page_content
stringlengths 0
46.9k
| metadata
dict |
|---|---|
### Bug description
The [title-block html template](https://github.com/quarto-dev/quarto-cli/blob/af5c051e8251d3a0535f2e8dcf62d011259c8fb2/src/resources/formats/html/templates/title-block.html) is applied to every page of an HTML book. It would be nice to have (partial) template which runs only on the book's title page and one which runs only on the other pages.
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": "2022-08-31T14:44:39Z",
"creator": "ThierryO",
"is_pull_request": false,
"labels": [
"bug",
"enhancement",
"books"
],
"locked": false,
"milestone": "v1.4",
"number": 2235,
"state": "open",
"title": "different template for html book title page",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2235"
} |
### Bug description
It's been a while since I reported a bug, here is a new one introduced in v1.1 (introduced between v1.1.67 and v1.1.149, and still in v1.1.165 or v1.2.15, likely to be c56d23e7690a5aec4e99b26310ffe12783807709).
This issue is platform/IDE independent.
Issue possibly related to #2166.
````
---
format: html
---
::: {#thm-line}
## Line (with or without the Lua filter error occurs)
```
1+1
```
:::
````
```bash
pandoc
to: html
output-file: Untitled-1.html
standalone: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
Error running filter /Applications/quarto/share/filters/crossref/crossref.lua:
/Applications/quarto/share/filters/crossref/crossref.lua:97: bad argument #1 to 'insert' (table expected, got nil)
stack traceback:
/Applications/quarto/share/filters/crossref/crossref.lua:97: in function 'tprepend'
/Applications/quarto/share/filters/crossref/crossref.lua:2057: in local 'fn'
/Applications/quarto/share/filters/crossref/crossref.lua:1154: in function </Applications/quarto/share/filters/crossref/crossref.lua:1148>
```
Currently the only way to use "Theorems and Proofs", is to fully specify those.
````
::: {#thm-line}
## Label
Some text
```
1+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://yihui.org/issue/#please-format-your-issue-correctly) 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": 0,
"created_at": "2022-08-31T12:24:15Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2228,
"state": "closed",
"title": "Theorems and Proofs with code blocks and no header/label cause Lua filter to error out",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2228"
} |
### Bug description
Pandoc offers two ways to create a block image,
```
```
and
```
![My Caption][ref]
[ref]: file.png
```
BUT, if you want to cross-reference these only the first works. See this testcase:
~~~markdown
---
title: "Crossref Test"
author: Jane Doe
lang: en
verbose: true
---
# Introduction #
Sed illum minimum, est mægna alienum mentitum ne.
{#fig-elephant}
Sint meis quo et (see @fig-elephant), vis ad fæcete dolorem!
![This is a medieval conception of an elephant fighting a dragon.][Elephant]{#fig-elephant2}
Ad pro quod definitiΓΈnem (see @fig-elephant2), mel no laudem delectus, te mei prompta maiorum pΓΈnderum!
[Elephant]: Elephant.jpg
~~~
Image used:
The result is this:
-----
macOS 12.5.1 and Quarto Version: 1.1.165
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": "2022-08-31T10:46:29Z",
"creator": "iandol",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2227,
"state": "closed",
"title": "Allow cross-referencing to work with reference-link images",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2227"
} |
### Bug description
Hello,
After creating a new Quarto blog project, I immediately get a permissions error (OS Error 5) when attempting to render `index.qmd` or `about.rmq`. Sometimes it'll render the website fine, but then I'll get the same error when clicking "About." Both R and RStudio are up to date. (RStudio 2022.07.1+554; R 4.2.1) I am the administrator on my PC, which shouldn't cause any permission issues. I didn't make any changes to the default template of the blog, this happened on my first attempt to render.
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": "2022-08-31T02:23:20Z",
"creator": "dinanajiarch",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "Future",
"number": 2225,
"state": "closed",
"title": "\"Access is denied\" (os error 5) when rendering. ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2225"
} |
### Bug description
A previously working document just failed after upgrading via `git pull` and `./configure.sh`. Then I used the installer, and it has the same error (v 1.1.165). This was working 2 days ago. When I do `quarto preview` the error I see is:
```
~/.../R_Pkgs/CSR(master β)> quarto preview
ERROR: Project _quarto.yml validation failed.
In file _quarto.yml
(line 9, columns 3--13) property name prefs-text is invalid
8: cookie-consent: true
9: prefs-text: "Cookies are used to track visits only"
~~~~~~~~~~
10: body-footer: <script data-goatcounter="https://chemospec.goatcounter.com/count" async src="//gc.zgo.at/count.js"></script>
βΉ The error happened in location website:prefs-text.
```
This is on MacOS 12.5.1. `quarto check` responds OK at each point. The full repo should you need it is [here](https://github.com/bryanhanson/CSR). | {
"assignee": null,
"comments": 1,
"created_at": "2022-08-31T02:18:02Z",
"creator": "bryanhanson",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2224,
"state": "closed",
"title": "Property name prefs-text is invalid",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2224"
} |
Our changes to override gt's default styles are over-eager and also change custom styles. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-08-30T19:54:42Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "v1.2",
"number": 2222,
"state": "closed",
"title": "fix style override for gt",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2222"
} |
It is probably a pandoc issue.
but would it be possible that the
```yaml
tbl-cap-location: top
fig-cap-location: top
```
work for docx output?
For the moment, they don't have any effect. | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-08-30T18:32:32Z",
"creator": "olivroy",
"is_pull_request": false,
"labels": [
"bug",
"crossref",
"tables",
"docx"
],
"locked": false,
"milestone": "v1.4",
"number": 2221,
"state": "open",
"title": "Add possibility to change the table, figure captions (docx)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2221"
} |
### Bug description
Hello
I was trying to change the font of a Reveal presentation following the themes in GitHub.
I was doing it by adding:
```scss
/*-- scss:defaults --*/
@import url(http://fonts.googleapis.com/css?family=Montserrat:300,300italic,800,800italic);
```
to my SCSS file.
Unfortunately, when Quarto renders the presentation it creates a `Quarto.css` file in `./rppresentation_files/libs/revealjs/dist/theme` with all the CSS rules adding another importing rule after mine, like this:
```css
@import"http://fonts.googleapis.com/css?family=Montserrat:300,300i,800,800i";@import"./fonts/source-sans-pro/source-sans-pro.css";:root{ ...
```
This overrules my Montserrat font.
I am running Linux Mint 21, with Quarto 1.1.163 and RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for Ubuntu 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://yihui.org/issue/#please-format-your-issue-correctly) 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": "2022-08-30T18:14:15Z",
"creator": "rgouveiamendes",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2219,
"state": "closed",
"title": "Font import through SCSS file",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2219"
} |
### Bug description
Trying to render any document with cache is not possible resulting in the message
```
The jupyter-cache package is required for cached execution
```
from [here](https://github.com/quarto-dev/quarto-cli/blob/9f91bdb4fbcc326944f8aea560f3a86797e2459e/src/resources/jupyter/notebook.py#L103)
The .qmd has nothing except for containing only Julia cells:
````
---
title: "test_quarto"
execute:
cache: true
---
## Quarto
Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
```{julia}
1
```
````
I use Windows. I do not know how to debug the error as I do have jupyter_cache, and my own python installation can find it without issue. The directory containing `jcache` is also in PATH
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": 4,
"created_at": "2022-08-30T16:13:07Z",
"creator": "justanothergithubber",
"is_pull_request": false,
"labels": [
"bug",
"windows"
],
"locked": false,
"milestone": "v1.2",
"number": 2217,
"state": "closed",
"title": "Julia cache does not seem to work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2217"
} |
Via Max Kuhn:
> Does quarto have built-in environmental variables (or similar) during qmd compilation that reflects the output type? Similar to knitr::is_html_output() but cross-language and more specific about the output type?
> Iβm trying to write single qmd files for books that get compiled in different formats. Any tools (e.g. chunk options etc) that make that easier would be fantastic.
| {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-08-30T16:04:27Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 2216,
"state": "open",
"title": "communicate format output to all engines ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2216"
} |
### Bug description
Hi, I use [BasicTeX](https://tug.org/mactex/morepackages.html), a small TeX Live 2022 install for macOS. When rendering to PDF I get a permission error when `tlmgr` tries to install a required package.
It would be nice if **I could enter my password when required**. I can also manually run `tlmgr` based on the output from quarto, but I do appreciate the fact quarto tries to do this for me so I just wish it could handle authorisation...
```
βΆοΈ quarto render Quarto.qmd --to pdf
pandoc
to: latex
output-file: Quarto.tex
standalone: true
pdf-engine: xelatex
variables:
graphics: true
tables: true
default-image-extension: pdf
toc: true
number-sections: true
metadata
documentclass: scrartcl
classoption:
- DIV=11
- numbers=noendperiod
papersize: letter
header-includes:
- '\KOMAoption{captions}{tableheading}'
block-headings: true
title: Quarto
author: Jane Doe
lang: en
bibliography:
- /Users/ian/.local/share/pandoc/Core.json
title-block-banner: true
colorlinks: true
running xelatex - 1
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
updating tlmgr
updating existing packages
finding package for tcolorbox.sty
> 1 package to install
> installing tcolorbox (1 of 1)
ERROR: tlmgr returned a non zero status code
You don't have permission to change the installation in any way,
specifically, the directory /usr/local/texlive/2022basic/tlpkg/ is not writable.
Please run this program as administrator, or contact your local admin.
tlmgr: An error has occurred. See above messages. Exiting.
```
------------
Quarto version:
```
βΆοΈ quarto check
[β] Checking Quarto installation......OK
Version: 1.1.163
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.3
Path: /Users/ian/.pyenv/versions/3.10.3/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.14
[β] 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://yihui.org/issue/#please-format-your-issue-correctly) 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": 0,
"created_at": "2022-08-30T16:01:29Z",
"creator": "iandol",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 2215,
"state": "open",
"title": "tlmgr cannot install using macOS 12.5.1 and a BasicTeX install",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2215"
} |
### Bug description
I had a document with a graphviz chart, and when I rendered to PDF I got the following error:
```
β· quarto render Quarto.qmd --to pdf
ERROR: NotFound: No such file or directory (os error 2)
Exception: quarto exited with 1
[tty 150], line 1: quarto render Quarto.qmd --to pdf
```
Rendering to HTML and there was no problem, and rereading the docs I realised I needed to install Chromium. After installing (`quarto install tool chromium`) then the error message goes away. It would be good if Quarto could offer a more descriptive error message when chromium is required.
```
βΆοΈ quarto check
[β] Checking Quarto installation......OK
Version: 1.1.163
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.3
Path: /Users/ian/.pyenv/versions/3.10.3/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
macOS 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://yihui.org/issue/#please-format-your-issue-correctly) 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": 34,
"created_at": "2022-08-30T15:54:35Z",
"creator": "iandol",
"is_pull_request": false,
"labels": [
"bug",
"mermaid",
"chromium"
],
"locked": false,
"milestone": "v1.3",
"number": 2214,
"state": "closed",
"title": "Cryptic error message when chromium is not yet installed",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2214"
} |
### Bug description
In a quarto website/blog project, I put this in `_quarto.yml` to set the "default" author:
```yaml
format:
html:
author: someAuthor
```
And I don't want to display it on the main page, so I put `author: Null` in `index.qmd`. This worked well with quarto ported with RStudio 2022.07.1 (seems to be v1.0.36), but after I installed quarto 1.1.163 in my system (Kubuntu 22.04.1), the project refuses to render, saying
```
ERROR: Validation of YAML front matter failed.
ERROR: In file index.qmd
(line 3, columns 9--12) Key author has value Null, which must be an object
2: title: "test"
3: author: Null
~~~
4: ---
β The value Null is a null value.
βΉ The error happened in location author.
```
I installed the 1.2.15 official pre-release and the problem remains.
The problem can be minimally reproduced by
1. Open a new quarto website project in RStudio
2. In `_quarto.yml`, set
```yaml
format:
html:
author: someAuthor
```
3. And set `author` to be `Null`, `null` or `~` in `index.qmd`. (BTW I remember having `author: null` renders as if `null` is a string with quarto 1.0.36, unsure though)
I guess it's the YAML validator that blocks the page from rendering. Since it worked fine in the earlier version, I suppose it's valid YAML...
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": "2022-08-30T13:23:16Z",
"creator": "mksinicus",
"is_pull_request": false,
"labels": [
"bug",
"yaml-validation"
],
"locked": false,
"milestone": "v1.3",
"number": 2210,
"state": "closed",
"title": "Project-wide YAML metadata cannot be suppressed",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2210"
} |
### Bug description
I have see this type of issue several time already: https://github.com/quarto-ext/lightbox/issues/9
````
Error running filter lightbox:
Could not find executable lightbox
````
It seems it is confusing for user what this means, especially as they tried to use an extension and the error does not mention anything. When you know filter can also be JSON filter, the error message makes sense: Extension was not found somehow.
What about making this error more clear to user ? We don't have specific syntax to know the filter asked is supposed to be in an extension, but we can assume most of the time that will be the usage (instead of JSON filter for Pandoc).
Maybe we can improve the error message saying. "If you tried to use an extension, please do check the extension is correctly installed for your project", or something like that.
Just an idea and opening this issue to get feedback on this situation when that happens.
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": "2022-08-30T09:06:26Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"duplicate"
],
"locked": false,
"milestone": null,
"number": 2207,
"state": "closed",
"title": "Better error when extension filter is not found",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2207"
} |
### Context
In looking to develop a [Format for Confluence](https://github.com/quarto-dev/quarto-cli/issues/2038), I've been investigating a minimal HTML reset format. It seems that some `link`s can't currently be removed from the HTML format when `minimal=true`. These scripts would be stripped out by Confluence so it seems wise to update the CLI to support a true HTML reset.
### Steps to Reproduce
1. Build the following example format
_extension.yml
```yaml
title: Min HTML Format
author: Al Manning
version: 0.0.1
contributes:
format:
html:
theme: none
minimal: true
template: min-template.html
```
min-template.html
```html
$body$
```
min-example.qmd
``` quarto
---
title: "Min HTML Format"
format: min-html
---
```
2. Expected Render
min-example.html
``` html
<html><body></body></html>
```
3. Actual Render
min-example.html
``` html
<html><head>
<link href="example_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
<link href="example_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"></head><body></body></html>
``` | {
"assignee": "allenmanning",
"comments": 4,
"created_at": "2022-08-30T08:03:49Z",
"creator": "allenmanning",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": null,
"number": 2206,
"state": "closed",
"title": "Enhancement: Min HTML Template / full reset with no scripts",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2206"
} |
I followed the following wizard in RStudio:
1) `New Project`
2) `New Directory`
3) `Quarto book`
4) typed in the directory name
Create project as subdirectory of: [on a local drive] D:/directoryname
5) select "use renv with this project"
6) click `Create Project`
I got this:
'C:/Program' is not recognized as an internal or external command,
operable program or batch file. | {
"assignee": "jjallaire",
"comments": 11,
"created_at": "2022-08-30T04:16:22Z",
"creator": "linlennypinawa",
"is_pull_request": false,
"labels": [
"bug",
"upstream"
],
"locked": false,
"milestone": "v1.2",
"number": 2208,
"state": "closed",
"title": "problem with creation of quarto book in RStudio IDE",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2208"
} |
I started this discussion a few months ago. I have a `book` project with a collection of chapters, which I'd like to render as separate `revealjs` presentations. Every way I've tried to do this either renders to the `html` format or returns the error `WARNING: The revealjs format is not supported by book projects`. But this exact workflow will work with `website` projects, as indicated by [this tweet](https://twitter.com/KellyBodwin/status/1552649491815227392), which I believe includes a slide from @mine-cetinkaya-rundel 's presentation at rstudio::conf(2022). So it seems to me like this is a bug.
