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### Bug description
Dear Quarto team,
This issue is on the web. Not on the CLI. I wanted to create the issue in the web repo, but I ended up here.
In any case, the following url is not working. In fact, the documentation for the citations is missing.
https://quarto.org/docs/visual-editor/technical.html#citations
Thanks.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 4,
"created_at": "2023-02-02T03:29:03Z",
"creator": "randrescastaneda",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 4188,
"state": "closed",
"title": "Missing hyperlink",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4188"
} |
We should fix this. The only thing I wonder about is whether we should support `kr` as a concession to backwards compatibility in quarto.
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4186
<div type='discussions-op-text'>
<sup>Originally posted by **jinhanpae** February 1, 2023</sup>
There is a typo in the illustration of the lang code for Korean. (the "Document Language" tab)
The language code of Korean is "ko", not "kr"
You may also consider changing the file name of the Korean language translation from "_language-**kr**.yml" to "_language-**ko**.yml"
</div> | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2023-02-02T00:51:48Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4187,
"state": "closed",
"title": "The language code of Korean",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4187"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3708
<div type='discussions-op-text'>
<sup>Originally posted by **JosiahParry** December 19, 2022</sup>
When using a title slide in revealjs with a line under it and an aside the aside is in the middle and very much not "aside".
How can this be fixed?
<img width="750" alt="image" src="https://user-images.githubusercontent.com/13534508/208440013-d1ecb752-1ffe-4cb9-a956-5f887006de5c.png">
```quarto
---
title: "title"
format: revealjs
---
# this a title slide
this is a sentence under it
:::{.aside}
here is a note about the title
:::
```
</div> | {
"assignee": "cderv",
"comments": 0,
"created_at": "2023-02-02T00:17:15Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"revealjs"
],
"locked": false,
"milestone": "v1.4",
"number": 4185,
"state": "open",
"title": "[revealjs] Allow to us aside in title / section slide ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4185"
} |
### Bug description
Using `link-citations: true` makes citations hyperlink to the corresponding bibliography entries. This works fine for html and pdf outputs. However, in ipynb the citation is a link, but the target is not defined.
Minimal example:
test.qmd
```
---
bibliography: references.bib
link-citations: true
---
Citation: a book @Author2006 and a paper @Author2020.
::: {#refs}
:::
```
Command:
```
quarto render temp.qmd --to ipynb
```
This results in a in notebook with a single markdown cell:
```
#
Citation: a book Author1 ([2006](#ref-author2006)) and
a paper Author3 ([2020](#ref-author2020)).
Author1, X., and Z. Author2. 2006. “Some title.” In *Some journal*, 1: 100-115
Author3, A. 2020. “Another title.” *Another journal.* 2: 304-315
```
Expected result (I think), markdown cell:
```
#
Citation: a book Author1 ([2006](#ref-author2006)) and
a paper Author3 ([2020](#ref-author2020)).
<span id="ref-author2006"></span>Author1, X., and Z. Author2. 2006. “Some title.” *Some journal*, 1: 100-115
<span id="ref-author2020"></span>Author3, A. 2020. “Another title.” *Another journal.* 2: 304-315
```
I am using VSCode to write qmd files, but render them on the command line (Mac OS 11.7), using quarto installed directly from the GitHub repo, commit id #82eae91a0 (which is why `quarto --version` gives `99.9.9`)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2023-02-01T15:17:36Z",
"creator": "lexnederbragt",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 4178,
"state": "open",
"title": "link-citations: true incompletely implemented in ipynb",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4178"
} |
### Bug description
Not sure how this relates to #4068, but the combination of panel-tabset and [nav-fill](https://getbootstrap.com/docs/5.0/components/navs-tabs/#fill-and-justify) doesnt work anymore.
```
---
title: "Untitled"
format: html
---
:::{.panel-tabset .nav-fill}
## A
## B
:::
```
With quarto 1.2.335:
and with quarto 1.3.146
Edit: This appears to work
```
:::{.nav-fill}
:::{.panel-tabset}
## A
## B
:::
:::
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2023-02-01T09:11:33Z",
"creator": "schochastics",
"is_pull_request": false,
"labels": [
"bug",
"ast"
],
"locked": false,
"milestone": "v1.3",
"number": 4174,
"state": "closed",
"title": "tabset and nav-fill not rendering correctly in prerelease",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4174"
} |
I don't think we have support for this ATM, but we should, since we're on tables anyway. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2023-01-31T23:14:38Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"crossref",
"tables"
],
"locked": false,
"milestone": "v1.4",
"number": 4171,
"state": "open",
"title": "Table API overhaul: computational subtables?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4171"
} |
(For our own reference)
Users want to be able to send a table and tell us this crossref should be treated as a Figure instead of a Table. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2023-01-31T19:51:03Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 4168,
"state": "open",
"title": "Crossref type override",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4168"
} |
Suppose that for some reason I want to store all the images that I want to use in a presentation in a location that is not the exact directory where the .qmd file itself lives, something like `things/stuff/imgs`.
This would clearly work
```
```
But gets very cumbersome to type.
with `xaringan` and using R, it seemed like I could create a variable that stored the long annoying path name and then recycle it for all my figures, for example by creating a variable called `pth`
```
pth = file.path("things", "stuff","imgs")
```
And then using that `pth` pbject in an inline code chunk in the figure path
```
`)
```
This doesn't seem to work in Quarto, at least when rendering to revealjs, since `file.path` returns a string and it seems like quarto expects the file path to the figure to be bare?
Is there a way to use programmatically generated file paths for figures in quarto when knitting to revealjs?
| {
"assignee": null,
"comments": 2,
"created_at": "2023-01-31T19:13:09Z",
"creator": "DanOvando",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 4183,
"state": "closed",
"title": "using programatic file paths for images in reavealjs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4183"
} |
### Bug description
Quarto 1.2.313 fails to render symlinked objects with website projects (Linux EndeavourOS).
Steps to reproduce:
1. Create a new quarto website project
2. Symlink to a directory `my-simlinked-dir` of `.qmd` and `.md` files
3. Symlink directly to a few `.qmd` and `.md` files
4. Render `index.qmd`
The directory now looks like
```
_site
.quarto
my-symlinked-dir
file.md
file.qmd
about.qmd
index.qmd
styles.css
_quarto.yml
```
`file.md` and `file.md` are direct symlinks to the contents of `my-simlinked-dir`
When you render `index.qmd` with
```
sidebar:
style: docked
contents:
- "file.qmd"
- "file.md"
- "my-simlinked-dir/file.qmd"
- "my-simlinked-dir/file.md"
```
no HTML files are generated from these files. Also quarto doesn't show any links on the side bar, presumably because it is unable to resolve these paths.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 4,
"created_at": "2023-01-31T18:45:48Z",
"creator": "KeAWang",
"is_pull_request": false,
"labels": [
"bug",
"file-systems"
],
"locked": false,
"milestone": "v1.4",
"number": 4167,
"state": "open",
"title": "Quarto fails to render symlinked content",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4167"
} |
### Bug description
If CSS chunk is included in `qmd` file, rendering (to HTML) fails with Quarto v1.3.142. Both CLI code and RStudio "Render" button behave the same way.
You may use this file to test:
[with-css.zip](https://github.com/quarto-dev/quarto-cli/files/10549594/with-css.zip)
### Details
If CSS chunk is included in `qmd` file like this:
---
knitr:
opts_chunk:
fig.height: 3
fig.width: 5
---
```{css}
h1 {
color: blue;
}
```
# Section 1
and Quarto v1.3.142 is used, rendering (to HTML) fails with the error:
```
Quitting from lines 10-13 (with-css.qmd)
Error in grepl(pattern, options$code) :
invalid regular expression '.*\Q/*\E\s*<[0-9]+>\s**\Q*/\E\s*$', reason 'Invalid use of repetition operators'
Calls: .main ... as.strict_list -> hook -> knitr_options_hook -> grepl
In addition: Warning message:
In grepl(pattern, options$code) :
TRE pattern compilation error 'Invalid use of repetition operators'
Execution halted
```
***
With Quarto v1.2.335 no error is present and CSS code is interpreted as CSS code (CSS changes the style of the document):
***
With both versions of Quarto, if YAML is excluded, e.g.:
```{css}
h1 {
color: blue;
}
```
# Section 1
rendering does not fail, but the contents of CSS chunk are displayed as (kind of) plain text and are not hidden.
CSS is not interpreted as CSS too:
### The result I expect
I expect the same behaviour as with Quarto v1.2.335.
(No error, CSS code is interpreted as CSS code, code is hidden)
### System details
RStudio Edition : Desktop [Open Source]
RStudio Version : 2023.3.0.277
OS Version : Windows 10 x64 (build 19045)
R Version : R version 4.2.2 (2022-10-31 ucrt)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 5,
"created_at": "2023-01-31T17:44:10Z",
"creator": "GegznaV",
"is_pull_request": false,
"labels": [
"bug",
"needs-discussion"
],
"locked": false,
"milestone": null,
"number": 4166,
"state": "closed",
"title": "Rendering `qmd` file with CSS cunk fails in Quarto 1.3.142",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4166"
} |
When using the `publish` [action on GHA as per documentation](https://quarto.org/docs/publishing/github-pages.html#publish-action), I ended up with the following error:
`ERROR: No _publish.yml file available (_publish.yml specifying a destination required for non-interactive publish)`.
As it turns out, the actual problem was that `quarto publish gh-pages` had not been run locally, as the [documentation for the action](https://github.com/quarto-dev/quarto-actions/tree/main/publish#github-pages) suggests one does before running the action. After doing this, the action ran as expected, without the need for any other tweaks and also without needing to include a `_publish.yml` file.
It would be helpful if
1. the error message were improved to point to the actual problem (probably a missing `gh-pages` branch?)
2. the [Quarto doc](https://quarto.org/docs/publishing/github-pages.html#publish-action) explicitly included the instruction to first run `quarto publish gh-pages` locally. | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2023-01-31T16:33:04Z",
"creator": "petrbouchal",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 4498,
"state": "open",
"title": "GHA to Github Pages: misleading error + need for documentation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4498"
} |
### Bug description
```quarto check``` stuck at ```Checking Jupyter engine render.... ``` as shown in the below image. iam also unable to render file.qmd to html. conversion stuck(freeze) after converting the qmd file to .ipynb and dont convert it further.
I am using Quarto 1.2.313
| {
"assignee": null,
"comments": 2,
"created_at": "2023-01-31T15:18:37Z",
"creator": "Mouli04",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4163,
"state": "closed",
"title": "quarto check stuck at Checking Jupyter engine render..",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4163"
} |
### Bug description
# Bug description
Running ``quarto publish gh-pages`` when ``output-dir`` is specified in ``_quarto.yml`` fails with error:
```sh
ERROR: NotFound: No such file or directory (os error 2)
```
# Minimal working example
Create a new project with
```sh
quarto create-project foo
```
and initialize it with a git repository
```sh
cd foo/
git init
git add .
git commit -m "Initial commit"
```
and set a remote for the repository.
Create an orphan ``gh-pages`` branch
```sh
git checkout --orphan gh-pages
git reset --hard
git commit --allow-empty -m "Initialising gh-pages branch"
git push origin gh-pages
```
Edit the ``_quarto.yml`` file so that
```yaml
project:
title: "foo"
output-dir: "_output"
```
Running ``quarto publish`` yields:
```
$ quarto --version
1.2.313
$ quarto publish gh-pages --no-browser
From github.com:dkubek/test
* branch gh-pages -> FETCH_HEAD
Rendering for publish:
pandoc
to: html
output-file: foo.html
standalone: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
title: foo
ERROR: NotFound: No such file or directory (os error 2)
```
Also tried running with the pre-release
```
$ quarto --version
1.3.142
$ quarto publish gh-pages --no-browser
From github.com:dkubek/test
* branch gh-pages -> FETCH_HEAD
Rendering for publish:
pandoc
to: html
output-file: foo.html
standalone: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
title: foo
ERROR: NotFound: No such file or directory (os error 2), stat '/home/dkubek/devel/foo/foo.html'
```
# OS information
```sh
$ uname -a
Linux fedora 6.1.7-100.fc36.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Jan 18 18:37:43 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] 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": 1,
"created_at": "2023-01-31T10:30:04Z",
"creator": "dkubek",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4158,
"state": "closed",
"title": "Quarto publish fails when project ``output-dir`` is specified",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4158"
} |
### Bug description
When using revealjs mode with Quarto if you set a slide to a dark background and include a footer the footer colour does not adjust to the dark background.
The footer appears to be moved outside of the slide section where revealjs sets `has-dark-background` class so it isn't possible to just apply scss logic within `src/resources/formats/revealjs/quarto.scss`.
## Steps to reproduce
Using the [attached file](https://github.com/quarto-dev/quarto-cli/files/10544325/footer-colour.txt) do the following:
```bash
$ mv footer-colour.txt footer-colour.qmd
$ quarto preview footer-colour.qmd
```
## OS Information
I've tested this on the most recent nightly release and still have this issue.
Running on macOS Ventura 13.1.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 4,
"created_at": "2023-01-31T08:33:17Z",
"creator": "Sparrow0hawk",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 4156,
"state": "open",
"title": "Footer text colour doesn't change with darker background colours",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4156"
} |
Trojan.PowerShell.Win32.488 from https://www.virustotal.com/gui/file/ee3cbc2eb52e258b4bfb862fdd51ec9e09d46dc511510fbeb4aeb2155e14ce12
From latest windows installer download on https://quarto.org/docs/get-started/ | {
"assignee": null,
"comments": 1,
"created_at": "2023-01-31T02:31:00Z",
"creator": "tyoc213",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 4177,
"state": "closed",
"title": "one report on virus total? should ignore?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4177"
} |
### Bug description
I am trying to embed videos on a book site using raw links from Dropbox. However, the video shortcode can't seem to parse the URL. For example, if a qmd document tries to include [this video file](https://www.dropbox.com/s/h3ezvnpyn8xe5ch/Section1_4_c.mp4?raw=1) using
````
Here is the video:
{{< video https://www.dropbox.com/s/h3ezvnpyn8xe5ch/Section1_4_c.mp4?raw=1 >}}
````
then rendering complains that "No video source specified for video shortcode".
