b12d777f-d1df-4803-9271-84f2985a1ad0.png">
The whole qmd file is [available here](https://github.com/cgoo4/quantumjitter/blob/main/content/project/happiness/index.qmd).
The whole output is [published here](https://www.quantumjitter.com/project/happiness/), with both dates printed in the details twistie at the foot of the page per the above snippet.
`lastmod: '`r Sys.Date()`'` in my other Rmarkdown files works okay.
Update 25/11 -- I've rebuilt the site with the html format to make fuller use of all the Quarto features including code-linking and date-modified etc.
RStudio IDE Version running on Mac OS:
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 12_6_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-10-06T12:27:36Z",
"creator": "cgoo4",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 2745,
"state": "open",
"title": "Not showing the last-modified date",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2745"
} |
### Bug description
Issue: For `revealjs` presentations, if `scrollable` is set to `true` in the yaml header, when viewing the slides on mobile, the user cannot swipe past the second slide (the slide that comes after the title slide). Swiping backward from the second slide does not work either.
Minimal qmd example [here](https://github.com/adamoshen/quarto-mobile-scrollable/blob/main/index.qmd) but also included below:
````
---
title: "Can't swipe on mobile"
format:
revealjs:
touch: true
scrollable: true
---
## Slide 1
I can swipe to this slide, but can't swipe any further on mobile.
## Slide 2
slide 2
. . .
blah
## Slide 3
slide 3
## Slide 4
slide 4
````
The rendered slides are [here](https://adamoshen.github.io/quarto-mobile-scrollable/#/title-slide) which you can try on your mobile device. I have also tried using Chrome's devtools to toggle between various other mobile devices such as the iPhone 12 Pro, iPad Air/Mini/Pro, Samsung Galaxy S20 Ultra, etc., none of which are able to swipe past the second slide either.
If you use the sidebar menu to go to the slide titled "Slide 2", swiping does not let you go through the `. . .` pause either.
The current workarounds to this is seem to be:
- display the navigation controls on the slides
- use the sidebar menu to jump between slides, but will need to do this for every slide, and cannot proceed between incremental phases of a slide (e.g. if there is a `. . .` pause)
- click on various portions of the progress bar to jump to a slide (very inaccurate)
```
> sessioninfo::platform_info()
setting value
version R version 4.1.3 (2022-03-10)
os Windows 10 x64 (build 19043)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_Canada.1252
ctype English_Canada.1252
tz America/New_York
date 2022-10-06
rstudio 2022.07.2+576 Spotted Wakerobin (desktop)
pandoc 2.17.1.1 @ C:\\Users\\Adam\\AppData\\Local\\Pandoc\\pandoc.exe
```
```
> quarto --version
1.2.188
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 3,
"created_at": "2022-10-06T04:53:31Z",
"creator": "adamoshen",
"is_pull_request": false,
"labels": [
"bug",
"upstream",
"revealjs"
],
"locked": false,
"milestone": "v1.4",
"number": 2743,
"state": "open",
"title": "`revealjs`: Cannot advance slides past second slide on mobile with `scrollable: true` in yaml header",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2743"
} |
### Bug description
I am trying to cross reference figures in a quarto book based of the example. It was inserted using the visual editor and uploaded to the images folder
But the figure is not showing as a cross reference
How can I fix this? Am I missing something?
2022.07.2 Build 576
Windows 10
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-10-06T03:56:58Z",
"creator": "GraceEMc",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2742,
"state": "closed",
"title": "Figures not identified to cross reference",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2742"
} |
https://github.com/ikatyang/tree-sitter-yaml looks to be unmaintained (last commit was 18 months ago)
Unfortunately, it parses YAML incorrectly: https://github.com/ikatyang/tree-sitter-yaml/issues/29
This is also coming from tree-sitter: https://github.com/quarto-dev/quarto-cli/discussions/2498
We don't have in-house tree-sitter expertise to take over that code base atm, but it feels like we will have to. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-10-05T18:40:46Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 2737,
"state": "open",
"title": "A fork of tree-sitter-yaml looks necessary",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2737"
} |
This happens inconsistently in renders that require puppeteer:
```
$ quarto render mermaid-clip.qmd
ERROR: No inspectable targets
Error: No inspectable targets
at defaultTarget (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/core/cri/deno-cri/chrome.js:63:15)
at Chrome._fetchDebuggerURL (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/core/cri/deno-cri/chrome.js:211:24)
at async Chrome._start (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/core/cri/deno-cri/chrome.js:158:19)
```
| {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-10-05T15:29:21Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"puppeteer"
],
"locked": false,
"milestone": "v1.2",
"number": 2733,
"state": "closed",
"title": "puppeteer bug: \"No inspectable targets\"",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2733"
} |
### Bug description
_No response_
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 13,
"created_at": "2022-10-05T14:41:51Z",
"creator": "GShotwell",
"is_pull_request": false,
"labels": [
"bug",
"third-party"
],
"locked": false,
"milestone": "v1.3",
"number": 2732,
"state": "closed",
"title": "Detect QUARTO_VERSION on Rstudio Connect",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2732"
} |
### Bug description
I create [this repo](https://github.com/huizezhang-sherry/quarto-include-graphics) to demonstrate the unexpected behavior when inserting figures with `knitr::inclue_graphics()` in qmd.
There are two qmd files:
1) `main.qmd `under the top level, and
2) `main-analysis.qmd` in the `analysis` folder.