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1433
<div type='discussions-op-text'>
<sup>Originally posted by **dhicks** July 16, 2022</sup>
I'm a university professor. For one of my classes, I like to present my lecture notes as both a presentation (eg, slidy or revealjs, for use in class) and a unified website (eg, gitbook, for students to consult out of class). With Rmarkdown, I could do this by having two different recipes in a Makefile: one that uses `bookdown::render_book()` to create the single gitbook, and another that uses `rmarkdown::render()` to create a presentation for each separate chapter `Rmd` file.
I'm playing around with Quarto, trying to figure out how I might be able to do this. Something like `quarto render chfile --to revealjs` in a book project generates a warning: `WARNING: The revealjs format is not supported by book projects`. (This should probably be an error, because Quarto doesn't go on to executive any code chunks or produce any output files.) Including `revealjs` as a `format` in `_quarto.yml` does the same thing. I tried setting up a separate metadata file, `_slides.yml`, but `quarto render` doesn't seem to have any flags to select which metadata file should be used.
So currently the best option seems to be to stick with `rmarkdown::render()` for the slides? </div> | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-08-30T00:36:49Z",
"creator": "dhicks",
"is_pull_request": false,
"labels": [
"bug",
"needs-discussion"
],
"locked": false,
"milestone": "v1.2",
"number": 2200,
"state": "closed",
"title": "book chapters can't be rendered as separate revealjs presentations",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2200"
} |
We should have a `lst-cap-location` to control the location of listing captions in the same way that we control figure and table caption locations.
While we're at it, `lst-cap-location` should also be controllable from `cap-location`. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-08-29T20:25:31Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 2196,
"state": "open",
"title": "`lst-cap-location`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2196"
} |
````
```{#lst-prefs .python lst-cap="Sum Function" filename=sum.py}
def sum(a, b):
sum = a + b
print(f'Sum: {sum}`)
return sum
```
````
<img width="896" alt="image" src="https://user-images.githubusercontent.com/285675/187291268-12dd5601-c98f-4502-8b6a-3517c5b949a0.png">
(Thanks, @jpmorr)
| {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-08-29T20:22:27Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2195,
"state": "closed",
"title": "listing caption interacts badly with listing filename",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2195"
} |
The following error message is very hard to read:
```
Key sidebar has value background: primary
logo: "images/logo.png"
...
- href: schedule.qmd
text: Schedule, which must be `true` or `false`
```
There are two problems here.
## Formatting
We can improve formatting in at least three ways. If we're going to print object values that violate the schema, we should always print them by themselves instead of wrapping text around them. That error should then read like so:
```
Key sidebar has value
background: primary
logo: "images/logo.png"
...
- href: schedule.qmd
text: Schedule
which must be `true` or `false`
```
I think we also shouldn't use the work `key`, we should use the word `field`.
Finally, when we're emitting error messages in contexts that have no color formatting, we should consistently use quotes (as we already do in `'true'` and `'false'`). The error should read
```
Field "sidebar" has value
background: primary
logo: "images/logo.png"
...
- href: schedule.qmd
text: Schedule
which must be "true" or "false"
```
## Better information in the case of short suggestions
This error is especially bad, though, in that it suggests that the replacement value _has_ to be `true` or `false`.
The problem is that although these replacements work, they are not the only options. The other alternatives, though, are more complicated schemas, and our short error report doesn't show that.
Our error heuristics should try to offer short suggestions, but they should not mislead.
| {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-08-29T15:59:58Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"yaml-validation"
],
"locked": false,
"milestone": "v1.2",
"number": 2191,
"state": "closed",
"title": "Improve YAML validation error messages",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2191"
} |
We had a bad validation error come from https://github.com/rstudio-conf-2022/teach-ds-course-website/blob/ef90e6111411bc9d2b6feb4b2e5b49dc6c24e55b/_quarto.yml under our v1.1 schema closure.
### Context
We recently closed a number of schemas, which introduces a large-scale change in the validation behavior. In this case specifically, `text` was mistakenly not a part of the `navigation-item` schema, which means that under the new schema, yaml validation fails (correctly, although using a wrong schema) :
- every array entry in `website:sidebar:contents` fails
- same for every array entry in `website:sidebar:tools`
- as a result, the entries `website:sidebar` and `website` fail
### Heuristics gone bad
We have heuristics that try to find "small" changes to fix the problem. Unfortunately, in this case, the small change suggested is to replace the `website:sidebar` object with `true` or `false`. It does this because we have a heuristic that says "a lot of internal errors to one object probably mean a single larger error in a containing object".
That heuristic is good in the case of interactive editing, where we expect errors to show up one at a time. But in this case, the schema change caused all errors to show up at once.
## Possible solutions
(All of these are a significant amount of work, but I'm writing them here so I don't need to keep them in my head for when I come back to this problem later.)
- We have a mechanism for identifying the "type" of error (`schemaPath`). Many errors with the same `schemaPath` should be an indication that it's actually the same error, and we should consider reporting that one instead.
- The bad heuristic comes from looking at the entire YAML at once. In this case, if we forced ourselves to look at "the first error to happen", then the error would be better, as long as we had a good definition of "first". Currently, we scan the full YAML object for errors. Instead, we could run the entire validation procedure on a sequence of YAML objects, from empty object to full YAML object, and then report the errors as they come. This is an attempt to mimic the "incremental typing" behavior, under which our validation works well.
- The logic of this is that there's always a path from a valid YAML (the empty object `{}`) to an invalid YAML (this object, `this`). Finding an error on a simpler partial YAML on the path from `{}` to `this` might make better validation errors. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-08-29T15:45:46Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"yaml-validation"
],
"locked": false,
"milestone": "Future",
"number": 2190,
"state": "open",
"title": "yaml validation error heuristics are not tuned for schema changes",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2190"
} |
### Bug description
This was encounter in https://community.rstudio.com/t/quarto-unable-to-locate-r-installation/144340/5
In some installation, it is possible that R defaults packages are not loaded. See https://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html
> If you want a different set of packages than the default ones when you start, insert a call to [options](https://stat.ethz.ch/R-manual/R-devel/library/base/help/options.html) in the β.Rprofileβ or βRprofile.siteβ file. For example, options(defaultPackages = character()) will attach no extra packages on startup (only the base package) (or set R_DEFAULT_PACKAGES=NULL as an environment variable before running R). Using options(defaultPackages = "") or R_DEFAULT_PACKAGES="" enforces the R system default.
Setting that and not loading **utils** will make Quarto fail the check
https://github.com/quarto-dev/quarto-cli/blob/2430b604b7651f9d40ee98bdd7b479208290eac0/src/resources/capabilities/knitr.R#L10-L11
Reprex:
````powershell
# No ENV set
> $env:R_DEFAULT_PACKAGES=$null
> quarto check knitr
(-) Checking R installation...........
[>] Checking R installation...........OK
Version: 4.2.1
Path: C:/PROGRA~1/R/R-42~1.1
LibPaths:
- C:/Users/chris/AppData/Local/R/win-library/4.2
- C:/Program Files/R/R-4.2.1/library
rmarkdown: 2.16.1
[>] Checking Knitr engine render......OK
# Setting the env var
> $env:R_DEFAULT_PACKAGES="NULL"
> quarto check knitr
(-) Checking R installation...........
Error in `packageVersion()`:
! could not find function "packageVersion"
Backtrace:
β
1. ββbase::cat(...)
2. ββbase::paste0(...)
Execution halted
[>] Checking R installation...........(None)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
````
By just namespacing our usage of `packageVersion()` we could avoid that
```r
> Rscript --vanilla -e "packageVersion('rmarkdown')"
Error in packageVersion("rmarkdown") :
could not find function "packageVersion"
Execution halted
> Rscript --vanilla -e "utils::packageVersion('rmarkdown')"
[1] '2.16.1'
```
| {
"assignee": "cderv",
"comments": 0,
"created_at": "2022-08-29T13:32:17Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2187,
"state": "closed",
"title": "Correctly namespace usage of R default package functions like utils",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2187"
} |
Would it be possible to enable the quarto options for code folding and linking to the hugo format (as per html)?
```
format:
hugo:
code-fold: true
code-link: true
``` | {
"assignee": "jjallaire",
"comments": 7,
"created_at": "2022-08-29T13:30:41Z",
"creator": "cgoo4",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.2",
"number": 2186,
"state": "closed",
"title": "Hugo code folding and linking",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2186"
} |
### Bug description
<img width="960" alt="image" src="https://user-images.githubusercontent.com/786803/187203159-ab45f23a-5612-483e-8006-b719c47350dd.png">
I am generating a blog site with quarto on windows 11 using vscode. Freeze directory is not generated on running quarto render command on cmd.exe or using Quarto render project command in vscode. (Additionally, I tried creating a _freeze directory manually before rendering . That directory got deleted after render command was executed)
My _quarto.yml is as follows
```
project:
type: website
pre-render: custom2qmd.py
website:
title: "qblog"
navbar:
right:
- about.qmd
- icon: github
href: https://github.com/
- icon: twitter
href: https://twitter.com
format:
html:
theme: cosmo
css: styles.css
execute:
freeze: auto
```
and _metadata.yml in posts directory is as follows:-
```
# options specified here will apply to all posts in this folder
# freeze computational output
# (see https://quarto.org/docs/projects/code-execution.html#freeze)
freeze: auto
# Enable banner style title blocks
title-block-banner: true
comments:
utterances:
repo: quarto-dev/quarto-docs
```
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": "2022-08-29T12:46:46Z",
"creator": "Rahuketu86",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2185,
"state": "closed",
"title": "Freeze directory not formed on windows 11",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2185"
} |
I was not able to create quarto document.
When I tped `quarto check` in cmd,an error occorred .
```
C:\Users\yuliang18\Documents>quarto check
[>] Checking Quarto installation......OK
Version: 1.1.149
Path: C:\Users\yuliang18\AppData\Local\Programs\Quarto\bin\
CodePage: unknown
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.8.13 (Conda)
Path: D:/programfiles/anaconda/python.exe
Jupyter: 4.9.2
Kernels: ir, javascript, python3
[>] Checking Jupyter engine render....OK
[>] Checking R installation...........OK
Version: 4.2.1
Path: D:/Program Files/R/R-4.2.1
LibPaths:
- D:/Program Files/R/R-4.2.1/library
rmarkdown: 2.16
(\) Checking Knitr engine render......ERROR: Error in source(file.path(res_dir, "hooks.R"), local = TRUE) :
C:\Users\yuliang18\AppData\Local\Programs\Quarto\share/rmd/hooks.R:787:3: unexpected symbol
786: comment_chars <- knitr_engine_comment_chars[[engine]] %||% "#"
787: comment_start
^
Calls: .main -> source
Ν£οΏ½οΏ½
[>] Checking Knitr engine render......OK
``` | {
"assignee": null,
"comments": 3,
"created_at": "2022-08-29T02:22:59Z",
"creator": "antonio-yu",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 2184,
"state": "closed",
"title": ">quarto check . Knitr engine render error.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2184"
} |
### Bug description
Render this document fails using the latest nightly release of Quarto
```
---
format: pdf
---
```
Example in R
``` r
file.create("test.qmd")
#> [1] TRUE
writeLines(c("---", "format: pdf", "---"), "test.qmd")
tryCatch(quarto::quarto_render("test.qmd"),
error = function(cnd) {
cnd$stderr
})
#> [1mpandoc [22m
#> to: latex
#> output-file: test.tex
#> standalone: true
#> pdf-engine: xelatex
#> variables:
#> graphics: true
#> tables: true
#> default-image-extension: pdf
#>
#> [1mmetadata[22m
#> documentclass: scrartcl
#> classoption:
#> - DIV=11
#> - numbers=noendperiod
#> papersize: letter
#> header-includes:
#> - '\KOMAoption{captions}{tableheading}'
#> block-headings: true
#>
#> [1mrunning xelatex - 1[22m
#> This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
#> restricted \write18 enabled.
#> entering extended mode
#>
#> [1mupdating tlmgr[22m
#>
#> [1mupdating existing packages[22m
#> [1m
#> compilation failed- error[22m
#> see test.log for more information.