This is in 1.2.280 on macos Ventura, in an empty default website template.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "allenmanning",
"comments": 5,
"created_at": "2023-01-30T22:20:04Z",
"creator": "tobydriscoll",
"is_pull_request": false,
"labels": [
"bug",
"enhancement",
"video"
],
"locked": false,
"milestone": "v1.4",
"number": 4153,
"state": "closed",
"title": "Can't embed video using raw Dropbox link",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4153"
} |
When rendering a quarto document:
```
Starting python3 kernel...ERROR:
object str can't be used in 'await' expression
```
This does not occur with `jupyter-client-8.0.1`.
I am using `quarto-1.2.329`. | {
"assignee": "dragonstyle",
"comments": 8,
"created_at": "2023-01-30T17:33:56Z",
"creator": "psads-git",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4151,
"state": "closed",
"title": "Cannot render quarto documents with the new jupyter-client-8.0.2",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4151"
} |
### Bug description
When I add a figure caption in the margin, Quarto doesn't respect the page layout options. I see that this makes sense in hindsight because there wouldn't be space for the caption, but I spent a while being confused why my figures weren't exapnding into the margin like I intended -- so maybe a warning would be helpful here when both options are toggled on?
## Minimal example
````
---
title: "test"
format: html
---
```{r}
#| column: page-right
#| fig-cap-location: margin
#| fig-cap: "This is a test"
#| fig-width: 12
#| fig-height: 8
plot(1:5)
```
```{r}
#| column: page-right
#| fig-cap-location: bottom
#| fig-cap: "This is a test"
#| fig-width: 12
#| fig-height: 8
plot(1:5)
```
````
## Output
<img width="901" alt="Screenshot 2023-01-30 at 10 12 51" src="https://user-images.githubusercontent.com/25734232/215531316-7390e7bd-db08-44c2-afb4-11bdd87f5c2b.png">
## Version
```
❯ quarto -V
1.2.313
```
```
setting value
version R version 4.2.1 (2022-06-23)
os macOS Ventura 13.1
system x86_64, darwin17.0
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Chicago
date 2023-01-30
pandoc 2.19.2 @ /usr/local/bin/pandoc
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2023-01-30T16:16:18Z",
"creator": "maxdrohde",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 4150,
"state": "open",
"title": "Margin figure caption in HTML interferes with page layout",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4150"
} |
### Bug description
**Note:** I [reported this](https://community.rstudio.com/t/quarto-presentation-render-fails-on-second-try-after-deleting-cache-when-using-cache-with-leaflet-addprovidertiles/158757) over at community.rstudio.com, but I suppose that this is a better place for it.
I am using RStudio 2022.12.0 Build 353 with R version 4.2.2 Patched (2022-11-10 r83330) and knitr-1.41 on a Ubuntu 20.04.5 LTS installation.
I have identified a problem using `cache: true` in a quarto document that uses the `leaflet` package, specifically when using `addProviderTiles`. An example document that demonstrates the problem is below:
````
---
title: "test"
format: revealjs
---
## Create some random spatial data
```{r}
library(sf)
library(leaflet)
# List of volcanos -----------------------------------------
v = c("Volcán Villarica, Chile","Volcán Lonquimay, Chile")
lon = c("Volcán Villarica, Chile"=-71.93,
"Volcán Lonquimay, Chile"=-71.58)
lon = lon[v]
lat = c("Volcán Villarica, Chile"=-39.42,
"Volcán Lonquimay, Chile"=-38.38)
lat = lat[v]
volcanoes = data.frame(name=v,lon=lon,lat=lat)
volcanoes = st_as_sf(volcanoes,coords=c("lon","lat"),crs=4326)
lf = volcanoes |> leaflet() |> addTiles() |> addMarkers()
```
## This works with cache
```{r}
#| cache: true
lf
```
## This fails with cache on second render
```{r}
#| cache: true
lf |> addProviderTiles(providers$OpenTopoMap)
```
````
The document renders without problem the first time before the `cache` exists, but the second time it fails with the following error about missing dependencies:
```
Error: path for html_dependency not found: /tmp/RtmpXpw2HT
Execution halted
```
Deleting the cache allows it to render again, but one looses the `cache` functionality.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 6,
"created_at": "2023-01-30T16:04:06Z",
"creator": "dmkaplan2000",
"is_pull_request": false,
"labels": [
"bug",
"third-party"
],
"locked": false,
"milestone": null,
"number": 4149,
"state": "closed",
"title": "Quarto presentation render fails on second try after deleting cache when using `cache` with `leaflet::addProviderTiles`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4149"
} |
### Bug description
Hi,
First of all, thanks for working so hard, Quarto is awesome!
I am generating docx report from R and I have to insert a signature page with a very specific format.
Previously, I was using Rmarkdown and officedown to generate my reports. The following code in the .Rmd allowed me to insert an external docx file (2 pages):
```
<!---BLOCK_POUR_DOCX{file: 'templates/TitleAndSignaturePages.docx'}--->
```
That doesn't work with Quarto (expected). Would it be possible to add this functionality?
Thanks,
Thomas.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2023-01-30T15:03:18Z",
"creator": "tdemarchin",
"is_pull_request": false,
"labels": [
"enhancement",
"docx"
],
"locked": false,
"milestone": "v1.4",
"number": 4148,
"state": "open",
"title": "[Feature request] possibility to include an external docx document into the quarto docx report",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4148"
} |
### Bug description
In a book project, using a label on a title, eg
```markdown
# title {#sec-stuff}
```
will normally result in a reference to "Chapter X" (where X is the number) when you do something like `@sec-stuff`. This worked well in 1.2.
However, somewhere in 1.3, it stopped working properly when a book contains appendices. All references to chapters in this way wind up as "Appendix X"
For example:
The cross references above should be to chapters 1 and 2.
To make it easy to reproduce, please see the latest commits on my quarto-test repo at: https://github.com/fuhrmanator/quarto-test
I'm using Windows 10, and Quarto's version is 1.3.129
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2023-01-30T03:45:28Z",
"creator": "fuhrmanator",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.3",
"number": 4145,
"state": "closed",
"title": "Cross references to labels on chapters show up as \"Appendix\" rather than \"Chapter\" when book contains appendices",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4145"
} |
### Bug description
Sorry if this has already been reported. I did a quick search to check, but didn't see anything...
It looks like Pandoc's div blocks for figures, under certain conditions, generate the LaTeX error - _Not in outer par mode_.
Here's an example:
````md
---
title: "figure divs"
format: pdf
::: {#fig-quarto}
{fig-align="center" width="2in"}
Caption here
:::
````
Here's what I think is the relevant Quarto output during render:
````md
updating tlmgr
updating existing packages
compilation failed- error
LaTeX Error: Not in outer par mode.
````
A few things to note:
1. This doesn't cause an error for the html format. Everything looks right.
2. If you move the figure options to the div block, as in `::: {#fig-quarto fig-align="center" width="2in"}`, the document renders but the figure options are ignored. Is this expected behavior?
3. Inspecting the .tex file, it appears that adding figure options inside the Pandoc div block, as in the example above, causes Quarto to wrap a LaTeX figure environment inside another figure environment (see below). I kinda wonder if this is what's causing the error, but I don't understand LaTeX sufficiently to say.
````md
\begin{figure}
{\centering
\begin{figure}
{\centering \includegraphics[width=2in,height=\textheight]{quarto.png}}
\end{figure}
}
\caption{\label{fig-quarto}Caption here}
\end{figure}
````
Here's my system info:
````md
> sessioninfo::session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.1 (2022-06-23 ucrt)
os Windows 10 x64 (build 22621)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.utf8
ctype English_United States.utf8
tz America/Denver
date 2023-01-29
rstudio 2022.12.0+353 Elsbeth Geranium (desktop)
pandoc 2.19.2 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
> quarto::quarto_version()
[1] ‘1.2.329’
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 3,
"created_at": "2023-01-29T19:37:26Z",
"creator": "kbvernon",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 4142,
"state": "open",
"title": "figure divs for pdf format cause LaTeX error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4142"
} |
Hey,
I'm trying to include numbered citations (https://github.com/citation-style-language/styles/blob/master/springer-basic-brackets-no-et-al.csl) into my Quarto project, which includes multiple .qmd documents.
I encounter the problem that with this style, the numbering is not consecutive across all documents.
Each document starts with 1 which does not match the numbering in the bibliography.
Is there a way to make the numbering consecutive across the whole document?
F | {
"assignee": "dragonstyle",
"comments": 7,
"created_at": "2023-01-29T13:13:21Z",
"creator": "faaa6",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.4",
"number": 4160,
"state": "open",
"title": "Consecutive citation numbering across multiple .qmd",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4160"
} |
### Bug description
The field bibliography now must be validated as a string, but existing filters for Pandoc sometimes use other types. Example:
```
bibliography:
primary: test/primary.bib
secondary: test/secondary.bib
```
This is the case of the [multi bib filter](https://github.com/pandoc-ext/multibib). Please see: https://github.com/pandoc-ext/multibib/issues/1
Is there any way to bypass this validation?
Thank you.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2023-01-28T22:16:26Z",
"creator": "bcdavasconcelos",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 4139,
"state": "closed",
"title": "Strict YAML validation collides with existing lua filters for Pandoc",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4139"
} |
### Bug description
# Introduction
After installing quarto on Windows 11, I couldn't get the example working from [this url](https://quarto.org/docs/get-started/hello/vscode.html).
# How to reproduce the issue
1. Install Quarto version 1.2.313
2. Create the example document and name it `test.qmd`
```md
---
title: "Quarto Basics"
format:
html:
code-fold: true
jupyter: python3
---
For a demonstration of a line plot on a polar axis, see @fig-polar.
```{python}
#| label: fig-polar
#| fig-cap: "A line plot on a polar axis"
import numpy as np
import matplotlib.pyplot as plt
r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(
subplot_kw = {'projection': 'polar'}
)
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()
```
3. Go to the directory where the document is and install the packages into a separate venv (in Powershell):
```
cd /directory/with/test/qmd/file
python -m venv "venv"
./venv/Scripts/Activate.ps1
python -m pip install jupyter matplotlib plotly
```
4. Run the following command with the activated venv:
```
quarto render test.qmd --to html
```
# What does happen
The command freezes and doesn't do anything. I doesn't write anything on the output. I noticed that it creates a correct `test.ipynb` file, but doesn't manage to execute it (the file doesn't have output cells).
Btw I also tried to run `quarto check jupyter` and it outputs the following:
It freezeson `Checking Jupyter engine render....`
# What should happen
It should render the html into `test.html`.
# Versions
## requirements.txt
<details>
<summary>Content of requirements.txt</summary>
```sh
anyio==3.6.2
argon2-cffi==21.3.0
argon2-cffi-bindings==21.2.0
arrow==1.2.3
asttokens==2.2.1
attrs==22.2.0
backcall==0.2.0
beautifulsoup4==4.11.1
bleach==6.0.0
cffi==1.15.1
colorama==0.4.6
comm==0.1.2
contourpy==1.0.7
cycler==0.11.0
debugpy==1.6.6
decorator==5.1.1
defusedxml==0.7.1
executing==1.2.0
fastjsonschema==2.16.2
fonttools==4.38.0
fqdn==1.5.1
idna==3.4
importlib-metadata==6.0.0
ipykernel==6.20.2
ipython==8.9.0
ipython-genutils==0.2.0
ipywidgets==8.0.4
isoduration==20.11.0
jedi==0.18.2
Jinja2==3.1.2
jsonpointer==2.3
jsonschema==4.17.3
jupyter==1.0.0
jupyter-console==6.4.4
jupyter-events==0.6.3
jupyter_client==8.0.1
jupyter_core==5.1.5
jupyter_server==2.1.0
jupyter_server_terminals==0.4.4
jupyterlab-pygments==0.2.2
jupyterlab-widgets==3.0.5
kiwisolver==1.4.4
MarkupSafe==2.1.2
matplotlib==3.6.3
matplotlib-inline==0.1.6
mistune==2.0.4
nbclassic==0.5.1
nbclient==0.7.2
nbconvert==7.2.9
nbformat==5.7.3
nest-asyncio==1.5.6
notebook==6.5.2
notebook_shim==0.2.2
numpy==1.24.1
packaging==23.0
pandocfilters==1.5.0
parso==0.8.3
pickleshare==0.7.5
Pillow==9.4.0
platformdirs==2.6.2
plotly==5.13.0
prometheus-client==0.16.0
prompt-toolkit==3.0.36
psutil==5.9.4
pure-eval==0.2.2
pycparser==2.21
Pygments==2.14.0
pyparsing==3.0.9
pyrsistent==0.19.3
python-dateutil==2.8.2
python-json-logger==2.0.4
pywin32==305
pywinpty==2.0.10
PyYAML==6.0
pyzmq==25.0.0
qtconsole==5.4.0
QtPy==2.3.0
rfc3339-validator==0.1.4
rfc3986-validator==0.1.1
Send2Trash==1.8.0
six==1.16.0
sniffio==1.3.0
soupsieve==2.3.2.post1
stack-data==0.6.2
tenacity==8.1.0
terminado==0.17.1
tinycss2==1.2.1
tornado==6.2
traitlets==5.8.1
uri-template==1.2.0
wcwidth==0.2.6
webcolors==1.12
webencodings==0.5.1
websocket-client==1.5.0
widgetsnbextension==4.0.5
zipp==3.12.0
```
</details>
## Python
```
Python 3.9.13
```
## Quarto
```
1.2.313
```
## Windows
Windows 11 Pro, Version 22H2, OS build 22621.1105
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2023-01-28T19:19:47Z",
"creator": "JanPalasek",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4138,
"state": "closed",
"title": "Getting Started Python example doesn't work on Windows",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4138"
} |
Many of our users are rightfully confused about the distinction between generating a quarto website, generating a shiny quarto document and publishing it to (eg) shinyapps.io, and how to have the former include the latter (which currently needs to happen with an iframe).
It would be ideal if our https://quarto.org/docs/interactive/shiny/index.html section included an explicit section about those distinctions. | {
"assignee": "cwickham",
"comments": 0,
"created_at": "2023-01-28T16:29:13Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 4497,
"state": "open",
"title": "clarify relationship between quarto shiny documents, quarto websites, etc",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4497"
} |
By default, MathJax does not have equation numbers when the LaTeX math environments are used. This:
```
---
title: "test6"
format: html
---
\begin{equation}\label{eq-a}
a
\end{equation}
```
produces this:
<img width="757" alt="image" src="https://user-images.githubusercontent.com/2545978/215232056-a2ab5e88-27c5-41b1-a348-803d96c652cb.png">
instead of this (with numbers)
<img width="918" alt="image" src="https://user-images.githubusercontent.com/2545978/215233374-23590d90-679e-4f4e-8be6-41ebef72dc3a.png">
The reason is that the default behavior for MathJax is to not show the equation numbers. This causes endless confusion for those who use the math environment, which is used for more complex math.