A single command is included in both qmd: `knitr::include_graphics(here::here("figures/R_logo.png"))`
Everything is fine when knitting the top level main.qmd, but when knitting `main-analysis.qmd`, the figure is not loaded when viewed in the Viewer window (also not in the browser when clicking the icon Show in a new window):
<img width="1904" alt="Screen Shot 2022-10-05 at 2 34 11 pm" src="https://user-images.githubusercontent.com/36781502/193976546-78d80826-8240-4f31-b315-fac74edb1b58.png">
The figure does appear when opening the `main-analysis.html`.
A quick inspection of HTML shows that the `figures` folder doesn't seem to be copied across
Maybe this is a bug?
Additional info:
- Rstudio IDE version: 2022.02.2
- Operating system: macOS Monterey version 12.5.1
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 3,
"created_at": "2022-10-05T03:50:32Z",
"creator": "huizezhang-sherry",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2730,
"state": "closed",
"title": "figures not rendered in local host when qmd is placed in a sub-directory",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2730"
} |
### Bug description
I just tested the Mermaid and Graphviz examples and Mermaid diagrams aren't rendered when the format is Hugo.
Graphviz diagrams are rendered. Mermaid diagrams are rendered if I chose html as the format.
Here is what I get with Hugo from the Mermaid examples of the documentation:
```
flowchart LR
A[Hard edge] --> B(Round edge)
B --> C{Decision}
C --> D[Result one]
C --> E[Result two]
```
and
```
sequenceDiagram
participant Alice
participant Bob
Alice->>John: Hello John, how are you?
loop Healthcheck
John->>John: Fight against hypochondria
end
Note right of John: Rational thoughts <br/>prevail!
John-->>Alice: Great!
John->>Bob: How about you?
Bob-->>John: Jolly good!
```
For info, here is my front matter:
```
---
title: Test
execute:
error: true
format: hugo
---
```
OS: 5.19.12-arch1-1
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-10-05T02:28:08Z",
"creator": "prosoitos",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2729,
"state": "closed",
"title": "Mermaid diagrams not rendered with format: hugo",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2729"
} |
### Bug description
I was looking at the "Quarto presentations using Reveal.js" gallery presentation.
On slide 22 it says to press 'm' to toggle the menu open and closed.
However, for me it only opens when pressing 'm '. Pressing 'm' again after opening it does *NOT* close it.
Browser: Safari 16.0
OS: macOS 12.6 (Monterey)
Viewed slide:
https://quarto.org/docs/presentations/revealjs/demo/#/easy-navigation
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 2,
"created_at": "2022-10-04T20:40:01Z",
"creator": "michaelaye",
"is_pull_request": false,
"labels": [
"bug",
"revealjs"
],
"locked": false,
"milestone": "v1.4",
"number": 2728,
"state": "open",
"title": "Presentation: Menu toggle via 'm' key doesn't toggle",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2728"
} |
From a discussion with @dragonstyle
> general thoughts : maybe we should have a dev version (or pre-release version) of the reference pages ? (probably more realistic than a dev version of the all doc).
> It would be very nice to have something like this (or perhaps even a version in the YAML schema that we can use to denote when a property become supported or ceased being supported). That would make it easy to generate version specific reference or a global reference that contains release information about availability... We still don't really have a great / consistent approach to documentation versions.
_Originally posted by @dragonstyle in https://github.com/quarto-dev/quarto-cli/issues/2718#issuecomment-1266974157_
Opening this to track the idea. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-10-04T13:50:04Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"yaml-validation"
],
"locked": false,
"milestone": "Future",
"number": 2724,
"state": "open",
"title": "Improve YAML schema to get notion of version availability",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2724"
} |
### Bug description
<https://quarto.org/docs/reference/metadata/citation.html> displays this example:
```
---
citation:
type: article-journal
container-title: ACM Transactions on Embedded Computing Systems
volume: 21
issue: 2
date: 3/2022
issn: 1539-9087
doi: 10.1145/3514174
---
```
Issues:
- `date` is not a valid CSL variable; use `issued` instead.
- `3/2022` is not a valid CSL YAML date format; only ISO-8601 dates are accepted, e.g., `2022`, `2022-03`, `2022-03-29` etc.
- Hence `date: 3/2022` above should be replaced by `issued: 2022-03`.
Further suggestions:
- In quarto output, citation metadata are introduced as `BibTeX citation:` -- which, strictly speaking is not true: Neither `url`, nor `doi`, `langid` exist in BibTeX -- while the BibTeX variant natbib has `url` and `doi`, many others that appear in quarto output, including `langid`, `eventdate`, `urldate`, `annote` are exclusive to BibLaTeX.
- It might be useful to offer output in CSL YAML format instead or alongside BibLaTeX.
- Possibly CSL JSON, too, which would allow lossless import into, e.g., Zotero. (CSL YAML import requires the BetterBibTeX plugin.)
- Empty BibLaTeX fields like `editor = {},` should be filtered out to reduce clutter.
- Markdown syntax in, e.g., `title` fields should be converted to the corresponding (La)TeX commands.
- E.g., `title: Foo **bar**` should be converted to `title = {Foo \textbf{bar}},
- Hence it might be easiest to use pandoc itself for converting `citation:` data from CSL to BibLaTeX, see <https://pandoc.org/MANUAL.html#specifying-bibliographic-data>.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 11,
"created_at": "2022-10-04T11:15:30Z",
"creator": "njbart",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2723,
"state": "closed",
"title": "Citation metadata: documentation issue",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2723"
} |
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