#> [1] "\033[1mpandoc \033[22m\n to: latex\n output-file: test.tex\n standalone: true\n pdf-engine: xelatex\n variables:\n graphics: true\n tables: true\n default-image-extension: pdf\n \n\033[1mmetadata\033[22m\n documentclass: scrartcl\n classoption:\n - DIV=11\n - numbers=noendperiod\n papersize: letter\n header-includes:\n - '\\KOMAoption{captions}{tableheading}'\n block-headings: true\n \n\033[1mrunning xelatex - 1\033[22m\n This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)\n restricted \\write18 enabled.\n entering extended mode\n \n\033[1mupdating tlmgr\033[22m\n\n\033[1mupdating existing packages\033[22m\n\033[1m\ncompilation failed- error\033[22m\nsee test.log for more information.\n"
quarto::quarto_version()
#> [1] '1.1.149'
tinytex::tlmgr_version()
#> tlmgr revision 63068 (2022-04-18 07:58:07 +0200)
#> tlmgr using installation: /Users/qiushi/Library/TinyTeX
#> TeX Live (https://tug.org/texlive) version 2022
xfun::session_info()
#> R version 4.2.0 (2022-04-22)
#> Platform: aarch64-apple-darwin20 (64-bit)
#> Running under: macOS Monterey 12.5
#>
#> Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8
#>
#> Package version:
#> askpass_1.1 base64enc_0.1.3 bslib_0.4.0 cachem_1.0.6
#> callr_3.7.2 cli_3.3.0 clipr_0.8.0 compiler_4.2.0
#> curl_4.3.2 digest_0.6.29 evaluate_0.16 fansi_1.0.3
#> fastmap_1.1.0 fs_1.5.2 glue_1.6.2 graphics_4.2.0
#> grDevices_4.2.0 highr_0.9 htmltools_0.5.3 jquerylib_0.1.4
#> jsonlite_1.8.0 knitr_1.40 later_1.3.0 lifecycle_1.0.1
#> magrittr_2.0.3 memoise_2.0.1 methods_4.2.0 openssl_2.0.2
#> packrat_0.8.1 pillar_1.8.1.9000 pkgconfig_2.0.3 processx_3.7.0
#> ps_1.7.1 purrr_0.3.4 quarto_1.2.0.9000 R.cache_0.16.0
#> R.methodsS3_1.8.2 R.oo_1.25.0 R.utils_2.12.0 R6_2.5.1
#> rappdirs_0.3.3 Rcpp_1.0.9.1 rematch2_2.1.2 reprex_2.0.2
#> rlang_1.0.4 rmarkdown_2.16 rprojroot_2.0.3 rsconnect_0.8.27
#> rstudioapi_0.14 sass_0.4.2 stats_4.2.0 stringi_1.7.8
#> stringr_1.4.1 styler_1.7.0.9001 sys_3.4 tibble_3.1.8
#> tinytex_0.41 tools_4.2.0 utf8_1.2.2 utils_4.2.0
#> vctrs_0.4.1 withr_2.5.0 xfun_0.32 yaml_2.3.5
```
<sup>Created on 2022-08-28 with [reprex v2.0.2](https://reprex.tidyverse.org)</sup>
[log file](https://gist.github.com/qiushiyan/97d9df61aa2ff1bf571f52af6dafa56f)
Although it is expected that tinytex produce no output with empty content, the quarto error could be improved to indicate this.
| {
"assignee": null,
"comments": 0,
"created_at": "2022-08-28T23:45:35Z",
"creator": "qiushiyan",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2183,
"state": "closed",
"title": "Render PDF fails with empty content",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2183"
} |
### Bug description
```md
Watching files for changes
Browse at http://localhost:3849/chapter/part01/myfile.html
GET: /chapter/part01/myfile.html
ERROR: AlreadyExists: Cannot create a file when that file already exists. (os error 183), mkdir 'H:\My Drive\...\site_libs\quarto-nav'
System: windows
IDE: Vscode
Type quarto: book
to directory in google drive
```
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": 8,
"created_at": "2022-08-28T12:55:55Z",
"creator": "jefferds",
"is_pull_request": false,
"labels": [
"bug",
"file-systems"
],
"locked": false,
"milestone": "v1.4",
"number": 2174,
"state": "open",
"title": "ERROR: AlreadyExists: (os error 183), mkdir 'H:\\My Drive\\...\\site_libs\\quarto-nav' on Google Drive",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2174"
} |
I was sketching a theorem using a bullet point list inside a div and stumbled upon the following issue.
The following minimal example using (un-)ordered lists inside a theorem div
```markdown
---
title: "unexpected caption item"
---
::: {#thm-unordered-list}
## This heading shouldn't have a bullet point
* This
* unordered list (unexpectedly) includes the caption
:::
::: {#thm-ordered-list}
## This heading shouldn't have a bullet point
1. This
2. ordered list (unexpectedly) includes the caption
:::
```
renders the theorem caption as part of the list:
| {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-08-27T15:05:16Z",
"creator": "vmichals",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2166,
"state": "closed",
"title": "Heading in theorem is included as item in list in theorem body",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2166"
} |
Mermaid allows theming / styling diagrams with
- ready-made built-in themes
- user-provided CSS
- combination of both above
If this can already be used through Quarto, please document how. (I didn't find anything about it in the documentation.)
If not, please consider adding a possibility to do so. (Best probably as YAML options as suggested at https://github.com/quarto-dev/quarto-cli/discussions/1521#discussioncomment-3225243, as that would allow project-wide, file-level and diagram-level control.) | {
"assignee": "cscheid",
"comments": 4,
"created_at": "2022-08-27T13:21:31Z",
"creator": "das-g",
"is_pull_request": false,
"labels": [
"enhancement",
"mermaid"
],
"locked": false,
"milestone": "Future",
"number": 2165,
"state": "closed",
"title": "allow theming & styling Mermaid diagrams",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2165"
} |
### Bug description
With the new quarto 1.1.147 release we see the following error when rendering a book
(https://github.com/mlr-org/mlr3book/runs/8047883939?check_suite_focus=true#step:13:16)
```bash
In file book/_quarto.yml
(line 67, column 7 through line 68, column 23) Key code-tools has value toggle: true
code-fold: false, which must be `true` or `false`
66: code-tools:
67: toggle: true
~~~~~~~~~~~~
68: code-fold: false
~~~~~~~~~~~~~~~~~~~~~~
69: highlight-style: printing
β The value toggle: true
code-fold: false is object.
βΉ The error happened in location format:html:code-tools.
```
AFAICS our source specification https://github.com/mlr-org/mlr3book/blob/main/book/_quarto.yml#L66-L68 looks still valid when compared to the [quarto documentation source](https://quarto.org/docs/output-formats/html-code.html#code-tools) - is this a bug in the new release?
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": 1,
"created_at": "2022-08-27T08:56:27Z",
"creator": "pat-s",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2161,
"state": "closed",
"title": "`code-tools` options mapping buggy in v1.1?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2161"
} |
I tried to create a new quarto document in Rstudio, through `File >> new file >> quarto document .`
Error occoured as mentioned in the title,
| {
"assignee": null,
"comments": 3,
"created_at": "2022-08-27T08:47:51Z",
"creator": "antonio-yu",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2160,
"state": "closed",
"title": "an error occourred when parsing json : offset :2",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2160"
} |
### Bug description
Hi,
I _think_ this is a bug and not a case of user error (if it's the latter, sorry!).
I am using the pre-release CLI 1.2.15 on an intel Mac (running 12.5.1) from the command line. This happens with both R and python posts.
I am trying to change the default twitter card (blog_title:title doesn't work for me because my blog has a long and stupid title. The title is also included elsewhere on the card). I can change the title but I can't make the description change. I've tested it on R and Python blogs and blogs with and without rendered maths in the title (because you never know). Both cases read the title from the twitter-card metadata but use the post description rather than the meta-card description.
A minimal reprex is here https://github.com/dpsimpson/blog/tree/quarto_bug
The full .qmd for the post is [(link)](https://github.com/dpsimpson/blog/blob/4103ca2b3762db9c33359c556e7c1518d1b8d643/posts/post_bad/post_bad.qmd)
```
---
title: "$(n-1)$-sane in the membrane (bad twitter card)"
subtitle: |
Windmills? Tilted. Topic? Boring. (n-1)? No.
date: 10-14-2021
categories: [Teaching, Fundamentals, Opinionated]
twitter-card:
title: "twitter title"
description: "twitter description"
creator: "@dan_p_simpson"
citation:
url: https://dansblog.netlify.app/n-sane-in-the-membrane
---
Stuff
```
but the generated html code is [(link)](https://github.com/dpsimpson/blog/blob/4103ca2b3762db9c33359c556e7c1518d1b8d643/_site/posts/post_bad/post_bad.html#L70)
```
<meta name="twitter:title" content="twitter title">
<meta name="twitter:description" content="Windmills? Tilted. Topic? Boring. (n-1)? No.">
<meta name="twitter:creator" content="@dan_p_simpson">
<meta name="twitter:card" content="summary">
```
which is using the default description.
I can't possibly imagine this being an important bug, but it's slightly odd behaviour.
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": "2022-08-27T08:07:45Z",
"creator": "dpsimpson",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2159,
"state": "closed",
"title": "(Small) Bug: Twitter card description not copied from twitter-card metadata",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2159"
} |
### Bug description
After pulling the commits today, I receive the following error on validation of the pre-render field in the project yaml file `_quarto.yml`:
```bash
ERROR: Project _quarto.yml validation failed.
In file _quarto.yml
(line 4, columns 3--13) property name pre-render is invalid
3: output-dir: docs
4: pre-render:
~~~~~~~~~~
5: - ./scripts/todo-pre.py
βΉ The error happened in location project:pre-render.
Error: Project _quarto.yml validation failed.
In file _quarto.yml
(line 4, columns 3--13) property name pre-render is invalid
3: output-dir: docs
4: pre-render:
~~~~~~~~~~
5: - ./scripts/todo-pre.py
βΉ The error happened in location project:pre-render.
at readAndValidateYamlFromFile (file:///home/julian/quarto-cli/src/core/schema/val
idated-yaml.ts:52:11)
at async projectContext (file:///home/julian/quarto-cli/src/project/project-contex
t.ts:123:28)
at async Command.fn (file:///home/julian/quarto-cli/src/command/preview/cmd.ts:230
:23)
at async Command.execute (file:///home/julian/quarto-cli/src/vendor/deno.land/x/cl
[email protected]/command/command.ts:1275:7)
at async quarto (file:///home/julian/quarto-cli/src/quarto.ts:104:3)
at async file:///home/julian/quarto-cli/src/quarto.ts:124:5
```
I am on Linux Ubuntu 22.04
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": "2022-08-26T20:02:07Z",
"creator": "juliantao",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2155,
"state": "closed",
"title": "failed yaml validation on \"pre-render\"",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2155"
} |
### Bug description
In chunk yaml, when I do "fig-cap-location: top" I still end up with the caption at the bottom. Setting it to "margin" works as expected. Published example is [here](https://quartopub.com/sites/356a4843-4b95-4082-9854-db5b0207f28f) on quarto-pub.
Might this be related to [this issue](https://github.com/quarto-dev/quarto-cli/issues/1990)? I don't know.
I have attached the qmd document that created the result linked to above that I published to quarto-pub:
````
---
title: "fig_caption_location_issue"
author: "John Goldin"
format: html
editor: visual
---
The fig-cap-location chunk option does not work as expected. I can do "bottom" or "margin" but "top" works the same way as "bottom".
```{r}
#| label: fig-a
#| fig-cap: "A Sample Figure"
#| fig-cap-location: top
plot(pressure)
```
Here is yaml for the code chunk:
#| label: fig-a
#| fig-cap: "A Sample Figure"
#| fig-cap-location: top
(I tried to find a function that would allow me to fetch these
values, but I didn't see one so I've pasted them here.)
RStudio version:
RStudio 2022.07.1+554 "Spotted Wakerobin"
Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22)
for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 12_5_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
quarto --version
1.1.140
When I run this I get the fig-cap at the bottom of the figure even if I try to specify "top".
## "Top" May Not Work, But "Margin" Does
Next I'll show I am able to change the location to "margin" and that works as expected (provided the html window is wide enough to allow for the caption
to appear in the margin).
#| label: fig-b
#| fig-cap: "Another Sample Figure"
#| fig-cap-location: margin
```{r}
#| label: fig-b
#| fig-cap: "Another Sample Figure"
#| fig-cap-location: margin
plot(pressure)
```
I wonder whether there is something else going on that I don't understand. The typography
when I use "margin" seems to be a smaller font. And when I use either "bottom" or "top"
there seems to be a lot of space between the bottom of the figure and the
caption.
session_info:
```{r}
print(devtools::session_info())
```
````
My system and session version info is all in the [published example](https://quartopub.com/sites/356a4843-4b95-4082-9854-db5b0207f28f) .
I also tried with quarto --version
1.2.8
I submit this with trepidation because it is a small, simple thing so the simplest explanation is that I made a simple mistake. But just in case I didn't, here's the report.
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": "2022-08-26T18:47:41Z",
"creator": "johngoldin",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 2154,
"state": "open",
"title": "fig-cap-location:top does place the caption above the figure",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2154"
} |
I just updated my quarto (to 1.1.140) and got the following error:
`ERROR: Project _quarto.yml validation failed.`
`In file www/_quarto.yml`
`(line 10, columns 3--14) property name reader-mode is invalid`
` 9: website:`
`10: reader-mode: true`
I see that reader-mode is still in the documentation. Any advice would be greatly appreciated. | {
"assignee": "dragonstyle",
"comments": 9,
"created_at": "2022-08-26T18:02:36Z",
"creator": "kmkinnaird",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 2153,
"state": "closed",
"title": "Help with error? property name reader-mode is invalid",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2153"
} |
### Bug description
gfm output that has pandas dataframes printed out, renders incorrectly on Github, possibly because of GitHub not respecting <style scoped> tags.
Input qmd:
````md
---
title: "Untitled"
format: gfm
---
```{python}
import pandas as pd
iris = pd.read_csv('https://raw.githubusercontent.com/mwaskom/seaborn-data/master/iris.csv')
iris.head()
```
````
Output md raw:
````
Untitled
================
``` python
import pandas as pd
iris = pd.read_csv('https://raw.githubusercontent.com/mwaskom/seaborn-data/master/iris.csv')
iris.head()
```
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
}
.dataframe tbody tr th {
vertical-align: top;
}
.dataframe thead th {
text-align: right;
}
</style>
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th>sepal_length</th>
<th>sepal_width</th>
<th>petal_length</th>
<th>petal_width</th>
<th>species</th>
</tr>
</thead>
<tbody>
<tr>
<th>0</th>
<td>5.1</td>
<td>3.5</td>
<td>1.4</td>
<td>0.2</td>
<td>setosa</td>
</tr>
<tr>
<th>1</th>
<td>4.9</td>
<td>3.0</td>
<td>1.4</td>
<td>0.2</td>
<td>setosa</td>
</tr>
<tr>
<th>2</th>
<td>4.7</td>
<td>3.2</td>
<td>1.3</td>
<td>0.2</td>
<td>setosa</td>
</tr>
<tr>
<th>3</th>
<td>4.6</td>
<td>3.1</td>
<td>1.5</td>
<td>0.2</td>
<td>setosa</td>
</tr>
<tr>
<th>4</th>
<td>5.0</td>
<td>3.6</td>
<td>1.4</td>
<td>0.2</td>
<td>setosa</td>
</tr>
</tbody>
</table>
</div>
````
Output md rendered:
```
Untitled
================
``` python
import pandas as pd
iris = pd.read_csv('https://raw.githubusercontent.com/mwaskom/seaborn-data/master/iris.csv')
iris.head()
```
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
}
.dataframe tbody tr th {
vertical-align: top;
}
.dataframe thead th {
text-align: right;
}
</style>
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th>sepal_length</th>
<th>sepal_width</th>
<th>petal_length</th>
<th>petal_width</th>
<th>species</th>
</tr>
</thead>
<tbody>
<tr>
<th>0</th>
<td>5.1</td>
<td>3.5</td>
<td>1.4</td>
<td>0.2</td>
<td>setosa</td>
</tr>
<tr>
<th>1</th>
<td>4.9</td>
<td>3.0</td>
<td>1.4</td>
<td>0.2</td>
<td>setosa</td>
</tr>
<tr>
<th>2</th>
<td>4.7</td>
<td>3.2</td>
<td>1.3</td>
<td>0.2</td>
<td>setosa</td>
</tr>
<tr>
<th>3</th>
<td>4.6</td>
<td>3.1</td>
<td>1.5</td>
<td>0.2</td>
<td>setosa</td>
</tr>
<tr>
<th>4</th>
<td>5.0</td>
<td>3.6</td>
<td>1.4</td>
<td>0.2</td>
<td>setosa</td>
</tr>
</tbody>
</table>
</div>
```
I am on Mac OS Big Sur and using VS Code 1.70.2.