It'd be great if Quarto turned on equation numbering in math environments by default so that html and PDF output behaves the same. All that is needed is to have this script in the header if the equation engine is mathjax:
```
<script>
MathJax = {
tex: {
tags: 'ams' // should be 'ams', 'none', or 'all' }
};
</script>
```
Obviously you can turn this on manually with
```
---
title: "test5"
html:
include-in-header: mathjax.html
---
```
with mathjax.html having the script above but most users spend hours and hours trying to debug lack of numbers until they stumble upon the right solution. What is worse, is that the solution depends on the MathJax version. The above is the method for the version being used by Quarto (by default).
I don't think there is any reason to have the numbering turned off. Anyone using the LaTeX math environment is likely to be a LaTeX user and we have a standard methods for selectively turning off numbers on an equation if that were wanted. | {
"assignee": "cscheid",
"comments": 7,
"created_at": "2023-01-28T00:59:18Z",
"creator": "eeholmes",
"is_pull_request": false,
"labels": [
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 4136,
"state": "open",
"title": "enhancement: add MathJax equation numbering for math environments in html",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4136"
} |
### Bug description
Hi!
I want to incluye a small Shiny app in a page of a website generated with quarto. To reproduce the error, create a new quarto website project with Rstudio.
This is the source code of the `index.qmd` file.
````
---
title: "Old Faithful"
format: html
server: shiny
---
```{r}
sliderInput("bins", "Number of bins:",
min = 1, max = 50, value = 30)
plotOutput("distPlot")
```
```{r}
#| context: server
output$distPlot <- renderPlot({
x <- faithful[, 2] # Old Faithful Geyser data
bins <- seq(min(x), max(x), length.out = input$bins + 1)
hist(x, breaks = bins, col = 'darkgray', border = 'white')
})
```
````
And this is the `_quarto.yml` generated by default by Rstudio.
````
project:
type: website
website:
title: "web-shiny"
navbar:
left:
- href: index.qmd
text: Home
- about.qmd
format:
html:
theme: cosmo
css: styles.css
toc: true
````
When I render de website, I get the error
```
Error in shiny_prerendered_html(input_rmd, render_args) :
Prerendered HTML file not found at /run/media/tmp/quarto/web-shiny/index.html
Calls: .main ... <Anonymous> -> shiny_prerendered_app -> shiny_prerendered_html
Execution halted
```
I am running quarto version 1.2.313 and Rstudio version 2022.12.0 Build 353 on Arch Linux.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2023-01-27T17:39:38Z",
"creator": "asalber",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4130,
"state": "closed",
"title": "Error including shiny app in quarto website",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4130"
} |
### Bug description
When using jupyter-client>=8.0.0, the python3 kernel hangs.
I am using a Windows 10 laptop, quarto version 1.2.269 to reproduce this bug, but I believe that this persists in later versions of quarto as well (initially stumbled across this when trying to render via a github action which had installed a later version of quarto).
Steps to reproduce:
1. Create a fresh python environment (I am currently using python 3.9)
2. Install requirements from a requirements.txt file:
```
notebook==6.5.2
jupyter_client==8.0.1
```
3. Create any .qmd with python code. Example `test.qmd`:
````
---
title: "test quarto"
format:
html:
code-fold: true
jupyter: python3
---
Run at least one python cell.
```{python}
print('Hello, World')
```
````
4. Try to render the file:
`quarto render test.qmd`
Quarto will hang on the line `Starting python3 kernel...`
If you change the jupyter_client version to 7.3.5 in the above requirements.txt file, the file will render.
Interestingly, if you just try to `pip install jupyter` into a fresh environment, it will also hang, but before it even reaches the the `Starting python3 kernel...` line.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 0,
"created_at": "2023-01-27T16:58:49Z",
"creator": "lindsay-fredrick",
"is_pull_request": false,
"labels": [
"bug",
"duplicate"
],
"locked": false,
"milestone": null,
"number": 4128,
"state": "closed",
"title": "Jupyter kernel hangs when using jupyter-client>=8.0.0",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4128"
} |
### Bug description
System: Debian 11
RStudio: RStudio 2022.12.0+353 "Elsbeth Geranium". All packages up to date, using default quarto version (could not check version)
In the yml file:
```
format:
pdf:
papersize: a4
include-in-header:
text: |
\usepackage{titlesec}
\titleformat{\chapter}[display]{\normalfont\huge\bfseries}{\chaptertitlename\ \thechapter}{20pt}{\Huge}
\titlespacing*{\chapter}{0pt}{-50pt}{40pt}
```
Use of titlesec package produces a compilation error:
```
compilation failed- error
Argument of \paragraph has an extra }.
<inserted text>
\par
l.1636 \ttl@extract\paragraph
```
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2023-01-27T16:36:32Z",
"creator": "vfacta",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4126,
"state": "closed",
"title": "Titlesec error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4126"
} |
### Bug description
System: Debian 11
RStudio: RStudio 2022.12.0+353 "Elsbeth Geranium". All packages up to date, using default quarto (could not check version)
In quarto book, using text commands inside equations, such as \text{} or \mathrm{}, produces a fatal error when a custom main font is used. Below, a code example:
```
\begin{align*}
a^n &= \underbrace{a \cdot a \cdot a \cdot \ldots}_{n \text{ times}} \\ \\
a^n &= p
\end{align*}
```
In the yml file, the main font is set to EB Garamond:
```
pdf:
mainfont: EB Garamond
```
This will generate the following error:
```
This is XeTeX, Version 3.14159265-2.6-0.999992 (TeX Live 2020/Debian) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
xdvipdfmx:fatal: Cannot proceed without the font: /usr/share/fonts/woff/ebgaramond/EBGaramond08-Regular.woff
No output PDF file written.
```
The removal of the \text command in the equation outputs a pdf file with no error and correct custom font.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 7,
"created_at": "2023-01-27T16:14:11Z",
"creator": "vfacta",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 4125,
"state": "open",
"title": "Custom font and Latex 's \\text{} error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4125"
} |
````powershell
cd $env:TEMP
mkdir test
cd test
quarto add https://github.com/quarto-ext/lightbox/archive/refs/tags/v0.1.4.tar.gz
````
Error is (in french here)
```
ERROR: La syntaxe du nom de fichier, de répertoire ou de volume est incorrecte. (os error 123), stat 'https://github.com/quarto-ext/lightbox/archive/refs/tags/v0.1.4.tar.gz'
```
Somehow we don't resolve as url it seems, or consider it a local extension maybe ?
Working ok on Ubuntu.
| {
"assignee": "cderv",
"comments": 1,
"created_at": "2023-01-27T16:07:43Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"windows"
],
"locked": false,
"milestone": "v1.3",
"number": 4124,
"state": "closed",
"title": "Installing extension from url fails on Windows",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4124"
} |
Quarto does not work with the latest version of jupyter_client that was recently released.
In the meantime, quarto devs have verified that the issue does not exist with version 7.4.9 of jupyter_client. So if you're a python quarto user, please pin your jupyter_client version to 7.4.9 while we diagnose and fix the issue.
In order to pin a version, the easiest way is to add the following line to your `requirements.txt` file in a venv (or similar)
```
jupyter_client < 8.0.0
``` | {
"assignee": "cscheid",
"comments": 8,
"created_at": "2023-01-27T12:53:02Z",
"creator": "JeremyBYU",
"is_pull_request": false,
"labels": [
"bug",
"jupyter"
],
"locked": false,
"milestone": null,
"number": 4122,
"state": "closed",
"title": "jupyter_client 8 issues",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4122"
} |
### Bug description
When using the quarto Render/Publish GitHub Action to create a quarto website embedded with Revealjs slides, I'm receiving:
```
ERROR: Error attempting to provision multiplex token from 'https://reveal-multiplex.glitch.me/': Unexpected token '<', "<html>
<h"... is not valid JSON
Error: Error: Error attempting to provision multiplex token from 'https://reveal-multiplex.glitch.me/': Unexpected token '<', "<html>
<h"... is not valid JSON
at revealMultiplexToken (file:///opt/quarto/bin/quarto.js:73046:15)
at async postprocessors (file:///opt/quarto/bin/quarto.js:72986:35)
at async renderPandoc (file:///opt/quarto/bin/quarto.js:69679:13)
at async Object.onRender (file:///opt/quarto/bin/quarto.js:79336:32)
at async renderFiles (file:///opt/quarto/bin/quarto.js:78709:21)
at async renderProject (file:///opt/quarto/bin/quarto.js:78844:25)
at async Command.fn (file:///opt/quarto/bin/quarto.js:79396:32)
at async Command.execute (file:///opt/quarto/bin/quarto.js:4107:13)
at async quarto (file:///opt/quarto/bin/quarto.js:107017:5)
at async file:///opt/quarto/bin/quarto.js:107028:9
Error: Process completed with exit code 1.
```
Visiting the URL:
```
https://reveal-multiplex.glitch.me
```
Yields:
```
This project has received too many requests, please try again later.
```
Is there a way to embed the necessary multiplex token?
---
Using:
quarto-1.2.313-linux-amd64.deb
r-4.2.2_1_amd64.deb
pandoc-2.19.2-1-amd64.deb
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2023-01-26T22:42:19Z",
"creator": "coatless",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 4117,
"state": "closed",
"title": "revealjs slides + quarto website publishing issue via github actions due to provisioning multiplex token",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4117"
} |
### Bug description
[quartodoc](https://machow.github.io/quartodoc/get-started/overview.html) uses a top-level config field in _quarto.yml, e.g.:
```yaml
project:
type: website
resources:
- objects.json
quartodoc:
style: single-page
dir: reference
package: quartodoc
sections:
- title: Some functions
desc: Functions to inspect docstrings.
contents:
- get_object
- preview
```
However, this fails validation, so `quarto render` raises:
```bash
ERROR: Project _quarto.yml validation failed.
In file _quarto.yml
(line 6, columns 1--10) property quartodoc does not match case convention _quarto
6: quartodoc:
~~~~~~~~~~
7: style: single-page
```
I'm not sure if this is a bug, or an indication that quartodoc would need to implement a custom project type 😅. (tested on Mac OSX).
Note that quartodoc uses this information prior to rendering, so the workflow right now looks like...
```bash
python -m quartodoc build
quarto preview
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2023-01-26T19:52:51Z",
"creator": "machow",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4114,
"state": "closed",
"title": "Custom config in _quarto.yml fails validation in v1.3.129",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4114"
} |
cc @dragonstyle
We want to do filters like this:
```
filters:
pre:
- pre.lua
render:
- render.lua
post:
- post.lua
```
The inspiration is the sweet positioning of asciidoc.lua and that's how everything else should be in our filter chain. | {
"assignee": "cscheid",
"comments": 6,
"created_at": "2023-01-26T18:38:47Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 4113,
"state": "open",
"title": "improve pre-post filter decomposition",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4113"
} |
Currently there's no way to globally adjust the font size used in speaker notes; see [stackoverflow](https://stackoverflow.com/questions/75213819/how-to-change-the-default-font-size-in-quarto-speaker-notes) and [RStudio Community](https://community.rstudio.com/t/create-a-div-that-will-reduce-font-size-of-speaker-notes/158274). This is an enhancement request.
I should add that `Ctrl- -` and `Ctrl- +` do the job, so it's not a showstopper, but a "nice to have". | {
"assignee": null,
"comments": 1,
"created_at": "2023-01-26T16:25:39Z",
"creator": "rmcd1024",
"is_pull_request": false,
"labels": [
"enhancement",
"revealjs"
],
"locked": false,
"milestone": "Future",
"number": 4112,
"state": "open",
"title": "Customize speaker note font size",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4112"
} |
### Bug description
System: Debian 11
RStudio: RStudio 2022.12.0+353 "Elsbeth Geranium". All packages up to date, using default quarto version (could not check version)
In quarto book, equations such as:
```
\begin{align*}
a^n &= a\cdot a \cdot a \cdot \ldots \\ \\
a^n &= p
\end{align*}
```
and
```
$\dfrac{a^n}{a^m} = a^{n - m}$
```
and:
```
$$\bar{x} = \frac{\sum_{x}^{2} x}{n}$$
```
and:
```
$a^{n \cdot m} = \underbrace{a^n \cdot a^n \cdot a^n \cdot \ldots}_{m}$
```
and:
```
$a^{\overbrace{n + n + n + \ldots}^{m}} = a^{n \cdot m}$
```
Are rendered as plain latex text in epub output. As I've tested, the error occurs when using the enviroments or commands \begin{align}, \begin{align*}, \dfrac{x}{y}, \sum_{x}^{y}, \underbrace and \overbrace. PDF and HTML outputs are not affected by this.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2023-01-26T16:16:25Z",
"creator": "vfacta",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4111,
"state": "closed",
"title": "Some Latex equations don't render correctly to epub output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4111"
} |
We could support loop or maybe more optional attributes available (https://developer.mozilla.org/en-US/docs/Web/HTML/Element/video#attributes)
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3060
<div type='discussions-op-text'>
<sup>Originally posted by **kir0ul** October 27, 2022</sup>
Hi,
Thanks for this super useful tool!
I was wondering if there's a way to add a `loop="true"` attribute to a `<video>` element in a `reveal.js` presentation?</div> | {
"assignee": null,
"comments": 1,
"created_at": "2023-01-26T11:59:21Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement",
"pandoc-lua"
],
"locked": false,
"milestone": null,
"number": 4106,
"state": "closed",
"title": "Support more attributes for video tag in video shortcode (e.g looping video)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4106"
} |
### Bug description
Hello,
I am starting a simple shiny interactive document with a simple drop-down menu selection:
`````
---
title: "LULCC_CH_model"
format: html
server: shiny
execute:
echo: false
---
````{r setup, include=FALSE}
# Install packages
packs <- c("data.table", "shiny")
new.packs <- packs[!(packs %in% installed.packages()[, "Package"])]
if (length(new.packs)) install.packages(new.packs)
# Load required packages
invisible(lapply(packs, require, character.only = TRUE))
# Source custom functions
invisible(sapply(list.files("Scripts/Functions", pattern = ".R", full.names = TRUE, recursive = TRUE), source))
````
````{r}
selectInput("OS", "Operating system:",
c("Windows", "GNU/Linux"))
textOutput("result")
````
````{r}
#| context: server
output$result <- renderText({
paste("You chose:", input$OS)
})
````
````{ojs}
viewof flavor = Inputs.checkbox(["Salty", "Spicy", "Sour", "Umami"], {label: "Flavor"})
````
`````
The 1st time I hit 'run document' the file renders with no problem when using either the viewer pane or window preview settings. However if I then make changes, save and hit 'run document' again. The preview disappears and is not replaced, the render tab displays the processing wheel to indicate something is happening but it just hangs and never updates. I get no error messages to the console and the last message printed to the render tab is: "Listening on http://127.0.0.1:7876"
I ran quarto check in the terminal and everything came back ok also I do not have such problems re-rendering non-interactive .qmd documents. Nor do I have a problem when re-running a .qmd with just interactive {ojs} chunks the problem seems to be limited to the shiny features.