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": 12,
"created_at": "2022-08-26T17:53:14Z",
"creator": "kalenkovich",
"is_pull_request": false,
"labels": [
"bug",
"upstream"
],
"locked": false,
"milestone": "v1.3",
"number": 2152,
"state": "closed",
"title": "gfm output of pandas dataframes rendered incorrectly on GitHub",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2152"
} |
the solution from that thread https://github.com/quarto-dev/quarto-cli/discussions/2060#discussioncomment-3455375 no longer works with the latest version 1.1.132. I've uninstalled that version and gone back to 1.1.57 which works fine with the `book.isbn` solution from the windows terminal. That's a workaround for me now.
_Originally posted by @jpmorr in https://github.com/quarto-dev/quarto-cli/issues/2143#issuecomment-1228607822_ | {
"assignee": "cscheid",
"comments": 14,
"created_at": "2022-08-26T15:25:23Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"yaml-validation"
],
"locked": false,
"milestone": "v1.2",
"number": 2148,
"state": "closed",
"title": "Using metadata under `book` key cannot be referenced anymore",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2148"
} |
### Bug description
I am trying to run Quarto for the first time. I have installed the deb package on my Ubuntu Focal machine. My first attempt to render the `hello.qmd` test file failed:
```
.../quarto/tutorialξ° quarto render hello.qmd --to html
Starting python3 kernel...Traceback (most recent call last):
File "/opt/quarto/share/jupyter/jupyter.py", line 21, in <module>
from notebook import notebook_execute, RestartKernel
File "/opt/quarto/share/jupyter/notebook.py", line 17, in <module>
from nbclient import NotebookClient
ModuleNotFoundError: No module named 'nbclient'
```
I resolved this with the following:
```
apt-get install python3-pip
python3 -m pip install nbclient
```
My next attempt to render failed with a new message:
```
quarto render hello.qmd --to html
Starting python3 kernel...ERROR:
No such kernel named python3
```
I'm not sure how to resolve this. Is there a list of Python dependencies for Quarto somewhere, and ideally instructions for installation that non-Python programmers can follow?
Maybe helpful:
```
quarto capabilities
{
"formats": [
"html",
"pdf",
"docx",
"odt",
"pptx",
"beamer",
"revealjs",
"gfm",
"hugo",
"epub",
"asciidoc",
"asciidoctor",
"commonmark",
"commonmark_x",
"context",
"docbook",
"docbook4",
"docbook5",
"dokuwiki",
"dzslides",
"epub2",
"epub3",
"fb2",
"haddock",
"html4",
"html5",
"icml",
"ipynb",
"jats",
"jats_archiving",
"jats_articleauthoring",
"jats_publishing",
"jira",
"json",
"latex",
"man",
"markdown",
"markdown_github",
"markdown_mmd",
"markdown_phpextra",
"markdown_strict",
"markua",
"mediawiki",
"ms",
"muse",
"native",
"opendocument",
"opml",
"org",
"plain",
"rst",
"rtf",
"s5",
"slideous",
"slidy",
"tei",
"texinfo",
"textile",
"xwiki",
"zimwiki"
],
"themes": [
"default",
"materia",
"lux",
"superhero",
"quartz",
"united",
"sandstone",
"spacelab",
"solar",
"journal",
"minty",
"sketchy",
"cosmo",
"flatly",
"vapor",
"darkly",
"yeti",
"cerulean",
"lumen",
"litera",
"morph",
"slate",
"cyborg",
"simplex",
"pulse",
"zephyr"
],
"python": {
"versionMajor": 3,
"versionMinor": 8,
"versionPatch": 10,
"versionStr": "3.8.10 (default, Jun 22 2022, 20:18:18) [GCC 9.4.0]",
"conda": false,
"execPrefix": "/usr",
"executable": "/usr/bin/python3",
"jupyter_core": "4.11.1",
"nbformat": "5.0.4",
"nbclient": "0.6.7",
"ipykernel": null,
"pyLauncher": false,
"kernels": [
{
"display_name": "Python 3",
"language": "python",
"name": "python3"
}
],
"venv": true
}
}
```
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": "2022-08-26T15:14:14Z",
"creator": "plantarum",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2147,
"state": "closed",
"title": "Missing Python dependencies in Ubuntu",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2147"
} |
### Bug description
The following mistake was entirely my fault but I found the behavior slightly unexpected compared to standard command line interfaces and the error message made it difficult to immediately identify what the issue was. Running the following render command produces the below error.
```
$ quarto render --to html unvotes.ipynb
ERROR: The specified directory ('.') is not a Quarto project
```
I'm fine with the ordering of input vs args but it seems like swapping the order is an easy mistake to make and more helpful error message would be appreciated (e.g. invalid file path, `--to` does not exist, or something similar).
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": "2022-08-26T15:06:55Z",
"creator": "rundel",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 2146,
"state": "open",
"title": "Confusing error with quarto render when swapping input and args",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2146"
} |
### Bug description
After installing the latest Quarto version on Windows 11, VS Code no longer finds the quarto app when clicking on the render button when working on a `.qmd` file. I've restarted Windows after the install.
This is despite being able to run `quarto check` from the VS code terminal
```
quarto check
[>] Checking Quarto installation......OK
Version: 1.1.132
Path: C:\Users\xxx\AppData\Local\Programs\Quarto\bin\
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.9.13 (Conda)
Path: C:/Users/xxx/anaconda3/python.exe
Jupyter: 4.11.1
Kernels: julia-1.4, julia-1.6, julia-1.7, 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/xxx/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
- [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://yihui.org/issue/#please-format-your-issue-correctly) 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": 23,
"created_at": "2022-08-26T12:23:51Z",
"creator": "jpmorr",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2143,
"state": "closed",
"title": "VS Code not finding Quarto after updating to latest version",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2143"
} |
### Bug description
I created a book project using RStudio and only added the `repo-url` and `repo-actions`
In `_quarto.yml` I have
```yaml
book:
title: "sidebarbug"
author: "Jane Doe"
date: "8/26/2022"
chapters:
- index.qmd
- intro.qmd
- summary.qmd
- references.qmd
repo-url: https://github.com/maelle/sidebarbug/
repo-actions: [edit, issue]
```
Source: https://github.com/maelle/sidebarbug
Now on the page where there is a TOC (because there are headers) the repo action links are present. https://maelle.github.io/sidebarbug/
But on the pages where there is no TOC (which is expected as there are no headers) the repo action links are not present (which I was not expecting). https://maelle.github.io/sidebarbug/intro.html
I don't think this is relevant but just in case, I am using
RStudio 2022.07.0+548 "Spotted Wakerobin" Release (34ea3031089fa4e38738a9256d6fa6d70629c822, 2022-07-06) for Ubuntu Bionic
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
Ubuntu 20.04.4 LTS
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": "2022-08-26T12:16:44Z",
"creator": "maelle",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2142,
"state": "closed",
"title": "repo-actions links do not appear if there is no TOC",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2142"
} |
### Bug description
I have a template where many files and resources needs to be added for correct pdf output. I opted to include some logos in the folder logos, which makes my _extension.yml look like this:
````
title: template
author: Simon Lidberg
version: 0.0.1
contributes:
format:
common:
number-sections: true
toc: true
reference-section-title: References
his-metadata:
sammanfattning: "Abstract in swedish"
publicationtype: dissertation
printshop: "Stema Specialtryck AB, BorΓ₯s"
isbn: 123-12-123456-X-X
seriesnumber: XX
pdf:
documentclass: his-thesis
classoption: english
biblio-config: false
cite-method: biblatex
suppress-bibliography: true
link-citations: true
colorlinks: false
template: his-template.tex
template-partials:
- "partials/doc-class.tex"
- "partials/_metadata.tex"
- "partials/title.tex"
- "partials/before-body.tex"
- "partials/after-body.tex"
format-resources:
- his-thesis.cls
- hismetadata.sty
- hisbibliography.sty
- histextformatting.sty
- hisownpublications.sty
- hisfont.sty
- hiscover.sty
- histitlepage.sty
- logos/
pdf-engine: lualatex
latex-min-runs: 3
has-frontmatter: true
papersize:
lof: true
lot: true
english: true
html:
theme: cosmo
````
But when the 'logos' folder is copied into the input folder, it retains the same permissions as regular files (555). This makes it impossible to remove in subsequent runs of quarto render. Directories would need to be (755) in order for them to be removed properly.
Here's the repo [https://github.com/verbalins/his-template](https://github.com/verbalins/his-template), sorry for the state it's in currently...
Debug information:
````
[β] Checking Quarto installation......OK
Version: 1.1.132
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.6
Path: /usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /usr/lib64/R
LibPaths:
- /home/verbalins/R/x86_64-pc-linux-gnu-library/4.2
- /usr/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
````
Output showing the error:
````
[1/3] index.qmd
[2/3] intro.qmd
[3/3] summary.qmd
pandoc
to: latex
output-file: index.tex
template: _extensions/his/his-template.tex
standalone: true
toc: true
number-sections: true
top-level-division: chapter
pdf-engine: lualatex
variables:
graphics: true
tables: true
default-image-extension: pdf
cite-method: biblatex
metadata
crossref:
chapters: true
documentclass: his-thesis
papersize: null
block-headings: true
reference-section-title: References
his-metadata:
sammanfattning: Abstract in swedish
publicationtype: licentiate
printshop: 'Stema Specialtryck AB, BorΓ₯s'
isbn: 123-12-123456-X-X
seriesnumber: XX
coverimage: foto.jpg
coverphoto: face.jpg
fullarticles: |
\fullarticle[scale=.9,trim={0mm 5mm 0mm 5mm},pages=-]{fischer2017doctoraldissertationmanual}{style-guide/manual.pdf}[\href{https://creativecommons.org/licenses/by-nc-nd/4.0/}{\ccbyncnd}]
\fullarticle[scale=.9,trim={0mm 5mm 0mm 5mm},pages=1]{fischer2017doctoraldissertationmanual}{style-guide/manual.pdf}[\copyright{} 2018 University of SkΓΆvde. Reprinted, with permission, from]
\fullarticle[scale=.9,trim={0mm 5mm 0mm 5mm},pages=1]{fischer2017doctoraldissertationmanual}{style-guide/manual.pdf}[Reprinted from][with permission from University of SkΓΆvde.]
acronyms: |
\newacronym{moo}{MOO}{Multi-Objective Optimization}
\newacronym{sbo}{SBO}{Simulation-Based Optimization}
\newacronym{ai}{AI}{Artificial Intelligence}
\newacronym{doe}{DOE}{Design of Experiments}
ownpublications: |
\authorspublication{fischer2017doctoraldissertationmanual}
\authorspublication[Design, manuscript preparation, review]{fischer2017doctoraldissertationmanual}
classoption:
- english
- final
- cover
biblio-config: false
suppress-bibliography: true
link-citations: true
colorlinks: false
has-frontmatter: true
lof: true
lot: true
english: true
bibliography:
- references.bib
title: Title for this example thesis
author: Author Authorsson
date: '2022-08-23'
abstract: Testing abstract
(ERROR) PermissionDenied: Permission denied (os error 13), remove '/path/to/folder/thesis/logos/laurelbranch-rubin.pdf'
````
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": "2022-08-26T11:02:09Z",
"creator": "verbalins",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2141,
"state": "closed",
"title": "quarto template format-resources folder not removed in linux",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2141"
} |
### Bug description
Change the default contents of index.qmd created in a new book project to:
````md
::: {.content-visible when-format="html"}
# Preface {.unnumbered}
This is a Quarto book.
To learn more about Quarto books visit <https://quarto.org/docs/books>.
:::
````
The compiled pdf file shows the chapter heading "Preface" but not the contents (This is a Quarto book...). It is my understanding that the chapter title should also be ignored?
quarto check:
````
[β] Checking Quarto installation......OK
Version: 1.1.132
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.6
Path: /usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /usr/lib64/R
LibPaths:
- /home/verbalins/R/x86_64-pc-linux-gnu-library/4.2
- /usr/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
````
quarto render -t all output:
````
1/4] index.qmd
[2/4] intro.qmd
[3/4] summary.qmd
[4/4] references.qmd
pandoc
to: latex
output-file: index.tex
standalone: true
toc: true
number-sections: true
top-level-division: chapter
pdf-engine: xelatex
variables:
graphics: true
tables: true
default-image-extension: pdf
metadata
crossref:
chapters: true
documentclass: scrreprt
papersize: letter
classoption:
- DIV=11
- numbers=noendperiod
header-includes:
- '\KOMAoption{captions}{tableheading}'
block-headings: true
bibliography:
- references.bib
title: repro
author: Jane Doe
date: 8/26/2022
running xelatex - 1
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022/Arch Linux) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
running xelatex - 2
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022/Arch Linux) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
Output created: _book/index.html
````
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": 7,
"created_at": "2022-08-26T09:08:48Z",
"creator": "verbalins",
"is_pull_request": false,
"labels": [
"bug",
"ast"
],
"locked": false,
"milestone": "v1.4",
"number": 2140,
"state": "open",
"title": "quarto book .content-visible ignored",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2140"
} |
### Bug description
When using the chalkboard feature and adding some annotations in a speaker view setting, the annotations are not mirrored to the main presentation.
This is an issue as usually one looks at the speaker view during a presentation on the laptop while the main audience looks at the mirrored slides behind/beside the speaker. For speakers, it's not easy to spot that things are not synchronized.
Adding annotations only on the main presentation view would require taking the mouse across screens which is fiddly and takes additional time.
quarto v1.1.120
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": 3,
"created_at": "2022-08-26T07:58:52Z",
"creator": "pat-s",
"is_pull_request": false,
"labels": [
"bug",
"upstream"
],
"locked": false,
"milestone": "Future",
"number": 2139,
"state": "open",
"title": "Chalkboard: annotations in speaker view are not mirrored to main presentation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2139"
} |
I set up a connection to a database but Quarto throws an error when rendering (not if I execute the chunk). The same code in Rmarkdown works smoothly.
```
library(dbplyr)
conn <- DBI::dbConnect(RMySQL::MySQL(),
host = "my_hostname",
user = "my_user",
password = Sys.getenv("PASSWORD_DB"),
dbname = "my_db",
port=3306)
my_table <- tbl(conn, "my_table")
```
This is the error:
```
#> Quitting from lines 11-28 (ECS_data_mining.qmd)
#> Error in .local(drv, ...) :
#> Failed to connect to database: Error: Access denied for user
#> my_user'@'2a01:57a0:1608:6300:8818:75ea:8b53:6933' (using password: NO)
#> Calls: .main ... eval -> <Anonymous> -> <Anonymous> -> .local -> .Call
#> Execution halted
``` | {
"assignee": null,
"comments": 7,
"created_at": "2022-08-26T07:37:35Z",
"creator": "jospueyo",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2145,
"state": "closed",
"title": "Problem when connecting to MySQL using environmental variables",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2145"
} |
### Bug description
Hello!