I have updated the shiny package and am runnnig the latest version of Quarto, Rstudio (2022.12.0 Build 353) and R (4.2.2 (2022-10-31 ucrt) on Windows 10.
Any help would be appreciated.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 7,
"created_at": "2023-01-26T08:26:27Z",
"creator": "blenback",
"is_pull_request": false,
"labels": [
"bug",
"upstream",
"rstudio"
],
"locked": false,
"milestone": "v1.4",
"number": 4105,
"state": "open",
"title": "Unable to re-render shiny interactive document ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4105"
} |
### Bug description
By chance, [I stumbled across the fact](https://fediscience.org/@andrew/109730300221529378) that Quarto (at least as of v1.3.56) supports nested tabsets, where a document like this:
````
---
title: Tabsets inside tabsets
---
:::: {.panel-tabset}
## A section
::: {.panel-tabset}
### A section within a section
### Another section inside a section
Neato.
:::
## Another section
::::
````
…would render like this, with a tabset inside the parent tabset:
<img width="852" alt="image" src="https://user-images.githubusercontent.com/73663/214765075-c9703d09-f4f3-4912-9f7c-ebde3d62c8ef.png">
Somewhere between v1.3.56 and v1.3.129, though, this broke. Using v1.3.129, that same example document renders like this, only showing the parent tabset:
<img width="848" alt="image" src="https://user-images.githubusercontent.com/73663/214765412-87b9e435-3880-4c0d-8839-303ec6096584.png">
I'm not sure when/at which version exactly the regression happened, or if it even counts as a regression since nested tabsets were never formally documented and perhaps never meant to be supported? I think it is a useful to have in more complicated notebook-type documents (checking lots of Bayesian diagnostic plots for a bunch of models in a compact way, for example—[see here for another use case](https://fediscience.org/@andrew/109730391347236604))
---
(This is all with R 4.2.2 on macOS Ventura 13.1 with Quarto v1.3.129)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 8,
"created_at": "2023-01-26T05:38:31Z",
"creator": "andrewheiss",
"is_pull_request": false,
"labels": [
"bug",
"regression",
"tabsets"
],
"locked": false,
"milestone": "v1.3",
"number": 4104,
"state": "closed",
"title": "Nested tabsets no longer work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4104"
} |
I tried to use Quarto for schoolwork and I have Rstudio 2022.07.1 installed. Also, I downloaded the latest version of Quarto v1.2.313. I tried to use Rstudio and Powershell to render and both gives me the same results and error message. I posted it on the Rstudio Community and I got an answer that it might because my computer language is not in UTF-8 and the ??? is some character in non-English language.
Here is the error message:
-------------------------------------------------------------
Error running filter C:/Quarto/share/filters/quarto-finalize/quarto-finalize.lua:
[string "..."]:268: cannot open file 'C:\Users\?????\AppData\Local\Temp\quarto-session5c7e9c46\44cf15db\7c187dce' (Invalid argument)
stack traceback:
[string "..."]:268: in function 'io.lines'
[string "..."]:1476: in field 'processDependencies'
C:/Quarto/share/filters/quarto-finalize/quarto-finalize.lua:41: in function <C:/Quarto/share/filters/quarto-finalize/quarto-finalize.lua:38> | {
"assignee": null,
"comments": 5,
"created_at": "2023-01-25T22:31:30Z",
"creator": "SelinaS37",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 4103,
"state": "closed",
"title": "Issue with renderring Quarto hellp.qmd file",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4103"
} |
(cc @machow)
Likely a mergeConfigs issue. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2023-01-25T18:04:26Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro",
"stale"
],
"locked": false,
"milestone": "v1.4",
"number": 4098,
"state": "open",
"title": "website:sidebar path resolution doesn't work with _metadata.yml",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4098"
} |
### Bug description
This doesn't work on Quarto v1.3.124 on macOS 13.0.1:
```swift
let foo = "bar" // <1>
```
1. Test
The code block is rendered with the `// <1>` as if it were standard code, and the ordered list a standard list.
Changing the `// <1>` to `# <1>` doesn't work either. Neither does changing `swift` to `javascript`. Changing it to `python` or `r` works, but syntax highlighting is wrong.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2023-01-25T12:26:47Z",
"creator": "seeM",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4091,
"state": "closed",
"title": "Code annotation doesn't work in some languages",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4091"
} |
Trying to embed a YouTube video in a reveal JS presentation.
Have tried using the shortcode for video with several variants of the URL for the video, and the embed code such as the following:
`{{< video https://www.youtube.com/watch?v=Ye8mB6VsUHw&t=16s width="850" height="475">}}` produces nothing.
`{{< video https://www.youtube.com/embed/Ye8mB6VsUHw width="850" height="475">}}` and `{{< video https://youtu.be/Ye8mB6VsUHw width="850" height="475">}}`
produce a black frame. When I inspect the frame in the browser I see the following with a long set of characters data where the ... are in the following for the src
```
<iframe src="data:text/html; ......................... .charset=utf-8;charset=utf-8, width="850" height="475" title="" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen=""></iframe>
```
If I edit the element in the browser to replace the src as follows,
```
<iframe src="https://www.youtube.com/embed/Ye8mB6VsUHw" width="250" height="175" title="" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen=""></iframe>
```
the video runs fine.
What am I missing to get it to render so it works?
Appreciate any suggestions.
| {
"assignee": null,
"comments": 4,
"created_at": "2023-01-24T23:28:29Z",
"creator": "rressler",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 4089,
"state": "closed",
"title": "YouTube video not playing in Reveal JS",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4089"
} |
This comes from discussion below
From @cderv
> should we maybe add a INSTALL file or something in the bundle ? Do we have a installation page somewhere ? I think we still need to add it in our doc.
From @dragonstyle
> Yes we should do a better job of this. For our AMD tarball installation, we have the following:
> [quarto.org/docs/download/tarball.html?version=1.2.313&idPrefix=download](https://quarto.org/docs/download/tarball.html?version=1.2.313&idPrefix=download)
> The specific commands provided are not RHEL specific, but the general outline of steps is accurate and could be used if you're familiar with configuring your environment.
> It would be great to improve our documentation for RHEL to include the same type of instructions...
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4074
<div type='discussions-op-text'>
<sup>Originally posted by **maxwellkonnaris** January 23, 2023</sup>
Hi, Im trying to install quarto on linux rhel7 server:
commands :
wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.2.313/quarto-1.2.313-linux-rhel7-amd64.tar.gz
tar -xvzf quarto-1.2.313-linux-rhel7-amd64.tar.gz
bash: quarto: command not found
I tried quarto.exe and quarto.cmd, both dont work
Do I have to place the path quarto somewhere like in .bashrc? suprised theres no .install file when you unzip the tar. Anyone deal with this / know what to do so I can use quarto? When I press render in Vscode it says I need to download quarto CLI so its definitely not recognizing. also if I type in quarto from terminal its not recognizing as well.
Thanks!
</div> | {
"assignee": "cwickham",
"comments": 1,
"created_at": "2023-01-24T21:39:12Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 4505,
"state": "open",
"title": "Add installation guide for our downloadable bundle",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4505"
} |
### Bug description
I am trying to use Quarto from my work computer in which I cannot write in the usual `C:/Program Files/R/R-4.2.2/library` and use a personal library instead (let's say `C:/user/r-lib`). I have therefore installed the `rmarkdown` package there.
When trying to render a document with Quarto, it cannot find the `rmarkdown` package as it is not in the system library. A `quarto check` command returns
```
$ quarto check
[>] Checking Quarto installation......OK
Version: 1.2.269
Path: C:\Program Files\RStudio\resources\app\bin\quarto\bin
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....(None)
Unable to locate an installed version of Python 3.
Install Python 3 from https://www.python.org/downloads/
[>] Checking R installation...........OK
Version: 4.2.2
Path: C:/PROGRA~1/R/R-42~1.2
LibPaths:
- C:/Program Files/R/R-4.2.2/library
rmarkdown: (None)
The rmarkdown package is not available in this R installation.
Install with install.packages("rmarkdown")
```
I wonder if it is possible to add my user library in the LibPaths checked by Quarto? Note that it is returned by the `.libPaths()` command in R.
I am using RStudio 2022.12.0 Build 353 on Windows 10.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2023-01-24T17:11:34Z",
"creator": "PierreMasselot",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4081,
"state": "closed",
"title": "Cannot find `rmarkdown` package from a user library",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4081"
} |
I believe we could have an issue in how we parse format and triage between supported Markdown variants and what we call modifiers (e.g `pdf+draft` and `pdf+final`).
This is what we get when running the command above
````
> quarto render doc.qmd --to docx+native_numbering
processing file: doc.qmd
output file: doc.knit.md
pandoc
to: docx
output-file: doc.docx
default-image-extension: png
metadata
title: test
Output created: doc.docx
````
No `native_numbering` in the `to` field for `pandoc`
From debugging within VSCode it seems we are seing `docx+native_numbering` not as the `+native_numbering` variants and then build the wrong format string.
Talking about this part of the code
https://github.com/quarto-dev/quarto-cli/blob/main/src/core/pandoc/pandoc-formats.ts#L171-L216
called
https://github.com/quarto-dev/quarto-cli/blob/main/src/core/pandoc/pandoc-formats.ts#L171-L12
I feel something is not right there but not sure as it seems the list to detect variants was built on the Markdown format supported ones.
https://github.com/quarto-dev/quarto-cli/blob/main/src/core/pandoc/pandoc-formats.ts#L218
@dragonstyle knows better this part of the code. If this is confirmed, we should transfer to an issue probably
Note that doing
````yaml
format: docx
variant: +native_numbering
````
seems to correctly pass the variant as quarto command prints
````
pandoc
to: docx+native_numbering
````
but we document variant only for `markdown` output.
Hope it helps
_Originally posted by @cderv in https://github.com/quarto-dev/quarto-cli/discussions/4020#discussioncomment-4732171_
| {
"assignee": "dragonstyle",
"comments": 5,
"created_at": "2023-01-24T15:02:57Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.4",
"number": 4080,
"state": "open",
"title": "Parsing format string with Pandoc's extensions ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4080"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4056
<div type='discussions-op-text'>
<sup>Originally posted by **aborruso** January 23, 2023</sup>
Hi,
if I open this sample page I have a very very useful TOC, on the side.
If I resize the window the TOC disappears and I do not have it in 1) and 2) (see below).
Is there a way to have it in hamburger menu, and not make it disappear when the window gets small, without putting it in the body, or to put automatically in the body only when the window is small?
Thank you
</div> | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2023-01-24T14:45:33Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.4",
"number": 4079,
"state": "open",
"title": "TOC Responsive Layout Collapse into Sidebar",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4079"
} |
### Bug description
Hello,
I tried the lastest pre-released 1.3.124 version of quarto and I observed a problem with the tabset in the html format. With the version 1.2.313 my tabset and their content (plot and text) are correctly created. But with the pre-released version the content of the tabset is not show.
I'm using R4.2.2 and RStudio 2022.12.0+353 on windows 11
Here is the code I use to generate my tabset:
````
::: panel-tabset
## LONGMIXR plot
::: {.panel-tabset group="GROUP"}
```{r}
#| results: 'asis'
rm(list = "ls2")
res <- list()
res[["FILES"]] <- ls
for (i in c("ALL", "A", "B", "C")) {
# create tab for each groups of individuals and prepare the sub-tabs for the different clustering on this group
cat("### ", i, "\n::: {.panel-tabset group='CLUSTERING'}\n")
for (j in rownames(ls)) {
if (!is.na(ls[j, i])) {
# check if the file exist
cat("#### ", j, "\n") # create the clustering sub-tabs
load(ifelse(i == "ALL",
paste0("./data/", permut, " permut/", ls[j, i]),
paste0("./data/", permut, " permut/", i, "/", ls[j, i])
))
cat("\n\n")
plot(cluster_model)
cat("\n\n")
}
}
cat("\n:::\n") # end CLUSTERING tabset
}
cat("\n:::\n") # end of GROUP tabset
```
:::
## Similarity index
some R plot
````
I trid a simplest code and tt look like the reason is that we can't add a tabset inside another tabset.:
````
::: panel-tabset
### Tab A
Content for Tab A
::: panel-tabset
### sub-Tab A
Content for Tab A
```{r}
plot(1)
```
### sub-Tab B
Content for Tab B
:::
### Tab B
Content for Tab B
:::
````
Would it be possible that in the full release it is possible to add a tabset inside another tabset? I use this feature a lot to present similar figures across different group/timepoint.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2023-01-23T14:53:20Z",
"creator": "Pierre9344",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4068,
"state": "closed",
"title": "Problem with procedural tabset in the pre-release 1.3.124",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4068"
} |
In RStudio, when a Quarto document with `output: gfm` is rendered, it shows the raw markdown in the Viewer. I think it would be more useful to see the HTML preview, to match what it will look like on GitHub. | {
"assignee": "dragonstyle",
"comments": 8,
"created_at": "2023-01-23T13:25:50Z",
"creator": "mine-cetinkaya-rundel",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.3",
"number": 4066,
"state": "closed",
"title": "HTML preview of `output: gfm` documents",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4066"
} |
Consider the following `quarto` document:
````
---
title: "Untitled"
format: pdf
jupyter: python3
---
```{python}
#|echo: false
%load_ext rpy2.ipython
```
```{python}
#| result: asis
%%R
x <- c(1, 2)
names(x) <- c('a', 'b')
print(x)
```
````
The output is misformatted:
| {
"assignee": null,
"comments": 1,
"created_at": "2023-01-23T13:05:57Z",
"creator": "psads-git",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 4133,
"state": "closed",
"title": "Misformatted Quarto R magic chunk output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4133"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4059
<div type='discussions-op-text'>
<sup>Originally posted by **witszymanski** January 23, 2023</sup>
Hi all!
According to this: https://quarto.org/docs/reference/formats/presentations/revealjs.html#slide-layout I can use width in percentage. However, when I do that, the presentation is not appearing at all. Blank screen.
```
---
title: "Title"
subtitle: "Subtitle"
author: "Me Me"
institute: Institute
date: "January 23, 2023"
date-format: "DD MMMM YYYY"
format:
revealjs:
theme: default
width: "100%"
height: "100%"
editor: source
---
# Hello
## What is Lorem Ipsum? {auto-animate="true"}
Lorem Ipsum is simply dummy text of the printing and typesetting industry. Lorem Ipsum has been the industry's standard dummy text ever since the 1500s, when an unknown printer took a galley of type and scrambled it to make a type specimen book. It has survived not only five centuries, but also the leap into electronic typesetting, remaining essentially unchanged.
- bullets
- bullet 1
- bullet 2
- bullet 3
- bullet 4
- boaleadasf
- again1
- again2
```
If I exchange the % with pixels, it works:
```
revealjs:
theme: default
width: 1600
height: 900
```
What am I doing wrong?
Greets</div> | {
"assignee": null,
"comments": 1,
"created_at": "2023-01-23T12:13:59Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"revealjs"
],
"locked": false,
"milestone": "v1.3",
"number": 4063,
"state": "closed",
"title": "[revealjs] `width` and `height` in % are not quoted in template",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4063"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4054
<div type='discussions-op-text'>
<sup>Originally posted by **jimjam-slam** January 22, 2023</sup>
Starter templates can [include a .quartoignore](https://quarto.org/docs/extensions/starter-templates.html#creating-a-template) file to manually specify which files to exclude from the template. It says it uses a `.gitignore`-type syntax, but one omission from this is that it doesn't appear to support a negation operator `!` to force Quarto to include a file that would otherwise be excluded using its default settings.
In my case, I'd like to include a `.gitignore` with my template, as it's designed to work with other file types, and I'd like to suggest to my users which files they should ignore (eg. `node_modules`) and which they should version control (eg. `.luarc.json`).
It'd be great if I could add `!.gitignore` to `.quartoignore` to force my suggested git ignore to be included with the template!</div> | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2023-01-23T11:51:56Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.3",
"number": 4061,
"state": "closed",
"title": "Feature request: support negation operator for .quartoignore",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4061"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4050
<div type='discussions-op-text'>
<sup>Originally posted by **jmgirard** January 22, 2023</sup>
When you share a video from youtube with "privacy-enhanced mode" enabled, the link will be `youtube-nocookie.com` instead of `youtube.com`. It would be great to support this in the video shortcode:
```qmd
{{< video https://www.youtube-nocookie.com/embed/mrvhj2XUfWo >}}
```
Currently (v1.3.124), you get a "No compatible source was found for this media" error.</div> | {
"assignee": "cderv",
"comments": 1,
"created_at": "2023-01-23T11:39:44Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.3",
"number": 4060,
"state": "closed",
"title": "Add support for privacy-enhanced youtube to video shortcode",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4060"
} |
Simple example
````markdown
---
title: "repex"
format: html
keep-md: true
---
```{r}
pander::pander(list("1", "2", 3, c(1, 2)))
```
````
Which gives us this results
Somehow the markdown list is not correctly formatted as sub bullet are introduced.
Our intermediary md is the one messed up somehow
````markdown
---
title: "reprex"
format: html
keep-md: true
---
::: {.cell}
```{.r .cell-code}
pander::pander(list("1", "2", 3, c(1, 2)))
```
::: {.cell-output-display}
* 1
* 2
* _3_
* _1_ and _2_
<!-- end of list -->
:::
:::
````
The knitted result with `knitr::knit("test.qmd")` gives us correct formatting
````markdown
---
title: "reprex"
format: html
keep-md: true
---
```r
pander::pander(list("1", "2", 3, c(1, 2)))
```
* 1
* 2
* _3_
* _1_ and _2_
<!-- end of list -->
````
So some processing somewhere is not correctly parsing. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2023-01-23T09:57:56Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 4057,
"state": "open",
"title": "Interaction issue with `pander` package as Markdown is not correctly formated in output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4057"
} |
### Bug description
In a website, when the navbar is turned off via `navbar: false`, the footer set via `page-footer` is not rendered.
Reproducible example
1. create website project
```bash
quarto create-project quarto-footer-bug --type website
```
2. edit `_quarto.yml` to turn off navbar and include footer text
```yaml
project:
type: website
website:
title: "quarto-footer-bug"
page-footer: "footer" # added
navbar: false # edited
format:
html:
theme: cosmo
css: styles.css
toc: true
```
3. render site
```bash
quarto render quarto-footer-bug
```
Quarto version: 1.3.124
MacOS 13.2 (22D49)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2023-01-22T22:57:51Z",
"creator": "petrbouchal",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4053,
"state": "closed",
"title": "`page-footer` does not render with navbar: false",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4053"
} |
(This seems like a bug.)
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4047
<div type='discussions-op-text'>
<sup>Originally posted by **aborruso** January 22, 2023</sup>
Hi,
if I run
```
quarto render ./report/4d9ceaa1-addd-43f0-a0a8-2623e818f348.qmd -o -
```
at the end I have, in the last line
```
</body></html>ERROR: NotFound: No such file or directory (os error 2)
```
If I add an output file, adding `>tmp.html` I have the file in the folder and `ERROR: NotFound: No such file or directory (os error 2)` message in the shell.
If I add `--metadata-file ../resources/only_content.yml` - it's a file to set `embed-resources: true` - the HTML output has no embedding.
How to solve it?
I'm using `1.3.115` in Debian 11.
Thank you</div> | {
"assignee": "cscheid",
"comments": 4,
"created_at": "2023-01-22T22:54:11Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 4052,
"state": "closed",
"title": "Error when I write to stdout: how to solve it?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4052"
} |
### Bug description
Using Revealjs, the footnote is appearing on top of the text no matter how little text I have on the slide. See the below example.
```
---
title: "Footnote"
format: revealjs
---
# Test
This needs a footnote^[Footnote]
```
Renders as:
<img width="401" alt="Screenshot 2023-01-21 at 1 05 41 PM" src="https://user-images.githubusercontent.com/6343832/213880808-7dacec03-fa74-4858-9d75-0e1e21954a6f.png">
The settings:
```
kevinreuning@Kevins-MacBook-Pro-4 R Bootcamp % quarto preview "/Users/kevinreuning/Dropbox/Teaching_Kevin/Spring_2023/R Bootcamp/
tmp.qmd" --no-browser --no-watch-inputs
pandoc
to: revealjs
output-file: tmp.html
standalone: true
title-prefix: Presentations
wrap: none
default-image-extension: png
html-math-method:
method: mathjax
url: >-
https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS_HTML-full
slide-level: 2
metadata
link-citations: true
width: 1050
height: 700
margin: 0.1
center: false
navigationMode: linear
controlsLayout: edges
controlsTutorial: false
hash: true
history: true
hashOneBasedIndex: false
fragmentInURL: false
transition: none
backgroundTransition: none
pdfSeparateFragments: false
lang: en
auto-stretch: true
author: Kevin Reuning
theme:
- default
title: Footnote
Output created: _site/tmp.html
```
Quarto version: 1.2.280
System Version: macOS 13.1 (22C65)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 4,
"created_at": "2023-01-21T18:19:28Z",
"creator": "reuning",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4044,
"state": "closed",
"title": "Footnote in Revealjs on top of text",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4044"
} |
### Bug description
First of all, congratulations on the wonderful work you have done at Quarto. I use Quarto with tinytex under WIN11 and Linux under Docker/WSL.
In a new Dockerfile, I tried the following:
- use of "quarto install tinytex" works fine (as user install)
- use of "quarto install tinytex --update-path " brings an error. (as root or user)
**Error -> "Outdated L3 programming layer for expl3.sty" if i try to make a pdf.**
_Source - https://github.com/rddaz2013/vscode-python_
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2023-01-21T07:49:55Z",
"creator": "rddaz2013",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro",
"latex"
],
"locked": false,
"milestone": "v1.4",
"number": 4043,
"state": "closed",
"title": "Outdated L3 programming layer for expl3.sty because of --update-path option?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4043"
} |
It would be good to migrate any provided classes (particularly as they may be Bootstrap classes) to the HTML table `<table>` element when they are present as Pandoc attributes (next to caption input). Here is an example of valid input:
```
| Default | Left | Right | Center |
|---------|:-----|------:|:------:|
| 12 | 12 | 12 | 12 |
| 123 | 123 | 123 | 123 |
| 1 | 1 | 1 | 1 |
: {#tbl-asdf .striped .hover .small tbl-colwidths="[15, 15, 35, 35]"}
```
This is a captionless table (though attributes can still be provided) and the ID, three classes, and the `tbl-colwidths` attribute (already supported) are provided. Note that these must be provided in that general order (id, classes, attributes). Also note that we should be flexible in allowing either `.table-striped` or the shorter `.striped` since we should resolve to the correct Bootstrap class names internally.
A final consideration is that the allowed classes should apply to the entire table (like the ones in the above example) since we will unconditionally apply them to the `<table>` element (and we don't have a sensible means to applying classes elsewhere in a table).
| {
"assignee": "rich-iannone",
"comments": 0,
"created_at": "2023-01-20T18:04:08Z",
"creator": "rich-iannone",
"is_pull_request": false,
"labels": [
"enhancement",
"tables"
],
"locked": false,
"milestone": "v1.3",
"number": 4036,
"state": "closed",
"title": "Support usage of classes given as Pandoc attributes (provided alongside table captions) ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4036"
} |
### Bug description
I have a problem rendering from `.qml` to Markdown (to use with Documenter.jl) and to me this seems like a bug. here is the .qml file (hopefully with the full config)=
(_edit_: I of course meant a `.qmd` file here, sorry)
```
---
title: "CommonMark Bug?"
execute:
freeze: auto
eval: true
echo: true
output: true
format:
commonmark:
variant: -raw_html
wrap: none
jupyter: julia-1.8
---
If I want to type something like $p^*$ so a p with a start upfront and run this
on Jupyter with Julia (not sure if relevant) to transfert to Commonmark (to use with Documenter.jl)
```
when running `quarto render my file.qmd` on this one gets
```
CommonMark Bug?
================
If I want to type something like *p*^(\*) so a p with a start upfront and run this on Jupyter with Julia (not sure if relevant) to transfert to Commonmark (to use with Documenter.jl)
```
which is not the `$p^*$` (or rendered here $p^*$) I initiallytypeset there; I would even prefer if inline LaTeX from cmd to md would just stay as it is?
This is running on Mac OS Ventura (13.0.1) using quarto installed via Homebrew with current version of Quarto being
```
❯ quarto --version
1.2.313
```
as an editor I use VS Code, IJulia from Julia 1.8.5, Jupyter installed via Conda.jl
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 8,
"created_at": "2023-01-20T18:02:07Z",
"creator": "kellertuer",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4035,
"state": "closed",
"title": "Rendering .qmd to Commonmark md breakes inline LaTeX ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4035"
} |
### Bug description
I created a Beamer presentation using Quarto, and noticed there was a blank slide after the title slide. After doing some testing, it seems that this issue is caused by having an R chunk before the first slide (I usually have one chunk before the first slide where I load packages etc). Doing some reading, I found that Pandoc causes this same issue when comments are placed before the first slide (https://tex.stackexchange.com/questions/480125/blank-slide-generated-between-the-title-and-the-first-content-slides-when-using) but I am wondering how having an R chunk plays into this. For context, I am using a Windows 10 machine and Rstudio 2022.12.0 Build 353.
See repex below:
````
---
title: "repex"
author: |
| None
date: "`r Sys.Date()`"
format:
beamer:
incremental: true
keep-tex: true
---
````{r,prepare-data}
#| echo: false
#| warning: false
#| message: false
#some code
z=3+4
````
# Slide 1
- Some text
# Slide 2
- Some text
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 7,
"created_at": "2023-01-20T16:19:03Z",
"creator": "aimundo",
"is_pull_request": false,
"labels": [
"bug",
"revealjs"
],
"locked": false,
"milestone": "v1.3",
"number": 4034,
"state": "closed",
"title": "Empty slide after title slide in Beamer",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4034"
} |
### Bug description
With Quarto 1.2.280 (included in recent RStudio daily builds), the presence of a `background-color` in a reveal.js presentation hides a configured `logo`, while the `footer` stays visible.
````markdown
---
title: "logo and footer"
format:
revealjs:
theme: simple
logo: posit-logo-black-TM.svg
footer: "the footer text"
---
## Nothing special
No background color. Footer and logo present.
## Background color {background-color="white"}
Background color. Footer, but no logo.
````
The first content slide, as rendered:
<img width="569" alt="image" src="https://user-images.githubusercontent.com/362187/213723798-f72a67b9-6731-421a-ab83-6755fd4b6656.png">
The final content slide, as rendered:
<img width="571" alt="image" src="https://user-images.githubusercontent.com/362187/213723876-14429cab-d7fe-48c4-9b8a-03b0c7291290.png">
The final slide is configured with a background color and the logo SVG does not display.
Note: I originally thought that this was a problem with `background-image`, but the disappearing `logo` appears connected to a background color, not image. My original example was providing both image and color as given in the documentation example <https://quarto.org/docs/presentations/revealjs/#image-backgrounds>
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2023-01-20T14:34:02Z",
"creator": "aronatkins",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4031,
"state": "closed",
"title": "background-color hides logo",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4031"
} |
About those new function missing in our doc
````lua
quarto.doc.input_file
quarto.doc.output_file
````
-----
Yep, it will available to any LUA code that is being executed (e.g. filter or shortcode)- it is public but you're right that it is omitted from the documentation (unintentionally)!
We also added some project related functions that are omitted:
```lua
quarto.project.directory
quarto.project.offset
quarto.project.profile
quarto.project.output_directory
```
Let's keep this issue open to track getting the documentation updated to reflect this.