I can't find functions for automating list of tables, list of figures and list of abbreviations in quarto book. These functionalities would be very useful for technical and academic reports.
Best
Ko Ko Zaw
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": 7,
"created_at": "2022-08-26T07:23:59Z",
"creator": "zawkzaw",
"is_pull_request": false,
"labels": [
"enhancement",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 2138,
"state": "open",
"title": "list of tables, list of figures and list of abbreviations in quarto book ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2138"
} |
### Bug description
I'm redoing my website using a Quarto blog. When I have post set to eval: false with a SQL code chunk and an R code chunk, it looks fine. When I remove the R part, it changes formatting.
To reproduce, I have a blog post with each of these options:
1) Blog post without R chunk.
````
---
title: "Test without R"
date: "2022-08-24"
execute:
eval: false
---
```{sql test}
SELECT * FROM EXAMPLE;
```
2) Same blog post, but with a blank R chunk at the end.
---
title: "Test with R"
date: "2022-08-25"
execute:
eval: false
---
```{sql test}
SELECT * FROM EXAMPLE;
```
```{r}
```
````
-----
The SQL section outputs are different.
Screenshot of the first blog post. Formatting does not have syntax highlighting.
Screenshot of the second blog post. This does have highlighting.
Screenshot of the home page.
I don't know why they don't match. I just updated to the newest Quarto version (but I think it was happening on the previous one too). This is on RStudio 2022.07.1 Build 554. "Spotted Wakerobin" for macOS, on Monterey.
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": "2022-08-26T00:37:26Z",
"creator": "WilliamTylerBradley",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 2137,
"state": "open",
"title": "SQL chucks appear different with R chunks when eval is false",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2137"
} |
### Bug description
Using MS code, Anaconda with python 3.9.12, when selecting 'file new' if I select a .ipynb file it does nothing, however if I create a .qmb file, and then create a .ipynb it then appears. The MS code extensions I have installed are:
ms-toolsai.jupyter
ms-toolsai.jupyter-keymap
ms-toolsai.jupyter-renderers
ms-python.vscode-pylance
ms-python.python
quarto.quarto
REditorSupport.r
RDebugger.r-debugger
This occurs on more than one machine, windows 10 professional:
Edition Windows 10 Pro
Version 20H2
Installed on β03/β08/β2022
OS build 19042.1706
Experience Windows Feature Experience Pack 120.2212.4170.0
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": 2,
"created_at": "2022-08-25T21:50:08Z",
"creator": "Eclecticdata",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "Future",
"number": 2135,
"state": "closed",
"title": "new ipynb file not appearing until a new .qmd file is created",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2135"
} |
### Bug description
test code
````md
---
title: 'debug code fold'
format:
html:
code-fold: true
embed-resources: true
standalone: true
execute:
cache: false
echo: false
---
```{ojs}
1+1
```
````
output:
This bug is caused by `code-fold: true` in the header. When remove this line, the rendering is ok. But it would better to check if echo == Ture before display the code fold mark.
### 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://yihui.org/issue/#please-format-your-issue-correctly) 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": 1,
"created_at": "2022-08-25T21:18:23Z",
"creator": "y9c",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2134,
"state": "closed",
"title": "code-fold still exist even if `echo` is set as false",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2134"
} |
I've been doing a lot of work on the shell scripts, and there's been some headache around platform-specific syntax. I saw some of that in my conda days. The only real way to avoid the headache is to strive for POSIX compliance, which can be something of a headache unto itself.
The first part of this proposal is to:
* Add a shellcheck step to our CI to show our status
* Make an effort to get our scripts into POSIX compliance
The second part of this proposal is to create native, standalone executables to replace our shell scripts. This is really only relevant to the `quarto` and `quarto.cmd` scripts. Native executables are not mutually exclusive with POSIX compatibility. Each part should be considered in terms of what goes into installers/packages and what only developers use.
The argument for POSIX compliance in our dev scripts is much weaker than the argument for it in the end-user scripts. It's reasonable to establish some BASH requirement for our dev scripts.
What this really boils down to is that it would be good to have the end-user scripts be POSIX compliant or be replaced by a standalone compiled executable (go, rust, whatever is easiest and most completely standalone). | {
"assignee": null,
"comments": 3,
"created_at": "2022-08-25T17:19:01Z",
"creator": "msarahan",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2128,
"state": "closed",
"title": "Proposal: posix compliance in shell scripts; native compiled launcher",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2128"
} |
<div type='discussions-op-text'>
<sup>Originally posted by **cbrnr** August 25, 2022</sup>
I created a website with `quarto create-project website --type website`. In `_quarto.yml` I changed the `theme` to `flatly` because the issue is more pronounced with this theme (but it also occurs with the default `cosmo` theme).
Then after `quarto preview`, repeatedly click on "Home" in the navbar (or switch between "Home" and "About"). Notice when the corresponding page is rendered, the main text jumps down a little. Here's a screen recording to show what I mean:
https://user-images.githubusercontent.com/4377312/186645355-abfbcc48-3137-4889-97ad-01a7e666f004.mov
Any ideas how to fix this behavior? I'm using Quarto 1.0.36 (part of RStudio) on macOS.</div> | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-08-25T16:09:46Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2126,
"state": "closed",
"title": "Website text \"jumps\" when rendered",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2126"
} |
e.g.
````markdown
```{python}
#| output: asis
%%javascript
// some JS code
```
````
This is because cell magics need to be the first line of the cell.
Note that the `keep-ipynb` feature is really designed for debugging rather than for producing a final notebook for distribution (e.g. markdown constructs like citations and crossrefs are not resolved in this version). We should either resolve this or make it more clear in the documentation that `keep-ipynb` is for debugging intermediate representations (we could even change the filename to make this more clear).
| {
"assignee": "jjallaire",
"comments": 7,
"created_at": "2022-08-25T12:25:17Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 2123,
"state": "open",
"title": "keep-ipynb notebook with cell magics and yaml options can't be executed",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2123"
} |
### Bug description
Currently in the doc for engine binding regarding computation chunk (https://quarto.org/docs/computations/execution-options.html#engine-binding) we have mention of two things regarding Markdown file :
* The table about auto-binding shows `.md` is supported, and no engine will be used
* `engine: markdown` can be used to deactivate engine
> You can also specify that no execution engine should be used via engine: markdown.
However, we have a check for computation chunk inside `.md` document that prevent any rendering at all
https://github.com/quarto-dev/quarto-cli/blob/71310bfd92ce7240042dd29f96a6f305690feb23/src/execute/markdown.ts#L67-L75
Which leads to
````
> quarto render test.md --to html
ERROR: You must use the .qmd extension for documents with executable code.
````
As discussed with @jjallaire
> That error is I think more helpful than not because if you have code cells in your .md you definitely aren't getting what you expected (the code won't execute). We could indeed silently send this to pandoc but I sort of view that as similar to eating bad YAML schema. Longer term its better for the user to clean this up.
Should we maybe update the documentation to clearly state that `.md` document works with quarto only if there is no computation chunk ? Or at least remove the `.md` line from the table ? | {
"assignee": null,
"comments": 1,
"created_at": "2022-08-25T11:54:31Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": null,
"number": 2122,
"state": "closed",
"title": "Adapt the documentation about .md document with computation chunk",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2122"
} |
{
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-08-25T11:34:32Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [
"books"
],
"locked": false,
"milestone": "v1.3",
"number": 2120,
"state": "closed",
"title": "support globs for book chapter lists",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2120"
} |
|
Issue https://github.com/quarto-dev/quarto-cli/issues/2113 is a problem that I caused by not considering that symlinks to the quarto binary may be relative. Our dev configuration makes absolute path symlinks, and we don't otherwise have a check for this use case. It seems like we should add something to the CI process to test this behavior. | {
"assignee": null,
"comments": 0,
"created_at": "2022-08-25T00:54:18Z",
"creator": "msarahan",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 2114,
"state": "open",
"title": "Need test for relative symlinks to Quarto",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2114"
} |
### Bug description
I am currently maintaining a set of homebrew formulae (for MacOS) for both quarto and quarto-dev, a user just reported (rundel/homebrew-quarto-cli#37) that as of v1.1.113 they are getting an error when running quarto installed using this formula. Specifically,
```
> quarto preview
usage: basename string [suffix]
basename [-a] [-s suffix] string [...]
ERROR: Cannot determine the Quarto source path. This script must be run from the bin or common folder.
```
this is still occurring with the latest pre-release (v1.1.119).
These formulae are installing the files from the `quarto-1.1.119-macos.tar.gz` assest into a homebrew cellar which are then symlinked into `/opt/homebrew`. The issue appears to be with how the primary quarto shell script is handling the construction of [`SCRIPT_PATH`](https://github.com/quarto-dev/quarto-cli/blob/1fbd4124cc00101f19601adbccd3ccc3474f6e1e/package/scripts/common/quarto#L4-L13) when the symlink is a relative path.
```
> ls -la /opt/homebrew/bin/quarto
lrwxr-xr-x 1 rundel admin 39 Aug 24 17:54 /opt/homebrew/bin/quarto -> ../Cellar/quarto-dev/1.1.119/bin/quarto
```
For this case it appears that https://github.com/quarto-dev/quarto-cli/blob/1fbd4124cc00101f19601adbccd3ccc3474f6e1e/package/scripts/common/quarto#L8
does not work as a relative path is not handled properly by `cd` since this is relative to where the script was invoked and not where the script lives.
The breaking changes seem to be part of #2015.
### Checklist
- [X] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)?
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. | {
"assignee": null,
"comments": 6,
"created_at": "2022-08-25T00:03:55Z",
"creator": "rundel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2113,
"state": "closed",
"title": "SCRIPT_PATH discovery is broken for relative symlinks ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2113"
} |
### Bug description
This bug is essentially #1141 but applied to citations in captions when using footnote citation styles. This Markdown doesn't work:
```md
---
csl: oxford-university-press-note.csl
---
![A schematic diagram of known types of viroid-like agents. This figure was published in [@Lee2021a].](figures/viroid-like-schematic.png)
```
The error message also parallels #1141:
```
compilation failed- error
Argument of \caption@ydblarg has an extra }.
<inserted text>
\par
l.324 ...1093/nar/gkab974}{10.1093/nar/gkab974}.}}
```
### Checklist
- [X] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)?
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-08-24T22:54:16Z",
"creator": "Benjamin-Lee",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2112,
"state": "closed",
"title": "Footnote-style citation in figure caption crashed PDF render",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2112"
} |
Per previous conversations @cscheid --
Quarto websites are fantastic for individual websites, but features are lacking for group or organization websites. The Hugo Academic framework enabled a taxonomy across the site for aggregating publications by author in a seamless manner. Quarto Listings are a start to this but need some ability to flag authors on publication entries and then aggregate each respective authors' publications on their individual page within the site.
| {
"assignee": "cscheid",
"comments": 6,
"created_at": "2022-08-24T20:56:34Z",
"creator": "kmasiello",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.4",
"number": 2110,
"state": "open",
"title": "Better frameworks for organization-centric websites ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2110"
} |
### Bug description
Code:
````md
---
title: "test webpage"
format:
html:
code-fold: true
execute:
cache: true
jupyter: python3
---
```{python}
#| label: fig-demo
#| fig-cap: "This is a demo figure for debug"
from bokeh.io import output_notebook
output_notebook(hide_banner=True)
from bokeh.palettes import Spectral5
from bokeh.plotting import figure, show
from bokeh.sampledata.autompg import autompg as df
from bokeh.transform import factor_cmap
df.cyl = df.cyl.astype(str)
group = df.groupby('cyl')
cyl_cmap = factor_cmap('cyl', palette=Spectral5, factors=sorted(df.cyl.unique()))
p = figure(height=350, x_range=group, title="MPG by # Cylinders", toolbar_location=None, tools="")
p.vbar(x='cyl', top='mpg_mean', width=1, source=group, line_color=cyl_cmap, fill_color=cyl_cmap)
show(p)
```
````
Output:
The subfigure 1b and 1c is empty and should be exist.
### Checklist
- [x] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)?
- [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [x] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well. | {
"assignee": "cscheid",
"comments": 9,
"created_at": "2022-08-24T19:19:42Z",
"creator": "y9c",
"is_pull_request": false,
"labels": [
"bug",
"needs-discussion"
],
"locked": false,
"milestone": "v1.3",
"number": 2107,
"state": "closed",
"title": "A single bokeh plot will be wrongly identified as several subfigures. ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2107"
} |
### Bug description
The ipynb may be there from keep-ipynb or just not cleaned up from a previous render error
### Checklist
- [ ] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)?
- [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included 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.
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well. | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-08-24T17:02:21Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2101,
"state": "closed",
"title": "index.qmd and index.ipynb causes rendering error in website",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2101"
} |
### Bug description
Hi, thank you for your amazing work.
I'm trying to add an audio file to my blog, and I get a Babushka-like bug: The audio is being rendered but every time a get another copy of "_site" inside the previous "_site" file.
I made a reprex of the problem:
### Rendered Blog (everything is working well here):
https://reproduce-bug-audio.netlify.app/about.html
### Github Links:
- Reprex of the blog: https://github.com/uriahf/reproduce_bug_audio
- YMAL call for resources: https://github.com/uriahf/reproduce_bug_audio/blob/a262d13fced8ab6010b33bdb1c6527d434db35f5/about.qmd#L16-L19
- Babushka-like _site files https://github.com/uriahf/reproduce_bug_audio/tree/main/_site/_site/_site/_site/_site/_site/_site/_site
- Commits (one for each time I rendered the quarto file): https://github.com/uriahf/reproduce_bug_audio/commits/main
### My Rstudio IDE version:
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for Windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
My OS is windows.
### Checklist
- [X] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)?
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-08-24T14:03:38Z",
"creator": "uriahf",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2097,
"state": "closed",
"title": "Adding audio file to quarto-blog creates \"_site\" new nested file each time that the site is being rendered.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2097"
} |
I've seen many users put document level YAML options in the `project` and `website` keys. This does not get reported as an error b/c those schemas aren't closed. I think we need to close up schemas that can be right away as the longer we wait the more projects/documents will be broken when we do (or at the limit we can never close them). | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-08-24T13:53:16Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [
"yaml-validation"
],
"locked": false,
"milestone": "v1.1",
"number": 2096,
"state": "closed",
"title": "close yaml schemas that can be closed",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2096"
} |
I've created a new Quarto book project. When I render the provided example in HTML format (without having made any changes), the search index appears to be incomplete.
Example: The file `intro.qmd` begins like this:
```
# Introduction
This is a book created from markdown and executable code.
See @knuth84 for additional discussion of literate programming.
```
The corresponding part in `search.json` however looks like this:
```
{
"objectID": "intro.html",
"href": "intro.html",
"title": "1Β Introduction",
"section": "",
"text": "See Knuth (1984) for additional discussion of literate programming."
}
```
The same issue occurs with `summary.qmd`.
```
R version 4.2.1 (2022-06-23)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.6.8
RStudio version: 2022.07.1 Build 554
Quarto version: 1.1.113
```
| {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-08-24T13:22:07Z",
"creator": "jderrfuss",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 2095,
"state": "closed",
"title": "search.json appears to be incomplete",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2095"
} |
### Bug description
Take this example where we have a very wide code chunk
`````markdown
---
title: "Untitled"
format: revealjs
execute:
echo: true
---
## Slides 1
```{r}
#| output-location: column
library(ggplot2)
ggplot(airquality, aes(Temp, Ozone)) + geom_point() + geom_smooth(method = "loess")
```
`````
This is what we get with stable quarto
This is what we get with pre-release
The second column is outside the slide
Possibly related to this change: https://github.com/quarto-dev/quarto-cli/commit/a43090353c454860dca50164f06896dec5a48968 to try fixing https://github.com/quarto-dev/quarto-cli/issues/1940 as `flex` is replacing `width`
This came up from a discussion in https://github.com/quarto-dev/quarto-cli/discussions/2088#discussioncomment-3464422
| {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-08-24T12:05:30Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 2093,
"state": "closed",
"title": "output-location to column does not work anymore for revealjs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2093"
} |
### Bug description
I don't know what `xfun::session_info()` is, hopefully the GH issue works without that?? (from the link with instructions to follow...)
I am following this tutorial:
https://quarto.org/docs/get-started/authoring/jupyter.html
and am using `nb_conda_kernel` to manage my Jupyter kernels from different environments.
This leads to notebook metadata having different kernelspec metadata than what are available.
However, this should not matter, as the YAML doc options should precede those kind of findings, but I find that that is not the case.
Here's my whole notebook:
```json
{
"cells": [
{
"cell_type": "raw",
"id": "563ca2fc-b9a0-4e94-ab33-a511b79debe4",
"metadata": {},
"source": [
"---\n",
"title: \"Quarto Document\"\n",
"author: \"Michael Aye\"\n",
"toc: true\n",
"number-sections: true\n",
"highlight-style: pygments\n",
"format:\n",
" html:\n",
" code-fold: false\n",
" html-math-method: katex\n",
" pdf:\n",
" geometry:\n",
" - top=30mm\n",
" - left=20mm\n",
" docx: default \n",
"jupyter: python3\n",
"---"
]
},
{
"cell_type": "markdown",
"id": "86065445-3aab-4e52-ad26-2edf63ff1670",
"metadata": {},
"source": [
"# Test\n",
"\n",
"This is a test."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "a5fa2a9c-093f-4558-a4b9-686e684c6d59",
"metadata": {},
"outputs": [],
"source": [
"2+2"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python [conda env:py310] *",
"language": "python",
"name": "conda-env-py310-py"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
```
Here are the available kernels, note the matching `python3` kernel name, fitting the doc options.
```bash
/Dropbox/src/quarto_hello β― jupyter kernelspec list
[ListKernelSpecs] WARNING | Config option `kernel_spec_manager_class` not recognized by `ListKernelSpecs`.
Available kernels:
python3 /home/ayek72/mambaforge/envs/py310/share/jupyter/kernels/python3
xonsh /usr/share/jupyter/kernels/xonsh
```
and here's what `quarto` says:
```
~/Dropbox/src/quarto_hello β― quarto render formats.ipynb --to html --execute
ERROR:
No such kernel named conda-env-py310-py
```
For reference, here's my output of `quarto check`:
```bash
~/Dropbox/src/quarto_hello β― quarto check
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.5 (Conda)
Path: /home/ayek72/mambaforge/envs/py310/bin/python
Jupyter: 4.11.1
Kernels: python3, xonsh
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........(None)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
I don't know what a QMD file is, but with above notebook json and the commands, it should be easily reproducible. It simply seems to be the case that `quarto` looks at the notebook metadata first instead of looking at the YAML docoptions first.
## OS
```
~/Dropbox/src/quarto_hello β― uname -a
Linux apollo.planet.fu-berlin.de 5.15.0-46-generic #49~20.04.1-Ubuntu SMP Thu Aug 4 19:15:44 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
```
Running a KDE Neon :
### Checklist
- [ ] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)?
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included 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.
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-08-24T10:55:16Z",
"creator": "michaelaye",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2091,
"state": "closed",
"title": "quarto --execute ignores jupyter kernel name in yaml doc options",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2091"
} |
At https://quarto.org/docs/presentations/revealjs/presenting.html, there is a section on the Navigation Menu. It gives an example of the `side`, `width` and `number` options:
```
format:
revealjs:
side: right
width: wide
```
However, this does not seem to work. Autocompletion in the yaml header also doesn't mention these options. Well, it does mention the `width` option, but that's for the overall presentation, not the nav menu.
Borrowing from the documentation for revealjs in RMarkdown (https://github.com/rstudio/revealjs), this does seem to work:
```
format:
revealjs:
menu:
side: right
width: wide
```
However, this implementation seems to obliviate the option to not show the hamburger, which is done as follows:
```
format:
revealjs:
menu: false
```
because you can either give `menu: false` OR `menu: <<options on following lines>>` in the yaml section. There is no option for not showing the hamburger thingy AND having options for the case where you do want to open the menu (hitting the `M` key).
So, two things:
* There's an error in the documentation
* A suboption in the `menu` option list (besides `side`, `width`, `numbers` and `use-text-content-for-missing-titles`) for not showing the hamburger would be nice (e.g., `show-hamburger: true/false`).
To be clear, the second bullet refers to something like this:
```
format:
revealjs:
menu:
side: right
width: wide
show-hamburger: false
```
| {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-08-24T07:48:45Z",
"creator": "mathijsdeen",
"is_pull_request": false,
"labels": [
"enhancement",
"revealjs"
],
"locked": false,
"milestone": "Future",
"number": 3376,
"state": "open",
"title": "documentation error on navigation menu in revealjs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3376"
} |
Really excited about quarto, but coming from blogdown/hugo world I'm struggling to understand how custom SASS themes work. In particular, I've read https://quarto.org/docs/output-formats/html-themes-more.html#bootswatch-sass-theme-files, which says:
> Weβve merged Bootswatch themes for Bootstrap 5 into this single file theme format in our repo here:
> https://github.com/twbs/bootstrap/blob/main/scss/_variables.scss
err... is that the correct link? That appears to be the (unmerged?) official bootstrap-5 sources of the Bootstrap team, not a merged scss file in "our repo"? (trying to better understand this single-file format deal).
More generally, it's not clear how I would go about bringing in external bootstrap-based SASS themes. For instance, I rather like the MIT-licensed bootstrap-5 themes from CreativeTim, like https://github.com/creativetimofficial/material-kit. It seems like to work with quarto, I need to refactor that whole sass stack into a single .scss file, ordered specifically as quarto expects, with the five decorations described in the above link? (e.g. ` /*-- scss:uses --*/`, `/*-- scss:functions --*/`). Is that correct? Or do I just need to convert my sass theme to a bootswatch theme (al al https://bootswatch.com/help/#customization) ?
Maybe just my ignorance here in these things, but manually refactoring perfectly good SASS code seems like a significant and somewhat cumbersome and needless design -- e.g. compared to converting material-kit or other bootstrap-based SASS templates into hugo themes which was super straight-forward. Maybe the answer is that users who want lower-level customization should just stick with hugo and this is out of scope for quarto? All the same, I had hoped that quarto would lower rather than raise the barrier for user-contributed themes. Sorry if I'm just confused?
| {
"assignee": null,
"comments": 2,
"created_at": "2022-08-24T00:35:56Z",
"creator": "cboettig",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2086,
"state": "closed",
"title": "Questions/ need more advice on extending themes ?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2086"
} |
This came up in https://github.com/quarto-ext/code-filename/issues/4
Quarto allows to install from a file (https://quarto.org/docs/extensions/distributing.html#archive-files) but expect a specific structure. When downloading from Github source, there is a parent folder to the repo folder.
We could maybe check for that structure instead of just directly looking for the `_extensions` folder.
See discussion in the issue link
cc @dragonstyle
| {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-08-23T19:11:17Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"extensions"
],
"locked": false,
"milestone": "v1.2",
"number": 2081,
"state": "closed",
"title": "Installing extension from Git archive repo does not work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2081"
} |
Tag @dragonstyle per discussion, here are the pre-release references. It might be helpful to formalize the strategy of if y'all do or do not want to indicate a minimum version when introducing new features that aren't backported.
Reference to 0.9: [Mermaid Diagrams](https://github.com/quarto-dev/quarto-web/blob/5a79cba1d466d55da139cd447c9f3fe1fc812d4d/docs/authoring/diagrams.qmd#L22)
Reference to 1.0.15: [Shortcodes](https://github.com/quarto-dev/quarto-web/blob/5a79cba1d466d55da139cd447c9f3fe1fc812d4d/docs/extensions/shortcodes.qmd#L105)
Reference to 0.9: [YAML Intelligence](https://github.com/quarto-dev/quarto-web/blob/5a79cba1d466d55da139cd447c9f3fe1fc812d4d/docs/tools/vscode.qmd#L124)
| {
"assignee": null,
"comments": 5,
"created_at": "2022-08-23T18:44:20Z",
"creator": "jthomasmock",
"is_pull_request": false,
"labels": [
"documentation",
"needs-discussion"
],
"locked": false,
"milestone": "v1.3",
"number": 4463,
"state": "closed",
"title": "Reference to old or pre-release RStudio/Quarto versions",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4463"
} |
Allowing variable overrides in batch scripts is hairy because of the need for complicated `startlocal enabledelayedexpansion` stuff. It makes our scripts fragile and limits the number of people who are willing to work on them. I propose that we cut `configure.cmd` completely, and run configure.sh on all platforms.
What this requires is the use of msys2 or git for windows. WSL is not useful here, it behaves like a linux system for the sake of our scripts instead of a bash-on-windows thing.
We clearly can't require this on end user systems for our quarto.cmd script. This proposal is only for development. The quarto.cmd script doesn't present the same override headaches anyway, so it's not a big deal there.
I will put up a PR showing that configure.sh can run fine on windows. If that is satisfactory, then maybe we can consider removing configure.cmd. | {
"assignee": null,
"comments": 3,
"created_at": "2022-08-23T13:47:26Z",
"creator": "msarahan",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 2071,
"state": "open",
"title": "Proposal: use bash on windows for configure",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2071"
} |
### Bug description
I'm unable to schedule a cron job to automatically render/publish a quarto website. The command get executed but the log just shows an empty line (like the output you get when you just execute quarto without any parameter).
This is the entry in my cron schedule file (linux/debian). The exact same command works when executed in the terminal.
`*/10 * * * * /usr/local/bin/quarto publish --no-prompt --no-browser quarto-pub '/home/rstudio/mine_2022/' >> '/home/rstudio/mine_2022/siteupdate.log' 2>&1`
I was not able to find documentation on how to schedule such a command.
Thank you in advance for your help. Best, Fabio
### Checklist
- [X] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)?
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. | {
"assignee": "jjallaire",
"comments": 2,
"created_at": "2022-08-23T09:42:54Z",
"creator": "fabiogiglietto",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2066,
"state": "closed",
"title": "Schedule quarto publish with cron",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2066"
} |
When using `quarto` to build websites, some static site generators, for instance `mkdocs`, create sites with "pretty" URLs by default. It would be great if Quarto also did this.
For instance, in a project containing the file `science.md`, `quarto render` will generate that as `science.html`, resulting in a URL like, `https://example.com/science.html`. In contrast, `mkdocs build` would generate it as `science/index.html`, meaning that, when published, it could be accessed at `https://example.com/science/`.
The current workaround would be to create the original file at `science/index.md`, in which case, both `quarto` and `mkdocs` would generate the same HTML in the same places.
This is important for sites that might be considering migrating to `quarto` that are not currently structured along the lines of the workaround. | {
"assignee": null,
"comments": 1,
"created_at": "2022-08-23T09:02:29Z",
"creator": "sellorm",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 2065,
"state": "open",
"title": "Quarto should output websites with \"pretty\" URLs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2065"
} |
I find the ability to insert tikz pictures by simply calling `{#label}` when rendering to PDF to be extremely elegant and practical, unfortunately the pictures do not seem to render for HTML outputs.
Trying to find a workaround I found the [TikZJax](https://github.com/kisonecat/tikzjax) library. It looks like it could be helpfu for this. | {
"assignee": null,
"comments": 0,
"created_at": "2022-08-23T07:41:08Z",
"creator": "Matrsz",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 2064,
"state": "open",
"title": "Feature Request: Rendering TikZ pictures for HTML output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2064"
} |
Currently the callout blocks visible text stays the same if the block is collapsed or expanded, like here:
Collapsed:
<img width="773" alt="image" src="https://user-images.githubusercontent.com/32404415/186082810-09ec1c12-fe70-4704-850f-d0e34c7d2410.png">
Expanded:
<img width="770" alt="image" src="https://user-images.githubusercontent.com/32404415/186082849-91ad430e-399a-4c70-b99f-75bfdac4459f.png">
Would it make sense to have different text for when be block is collapsed: "Expand to see me" and different when it's expanded: "Collapse to hide me"? | {
"assignee": null,
"comments": 0,
"created_at": "2022-08-23T06:10:17Z",
"creator": "miwojc",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 2063,
"state": "open",
"title": "[feature request] change visible text for callout blocks when collapsed/expanded",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2063"
} |
### Bug description
When I choose `revealjs` as a `format` for a `qmd` document, it does not render `width` variable from `ojs` properly.
````{qmd}
---
format: revealjs
---
## DEMO
```{ojs}
md`${width}`
```
````
When I render it as `html`, it works well.
OS: mac air m1 Venture 13.0 Beta 22A5321d
### Checklist
- [X] upgraded to the [latest nightly quarto version](https://github.com/quarto-dev/quarto-cli/releases)?
- [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included 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.
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well. | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-08-22T19:45:45Z",
"creator": "kwangkim",
"is_pull_request": false,
"labels": [
"bug",
"ojs-engine"
],
"locked": false,
"milestone": "v1.2",
"number": 2058,
"state": "closed",
"title": "[revealjs] ojs runtime error: Cannot read properties of null (reading 'clientWidth') from width",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2058"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2056
<div type='discussions-op-text'>
<sup>Originally posted by **Hedonical** August 22, 2022</sup>
Hi everyone,
I am trying to make it so only the header of a section is centered and center text as seen in the live editor view:
But when I render the HTML document, it applys the centering and color to the entire section:
Is there an easy way to make it so the css elements only apply to the header and not all of the text under?
</div> | {
"assignee": null,
"comments": 7,
"created_at": "2022-08-22T18:51:32Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2057,
"state": "closed",
"title": "How to stop CSS styling of a header applying to entire section?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2057"
} |
I have created a Blog and I use Github Pages to deploy it.