_Originally posted by @dragonstyle in https://github.com/quarto-dev/quarto-cli/issues/2249#issuecomment-1397066585_
| {
"assignee": "cwickham",
"comments": 1,
"created_at": "2023-01-19T14:33:42Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 4499,
"state": "open",
"title": "Document all public functions from quarto Lua API",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4499"
} |
Currently https://quarto.org/docs/authoring/markdown-basics.html has no mention of Raw Block and Raw Inline syntax based on https://pandoc.org/MANUAL.html#extension-raw_attribute
| {
"assignee": "cwickham",
"comments": 0,
"created_at": "2023-01-19T13:54:45Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 4500,
"state": "open",
"title": "Document raw block syntax in our Basic Markdown Guide",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4500"
} |
### Bug description
I'm following the tutorial [here](https://quarto.org/docs/get-started/computations/vscode.html#overview).
Using the following `computations.qmd` code example, the matplotlib image is rendered okay, but the plotly image does not get rendered in the preview both in visual studio code and in the browser:
````
---
title: Quarto Computations
jupyter: python3
---
## NumPy
```{python}
import numpy as np
a = np.arange(15).reshape(3, 5)
a
```
## Matplotlib
```{python}
import matplotlib.pyplot as plt
fig = plt.figure()
x = np.arange(10)
y = 2.5 * np.sin(x / 20 * np.pi)
yerr = np.linspace(0.05, 0.2, 10)
plt.errorbar(x, y + 3, yerr=yerr, label='both limits (default)')
plt.errorbar(x, y + 2, yerr=yerr, uplims=True, label='uplims=True')
plt.errorbar(x, y + 1, yerr=yerr, uplims=True, lolims=True,
label='uplims=True, lolims=True')
upperlimits = [True, False] * 5
lowerlimits = [False, True] * 5
plt.errorbar(x, y, yerr=yerr, uplims=upperlimits, lolims=lowerlimits,
label='subsets of uplims and lolims')
plt.legend(loc='lower right')
plt.show(fig)
```
## Plotly
```{python}
import plotly.express as px
import plotly.io as pio
gapminder = px.data.gapminder()
gapminder2007 = gapminder.query("year == 2007")
fig = px.scatter(gapminder2007,
x="gdpPercap", y="lifeExp", color="continent",
size="pop", size_max=60,
hover_name="country")
fig.show()
```
````
I can execute the plotly cell and see the correct cell output in visual studio code, but when I try to preview it, either inside visual studio code or in a web browser, the plotly output is not rendered.
In the browser's devtools console, I see the following error:
```
Uncaught TypeError: Cannot read properties of undefined (reading 'newPlot')
at computations.html:268:436
at Object.execCb (require.min.js:1:16727)
at e.check (require.min.js:1:10499)
at e.<anonymous> (require.min.js:1:12915)
at require.min.js:1:1542
at require.min.js:1:13376
at each (require.min.js:1:1020)
at e.emit (require.min.js:1:13344)
at e.check (require.min.js:1:11058)
at e.enable (require.min.js:1:13242)
```
I am usring quarto 1.2.313 running on Ubuntu 22.04 on WSL2.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2023-01-19T13:31:52Z",
"creator": "aaronsgithub",
"is_pull_request": false,
"labels": [
"bug",
"third-party"
],
"locked": false,
"milestone": null,
"number": 4018,
"state": "closed",
"title": "plotly cell output is not being rendered",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4018"
} |
### Bug description
# What happens
In a Quarto Website project, when, in `index.qmd`
- the `listing` `type` is set to `grid` and
- `lang` is set to `cs` (which is a supported language) either in `quarto.yml` or in the YAML header of `index.qmd`
- the listed ("child") document contains a valid date in the `date` field
...the listing comes out like this:
<img width="851" alt="image" src="https://user-images.githubusercontent.com/1666657/213404565-934486d3-02d6-4e57-a3c2-f8127f634f10.png">
The bug disappears i.e. the listing comes out correct when:
- the `lang` field is removed or set to other languages (including non-ascii like `pl` and `kr`)
- the `date` field contains non-date text - the listing looks correct and correctly displays "Invalid date"
- the `type` of listing is set to `default`
- (!) `lang: cs` is replaced with `language: _language-cs.yml`, where `_language-cs.yml` is a local copy of [the quarto language file for Czech](https://github.com/quarto-dev/quarto-cli/blob/main/src/resources/language/_language-cs.yml)
# How to reproduce:
1. In RStudio, create a new quarto website project.
2. In index.qmd, set the following YAML header:
```yaml
title: "quarto-listing-bug"
lang: cs
listing:
type: grid
```
3. Create `test.qmd` with the following yaml header:
```yaml
title: "Untitled"
date: 2022-01-01
```
and remove any contents (for minimal reproducibility, the content makes no difference to the bug).
5. Leave other files untouched, including `_quarto.yml`:
```yaml
project:
type: website
website:
title: "quarto-listing-bug"
navbar:
left:
- href: index.qmd
text: Home
- about.qmd
format:
html:
theme: cosmo
css: styles.css
toc: true
```
6. Click `Render` on `index.qmd`. (Running `quarto render` or `quarto render index.qmd` has the same result.) No unusual Quarto output appears on the console.
# Versions
- Quarto: 1.2.313 - I wasn't able to test on the daily release, since the daily returned an error referring to missing Lua filters in a quarto shared directory.
- RStudio: Version 2023.03.0-daily+41 (2023.03.0-daily+41)
- OS: MacOS 13.2 (a) Beta (22D7750270d)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2023-01-19T09:50:47Z",
"creator": "petrbouchal",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4017,
"state": "closed",
"title": "Grid listing garbled with `lang: cs` and a valid `date` in listed document",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4017"
} |
### Bug description
When rendering a document using the margin layout with a full-width figure the HTML render makes a full-width caption, which is probably the desired layout. In the PDF layout, the figure is full-width, but the caption is limited to the text column, which is a bit hideous. Running Mac OS.
Example:
````md
---
format:
pdf:
execute:
echo: false
html:
code-fold: true
reference-location: margin
---
```{r}
#| label: fig-test
#| fig-column: page-right
#| fig-cap: Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
#| warning: false
library(tidyverse)
data(iris)
iris %>% ggplot(aes(Sepal.Length, Sepal.Width, color = Species)) + geom_point()
```
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2023-01-19T01:56:45Z",
"creator": "mikheyev",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4014,
"state": "closed",
"title": "Figure caption width not the same when rendering HTML vs pdf in margin layout when using full-width figures",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4014"
} |
If a plot is programmatically generated, it produces an error: `LaTeX Error: Not in outer par mode` when rendering. Here is a simple example:
````
---
format:
pdf:
execute:
echo: false
---
This is some text
::: {.column-margin}
#### Subtitle
```{r}
#| label: fig-test
#| fig-cap: Test captions
#| warning: false
library(tidyverse)
data(iris)
iris %>% ggplot(aes(Sepal.Length, Sepal.Width, color = Species)) + geom_point()
```
:::
```` | {
"assignee": null,
"comments": 3,
"created_at": "2023-01-18T22:49:59Z",
"creator": "mikheyev",
"is_pull_request": false,
"labels": [
"wontfix",
"lint"
],
"locked": false,
"milestone": "Future",
"number": 4011,
"state": "open",
"title": "margin figures errors in pdf when generating plots",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4011"
} |
[Page layout](https://quarto.org/docs/output-formats/page-layout.html) gives a code example that produces an error of "ERROR: Render failed due to invalid YAML."
The example shows as:
```
format:
html:
page-layout: full
```
I believe the example should be shown as:
```
format: html
page-layout: full
``` | {
"assignee": null,
"comments": 2,
"created_at": "2023-01-18T19:01:20Z",
"creator": "SPLOpenData",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 4010,
"state": "closed",
"title": "YAML code example error for page layout",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4010"
} |
The following code works in Rmarkdown but not in Quarto to produce side-by-side plots:
`.Rmd` file:
````
---
title: "Side-by-side plot test"
output: html_document
---
```{r, fig.show='hold', out.width='50%'}
plot(1, 2)
plot(3, 4)
```
````
Correct output: plots appear in one *row* in `.html` output file.
`.qmd` file
````
---
title: "Side-by-side plot test"
format: html
---
```{r}
#| fig-show: hold
#| out-width: 50%
plot(1, 2)
plot(3, 4)
```
````
Incorrect output: plots appear in one *column* in `.html` output file.
I tested on the latest nightly release: 1.3.115
RStudio version: 2022.07.2
OS: macOS Monterey 12.5.1
_No response_
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 6,
"created_at": "2023-01-18T16:03:22Z",
"creator": "jtr13",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 4007,
"state": "closed",
"title": "Side-by-side plots with fig-show: hold not working in Quarto",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4007"
} |
When rendering a file that includes conditional content e.g.:
```
---
title: "exerc"
---
::: {.content-visible when-profile="solutions"}
This content will only appear in the advanced version.
:::
```
The conditional content is not included in the output when rendered using quarto version 1.3.115. In version 1.2.313 everything works as expected.
```
quarto render exerc.qmd --profile solutions
```
System: Windows 10 | {
"assignee": "cscheid",
"comments": 13,
"created_at": "2023-01-18T15:40:10Z",
"creator": "PeterReiter",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 4006,
"state": "closed",
"title": ".content-visible when-profile= ignored in version 1.3.115",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4006"
} |
It'd be nice to change how this is laid out for the reasons pointed out, but we currently hard code that decision.
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3999
<div type='discussions-op-text'>
<sup>Originally posted by **jtrecenti** January 17, 2023</sup>
Hi! Thank you very much for developing Quarto. It is awesome.
I was trying to tweak table styles in MS Word (painful, but needed) when I realized that this code:
```
---
title: "Untitled"
format: docx
---
Lets's see @fig-aaa.
```{r}
#| label: fig-aaa
#| fig-cap: a nice figure.
plot(1:10)
```
generates this document:
Note the "+" sign on the top left of the image and the table styling options at the top menu, indicating that we are inside a table.
So, apparently, when we use `fig-cap:`, it wraps the figure and the caption inside a 1-cell table.
Two questions
1. Is this the desired behavior?
2. Is it possible to turn it off?
Thanks!
</div> | {
"assignee": "rich-iannone",
"comments": 5,
"created_at": "2023-01-18T15:09:58Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"crossref",
"tables"
],
"locked": false,
"milestone": "v1.4",
"number": 4004,
"state": "open",
"title": "Figure rendered inside a table in MS Word when using fig-cap",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4004"
} |
### Bug description
Quarto is a far bigger platform than R markdown. But, this is limited to only rendering markdown or its flavours with R or the like code sequences only.
Asciidoc is simpler and has only one flavour with distinct features for writings very good books, articles and what not?
Therefore, I request its developer's to incorporate rendering facilities for Asciidoc documents to be written in Asciidoc quarto.
First, I raised this issue at RStudio.com community forum. But, andresrcs (the Sustainer) suggested me to raise Quarto related issues at this forum.
So, I would like to clarify it further that Quarto does provide one format option of "Asciidoc". But, that feature, in fact converts the document written in Quarto Markdown (Pandoc Markdown) to Asciidoc format with asciidoc codes, which should be rendered elsewhere. And what I mean is that the input file of quarto document should contain asciidoc codes, which can be rendered by Quarto to an output file, not with asciidoc codes, but a file rendered into html, pdf or docx.
To be more clear, what I am expecting from Quarto is that we should be able to write the document, along with R scripts in RStudio in .asciidoc (or .adoc) codes, instead of Rmarkdown or Markdown, which could be rendered to html, pdf, docx or docbook.
Wishing all the best hopefully,
Dr. A.K Singh
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 11,
"created_at": "2023-01-18T13:14:22Z",
"creator": "aksigkvgithub",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 4003,
"state": "open",
"title": "Quarto should incorporate Asciidoc rendering facilities",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4003"
} |
### Bug description
Not all the chapters in my book have headers. I've noticed that in the chapters without headers (and therefore no TOC on the right), the `repo-actions` I specified are missing.
## Minimal example
### Input:
#### `_quarto.yml`
```
project:
type: book
format:
html:
theme: darkly # just to make the screenshots more clear
book:
repo-url: https://github.com/test/test
repo-actions: [edit]
chapters:
- index.qmd
- chapter1.qmd
```
#### `index.qmd`
```
# A header
```
#### `chapter1.qmd`
```
no header
```
### Output
#### `index.html`
(notice how `Edit this page` is available)
#### `chapter1.html`
(notice how `Edit this page` is *not* available)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2023-01-17T22:51:36Z",
"creator": "ratnanil",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3998,
"state": "closed",
"title": "book output: repo-actions only available if chapter has headers",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3998"
} |
### Bug description
The slide numbering gets messed up by h1 (i.e., `#`) sections when using `print-pdf` with RevealJS. If you create a MWE presentation using the code below, it will correctly number the slides 1 to 4 in the IDE and web browser. But when you go to `http://localhost:6600/?print-pdf` (or whatever your port is) or open the presentation in Chrome and hit `e` on the keyboard, each h1 section will increment the slide number by 2 instead of 1. It will also change back to the `c` format, even if you change it in YAML, and it will add an empty page at the end.
```` qmd
---
format:
revealjs:
slide-number: c/t
show-slide-number: all
---
# Section 1
## Slide
# Section 2
## Slide
````
Correct display in RStudio IDE: (i.e., `1 / 4`, `2 / 4`, `3 / 4`, `4 / 4`)
Incorrect numbering and format in PDF Output: (i.e., `2`, `3`, `5`, `6`, Blank)
See the PDF here generated by Chrome
[mwe.pdf](https://github.com/quarto-dev/quarto-cli/files/10439373/mwe.pdf)
---
### Versions
RStudio 2022.12.0+353 "Elsbeth Geranium" Release (7d165dcfc1b6d300eb247738db2c7076234f6ef0, 2022-12-03) for Windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2022.12.0+353 Chrome/102.0.5005.167 Electron/19.1.3 Safari/537.36
Microsoft Windows version 22H2 (OS Build 22623.1095) (64-bit)
Google Chrome version 109.0.5414.75 (Official Build) (64-bit)
Quarto CLI 1.2.269
---
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 15,
"created_at": "2023-01-17T21:14:21Z",
"creator": "jmgirard",
"is_pull_request": false,
"labels": [
"bug",
"revealjs"
],
"locked": false,
"milestone": "v1.4",
"number": 3997,
"state": "open",
"title": "Slide Number Issues with RevealJS's print-pdf and h1 sections",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3997"
} |
I get an error when I run the example on this webpage ("Print Options" section):
[https://quarto.org/docs/presentations/revealjs/presenting.html#print-options](https://quarto.org/docs/presentations/revealjs/presenting.html#print-options)
```
---
title: "Presentation"
format:
revealjs:
show-notes: separate-page
slide-number: true
---
```
When I run "Quarto: Render" in VS Code, the error message is:
`ERROR: Validation of YAML front matter failed.`
```Field "show-notes" has value separate-page, which must instead be `true` or `false` ```
FYI, the example compiles and runs perfectly when I replace `separate-page` with `true` or `false`.