However, my blog struggles to get updated on the web when I have modified something in an old post.
What I do, is that I push the changes to the main repo and then I go to the terminal and just type the usual command: `quarto publish `
I have tried to delete my cache in the browser, but the blog fails to update.
I honestly cannot understand what is the process to update a blog manually, i.e. without GithubActions, when one is using Github Pages for deployment.
| {
"assignee": null,
"comments": 9,
"created_at": "2022-08-22T17:35:24Z",
"creator": "ghost",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 2055,
"state": "closed",
"title": "Deployment with Github Pages ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2055"
} |
Fixes `colorlinks` issue in pdf output | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-08-22T17:08:11Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 2054,
"state": "closed",
"title": "Update pandoc template to 2.19.1",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2054"
} |
### Bug description
It is [documented](https://quarto.org/docs/computations/r.html#chunk-options) that `!expr` works with `fig-cap`, but it doesn't work with `fig-subcap`.
````md
```{r}
#| label: fig-charts
#| fig-cap: Charts
#| fig-subcap: !expr c("First", "Second")
plot(cars)
plot(pressure)
```
````
I get the following error when running `quarto render` on the file:
```
ERROR: Validation of YAML cell metadata failed.
In file subfig-eval-yaml.qmd
(line 4, columns 16--42) Key fig-subcap has value !expr c("First", "Second"), which must be 'true'
3: #| fig-cap: Charts
4: #| fig-subcap: !expr c("First", "Second")
~~~~~~~~~~~~~~~~~~~~~~~~~~
ERROR: Render failed due to invalid YAML.
```
### `quarto check` Output
```
[>] Checking Quarto installation......OK
Version: 1.0.38
Path: C:\scoop\apps\quarto\current\bin\
CodePage: 1250
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.10.6
Path: C:/msys64/mingw64/bin/python.exe
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python -m pip install jupyter
[>] Checking R installation...........OK
Version: 4.2.1
Path: C:/scoop/apps/r-release/current
LibPaths:
- C:/scoop/apps/r-release/4.2.1/library
rmarkdown: 2.15
[>] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
[>] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex External Installation --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 6,
"created_at": "2022-08-22T15:25:06Z",
"creator": "svraka",
"is_pull_request": false,
"labels": [
"bug",
"yaml-validation"
],
"locked": false,
"milestone": "Future",
"number": 2047,
"state": "open",
"title": "Evaluating R code with `!expr` in `fig-subcap` doesn't work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2047"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2043
<div type='discussions-op-text'>
<sup>Originally posted by **maelle** August 22, 2022</sup>
Say I have a chapter file called `abb-blurb.qmd`.
How can I make the corresponding HTML file something else than `abb-blurb.HTML`? Do I need to use a YAML field in the file?</div> | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-08-22T15:13:09Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 2045,
"state": "closed",
"title": "How to change the rendered file path in Quarto books",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2045"
} |
### Bug description
This is a minimal sample project.
[quarto_minimal.zip](https://github.com/quarto-dev/quarto-cli/files/9394347/quarto_minimal.zip)
The post content is simply:
````qmd
---
title: test
---
```{r}
plot(1)
```
````
The rendered site will not display the picture stated in post.
Error message from console is as follows:
```r
#> GET: /
#> /index_files/figure-html/unnamed-chunk-1-1.png (404: Not Found)
#> /index_files/figure-html/unnamed-chunk-1-1.png (404: Not Found)
```
<sup>Created on 2022-08-22 with [reprex v2.0.2](https://reprex.tidyverse.org)</sup>
<details style="margin-bottom:10px;">
<summary>
Session info
</summary>
``` r
sessioninfo::session_info()
#> β Session info βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
#> setting value
#> version R version 4.2.1 (2022-06-23 ucrt)
#> os Windows 10 x64 (build 22000)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate Chinese (Simplified)_China.utf8
#> ctype Chinese (Simplified)_China.utf8
#> tz Asia/Taipei
#> date 2022-08-22
#> pandoc 2.18 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> β Packages βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
#> package * version date (UTC) lib source
#> cli 3.3.0 2022-04-25 [1] CRAN (R 4.2.1)
#> digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.1)
#> evaluate 0.16 2022-08-09 [1] CRAN (R 4.2.1)
#> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.1)
#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.1)
#> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.1)
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.1)
#> highr 0.9 2021-04-16 [1] CRAN (R 4.2.1)
#> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.1)
#> knitr 1.39 2022-04-26 [1] CRAN (R 4.2.1)
#> lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.1)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.1)
#> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.1)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.1)
#> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.1)
#> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.1)
#> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0)
#> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0)
#> R.utils 2.12.0 2022-06-28 [1] CRAN (R 4.2.1)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.1)
#> rlang 1.0.4 2022-07-12 [1] CRAN (R 4.2.1)
#> rmarkdown 2.15 2022-08-16 [1] CRAN (R 4.2.1)
#> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.2.1)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1)
#> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.1)
#> stringr 1.4.1 2022-08-20 [1] CRAN (R 4.2.1)
#> styler 1.7.0 2022-03-13 [1] CRAN (R 4.2.1)
#> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.1)
#> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.1)
#> vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.1)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.1)
#> xfun 0.32 2022-08-10 [1] CRAN (R 4.2.1)
#> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.1)
#>
#> [1] C:/Users/lenovo/AppData/Local/R/win-library/4.2
#> [2] C:/Program Files/R/R-4.2.1/library
#>
#> ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
```
</details>
### `quarto check` Output
```bash
[>] Checking Quarto installation......OK
Version: 1.0.38
Path: C:\PROGRA~1\Quarto\bin\
CodePage: 936
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.9.5 (Conda)
Path: C:/Users/lenovo/miniconda3/python.exe
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with conda install jupyter
(/) Checking R installation...........
```
### `quarto tools check` Output
```bash
[>] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 9,
"created_at": "2022-08-22T12:40:13Z",
"creator": "psychelzh",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2042,
"state": "closed",
"title": "For website project, images generated by R code does not display normally in listing page",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2042"
} |
See discussion and example in https://github.com/quarto-dev/quarto-cli/issues/1581
In short, some **knitr** option could be useful with other computation engine and this require broader Quarto support
This could maybe even be done using Lua filter in an extension (TBC) | {
"assignee": null,
"comments": 0,
"created_at": "2022-08-22T07:49:51Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 2040,
"state": "open",
"title": " Consider support for `class.source` `class.output` `attr.source` `attr.output` equivalent (not only available for knitr cells)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2040"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2003
<div type='discussions-op-text'>
<sup>Originally posted by **andrewcstewart** August 19, 2022</sup>
Looking under the list of formats under https://quarto.org/docs/output-formats/all-formats.html, one format that would be nice to add is Confluence's. I think there are probably a few different options there, but one would be https://confluence.atlassian.com/doc/confluence-storage-format-790796544.html
Just starting this conversation to see if there is similar interest out there.</div> | {
"assignee": "allenmanning",
"comments": 3,
"created_at": "2022-08-22T07:05:16Z",
"creator": "allenmanning",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.3",
"number": 2038,
"state": "closed",
"title": "Publish to Confluence",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2038"
} |
### Bug description
````markdown
---
title: "test"
format:
html:
self-contained: true
keep-md: true
---
```{r}
plot(mtcars)
```
````
This will produce with quarto 1.1.107 on the RStudio Viewer preview pane on Windows
This is due to a bug in Pandoc introduced in version 2.19.1 when base64 package was changed.
See https://github.com/jgm/pandoc/issues/8239
We should probably wait for new Pandoc release before new Quarto release
FWIW I check with R Markdown document that using Pandoc 2.19 works, and 2.19.1 does not. | {
"assignee": null,
"comments": 2,
"created_at": "2022-08-22T06:56:20Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2037,
"state": "closed",
"title": "self-contained document have broken images",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2037"
} |
Hi,
I was running a simple Quarto document that just takes the mean of `c(1,2,3)` and wanted to know how `code-link` and `code-line-numbers` work.
The versions are Quarto 1.0.11, R 4.2.1 and RStudio 2022.07.1 Build 554.
Hopefully the issue reported can be reproduced.
I understand that both R packages `downlit` and `xml2` need to be installed.
Below is the content of the Quarto document.
```
---
title: "CodeNumberVSCodeLink"
format:
html:
code-link: true
code-line-numbers: true
---
## Quarto
Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
```{r}
mean(c(1,2,3))
```
If I set `code-link: true` and `code-line-numbers: false` and click render, the hyperlink works
If I set `code-link: false` and `code-line-numbers: true` and click render, the code numbering works
However when I set both `code-link: true` and `code-line-numbers: true` and click render, **only** the the code numbering works.
Is there a reason for this behaviour ?
| {
"assignee": null,
"comments": 2,
"created_at": "2022-08-22T04:55:25Z",
"creator": "JauntyJJS",
"is_pull_request": false,
"labels": [
"bug",
"upstream"
],
"locked": false,
"milestone": "Future",
"number": 2036,
"state": "open",
"title": "`code-link` and `code-line-numbers` does not work together when both set to true",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2036"
} |
### Bug description
I keep getting the error "\Quarto\bin\ was unexpected at this time" when trying to use a fresh install of Quarto.
The only command I have found so far that works is "quarto -- version" which outputs:
"1.0.38"
Windows 10
Version 10.0.19044 Build 19044
I have verified that quarto is in my path.
### `quarto check` Output
\Quarto\bin\ was unexpected at this time.
### `quarto tools check` Output
\Quarto\bin\ was unexpected at this time.
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 2,
"created_at": "2022-08-22T04:37:27Z",
"creator": "kpjmcg",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2035,
"state": "closed",
"title": "\"\\Quarto\\bin\\ was unexpected at this time\" error for all commands",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2035"
} |
### Bug description
More a question than a bug but wondering if I have multiple Jupyter Notebooks in my project, each of those with different figures that I would like to reference from other notebook, how can I do that?
In the "testing copy.ipynb" notebook I put two cross references: @fig-plot and @fig-plot-copy
fig-plot belongs to testin.ipynb and as shown in the image below, not rendering. Also getting `WARNING: Unable to resolve crossref @fig-plot`
Minimal Reproducible Example here:
https://lgonzalezsa.github.io/hello_quarto/cross_copy.html
https://github.com/lgonzalezsa/hello_quarto/blob/main/test/testing%20copy.ipynb
### `quarto check` Output
_No response_
### `quarto tools check` Output
_No response_
### Checklist
- [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included 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.
- [ ] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [ ] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 1,
"created_at": "2022-08-22T00:43:47Z",
"creator": "lgonzalezsa",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2034,
"state": "closed",
"title": "How to cross reference figures from distinct Jupyter Notebooks ?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2034"
} |
### Bug description
Creating quarto website with a Jupyter Notebook using Python [Holoviz](https://holoviz.org/) plot but getting `Unable to display output for mime type(s):`
I also tested seaborn package and the plots render properly.
Do I need to configure a property for Holoviz plots to render properly with Quarto?
Please check my minimal reproducible example here:
https://lgonzalezsa.github.io/hello_quarto/testing.html#fig-plot
https://github.com/lgonzalezsa/hello_quarto/blob/main/test/testing.ipynb
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.38
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.12 (Conda)
Path: /home/gonluisr/miniconda3/envs/conda_dev/bin/python
Jupyter: 4.10.0
Kernels: julia-(8-threads)-1.7, julia-1.7, python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........(None)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
Linux OS:
```bash
OS: Pop!_OS 22.04 LTS x86_64
Kernel: 5.19.0-76051900-generic
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 2,
"created_at": "2022-08-22T00:07:04Z",
"creator": "lgonzalezsa",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2033,
"state": "closed",
"title": "Quarto not rendering Holoviz plots | Unable to display output for mime type(s):",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2033"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2030
<div type='discussions-op-text'>
<sup>Originally posted by **lukefullard** August 21, 2022</sup>
Hi,
I'm trying to add a table to my quarto document using the [Panel Tabulator widget](https://panel.holoviz.org/reference/widgets/Tabulator.html).
While the table displays nicely and is interactive, I get a warning printed into my pdf:
_Unable to display output for mime type(s)_
I googled and found [another document with a similar warning](https://nasa-openscapes.github.io/2021-Cloud-Hackathon/tutorials/05_Data_Access_Direct_S3.html#plot-the-hls-s3-object).
I tried adding
#| warning: false
#| error: false
to my Python block, bit the warning text still appeared.
Could anyone tell me how to suppress this warning?
Thanks.
</div> | {
"assignee": "jjallaire",
"comments": 3,
"created_at": "2022-08-21T21:09:33Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 2031,
"state": "closed",
"title": "Warning: \"Unable to display output for mime type(s)\"",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2031"
} |
### Bug description
````markdown
---
title: "test"
format: docx
---
:::{.callout-caution}
## Running Code
```{r}
1 + 1
```
:::
````
This causes this issue :
````bash
An error occurred
Found a nested callout in the document. Please fix this issue and try again.
````
This does not happen in PDF and HTML.
This error is thrown from
https://github.com/quarto-dev/quarto-cli/blob/852c9bb99e54e0163575ceecf7dde372b4b73321/src/resources/filters/quarto-pre/callout.lua#L533-L538
where we check for nested Divs.
The Markdown generated by Quarto before Pandoc rendering is the following
````markdown
:::{.callout-caution}
## Running Code
::: {.cell}
```{.r .cell-code}
1 + 1
```
::: {.cell-output .cell-output-stdout}
```
[1] 2
```
:::
:::
:::
````
Hence the error thrown.
I believe this should be fixed - not sure about the context of nested Divs not allowed in Docx @dragonstyle (https://github.com/quarto-dev/quarto-cli/commit/688fd1c070739e3d629d65773da6760ad1d74e41) but it does seem something we should allow for our own expected div right ?
Initially reported in https://community.rstudio.com/t/quarto-render-to-docx-word-fails-if-callout-has-a-code-chunk/145189
### `quarto check` Output
````
quarto check
[>] Checking Quarto installation......OK
Version: 1.1.80
Path: C:\Users\chris\scoop\apps\quarto-prerelease\current\bin\
CodePage: unknown
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.9.13
Path: C:/Users/chris/scoop/apps/pyenv/current/pyenv-win/versions/3.9.13/python3.exe
Jupyter: 4.11.1
Kernels: bash, julia-1.7, python3
[>] Checking Jupyter engine render....OK
(-) Checking R installation...........++ Activating rlang global_entrace
++ Setting QUARTO_PYTHON
[>] Checking R installation...........OK
Version: 4.2.0
Path: C:/PROGRA~1/R/R-42~1.0
LibPaths:
- C:/Users/chris/AppData/Local/R/win-library/4.2
- C:/Program Files/R/R-4.2.0/library
rmarkdown: 2.14.3
[>] Checking Knitr engine render......OK
````
| {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-08-21T15:38:13Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"verify-fixed"
],
"locked": false,
"milestone": null,
"number": 2027,
"state": "closed",
"title": "Nested callout error in Docx when include code chunk in callout block",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2027"
} |
Tracking issue for this PR: https://github.com/quarto-dev/quarto-cli/pull/2015 | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-08-21T13:12:42Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 2025,
"state": "closed",
"title": "merge conda PR",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2025"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2009
@dragonstyle You should read to the bottom of the discussion to see the clearest explanation of what the bug is.