The documentation in the link above (Print Options section) states that `shownotes` option can take the value of either `true, false, or separate-page`.
In terms of version, I am running using the latest update of Google Chrome and Mac OS, and I just downloaded and installed Quarto two weeks ago.
| {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2023-01-17T09:44:26Z",
"creator": "code86",
"is_pull_request": false,
"labels": [
"bug",
"yaml-validation",
"revealjs"
],
"locked": false,
"milestone": "v1.3",
"number": 3996,
"state": "closed",
"title": "Reveal js error for `show-notes: separate-page`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3996"
} |
### Bug description
```
# This will create a file named "template.qmd" in the current folder.
# Used in: the "template.qmd" is a parametrized report and in a package. The report
# will be compiled in a temporary directly which will be cleaned afterwards.
f <- c("---", "title: \"Test\"", "format: html", "---", "", "## Set a variable",
"", "```{r}", "OK <- FALSE", "```", "", "## Running Code depending on value of `OK`",
"", "```{r}", "#| eval: !expr OK", "print(\"OK is TRUE - otherwise you won't see anything here.\")",
"```", "")
writeLines(f, "template.qmd")
name <- "Test_Report"
output_format <- "html"
output_file <- paste0(name, ".html")
tmpdir <- tempfile()
dir.create(tmpdir)
template <- file.path(tmpdir, "template.qmd")
file.copy(
file.path(".", "template.qmd"),
template
)
report <- quarto::quarto_render(
input = template,
output_format = output_format,
output_file = output_file
)
# Here the error occurs:
#
# processing file: template.qmd
# |.............. | 20%
# ordinary text without R code
#
# |............................ | 40%
# label: unnamed-chunk-1
# |.......................................... | 60%
# ordinary text without R code
#
# |........................................................ | 80%
# label: unnamed-chunk-2 (with options)
# List of 1
# $ eval: logi FALSE
#
# |......................................................................| 100%
# ordinary text without R code
#
#
# output file: template.knit.md
#
# pandoc --output ../../../../../../../Users/rainerkrug/tmp/test/Test_Report.html
# to: html
# standalone: true
# section-divs: true
# html-math-method: mathjax
# wrap: none
# default-image-extension: png
#
# metadata
# document-css: false
# link-citations: true
# date-format: long
# lang: en
# title: Test
#
# pandoc: ../../../../../../../Users/rainerkrug/tmp/test/Test_Report.html: openFile: does not exist (No such file or directory)
# Error in `processx::run(quarto_bin, args, echo = TRUE)`:
# ! System command 'quarto' failed
# ---
# Exit status: 1
# stdout & stderr: <printed>
# ---
# Type .Last.error to see the more details.
# And I would like to continuye as follows:
file.copy(
file.path(tmpdir, output_file),
file.path(".", output_file),
)
unlink(tmpdir)
```
```
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Ventura 13.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 ps_1.7.2 digest_0.6.30 later_1.3.0 R6_2.5.1 jsonlite_1.8.4
[7] evaluate_0.19 rlang_1.0.6 cli_3.6.0 rstudioapi_0.14 rmarkdown_2.18 tools_4.2.2
[13] yaml_2.3.6 xfun_0.36 fastmap_1.1.0 compiler_4.2.2 processx_3.8.0 htmltools_0.5.3
[19] knitr_1.41 quarto_1.2
> quarto::quarto_version()
[1] ‘1.2.313’
> pandoc::pandoc_version()
[1] ‘2.19.2’
```
The example runs on Ubuntu, but not on a Mac.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 13,
"created_at": "2023-01-17T09:32:18Z",
"creator": "rkrug",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 3992,
"state": "open",
"title": "Compile quarto document in temporary directory in R fails when using `output_file = ...`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3992"
} |
### Bug description
The function `profvis::profvis()`, somehow, messes up the syntax highlighting of R code blocks.
## Example
File:
````Rmd
---
format: html
---
```{r}
library(profvis)
f <- function() {
pause(0.1)
}
# profvis(f())
```
````
Normal syntax highlighting:
With `profvis::profvis()`:
````Rmd
---
format: html
---
```{r}
library(profvis)
f <- function() {
pause(0.1)
}
profvis(f())
```
````
Syntax highlighting totally messed up:
## Context
Same behaviour with any highlight style, with `format: revealjs` and `format: html`, within a website or outside.
*Note: this might be something weird that the function is doing and may not be a Quarto bug per se.*
## OS
Arch Linux (6.1.6-arch1-1)
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 7,
"created_at": "2023-01-17T06:46:04Z",
"creator": "prosoitos",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3991,
"state": "closed",
"title": "Syntax highlighting messed up by profvis::profvis()",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3991"
} |
### Bug Description
My issue is exactly the same as issue #3941. I have tried everything mentioned in it, and still unable to publish on quarto pub. Every time I attempt, I am asked to re-authorize my account. And even after re-authorization, the publishing process doesn't go ahead at all. I updated RStudio version to 2023.03.0 +79 and quarto to version 1.3.112. But still the issue persists.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "softwarenerd",
"comments": 5,
"created_at": "2023-01-17T06:46:04Z",
"creator": "bhattmaulik",
"is_pull_request": false,
"labels": [
"bug",
"publishing"
],
"locked": false,
"milestone": null,
"number": 3990,
"state": "closed",
"title": "Unable to publish on quartopub blog",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3990"
} |
### Bug description
I'm not sure if this is an RStudio issue or a Quarto issue (it doesn't happen when using VS Code, so it might be an RStudio thing; but there also might be some setting in Quarto that I'm missing that could fix it).
*(This is all with Quarto 1.3.49 in RStudio 2022.12.0+353 on macOS Ventura 13.1)*
An RStudio Project in a subfolder in a Quarto project inherits the Quarto-ness of the parent directory, so that .Rmd files in the child directory are rendered with Quarto instead of `rmarkdown::render()`.
As a reproducible example, consider a Quarto project folder structured like this:
```
.
├── _quarto.yml
├── child-project
│ ├── child-project.Rproj
│ └── rmd_document.Rmd
├── index.qmd
└── quarto-parent.Rproj
```
<img width="220" alt="image" src="https://user-images.githubusercontent.com/73663/212736802-4449b763-a712-4cbb-9edc-1a0f16624e1b.png">
**index.qmd**
```markdown
---
title: "Parent project"
---
This is a Quarto file in the overarching project. It gets rendered with Quarto.
```
**child-project/rmd_document.Rmd**
```markdown
---
title: "R Markdown document"
---
This is an R Markdown document. It should get rendered with `rmarkdown::render()`, but sometimes
it gets rendered with Quarto
```
### Main problem
When the `child-project` folder is placed inside the `quarto-parent` folder, it inherits the fact that it's part of a larger Quarto project and when it is knit, it goes through Quarto instead of `rmarkdown::render()`.
<img width="629" alt="image" src="https://user-images.githubusercontent.com/73663/212737680-f860317e-2530-46fd-a82f-eda4ceb75142.png">
The "Knit" button in RStudio is replaced with the "Render" button that appears with .qmd files
<img width="405" alt="image" src="https://user-images.githubusercontent.com/73663/212737707-1154603a-f7a0-498a-a5fe-182c353833bd.png">
When the `child-project` folder is placed elsewhere (i.e. if I move it to not be inside a Quarto folder), the document is built with `rmarkdown::render()` as expected…
<img width="630" alt="image" src="https://user-images.githubusercontent.com/73663/212738037-e67332f3-c2f5-4e61-8346-5d888f5cdec9.png">
…and RStudio shows a "Knit" button.
<img width="392" alt="image" src="https://user-images.githubusercontent.com/73663/212737980-ade1e199-f89f-4482-b456-220ba18bb5d5.png">
### Why it's a problem
Often R Markdown files use specific output format options that aren't directly compatible with Quarto. For instance, in [this Quarto project](https://github.com/andrewheiss/evalsp23.classes.andrewheiss.com) I use Quarto to build a website, but the slides for the course are built using {{xaringan}} and are still .Rmd files. Those .Rmd files all live in a [slides subdirectory](https://github.com/andrewheiss/evalsp23.classes.andrewheiss.com/tree/main/slides), and each contains extra metadata in their YAML headers specifying that they should be rendered using {{xaringan}}:
```yaml
output:
xaringan::moon_reader:
...
```
If I open `slides/evalsp23-slides.Rproj` and edit slide files there and then knit the document, Quarto takes over and tries to render the .Rmd file (and can't, since {{xaringan}} isn't one of Quarto's outputs).
Right now, my workaround is to move that `slides` child directory outside of the main Quarto project folder (like to the Desktop), work on edits and knit documents there (so that R Markdown handles the knitting instead of Quarto), and then move the child directory back into the main Quarto project folder to build the website and upload it. It's a hassle, but it works.
It would be nice if child project directories didn't inherit the Quarto rendering properties of their parent folders so that .Rmd files in those child projects can be build with `rmarkdown::render()` instead of Quarto.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 6,
"created_at": "2023-01-16T17:52:22Z",
"creator": "andrewheiss",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3985,
"state": "closed",
"title": "Projects stored in subfolders inherit the rendering settings from the parent directory",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3985"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3813
<div type='discussions-op-text'>
<sup>Originally posted by **howardm** December 31, 2022</sup>
Hi,
I'm trying to use the following functionality in a particular portion of a web page:
```
<details><summary>Content to be revealed</summary>
Content that is revealed.
</details>
```
It works, but this screenshot shows the placement of it (truncated) in the left margin
---
---
Is the fact that the code precedes content that includes a `::: {.panel-tabset .column-page}` section the cause ?
This problem with the code doesn't occur elsewhere in the document.
Howard</div> | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2023-01-16T16:48:55Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"bug",
"articles"
],
"locked": false,
"milestone": "Future",
"number": 3983,
"state": "open",
"title": "Details tag not well supported for article layout",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3983"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3970
<div type='discussions-op-text'>
<sup>Originally posted by **Zegeri** January 14, 2023</sup>
Some mathematical texts might use axioms and it would be nice if it were supported by quarto. I suggest using "axm" as tag prefix. For example:
```
::: {#axm-pairing}
## Pairing
If $x$ and $y$ are sets, then there exists a set which contains $x$ and $y$ as elements.
:::
```
</div> | {
"assignee": "cscheid",
"comments": 6,
"created_at": "2023-01-16T13:18:33Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 3979,
"state": "open",
"title": "[Feature Request] Add more theorem types from amsthm (e.g. axiom, assumption, ...)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3979"
} |
I've been testing teaching using Journal templates for Quarto, but I keep hitting the same issue every time:
What is the best workflow for using a template, knowing you are likely to switch to another template at a later stage?
Academic publishing often leads us into several rejections from various journals, meaning the need to switch template.
But I have yet to find a workflow that I find particularly satisfying to recommend.
I usually start with recommending to `quarto use template` as this provides also a template.qmd to start filling in, often with useful links to journal publishing guidelines. This, however, forces the use of a sub-directory, and the need to either:
1. move `_extensions` folder to the project root for use with the main doc and possibility to add more extension + transfer the template yaml to your document and start adapting
2. copy your document content to the template.qmd and adapt the yaml + do the same for every new extension, overpopulating the the project with unnecessary sub-directories.
Having the template.qmd is so very useful to know what yaml options the template has or needs, but the subdirectory (though understamdably needed) makes a messy project.
When trying to show the second way of installing a template `quarto install extension` the project structure is nicely maintained, but there is not template.qmd to aid in yaml option settings. It requires exploring the root repo the template is in on github and opening the qmd there to see the tempalte. This is not so convenient.
Do you have any recommendations for how a workflow for this would look like? | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2023-01-16T09:03:47Z",
"creator": "drmowinckels",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 3978,
"state": "open",
"title": "[Docs request] Workflow for working with academic templates",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3978"
} |
### Bug description
Following the [documentation on sizing mermaid diagram](https://quarto.org/docs/authoring/diagrams.html#sizing), the latest nightly build (1.3.107) running on Ubuntu 20.04 no longer sizes the diagrams differently regardless of the fig-width parameter. I also tried this with the latest stable (1.2.313) and it has the same issue.
For example, in the following script the diagram under #Slide 1 is the exact same size as the diagram in #Slide 2. I have tried playing with both and fig-width and fig-height but neither seems to have any effect.
````md
---
title: Bad Mermaid Sizing
format:
revealjs
---
# Slide 1
```{mermaid}
%%| fig-width: 5
flowchart LR
A[Hard edge] --> B(Round edge)
B --> C{Decision}
```
# Slide 2
```{mermaid}
%%| fig-width: 15
flowchart LR
A[Hard edge] --> B(Round edge)
B --> C{Decision}
```
````
Maybe related to some of the fixes for https://github.com/quarto-dev/quarto-cli/issues/2607?
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 6,
"created_at": "2023-01-14T23:34:06Z",
"creator": "d-chambers",
"is_pull_request": false,
"labels": [
"bug",
"mermaid"
],
"locked": false,
"milestone": "v1.4",
"number": 3973,
"state": "open",
"title": "Mermaid fig-width no longer works",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3973"
} |
The file https://github.com/quarto-dev/quarto-web/blob/50b8e37ab46690f04be9d96a5955928132810449/docs/reference/projects/book.json, contains duplicate entries, some that do not seem to correspond to the quarto book type.
I am submitting a quick PR to fix this issue. | {
"assignee": null,
"comments": 1,
"created_at": "2023-01-14T16:12:00Z",
"creator": "jmcastagnetto",
"is_pull_request": false,
"labels": [
"bug",
"enhancement",
"yaml-validation"
],
"locked": false,
"milestone": "v1.3",
"number": 3981,
"state": "closed",
"title": "Clean up schemas in the presence of overlapping entries",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3981"
} |
### Bug description
The file https://github.com/quarto-dev/quarto-web/blob/50b8e37ab46690f04be9d96a5955928132810449/docs/reference/projects/book.json, contains duplicate entries, some that do not seem to correspond to the quarto book type.