<div type='discussions-op-text'>
<sup>Originally posted by **sammo3182** August 19, 2022</sup>
Recently I asked a question about varying the reference allocation with Quarto in #1728. Then I find the problem that made the old rmarkdown tricks not work was because I used the [`article-format-template`](https://github.com/quarto-journals/article-format-template). The reference was in the right place I want when rendering the plain pdf but then moved to the very end of the document when rendering the `aft`.
A replicable example:
```qmd
---
format:
pdf:
number-sections: true
aft-pdf:
keep-tex: true
aft-html: default
bibliography: bio.bib
title: A test
---
content @Hu2020
# Reference
::: {#refs}
:::
# Online Supplementary Materials
```
[bio.zip](https://github.com/quarto-dev/quarto-cli/files/9386033/bio.zip)
See the difference of the reference when choosing the following options respectively:
How could I allow the `aft` to recognize my reference setting? Any suggestion will be very helpful.
Moreover, a more detailed instruction and examples about how to customize the template than the current [brief version](https://github.com/quarto-journals/article-format-template/blob/main/README.md) under aft repo and Quarto.org will be super welcomed---details like how to arrange the author area, showing the corresponding author, adding the key words and acknowledge, etc.</div> | {
"assignee": "dragonstyle",
"comments": 5,
"created_at": "2022-08-21T13:04:30Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.4",
"number": 2024,
"state": "open",
"title": "Varying the reference position in `quarto-journals` template",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2024"
} |
### Bug description
Would be great if collapsed sections would be accessible for follow hints, for example in qutebrowser or vimium/vimium-FF
In this screenshot the collapsed section doesn't get it's own follow hint, making it not possible to navigate to it without mose. This website was generated by quarto from markdown files using github workflow actions from this repo: https://github.com/miwojc/mlq
Website is built to `gh-pages` branch as per quarto instructions.
<img width="1440" alt="image" src="https://user-images.githubusercontent.com/32404415/185790106-1041929f-8c94-4fce-bc5e-5d171b26c24e.png">
### `quarto check` Output
```bash
quarto check
[β] Checking Quarto installation......OK
Version: 0.9.476
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.13 (Conda)
Path: /Users/username/mambaforge/bin/python
Jupyter: 4.10.0
Kernels: python3, dyalog-kernel
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........(None)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
### `quarto tools check` Output
```bash
quarto tools check
(\) Reading Tool DataDownload https://deno.land/x/[email protected]/directories.ts
(|) Reading Tool DataDownload https://deno.land/x/[email protected]/deps.ts
[β] Reading Tool Data
Tool Status Installed Latest
tinytex Not installed ---- v2022.08
chromium Not installed ---- 869685
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "jooyoungseo",
"comments": 0,
"created_at": "2022-08-21T12:10:32Z",
"creator": "miwojc",
"is_pull_request": false,
"labels": [
"bug",
"accessibility"
],
"locked": false,
"milestone": "v1.4",
"number": 2023,
"state": "open",
"title": "Add follow hint to collapsed section",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2023"
} |
It's fairly common for data scientists to produce reports which end up in Google Slides and it would be great if there were a pattern which let them use quarto to generate these slides. I know that people have asked for this in the Rmarkdown world and it was tricky to implement, but I was wondering if it would be possible to implement it in quarto.
The only project that I'm aware of that kind of helps is this [md2googleslides](https://github.com/googleworkspace/md2googleslides) project. | {
"assignee": null,
"comments": 6,
"created_at": "2022-08-20T23:13:26Z",
"creator": "GShotwell",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 2022,
"state": "open",
"title": "Feature request: Google slides output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2022"
} |
Hi,
just getting started with quarto (thanks), and not sure I've got the jupyter side of things sorted out. I think I've installed the irkernel for R okay. but am struggling to convert a .qmd file to .ipynb.
Running 'quarto check' in the folder I see the error (at bottom):
```
stephen@blur estimateq % quarto check
[β] Checking Quarto installation......OK
Version: 1.0.38
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.6
Path: /opt/homebrew/opt/[email protected]/bin/python3.10
Jupyter: 4.11.1
Kernels: ir
[β] Checking Jupyter engine render....OK
ERROR: Invalid jupyter YAML metadata found in file (must be string or object)
```
where might I find the invalid YAML? If the check script knows the location (file/line number) of the error, is there any chance it could report that?
As far as I can tell, the only yaml file I've got in the folder is the following
```
---
title: "Example quarto document: estimating PI"
author: "Stephen J Eglen"
date: "2022-08-20"
bibliography: refs.bib
format:
html:
code-fold: false
---
```
(what I'd like to do is specify the ir kernel).
(As a minor aside, when I saw the rstudioconf talk that quarto was 'batteries included', I had falsely assumed that it would include all the python/jupyter machinery. but I don't think it did, so I've done the following:
```
python3 -m pip install jupyter
```
and from the R side, installed the irkernel package and installed the kernel
```
install.packages('IRkernel') # Donβt forget step 2/3!
IRkernel::installspec()
```
) | {
"assignee": null,
"comments": 5,
"created_at": "2022-08-20T22:28:04Z",
"creator": "sje30",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2020,
"state": "closed",
"title": "ERROR: Invalid jupyter YAML metadata found in file (must be string or object)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2020"
} |
### Bug description
The "On this page" table of contents drop down menu sometimes glitches in and out when scrolling through a part of the page with margin elements.
Here's an example from the Quarto website: [https://quarto.org/docs/authoring/article-layout.html]()
with a screen recording of the behavior:
https://user-images.githubusercontent.com/25734232/185762861-22533a12-ac99-4b67-9fdf-993ec86a120c.mov
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 1.0.38
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.12
Path: /usr/local/opt/[email protected]/bin/python3.9
Jupyter: 4.10.0
Kernels: ir, julia-1.6, juliapro_v1.5.0-1-1.5, julia-1.5, python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.1.2
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.1/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-08-20T19:18:01Z",
"creator": "maxdrohde",
"is_pull_request": false,
"labels": [
"bug",
"duplicate",
"verify-fixed"
],
"locked": false,
"milestone": "v1.1",
"number": 2019,
"state": "closed",
"title": "\"On this page\" menu glitches when scrolling through margin elements on page",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2019"
} |
RStudio 2022.07.1 Build 554
OS Mac M1 Air
### Bug description
What happens depends on the document class. Described below.
If one passes in `hyperrefoptions: `
```
pdf:
documentclass: scrbook
keep-tex: true
hyperrefoptions:
- "colorlinks=true"
- "linkcolor=blue"
- "urlcolor=cyan"
```
This is correctly passed to hyperref in the tex output. At top of generated tex:
```
\PassOptionsToPackage{unicode,colorlinks=true,linkcolor=blue,urlcolor=cyan}{hyperref}
```
But below that (after line 100 in the generated tex) is this `\hypersetup` command which overrides that.
**`documentclass: scrbook` and `book`**
No hyperlink color are seen because the `\hyperref` setup is not changed and includes `hidelinks`.
```
\hypersetup{
pdftitle={title},
pdfauthor={author},
hidelinks,
pdfcreator={LaTeX via pandoc}}
```
**`documentclass: scrarticle`, `article`, `krantz`, `svmono`, `report`, `memoir`**
Passing in any `hyperrefoptions: `, including `colorlinks=false`, triggers a change to `\hypersetup` to turn on colorlinks but none of the info in `hyperrefoptions` is used.
The code the generated tex is this
```
\hypersetup{
pdftitle={title},
pdfauthor={the author},
colorlinks=true,
linkcolor={blue},
filecolor={Maroon},
citecolor={Blue},
urlcolor={Blue},
pdfcreator={LaTeX via pandoc}}
```
whether one puts this
```
hyperrefoptions:
- "colorlinks=false"
```
or this (or anything else)
```
hyperrefoptions:
- "colorlinks=true"
- "urlcolor=red"
```
in the format pdf YAML.
Note in all cases the hyperref options are passed to hyperref at the top of the tex file, it's just that they are being overridden later by `\hypersetup`
Personally as a LaTeX user, I find this preferable
```
hyperrefoptions:
- "colorlinks=true"
- "linkcolor=blue"
- "urlcolor=cyan"
```
over this
```
colorlinks: true
linkcolor: blue
urlcolor: cyan
```
The former is what I use for `classoptions` and `geometry` and it is 100% clear what I am doing, i.e. I am setting the hyperref package options and I can look up all the possible options for that package. But the can co-exist just need the `\hyperrefoptions` commands to make it into `\hypersetup`.
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 1.0.38
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.12
Path: /opt/homebrew/opt/[email protected]/bin/python3.9
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.1.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Users/eli.holmes/Library/R/x86_64/4.1/library
- /Library/Frameworks/R.framework/Versions/4.1/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex External Installation --- v2022.08
```
MWE qmd
```
---
title: title
author:
- name: the author
editor: source
format:
pdf:
documentclass: scrbook
keep-tex: true
hyperrefoptions:
- "colorlinks=true"
- "linkcolor=blue"
- "urlcolor=cyan"
---
# Intro
[Quarto](https://quarto.org/) is great.
```
### Checklist
- [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [x] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [x] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [x] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 10,
"created_at": "2022-08-20T16:48:21Z",
"creator": "eeholmes",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2017,
"state": "closed",
"title": "For PDF, hyperrefoptions being overridden by \\hypersetup",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2017"
} |
I am trying to replicate the example shown here : https://quarto.org/docs/interactive/ojs/ but instead of using the csv file I am using the penguins data set and I am not able to get the plots showing up when I used the transpose function but it work when I use the csv file found [here](https://github.com/quarto-dev/quarto-web/blob/main/docs/interactive/ojs/palmer-penguins.csv) .
````
---
title: "test observ"
format: html
execute:
echo: false
---
## Quarto
``` {r, include=FALSE}
library("palmerpenguins")
ojs_define(data = penguins)
```
```{ojs}
viewof bill_length_min = Inputs.range(
[32, 50],
{value: 35, step: 1, label: "Bill length (min):"}
)
viewof islands = Inputs.checkbox(
["Torgersen", "Biscoe", "Dream"],
{ value: ["Torgersen", "Biscoe"],
label: "Islands:"
}
)
```
```{ojs}
filtered = transpose(data).filter(function(penguin) {
return bill_length_min < penguin.bill_length &&
islands.includes(penguin.island);
})
Plot.rectY(filtered,
Plot.binX(
{y: "count"},
{x: "body_mass", fill: "species", thresholds: 20}
))
.plot({
facet: {
data: filtered,
x: "sex",
y: "species",
marginRight: 80
},
marks: [
Plot.frame(),
]
}
)
```
````
This is what I get the plots are not showing. When I use the csv the plots show up.
| {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-08-20T16:45:34Z",
"creator": "meldarionqeusse",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 2018,
"state": "closed",
"title": "ObservableJS penguins exmaple does not work with transpose but works if you load csv file.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2018"
} |
### Bug description
Setting either `none-in` or `none-out` results in fading instead of nothing.
Reprex:
````md
---
format: revealjs
---
## slide 1
## slide 2 {transition="none-in none-out"}
## slide 3
````
results:
## RStudio about
Using MacOS
<img width="299" alt="Screen Shot 2022-08-20 at 6 26 41 PM" src="https://user-images.githubusercontent.com/14034784/185756882-57d02ad1-b044-4c2f-b661-f4e947a67d0b.png">
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.38
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.9
Path: /Library/Developer/CommandLineTools/usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources
LibPaths:
- /Users/emilhvitfeldt/Library/R/arm64/4.2/library
- /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Update available v2021.12 v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 2,
"created_at": "2022-08-20T16:27:23Z",
"creator": "EmilHvitfeldt",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2016,
"state": "closed",
"title": "Setting transition=\"none-*\" turns on fading",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2016"
} |
### Bug description
**distill** has also a `layout` option, and for now if the option is not correctly converted to Quarto supported one then there is an useful error
* Content from distill without using YAML syntax
````markdown
---
title: "A small example"
format: html
page-layout: article
---
```{r setup, layout="l-body-outset"}
mtcars[,1:3] |> head()
```
````
* After conversion using `knitr::convert_chunk_header()`
````markdown
---
title: "A small example"
format: html
page-layout: article
---
```{r}
#| layout: l-body-outset
mtcars[,1:3] |> head()
```
````
in both case, we'll have this issue
````
Error running filter C:/Users/chris/scoop/apps/quarto-prerelease/current/share/filters/layout/layout.lua:
...prerelease\current\bin\..\share\pandoc\datadir\_json.lua:167: bad 'for' initial value (number expected, got nil)
stack traceback:
...prerelease\current\bin\..\share\pandoc\datadir\_json.lua:381: in function '_json.decode'
...uarto-prerelease/current/share/filters/layout/layout.lua:3641: in function 'parseLayoutWidths'
...uarto-prerelease/current/share/filters/layout/layout.lua:4274: in function 'layoutCells'
...uarto-prerelease/current/share/filters/layout/layout.lua:4098: in function <...uarto-prerelease/current/share/filters/layout/layout.lua:4091>
ERROR: unexpected character 'l' at line 1 col 1
`````
Not so useful.
And in the second case, YAML validation does not help to detect that. No error detected for the `layout` field in the chunk for me.
Can we do better in the error or at least in the validation ?
### `quarto check` Output
````
$ quarto check
[>] Checking Quarto installation......OK
Version: 1.1.80
Path: C:\Users\chris\scoop\apps\quarto-prerelease\current\bin\
CodePage: unknown
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.9.13
Path: C:/Users/chris/scoop/apps/pyenv/current/pyenv-win/versions/3.9.13/python3.exe
Jupyter: 4.11.1
Kernels: bash, julia-1.7, python3
[>] Checking Jupyter engine render....OK
(\) Checking R installation...........++ Activating rlang global_entrace
++ Setting QUARTO_PYTHON
[>] Checking R installation...........OK
Version: 4.2.0
Path: C:/PROGRA~1/R/R-42~1.0
LibPaths:
- C:/Users/chris/AppData/Local/R/win-library/4.2
- C:/Program Files/R/R-4.2.0/library
rmarkdown: 2.14.3
[>] Checking Knitr engine render......OK
```` | {
"assignee": "cscheid",
"comments": 8,
"created_at": "2022-08-20T13:21:25Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement",
"yaml-validation"
],
"locked": false,
"milestone": "Future",
"number": 2013,
"state": "open",
"title": "Improve validation for layout to help distill conversion ? ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2013"
} |
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