I am submitting a quick PR to fix this issue
| {
"assignee": null,
"comments": 1,
"created_at": "2023-01-14T16:09:28Z",
"creator": "jmcastagnetto",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3972,
"state": "closed",
"title": "duplicate entries in books.json",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3972"
} |
### Bug description
Hello! I am getting an issue when I press the render button in Rstudio vs running `quarto render` in the CLI. When I press Render in Rstudio, my python installation is not being found, but when I run 'quarto render' everything works just as expected.
Here are the outputs from trying to press Render and running 'quarto check jupyter` in the CLI respectively.
I am using Windows 10 and RStudio 2022.12.0+353 "Elsbeth Geranium" Release (7d165dcfc1b6d300eb247738db2c7076234f6ef0, 2022-12-03) for Windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2022.12.0+353 Chrome/102.0.5005.167 Electron/19.1.3 Safari/537.36
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 3,
"created_at": "2023-01-13T23:28:56Z",
"creator": "sweiner123",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3968,
"state": "closed",
"title": "Quarto Render button not working but `quarto render` in command line works",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3968"
} |
Just getting started with quarto. I used it in VSC and it rendered with python code..but with r code, using the file from the official site
https://quarto.org/docs/get-started/hello/rstudio/_hello.qmd
from here
https://quarto.org/docs/get-started/hello/rstudio.html
the following error occured when trying to render this r code both in vsc and rstudio
Output:
```
processing file: hello.qmd
|.............. | 20%
ordinary text without R code
|............................ | 40%
label: load-packages (with options)
List of 1
$ include: logi FALSE
|.......................................... | 60%
inline R code fragments
|........................................................ | 80%
label: plot-penguins (with options)
List of 3
$ warning: logi FALSE
$ echo : logi FALSE
$ message: logi FALSE
Quitting from lines 28-43 (hello.qmd)
Error in png(..., res = dpi, units = "in") : unable to start png() device
Calls: .main ... in_dir -> plot2dev -> do.call -> <Anonymous> -> png
In addition: Warning messages:
1: In png(..., res = dpi, units = "in") :
unable to open file 'hello_files/figure-html/plot-penguins-1.png' for writing
2: In png(..., res = dpi, units = "in") : opening device failed
Execution halted
```
Thanks a lot | {
"assignee": "cderv",
"comments": 5,
"created_at": "2023-01-13T20:50:51Z",
"creator": "AbdurrahmanMN",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3967,
"state": "closed",
"title": "Error on rendering r code",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3967"
} |
### Bug description
As far as I can tell, there are no tests of rendering `.qmd` files with Julia code. E.g.
```bash
paul@pts2 tests [main] $ grep -rnw . -e "{julia}" | wc -l
0
paul@pts2 tests [main] $ grep -rnw . -e "{python}" | wc -l
15
paul@pts2 tests [main] $ grep -rnw . -e "{r}" | wc -l
130
```
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2023-01-13T20:25:33Z",
"creator": "schrimpf",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 3965,
"state": "open",
"title": "there are no tests for Julia",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3965"
} |
````
> quarto use template quarto-journals/acs
Quarto templates may execute code when documents are rendered. If you do not
trust the authors of the template, we recommend that you do not install or
use the template.
? Do you trust the authors of this template (Y/n) » Yes
? Directory name: » test-quarto-acs
[>] Downloading
[>] Unzipping
Found 1 extension.
[>] Copying files...
Files created:
- bibliography.bib
- placeholder.png
- style-guide
- test-quarto-acs.qmd
- _extensions
> cd .\test-quarto-acs\
````
Then rendering to `acs-html` does "work" as no warning or error is thrown but
* `html` is not defined in the `_extensions.yml`
* document is rendered to HTML without using the `common` information defined in `_extensions.yml` (like the CSL file)
So it seems if the format is not explicitly defined, it will just pass through to main one, here HTML
<details>
<summary>Details of the render </summary>
````markdown
> quarto render .\test-quarto-acs.qmd --to acs-html
pandoc
to: html
output-file: test-quarto-acs.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
author:
- name: Andrew N. Other
note: A shared note
- name: Fred T. Secondauthor
affiliations:
- name: Current address
city: Some other place
country: Germany
- name: I. Ken Groupleader
email: [email protected]
phone: +123 (0)123 4445556
fax: +123 (0)123 4445557
affiliations:
- id: unknown1
name: Unknown University
department: Department of Chemistry
town: Unknown Town
- id: second-uni
name: Second University
department: Department of Chemistry
town: Nearby Town
note: A shared note
- name: Susanne K. Laborator
email: [email protected]
affiliations:
- name: BigPharma
town: Big Town
country: USA
- name: Kay T. Finally
affiliations:
- ref: second-uni
- ref: unknown1
title: 'A demonstration of the _achemso_ {{< latex >}} class^[A footnote for the title]'
title-short: An _achemso_ demo
keywords: 'American Chemical Society, LaTeX'
abstract: |
This is an example document for the _achemso_ documentclass, intended for submissions to the American Chemical Society for publication. The class is based on the standard LaTeXe _report_ file, and does not seek to reproduce the appearanceof a published paper.
This is an abstract for the _achemso_ document class demonstration document. An abstract is only allowed for certain manuscript types. The selection of `journal` and `manuscript` will determine if an abstract is valid. If not, the class will issue an appropriate error.This is the abstract.
bibliography:
- bibliography.bib
Output created: test-quarto-acs.html
````
</details>
I believe it should error if we expect to have explicitly a defined format in the extensions i.e at least adding `html: default`
<details>
<summary>YAML would be </summary>
````yaml
title: ACS Journal Format
author: Charles Teague
version: 0.9.1
contributes:
formats:
common:
csl: american-chemical-society.csl
shortcodes:
- fancy-text
filters:
- latex-environment
environments:
- scheme
- chart
- graph
- tocentry
- acknowledgement
- suppinfo
commands:
- ce
pdf:
cite-method: natbib
biblio-config: false
format-resources:
- achemso.bst
template-partials:
- "doc-class.tex"
- "title.tex"
- "_affiliation.tex"
html: default
````
</details>
Or we should at least use the `common` information in format as someone passing explicitly a custom format e.g `acs-html` would expect that (I was) | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2023-01-12T17:12:35Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 3955,
"state": "open",
"title": "Rendering to a non declared custom format silently renders to quarto default format",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3955"
} |
### Bug description
When we include R code in quarto files, the same code chunk (with our current setup) is split into multiple rendered junks (even though it belongs to the same junk in the source code. Each of these rendered junks starts with the number 1, which is not desirable as it prevents referring to the line numbers correctly.
E.g. in the image below, we might have something like this in the qmd file:
```r
task_mtcats$nrow
task_mtcars$ncol
```
I would expect the first line to get the number 1 and the second line to get the number 2, but both get number 1 because in the rendered output they become two junks.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2023-01-12T16:51:14Z",
"creator": "sebffischer",
"is_pull_request": false,
"labels": [
"bug",
"verify-fixed"
],
"locked": false,
"milestone": null,
"number": 3954,
"state": "closed",
"title": "Line numbers of code blocks are not ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3954"
} |
### Bug description
Hi. As always, thank you, thank you, thank you for this awesome software.
As the title states, for revealjs documents, fontawesome icons used in section headers do not appear in the presentation outline. Unicode/HTML does, though.
````md
---
title: "Test Prez"
format: revealjs
---
## Slide 1 📋
## Slide 2 {{< fa brands r-project >}}
## Slide 3 🎯
````
Output:
<img width="338" alt="image" src="https://user-images.githubusercontent.com/53311626/212113357-6aae228e-65b4-4c6e-8e52-62ac7bde7ea1.png">
```
> sessioninfo::session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.1 (2022-06-23 ucrt)
os Windows 10 x64 (build 22621)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.utf8
ctype English_United States.utf8
tz America/Denver
date 2023-01-12
rstudio 2022.12.0+353 Elsbeth Geranium (desktop)
pandoc NA
```
Not sure why it's not showing my pandoc version, but here's this:
```
> rmarkdown::find_pandoc()
$version
[1] ‘2.19.2’
$dir
[1] "C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools"
```
Thanks!
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 6,
"created_at": "2023-01-12T15:54:50Z",
"creator": "kbvernon",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3950,
"state": "closed",
"title": "revealjs - fontawesome icon in section header does not appear in presentation outline",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3950"
} |
### Bug description
Putting `references.bib` (or a csl file, as I was attempting) in a subdirectory Quarto does not find it for HTML only.
For a reprex, create a Quarto book from template (say, `quarto create-project mybook --type book`)
Then place the .bib fiile in a new directory called `subdir` then modify `_quarto.yml`, line 15.
That should create the following key files:
#### index.qmd
```
# Preface {.unnumbered}
See @knuth84 for additional discussion of literate programming.
```
#### references.qmd
```
# References {.unnumbered}
::: {#refs}
:::
```
#### _quarto.yml
```
project:
type: book
book:
title: "issue3949"
author: "Jane Doe"
date: "12/01/2023"
chapters:
- index.qmd
- references.qmd
bibliography: subdir/references.bib
format:
html:
theme: cosmo
pdf:
documentclass: scrreprt
````
#### subdir/references.bib
```
@article{knuth84,
author = {Knuth, Donald E.},
title = {Literate Programming},
year = {1984},
issue_date = {May 1984},
publisher = {Oxford University Press, Inc.},
address = {USA},
volume = {27},
number = {2},
issn = {0010-4620},
url = {https://doi.org/10.1093/comjnl/27.2.97},
doi = {10.1093/comjnl/27.2.97},
journal = {Comput. J.},
month = may,
pages = {97–111},
numpages = {15}
}
```
If I render to PDF this works fine, Rendering to HTML leads to
> File subdir.bib not found in resource path
> ERROR: File subdir.bib not found in resource path
Dashes seem to preserve some of the name as `bibliography: subdir/references-2.bib` leads to
> File subdir-2.bib not found in resource path
This is on Quarto version 1.2.313,
<details><summary>RStudio Version</summary>
RStudio 2022.12.0+353 "Elsbeth Geranium" Release (7d165dcfc1b6d300eb247738db2c7076234f6ef0, 2022-12-03) for Windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2022.12.0+353 Chrome/102.0.5005.167 Electron/19.1.3 Safari/537.36
</details>
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 5,
"created_at": "2023-01-12T15:22:34Z",
"creator": "nclJoshCowley",
"is_pull_request": false,
"labels": [
"bug",
"windows"
],
"locked": false,
"milestone": null,
"number": 3949,
"state": "closed",
"title": "References (in subdirectory) not found for HTML book",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3949"
} |
I tried to render the quarto example document "hello.qmd" to pdf. This throws an error, because an external image is linked in Markdown (the same problem would appear in R Markdown). As soon as I comment out the image the pdf document can be created.
I think it is not ideal to use an example document that cannot be rendered in all widely used formats html, pdf, docx. | {
"assignee": null,
"comments": 11,
"created_at": "2023-01-12T14:00:36Z",
"creator": "hemonika",
"is_pull_request": false,
"labels": [
"bug",
"windows"
],
"locked": false,
"milestone": "v1.3",
"number": 3982,
"state": "closed",
"title": "rendering a document with online image to pdf is not possible on Windows",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3982"
} |
### Bug description
Code annotations in the v1.3.97 pre-release are not working when `code-link: true`:
A reproducible example may be made in RStudio with New Project > Quarto Website, then add `code-link: true` to the _quarto.yml.
````markdown
---
title: "Reprex"
---
This is a Quarto website.
To learn more about Quarto websites visit <https://quarto.org/docs/websites>.
```{r}
1 + 2 # <1>
```
1. Simple calculation
````
Sample Quarto site with `code-link: true` added:
<img width="829" alt="image" src="https://user-images.githubusercontent.com/32419319/212060887-c1fdcf78-94fe-4576-a65a-5a7b55862eea.png">
Sample Quarto site without
<img width="829" alt="image" src="https://user-images.githubusercontent.com/32419319/212061613-fefccb21-ac24-4731-b228-0c159bb55fd8.png">
RStudio Version 2022.12.0+353 (2022.12.0+353)
macOS Monterey v12.6
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2023-01-12T12:10:14Z",
"creator": "cgoo4",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3945,
"state": "closed",
"title": "Code annotations in the v1.3.97 pre-release are not working when `code-link: true`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3945"
} |
I'm having a related bug when the csl is defined in an extension. Both in 1.2.313 and 1.3.97 on Windows. It works fine on Ubuntu.
```
File _extensions-institute-for-nature-and-forest.csl not found in resource path
ERROR: File _extensions-institute-for-nature-and-forest.csl not found in resource path
```
The report and extension are available at https://github.com/inbo/inboqmd_examples/tree/main/source/report/en
_Originally posted by @ThierryO in https://github.com/quarto-dev/quarto-cli/issues/2945#issuecomment-1380175605_
| {
"assignee": "cderv",
"comments": 7,
"created_at": "2023-01-12T11:49:34Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"windows"
],
"locked": false,
"milestone": "v1.3",
"number": 3944,
"state": "closed",
"title": "CSL is not found when defined in an extension. ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3944"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3940
<div type='discussions-op-text'>
<sup>Originally posted by **pnavaro** January 12, 2023</sup>
I am trying to publish on quarto-pub and I am stuck in a loop hole. I always get this message
```
The authorization saved for Quarto Pub is no longer valid.
Please be sure you are logged into the correct Quarto Pub account in your
default web browser, then press Enter to re-authorize.
[✓] Creating quarto-pub site
? Re-authorize account (Y/n) › Yes
? Authorize (Y/n) › Yes
```
I try a lot of things:
- Delete my account on quarto-pub and recreate (I used github and I change to email+passwd)
- Remove my account with `quarto publish accounts`
- Remove the directory `.quarto`
- Change my default browser (Safari, Firefox, Chrome)
- create a token and set the env variable `QUARTO_PUB_AUTH_TOKEN`
Thanks for your help
Pierre</div> | {
"assignee": "softwarenerd",
"comments": 3,
"created_at": "2023-01-12T11:04:47Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3941,
"state": "closed",
"title": "Can't publish on quarto-pub",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3941"
} |
Hi,
Is there a way to include an appendix when using quarto to produce a .pdf? In that case, tables and figures should have the caption: "table A1." and "Figure A1." respectively. | {
"assignee": null,
"comments": 0,
"created_at": "2023-01-12T09:29:46Z",
"creator": "ygalanak",
"is_pull_request": false,
"labels": [],
"locked": true,
"milestone": null,
"number": 3942,
"state": "closed",
"title": "appendix in pdf",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3942"
} |
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